NAME:

 __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  

 
GRAM  POSITIVE  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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NOTES:  

 
 
 
 
 
 
 
 
 

  1  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO=   TRANS-­‐ TREATMENT  AND  
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   MISSION   PREVENTION  
GRAM  POSITIVE  COCCI  
  Humans   Hands   • Catalase-­‐positive   • Protein  A:  binds   • Exofoliatin:  Scaled   • Skin  and  Soft  Tissue  Infections   • Methicillin-­‐sensitive  SA   • Gram-­‐stain   • 95%  resistance  
Staphylococcus   (nasal)   Food   • Coagulase-­‐positive   IgG,  preventing   skin  syndrome   o bullous  impetigo,  folliculitis,  furuncles,   (MSSA)     o Reveals  gram-­‐positive  cocci   to  penicillins  
aureus       • Facultative   opsonization  and   • Enterotoxin:  food   carbuncles,  cellulitis,     o Penicillinase-­‐resistant   in  cluster     • 60%  MRSA  in  
      anaerobe   phagocytosis   poisoning   o hidradenitis  suppurativa,  mastitis,  surgical   penicillins   • Culture   the  Philippines  
        • Coagulase:  Allows   • Toxic  shock   site  infections   o Nafcillin,  oxacillin,   o Beta-­‐hemolytic   • mecA  gene  
      fibrin  formation   syndrome  toxin   • Acute  Endocarditis   and  dicloxacillin   o Produces  a  golden  yellow   • Panton-­‐
        around  organism   (TSST-­‐1)   o Most  common  cause  of  acute  endocarditis   • Methicillin-­‐resistant  SA   pigment.   Valentine  
    • Hemolysins   o Native  valve  (tricuspid  valve)  in  IV  drug   (MRSA)   • Polymerase  chain  reaction   leukocidin  
• Penicillase     abusers   o Contain  altered  PBP   (PCR)      
• Hyaluronidase:   • Pneumonia   o DOC  is  vancomycin   o mecA  gene  for  MRSA    
breaks  down   o Nosocomial,  necrotizing,  complicated  by   • Vancomycin-­‐resistant    
connective  tissue   empyema,  abscess  or  pneumatocele   SA  (VRSA)  
• Staphylokinase:   o Post-­‐viral   o DOC  is  linezolid  
lyses  formed   • Osteomyelitis  and  Septic  Arthritis  
• Lipase     • Gastroenteritis  
o Acute  onset  (4  hrs)  of  vomiting  and  
diarrhea  due  to  ingestion  of  preformed  
heat-­‐stable  enterotoxin  
o Source:  salad  made  with  mayonnaise  
(potato  or  tuna  salad)  
• Scalded  Skin  Syndrome  (Ritter  Disease)  
o Exfoliatin  cleaves  desmoglein  in  
desmosomes  
• Toxic  Shock  Syndrome  
o Fever,  hypotension,  strawberry  tongue,  
desquamating  rash  and  multi-­‐organ  
involvement  (>3)  
o Usually  no  site  of  pyogenic  inflammation;  
blood  CS  negative  
o Tampon-­‐using  menstruating  women  or  in  
patients  with  nasal  packing  for  epistaxis  
  Humans   Nosocomial   • Catalase-­‐positive   • Polysaccharide     • Prosthetic  device  infections  (valves,  joints,   • Vancomycin  (50%   • Gram-­‐stain      
Staphylococcus   • Coagulase-­‐negative   capsule:  adheres  to   plates)   methicillin  resistance)   o Gram-­‐positive  cocci  in  cluster  
epidermidis   • Facultative   a  variety  of   • Culture  
anaerobe   prosthetic  devices.   o White  colonies  on  blood  
• Catalase-­‐positive   Forms  a  biofilm.   agar,  non-­‐hemolytic  
• Highly  resistant  to   • Metabolism  
antibiotics   o Catalase-­‐positive  
  o Coagulase-­‐positive  
nd
  Humans     • Coagulase-­‐negative       • UTI  in  women   • Fluoroquinolones   • Gram-­‐stain   • 2  most  
Staphylococcus   • Facultative   • TMP-­‐SMX   o Gram-­‐positive  cocci  in  cluster   common  
saphrophyticus   anaerobe   • Culture   cause  of  UTI  
• NOVOBIOCIN   o Gamma-­‐hemolytic   in  sexually  
RESISTANT   • Metabolism   active  women  
  o Catalase-­‐positive  
• NO  STRES   • Coagulase-­‐positive  
 
  2  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐ TRANS-­‐ TREATMENT  AND  
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   MISSION   PREVENTION  
  Humans   Respiratory   Catalase-­‐ • Erythrogenic  toxin:   • Hyaluronidase:   • Impetigo  contagiosa   • DOC  is  Penicillin  G   • Gram-­‐positive  cocci  in   • Disease  of  poverty  
Streptococcus   droplets   negative   produces  scarlet   degrades  hyaluronic   • Erysipelas   • Patients  with  a  history  of   chains  
pyogenes   fever   acid  (spreading  factor)   • Cellulitis   rheumatic  fever  require   • Catalase-­‐negative  
  • Streptolysin  O   • Streptokinase   • Necrotizing     long-­‐term  antibiotic   • Beta-­‐hemolytic  
GABHS  (Group   (oxygen-­‐labile):   (fibrinolysin)     • Pharyngitis   prophylaxis  to  prevent   • Bacitracin-­‐sensitive  
A  Beta   highly  antigenic,   • DNase   o Most  common  bacterial  cause  of   recurrence  of  the  disease   • Lancefield  group  A  
Hemolytic   causes  AB   (streptodornase):   sore  throat     • positive  PYR  test  
Strep)   formation   degrades  DNA  in   • Scarlet  Fever    
    • Streptolysin  S   exudates  or  necrotic   • Streptococcal  Toxic  Shock  Syndrome  
(oxygen-­‐stable)   tissue     o Clinically  similar  but  milder  than  S.  
• Pyogenic  exotoxin   • C5a  peptidase:   aureus  TSS  
A:  superantigen   inactivates  complement   o Due  to  pyogenic  exotoxin  A  
similar  to  TSST   C5a   o Recognizable  site  of  pyogenic  
• Exotoxin  B:   inflammation  
protease  that   o Blood  cultures  are  often  positive    
rapidly  destroys   • Acute  Rheumatic  Fever  
tissue  →   • APSGN  
necrotizing  fasciitis  
  Vagina   • Trans-­‐       • UTI  in  pregnant  women     • Gram-­‐positive  cocci  in   • Most  common  cause  of  
Streptococcus   vaginally   • Neonatal  sepsis  (meningitis,   chains   neonatal  sepsis  in  the  
agalactiae   • Trans-­‐ pneumonia)   • Beta-­‐hemolytic   world  (the  universe,  
placentally   • Endometritis   • Catalase-­‐negative   rather)  J  
  o Most  commonly  polymicrobial   • Bacitracin-­‐resistant  
  o Foul-­‐smelling  lochia     • Hydrolyzes  hippurate    
    • CAMP  test–positive  
    • Lancefield    group  B  
  • Grows  using  Lim  
  broth      
  • Human  colon   • May  enter         • UTIs  due  to  indwelling  urinary   • Penicillin  plus  gentamicin   • Gram-­‐positive  cocci  in    
Group  D   • Urethra  and   bloodstrea catheters  and  urinary  tract   • Vancomycin  for  penicillin-­‐ chains  
streptococci   female   m  during   instrumentation     resistance   • Catalase-­‐negative  
genital  tract   GIT  or  GUT   • Biliary  tract  infections   • Linezolid  for  vancomycin-­‐ • Gamma  hemolytic  
can  be   surgery   • Endocarditis  in  patients  who   resistant  strains   colonies  
colonized   underwent  GIT  surgery  due  to  E.  
faecalis  
GRAM  POSITIVE  BACILLI  
  • Herbivores   • Endopores         • Aerobic  (but     • Protein  capsule   • Exotoxin:  3  proteins             • Anthrax                           • Ciprofloxacin  (DOC)   • Gram  stain:  box-­‐car   • Protein  capsule  
Bacillus   (zoonotic):   since  it  can     (polymer  of     • Protective  antigen  (PA)               • Cutaneous  (95%)    painless  black   • Doxycycline   shaped  bacteria   • Medusa  head  
anthracis   Sheep  Goats   grow  without   gamma-­‐D-­‐ • Edema  factor  (EF)                                   vesicles;    can  be  fatal  if  untreated           • Vaccine:  for  high-­‐risk   • Culture   • MCC  of  death  in  
Cattle   oxygen.  It  is     glutamatic  acid):   • Lethal  factor  (LF)     • Pulmonary  (woolsorter’s        disease)             individuals     • Serology   woolsorter’s  disease  is  
classified  as  a   antiphagocytic             • GI:  abdominal  pain,    vomiting  and   • Vaccine  is  composed  of   • PCR  of  nasal  swab   pulmonary  hemorrhage  
facultative     • Non-­‐motile           bloody    diarrhea                 the  protective  antigen     • MCC  of  death  is  
anaerobe                                                                                                                                           • Infections  result  to     (PA)     pulmonary  hemorrhage  
  • Permanent  immunity     • Animal  vaccine  is   in:  Anthrax,  Leptospirosis  
  composed  of  a  live  strain,   (Weil’s  syndrome),  
  attenuated  by  loss  of  its   Congenital  syphilis  
 
protein  capsule  

  3  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐ TRANS-­‐ VIRULENCE  
RESERVOIR   METABOLISM   TOXINS   CLINICAL  SYNDROMES   TREATMENT  AND  PREVENTION   DIAGNOSIS   NOTES  
ORGANISM   MISSION   FACTORS  
    Endospores   • Aerobic   • No  capsule   • Enterotoxins   • Food  poisoning:  nausea,   • Vancomycin   • Culture  specimen   • Chinese  fried  rice  
Bacillus  cereus   • Motile   o Heat  labile:  similar  to   vomiting     • Clindamycin   from  suspected  food   syndrome  
  interotoxin  of  cholera  and   • Resistant  to  beta-­‐lactam   source  
  E.  coli  (diarrheal  form)   antibiotics    
o Heat  stable:  produces   • No  treatment  for  food  
syndrome  similar  to  that   poisoning  
of  Staphylococcus  aureus  
food  poisoning,  but  with  
limited  diarrhea  (emetic  
form)  
  • Soil   Endospores   • Anaerobic   Motile:  flagella   • Neurotoxins  inhibits  release   • Food-­‐Borne  botulism:   • Antitoxin     • Gram  stain   • Flaccid  paralysis  
Clostridium   • Stored   (heat  resistant)   • Anaerobes:   (so  H-­‐antigen   of  acetylcholine  from   cranial  nerve  palsies,  muscle   o For  food-­‐borne  and  wound   • Culture   • Floppy  baby  syndrome  
botulinum   vegetables:   ABC   positive)   peripheral  nerves   weakness,  respiratory   botulism   o Requires  anaerobic   • Botox  neurotoxin  
home-­‐canned   Actinomyces   • Toxin  is  not  secreted,  rather   paralysis   • Human  botulism:     condition    
zip-­‐lock  storage   Bacteroides   it  is  released  upon  the  death   • Infant  botulism:   o Immunoglobulin  (for  infant   (thioglycollate-­‐
bags   Clostridium   of  the  bacterium   constipation,  flaccid   botulism)   enriched  agar)  
• Smoked  fish       paralysis  (floppy  baby   • Penicillin   • Patient’s  serum  
• Wild,  raw  honey:       syndrome)   • Supportive  therapy   injected  into  mice  
associated  with   • Wound  botulism:  similar  to   o Including  incubation  and   results  in  death  
infant  botulism   food-­‐borne  except  absence   ventilator  assistance    
of  GI  prodromal  symptoms  
  • Soil   Endospores:   • Anaerobic   Motile  flagella   • Tetanospasmin:  inhibits   • Tetanus   • Tetanus  toxoid:  vaccination   • Gram  stain   • Spastic  paralysis  
Clostridium   introduced   (so  H-­‐antigen-­‐ release  of  GABA  and  glycine   o Muscle  spasm   with  formalin-­‐  inactivated   o Gram-­‐positive  rods,   • Drumstick,  tennis  
tetani   through  wound   positive)   (both  inhibitory   o Lockjaw  (trismus)   toxin  (toxoid),  part  of  the  DPT   often  with  an   racquet,  lollipop  
neurotransmitters)  from   o Risus  sardonicus   vaccine   endospore  at  one   appearance  
nerve  cells,  resulting  in   o Respiratory  muscle   • Antitoxin:  human  tetanus   end,  giving  them    
sustained  muscle   paralysis   immnue  globulin  (pre-­‐formed   the  appearance  of  a    
contraction     anti-­‐tetanus  antibodies)   drumstick    
  • Clean  the  wound   • Requires  anaerobic    
  • Penicillin  (DOC)   conditions    
  • Supportive  therapy:  may    
  require  ventilator  assistance    
  • Vaccine  DPT:    
o diphtheria    
o pertussis    
o tetanus  
  • Ubiquitous:   Endospores   • Anaerobic   NON-­‐motile   • Alpha  toxin:  lecithinase   • Cellulitis/wound  infection   • Radical  surgery  (may  require   • Gram  stain   • Double  hemolysis  on  
Clostridium   • Soil   (splits  lecithin  into   • Clostridial  myonecrosis:  fatal   amputation)   • Culture   blood  agar  
perfringens   • G  tract  of  humans   phosphocoline  and   if  untreated     • Penicillin   o Requires  anaerobic   • Looks  motile,  but  not  
and  mammals   diglyceride)   • Watery  diarrhea:  associated   • Hyperbaric  oxygen     conditions   motile  on  blood  agar  à  
• 11  other  tissue  destructive   with  food-­‐borne  ingestion     due  to  avidity  for  lecithin  
enzymes   in  the  blood  membranes  
  • Intestinal  tract   Fecal-­‐oral:   • Anaerobic   Motile  flagella   • Toxin  A:  diarrhea   • Pseudomembranous   • Metronidazole   • Immunoassay  for  C.   • PO  vancomycin  because  
Clostridium   • Endospores   ingestion  of   (so  H-­‐antigen-­‐ • Toxin  B:  cytotoxic  to  colonic   enterocolitis:  antibiotic-­‐ • Oral  vancomycin   difficile  toxin   it  has  poor  intestinal  
difficile   found  in  hospitals   endospores   positive)   epithelial  cells   associated  diarrhea   • Terminate  use  of  the   • Examine  colon  with   absorption,  hence,  
and  nursing     responsilbe  antibiotic   colonoscopy   “coats”  the  lesions  with  
homes     antibiotic  
 

  4  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐ VIRULENCE  
RESERVOIR   TRANSMISSION   METABOLISM   TOXINS   CLINICAL  SYNDROMES   TREATMENT  AND  PREVENTION   DIAGNOSIS   NOTES  
ORGANISM   FACTORS  
  Throat   Respiratory  
 

• Facultative   • Pseudo-­‐ • Exotoxin  (coded  by  a   • Diphtheria   • Antitoxins   • Gram-­‐stain   • Obtains  exotoxin  from  a  
Corynebacterium   droplets  from   anaerobe   membrane   bacteriophage)   o Mild  sore  throat  with   • Penicillin  or  Erythromycin   o Gram-­‐positive   temperate  bacteriophage  
diphtheriae   carrier   • Catalase-­‐ forms  in  the   o Subunit  A:  blocks   fever  initially   • vaccine  DPT:   pleomorphic  rods   by  lysogenic  conversion  
positve   pharynx,  which   protein  synthesis  by   o Pseudomembrane  forms   diphtheria:  formalin   (sometimes   • Schick  test:  injection  of  
serves  as  a   inactivating  EF2   on  pharynx   inactivated  exotoxin,  as   describe  as  looking   diphtheria  exotoxin  into  
base  from   o Subunit  B:  provides   o Myocarditis  causing  A-­‐V   antibodies  to  the  B-­‐subunit  are   like  Chinese  letters)   the  skin,  to  determine  
where  it   entry  into  cardiac  and   condution  block  and   protective   • Culture   whether  a  person  is  
secretes  its   neural  tissue   dysrhythmia   pertussis   o Potassium  tellurite:   susceptible  to  infection  
toxin   • Exotoxin  is  like  a  human   o Neural  involvement:   tetanus   dark  black  colonies   by  diphtheria  
antibiotic,  as  it  inhibits   perpheral  nerve  palsies,   o Loeffler’s  medium:   • Modified  Elek  test:  for  
eukaryotic  protein   GBS,  palatal  paralysis,  and   after  12  hours  of   detection  of  toxigenicity  
synthesis,  just  as   neuropathies   growth,  stain  with  
tetracycline  inhibits   methylene  blue.  
protein  synthesis  in   Reddish  (Babes-­‐
bacteria   Ernst)  granules  can  
be  seen  
  • Ubiquitous   • Ingestion  of   • Facultative   • Motile  (via   • Listeriolysin  O  and   • Neonatal  meningitis   • Ampicillin   • Gram-­‐stain   • Facultative  intracellular  
Listeria   • Plants   contaminated   anaerobe   flagella):  so  has   phospholipases:  allows   • Meningitis  in  immune-­‐ • TMP-­‐SMX   o Gram-­‐positive  rods   parasite  
monocytogenes   (vegetables)   raw  milk  or   • Catalase-­‐ H-­‐antigen  à   escape  from  the   suppressed  patients  and  the   • NOT  CEPHALOSPORINS:   • Culture   • Cell-­‐mediated  immunity  
  cheese  from   positive   tumbling   phagolysosomes  of   elderly  (>50)   NONE  OF  THE   o :Can  grow  at   is  protective  
infected  cows   • Beta-­‐ motility   macrophages   • Septicemia  in  pregnant   CEPHALOSPORINS  ARE  ACTIVE   temperature  as  low   • Listeriolysin  
• Vaginally   hemolytic  on   • Hemolysin:   women   AGAINST  MRSA,  LISTERIA,   as  0  C  so  use  cold    
(during  birth)   blood  agar   (like   AND  ENTEROCOCCI   enrichment   Actin  rockets  
• Tranplacental   streptolysin  O)   technique  to  isolate    
infection  of     from  mixed  flora   Tumbling  motility  
fetus  from    
bacteremic  
mother  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

  5  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
GRAM  NEGATIVE  
 
 
 
 
 
 
 
 
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NOTES:  

 
 
 
 
 
 
 
 
 
  6  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TRANS-­‐ TREATMENT  AND  
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   MISSION   PREVENTION  
GRAM  NEGATIVE  COCCI  
  Respiratory   Respiratory   • Ferments  both   • Antiphagocytic  polysaccharide     • MENINGITIS:  most  common  cause   • Penicillin   • Gram-­‐negative,   • Complement  deficiencies  
Neisseria   tract   droplets   maltose  and   capsule     among  aged  2-­‐18  yrs   Ceftriaxone  (or   aerobic,  encapsulated   in  the  late-­‐acting  
meningitidis   glucose   • Endotoxin  (LOS):   • MENINGOCOCCEMIA   cefotaxime)  -­‐  DOC  for   diplococcus   complement  components  
• Oxidase-­‐ o An  LOS  can  be  shed  in  large   o Dissemination  of  meningococci   meningococcal  meningitis   • Culture   (C5–C9)  predispose  to  
positive   amounts  by  a  process  called   (Neisseria  meningitidis)  into  the   and  septicemia   o Grows  best  on   illness  
colonies  on   blebbing,  causing  fever,  shock,   bloodstream   • Rifampin   enriched  media,   • Most  patients  with  
chocolate  agar   and  other  pathophysiology.     o Multiorgan  disease,  consumptive   chemoprophylaxis  to  close   such  as  Mueller-­‐ meningococcal  
  o This  is  considered  the   coagulopathy   contacts   Hinton  or  chocolate   meningitis,  caused  by  the  
principal  factor  that  produces   o petechial  or  purpuric  rash   • Vaccine  contains  capsular   agar,  at  37°C  and  in   gram-­‐negative  
the  high  endotoxin  levels  in   (purpura  fulminans)   polysaccharide  of  strains   an  atmosphere  of   diplococcus  Neisseria  
meningococcal  sepsis.     o Patients  with  acute   A,  C,  Y,  and  W-­‐135   5-­‐10%  carbon   meningitidis,  recover  
o Meningococcal  LOS  interacts   meningococcemia  may  present   coupled  to  a  carrier   dioxide   completely  if  appropriate  
with  human  cells,  producing   with  (1)  meningitis  (2)  meningitis   protein  (diphtheria     antibiotic  therapy  is  
proinflammatory  cytokines   with  meningococcemia,  or  (3)   toxoid)  to  enhance   instituted  promptly.    
and  chemokines,  including   meningococcemia  without   immunogenicity   • Nonetheless,  the  disease  
interleukin  1  (IL-­‐1),  IL-­‐6,  and   clinically  apparent  meningitis.   • Currently,  vaccinations   still  is  associated  with  a  
tumor  necrosis  factor  (TNF).   • WATERHOUSE-­‐FRIDERICHSEN   against  meningococcus  A,   high  mortality  rate  and  
o LOS  is  one  of  the  important   SYNDROME   C,  W,  and  Y  are  available.     persistent  neurologic  
structures  that  mediate   o Most  severe  form  of   • The  first  meningococcal   defects,  particularly  
meningococcal  attachment  to   meningococcemia   vaccine  for  serogroup  B   among  infants  and  young  
and  invasion  into  epithelial   o High  fever,  shock,  widespread   was  approved  in  October   children.  
cells.   purpura,  disseminated   2014.    
o LOS  triggers  the  innate   intravascular  coagulation,    
immune  system  by  activating   thrombocytopenia,  and  adrenal  
the  Toll-­‐like  receptor  4MD2   insufficiency  à  bilateral  
cell  surface  receptor  complex   hemorrhagic  destruction  of  the  
and  myeloid  in  non-­‐myeloid   adrenal  glands    
human  sounds.  The  degree  of    
activation  of  complement  then  
coagulation  system  is  directly  
related  to  the  bacterial  load.  
• IgA  protease      
o At  least  13  serogroups  have  
been  described:  A,  B,  C,  D,  E,  
H,  I,  K,  L,  W-­‐135,  X,  Y,  and  Z.  
Serogroups  B  and  C  have  
caused  most  cases  of  
meningococcal  meningitis  in  
the  United  States  since  the  
end  of  World  War  II  
o Before  that,  group  A  was  more  
prevalent.  More  than  99%  of  
meningococcal  infections  are  
caused  by  serogroups  A,  B,  C,  
 
29E,  or  W-­‐135.  
 
  7  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TRANS-­‐ TREATMENT  AND  
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   MISSION   PREVENTION  
  Humans  only   • Sexually   • Facultative-­‐ • Pili:   • Endotoxin:   • Asymptomatic  (but  still   • Antibiotic  of  choice   • Gram-­‐stain  of  urethral  pus     • Kidney  bean  shaped  
Neisseria   (no  immunity  to   • Birth   anaerobe   Adherence  to   lipooligosaccharide   infectious)   o Third  generation   o Reveals  the  tiny  gram-­‐ with  concave  sides  
gonorhoeae   repeated     • Grows  best  in   epithelial  cells   (LOS)   • Men:  urethritis   cephalosporin  such  as   negative  doughnut-­‐ facing  each  other  
infections)   high  CO2   Antigenic  variation   • No  exotoxins   • Women   ceftriaxone  (Add   shaped  diplococci  within   forming  the  
environment   Antiphagocytic,     o Cervical  gonorrhea,  which  can   doxycycline  to  cover   white  blood  cells   appearance  of  
• Ferments  only   binds  bacteria   progress  to  pelvic   incubating  Chlamydia   • Culture   doughnut  
glucose  (not   tightly  to  host  cell   inflammatory  disease  (PID)   trachomatis  and  syphilis)   o Specimen  on  chocolate   • Gram-­‐negative  
maltose)-­‐  easy  to   protecting  it  from   complications  of  PID   • The  Centers  for  Disease   agar   diplococci  
remember,  since   phagocytosis   o Lower  abdominal  pain:  Most   Control  (CDC)  recommends   o Selective  media:   • Reinfection  because  
there  is  only  a  “g”   • IgA  protease   consistent  symptom  of  PID   that  all  patients  with   prevents  growth  of   there  is  no  immunity  to  
(no  “m”)  in   • Outer  membrane   • Both  men  and  women:     gonorrheal  infection  also  be   other  bacteria   previous  infections  
gonorrhoeae   proteins:     o Gonococcal  bacteremia   treated  for  presumed  co-­‐ o Thayer  Martin  with  VCN   • Fitz-­‐Hugh-­‐Curtis  
  o Protein  I:  porin     o Septic  arthritis:  gonococcal   infection  with  Chlamydia   o Cell  wall  contains   syndrome  
o Protein  II  (opacity   arthritis  is  the  most  common   trachomatis  (2015)   cytochrome  oxidase   Septic  arthritis  in  
protein):   cause  of  septic  arthritis  in   • Second  line,  but  not   which  oxidizes  dye   sexually  active  patients  
presence   sexually  active  individuals   effective  against  syphilis:   tetramethylphenylene   Well-­‐characterized  
associated  with   • Neonates   o Flouroquinolones   diamine  from  colorless   plasmids  commonly  
dark,  opaque   o Ophthalmia  neonatorum   o Spectinomycin   to  deep  pink.     carry  antibiotic-­‐
colonies   (conjunctivitis  in  newborns)   • For  opthalmia  neonatorum:   o Used  to  ID  colonies   resistance  genes,  most  
• For  adherence:   o N.  gonorrhoeae  is  acquired   o Erythromycin  eye  drops   PCR  in  bacterial  DNA  in   notably  penicillinase.  
Has  unique  protein   during  passage  through  an   should  be  given   clinical  specimens   Plasmid  and  
that  can  extract   infected  birth  canal   immediately  following   nonplasmid  genes  are  
iron  from   o Conjunctivitis  usually  erupts   birth,  for  prophylaxis   transmitted  freely  
transferrrin,   within  the  first  5  days     against  both  N.   between  different  
lactoferrin  and   gonorrhoeae  and   subtypes.  The  ensuing  
hemoglobin   Chlamydia  trachomatis   exchange  of  surface  
conjunctivitis   protein  genes  results  in  
o Infants  with  ophthalmia   high  host  susceptibility  
neonatorum  require   to  reinfection.  The  
systemic  treatment  with   exchange  of  antibiotic  
ceftriaxone.     resistance  genes  has  
o Erythromycin  syrup   led  to  extremely  high  
should  also  be  provided  to   levels  of  resistance  to  
cover  for  possible   beta-­‐lactam  antibiotics.  
concurrent  chlamydial  
disease  (this  is  important,  
as  failure  to  treat  neonatal  
Chlamydia  conjunctivitis  
can  lead  to  chlamydial  
pneumonia)  
  Part  of  the           • Otitis  media  in  children   • Azithromycin  or     • Resistant  to  penicilins  
Moraxella   normal  flora   • Can  cause  other  respiratory  tract   clarithromycin  
(Branhamella   infections,  such  as  sinusitis,   • Amoxicillin  with  clavulanate  
catarrhalis)   bronchitis  and  pneumonia   • Oral  second  or  third  
• COPD  exacerbation   generation  cephalosporin  
 
  • TMP-­‐SMX  
 
  8  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TRANS-­‐
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   TREATMENT  AND  PREVENTION   DIAGNOSIS   NOTES  
ORGANISM   MISSION  
GRAM  NEGATIVE  BACILLI  
  • Man  only   • Transmitted   • Haemophilus   • Some  strains  of  H.     • Hib  meningitis   • Second  or  third  generation   • Gram  stain     • NTHi  strains  form  
Haemophilus   (obligate   via   influenzae   influenzae  possess  a   o Most  serious  manifestation   cephalosporins  (since  H.   • Culture  specimen:   biofilm  in  vitro  and  
influenzae   human   respiratory   requires  two   polysaccharide  capsule,   of  Hib  infection   influenzae  can  acquire  ampicillin   o Blood  agar  that  has  been   ex  vivo  and  have  
o
parasite   route   factors  for   and  these  strains  are   o Antecedent  upper   resistance  by  plasmids)   heated  to  80 C  for  15   been  implicated  in  
• NTHi  strains   growth  (both   serotyped  into  6   respiratory  tract  infections   • Hib  vaccine:  H.  influenzae   minutes  (now  called   chronic  infection  
colonize  the   found  in   different  types  (a-­‐f)   are  common   polysaccharide  capsule  of  type  b   chocolate  agar).  This  high   such  as  otitis  
nasopharynx   blood):   based  on  their   o Hib  meningitis   strain  (Hib)  is  conjugated  to   temperature  lyses  the  red   media,  sinusitis,  
in  up  to  80%   o X  factor:   biochemically  different   manifestations   diphtheria  toxoid     blood  cells  releasing  both   and  bronchitis.    
of  individuals   Hematin   capsules.     indistinguishable  from  other   • Passive  Immunization:  mother  is   hematin  (called  X  factor)   • NTHi  biofilm  
  o V  factor:   • The  most  virulent  strain   bacterial  meningitis  causes   immunized  during  8th  month  of   and  NAD+  (called  V   formation  was  
NAD+   is  H.  influenzae  type  b   • Cellulitis   pregnancy  to  increase  passive   factor).     found  in  patients  
• Satellite   (Hib)   o Most  commonly  involves   antibody  transfer  in  breast  milk   o Like  the  Neisseria,  H.   with  CF  on  the  
growth  around   • Some  H.  influenzae   the  buccal  and  periorbital   • The  Centers  for  Disease  Control   influenzae  grows  best   apical  surface  of  
Staphylococcus   strains  have  no  capsule   regions   and  Prevention  (CDC)  Advisory   when  the  chocolate  agar   airway  epithelia  
aureus   and  are  termed   o Usually  associated  with   Committee  on  Immunization  has   is  placed  in  a  high  CO2   with  decreased  
o
nonencapsulated  H   fever   released  updated  2014   environment  at  37 C   antibiotic  
influenzae  or   • Epiglottitis   vaccination  recommendations   • Fluorescently  labeled   susceptibility.  
nontypeable  H   o Fever,  sore  throat,   for  adults  aged  19  years  and   antibodies  (ELISA  and  latex   • Approximately  6%  
influenzae  (NTHi).   dysphagia,  drooling,  and   older.  Key  changes  in  the   particle  agglunation)   of  individuals  with  
  difficulty  breathing   recommendations  include  the   • Positive  Quellung  test:  due   Hib  meningitis  
• Hib  pneumonia   following:   to  its  capsule,  similar  to   experience  
o Clinically  indistinguishable   o (1)  certain  adults  at  increased   Streptococcus  pneumoniae   permanent  
from  other  bacterial   risk  for  Hib  who  have  not     sensorineural  
pneumonias—except  for  its   previously  received  the   hearing  loss.  
insidious  onset  and  a  history   vaccine—except  for  individuals  
of  fever,  cough,  and   with  human  immunodeficiency  
purulent  sputum  production   (HIV)  infection,  who  have  a  
• Hib  pericarditis   low  risk  for  Hib  infection;  and    
o Fever,  respiratory  distress,   o (2)  adults  who  have  
and  tachycardia   undergone  a  successful  
• Septic  arthritis   hematopoietic  stem  cell  
o Joint  pain,  swelling,  and   transplant  (HSCT).  (Administer  
decreased  mobility   a  3-­‐dose  series  of  Hib  vaccine  
• Occult  bacteremia   6-­‐12  mo  posttransplantation,  
o Fever,  anorexia,  and   regardless  of  Hib  vaccination  
lethargy   status.)  
• NTHi  infections  
o Commonly  causes  various  
mucosal  infections,  
including  otitis  media  and  
conjunctivitis  
 
 
 
 
  9  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TRANS-­‐ TREATMENT  AND  
RESERVOIR   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   MISSION   PREVENTION  
GRAM  NEGATIVE  GI  AND  GU  
  • Humans   • Fecal-­‐oral   • Indole-­‐positive   • Fimbriae  (pili):   • Enterotoxins   • Neonatal  meningitis   • Penicillins   • Gram-­‐negative    
Escherichia   GI  and   • Ascending   • Beta-­‐hemolytic     attachment/   o LT  (heat-­‐labile):   • UTI     • Aminoglycosides   • Culture  
coli   urinary  tract   infection  to   • Ferments   colonization  factor     increases  cAMP   • Nosocomial  sepsis  
nd rd
• 2  and  3  gen   o Specimen  may  be  urine,  
  the  urethra   lactose   • Siderophore   (same  as  cholera   • Nosocomial  pneumonia   cephalosporins   sputum,  CSF  or  blood  
  • Colonization     • Adhesins   toxin)   • Diarrhea   • Fluoroquinolones   o Can  grow  at  45.5  C  
  of  catheters     • Capsule  (K-­‐antigen)   o ST  (heat-­‐stable)   • ETEC     o Pathogenic  strains  may  
  in     • Flagella  (H-­‐antigen)   Increases  cGMP   o Releases  LT  and  ST  toxins,     be  isolated  from  stool  
hospitalized       • Shiga-­‐like  toxin   traveler’s  diarrhea     o E.  coli  ferments  lactose,  
patients         (verotoxin):  inhibits   • EHEC/STEC  (Shiga-­‐like  toxic     so  colonies  appear  
• Aspiration     protein  synthesis  by   producing  E.  coli)   purple  to  black  on  EMB  
inactivating  the  60S   o No  fever,  no  pus  in  stool     agar  and  pink  to  purple  
ribosomal  subunit  of   o Secretes  shiga-­‐like  toxin   on  MacConkey  agar  
eukaryotic  cells  (E.   (verotoxin)  
coli  O157:H7,  STEC,   o Causes  hemorrhagic  colitis  and  
EHEC)   hemolytic  uremic  syndrome  (E.  
coli  strain  O157:H7)  
• EIEC  
o With  pus  in  the  stool  and  fever  
      • Urease:   • Swarming  motility   • No  toxins   • UTI:  high  urine  pH  due  to  urease   • Ampicilin   • Culture   • Weil-­‐Felix  reaction:  a  test  
Proteus   hydrolyzes   production  -­‐>  struvite  calculi   • TMP-­‐SMX   o Colonies  swarm  over   that  uses  antibodies  
mirabilis   ureas  into  NH3   formation;  staghorn  calculi  (tx  with     entire  culture  plate   against  certain  strains  of  
and  CO2     surgery)   • Alkaline  urine  (high  pH)   Proteus  to  diagnose  
• Indole-­‐negative   • Sepsis     rickettsial  disease  (as  
• Does  not     certain  rickettsiae  share  
ferment  lactose   similar  antigens)  
• See  also:  Rickettsia  
species  
  • Humans   • Fecal-­‐oral   • No  H2S   • Invades  submucosa   • Shiga  toxin     • Bloody  diarrhea  with  mucus  and   • Floruoquinolones   • Stool  culture:  because   • IgA  is  best  for  immunity  
Shigella   production   of  intestinal  tract,   o MOA:  inactivates   pus  (similar  to  enteroinvasive  E.   • Azithromycin   Shigella  is  never  a  part  of   • Shigella  is  more  toxic  and  
dysenteriae   • Does  not   but  not  the  lamina   the  60S  ribosome,   coli)   • TMP-­‐SMX   the  normal  intestinal  flora   invasive  than  Salmonella  
ferment  lactose   propria  à  ulcers  à   inhibiting  protein    
  bleeding   synthesis  and  killing    
• NON-­‐motile:  No  H-­‐ intestinal  epithelial    
antigen  (since  they   cells  
have  no  flagella)   o Protein  synthesis  
inhibitor  of  
EUKARYOTES  
 
 
 
 
 
 
 
  10  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   METABOLIS TREATMENT  AND  
RESERVOIR   TRANS-­‐MISSION   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   M   PREVENTION  
  • S.  typhi  is   • S.  typhi  is   • Produces   • Motile  (H-­‐antigen)     • Enteric  fever     • Ciprofloxacin   • Culture:  blood  stool   • Facultative  intracellular  
Salmonella   found  only  in   transmitted  via   H2S   • Capsule  (called  the   • Typhoid  fever   • Ceftriaxone   or  urine  may  contain   parasite:  
typhi   humans   fecal-­‐oral  route     • Does  not   Vi  antigen):   • Parathypoid  -­‐  fever  (similar  to   • TMP-­‐SMX   S.  typhi   o Lives  within  macrophages  in  
  • Zoonotic:   ferment   protects  from   typhoid  fever,  but  caused  by   • Azithromycin     • Never  part  of  the   lymph  nodes    
Non-­‐typhoidal   1.  Pet  turtles   lactose   intracellular  killing   non-­‐typhoidal  Salmonella)   • *Salmonella   intestinal  flora   o Can  live  in  gall  bladder  for  
groups  of   2.  Chickens     • Siderophores   • Chronic  carrier  state  in  the  gall   gastroenteritis:  there     years  (carriers  secrete  S.  typhi  
Salmonella   3.  Uncooked       bladder   is  little  benefit  from     in  stool)  
    eggs       • Gastroentritis   antibiotic  treatment;     • Persons  who  are  asplenic  or  
          • Sepsis     it  may  prolong  carrier     have  non-­‐functioning  spleens  
          • Osteomyelitis:  Especially  in  sickle   state     (sickle  cell  anemia)  are  at  
          cell  patients  (Salmonella   • In  the  Philippines,   increased  risk  of  infection  by  
      choleraesuis)   first  line  drug  for   this  organism  
    typhoid:  Amoxicillin,   • Gastric  acid  is  protetive  against  
TMP-­‐SMX,   salmonellosis,  hence,  
Chloramphenicol   gastrectomy/antacids  increase  
the  risk  
    • Zoonotic:  can   • Ingestion  of   • Non-­‐ • V  and  W  antigens   • Enterotoxin  similar  to   • Pseudoappendicitis  (RLQ  pain)  à   • Antibiotics  do  not   • Stool  or  blood   • Survives  refrigeration  
Yersinia   be  found  in   contaminated   lactose   • Motile   the  heat  stable  toxin   mesenteric  lymphadenitis   alter  the  course  of   cultures  mat  be   • Closely  related  to  Yersinia  pestis  
enterocolitica   pigs   food  or  water     fermenter     of  E.  coli    increases   • Acute  enterocolitis,  with  fever,   the  diarrhea.     positive     • Mesenteric  lymphadenitis  in  
• Unpasteurized   • Virulence     cGMP  levels   diarrhea  and  abdominal  pain     • However,  patients   • Examination  of  the   children  à  pseudoappendicitis  
milk   factors  are     • Diarrhea  -­‐  The  most  common   with  positive  blood   terminal  ilium  with    
  temperatu   clinical  manifestation  of  this   culture  should  be   colonoscopy  will    
  re  sensitive   infection;  diarrhea  may  be   treated  with   reveal  mucosal    
  expressed   bloody  in  severe  cases     antibiotics   ulceration    
o
  at  37 C     • Low-­‐grade  fever      
• Abdominal  pain  -­‐  May  localize  to  
the  right  lower  quadrant    
• Vomiting  -­‐  Present  in  
approximately  15-­‐40%  of  cases  
  • Humans  only   • Fecal-­‐oral   • Oxidase-­‐ • Motile  (H-­‐antigen)   • Choleragen   • Cholera   • Fluid  and  electrolyte   • Dark  field  microscopy   • Death  by  dehydration:  children  
Vibrio  cholerae   transmission   positive   à  Shooting  star   (enterotoxin):  like  LT   o Severe  diarrhea  with  rice   replacement   of  stool  reveals  motile   affected  in  endemic  areas  1991:  
• Morphology:   • Ferments   motility   of  E.  coli,  increases   water  stools.     • Doxycycline   organism  that  are   Latin  America  epidemic    
Short,  comma   sugar   • Digest  mucous  layer   levels  of  cAMP,   o No  pus  in  stools   • Flouroquinolones   immobilized  with   • 1993:  Epidemic  in  Bangladesh  
shaped,  with  a   (except   so  V.  cholera  can   causing  secretion  of     antiserum   and  India    
single  polar   lactose)   attach  to  cells     electrolytes  from  the     • Grows  as  flat  yellow   • Washer  woman’s  hands  sign  à  
flagellum     • Fimbrae:  helps  with   intestinal  epithelium.       colonies  on  selective   wirnkled  skin  due  to  loss  of  skin  
    attachment  to  cells     • This  results  in     media:  thiosulfate-­‐ turgor  due  to  dehydration  
    • Non-­‐invasive   secretion  of  fluid  into   citrate-­‐bile-­‐salts-­‐
    the  intestinal  tract.   sucrose  (TCBS)  agar  
  à  secretory  diarrhea  
  • Fish   • Consumption  of   • Halophilic   • Motile  (H-­‐antigen)   • Hemolytic  cytotoxins   • Cause  of  25%  of  food  poisoning   • Doxycycline   • TCBS   • Diarrhea  after  ingestion  of  raw  
Vibrio  para-­‐ • Seafood   raw  fish     (likes  salt)   • Capsule   in  Japan  (diarrhea  for  3  days)  à   • Fluoroquinolone     seafood  
haemolyticus   • Morphology:     because  Japanese  love  seafood   • Unclear  if  antibiotics   • Also  consider  Norwalk  virus    
short,  comma   change  clinical  course   • Important  to  distinguish  viral  
shaped,  with  a   of  the  disease   from  bacterial  
single  polar  
 
flagellum      
 

  11  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   VIRULENCE  
RESERVOIR   TRANSMISSION   METABOLISM   TOXINS   CLINICAL  SYNDROMES   TREATMENT  AND  PREVENTION   DIAGNOSIS   NOTES  
ORGANISM   FACTORS  
  • Zoonotic:   • Uncooked  meat   • Microaerophilic   • Motile  (H-­‐ • Enterotoxin:   • Secretory  or  bloody   • Fluoroquinolone   • Microscopic   • One  of  the  three  most  
Campylobacter   wild  and   (especially  poultry)   • Oxidase   antigen)   similar  to  cholera   diarrhea   • Erythromycin     exam  of  stool   common  causes  of  
jejuni   domestic   • Unpasteurized  milk   Positive   • Invasive   toxin  and  the  LT   • Associated  with  Guillain-­‐   reveals  motile,   diarrhea  in  the  world  
animal  and   • Fecal-­‐oral   • Optimum     of  E.  coli   Barre  syndrome     curved  gram-­‐ • Most  common  cause  of  
poultry;   • Morphology:   temperature  is     • Cytotoxins:     negative  rods     bacterial  gastroenteritis  
o
undercooked   curved  gram-­‐ 42 C  –  to   destroy  mucosal   • Selective  media    
chicken   negative  rods  with   inhibit  the   cells   with  antibiotic  at  
o
a  single  polar   growth  of     42 C  
flagellum   other  fecal     • Skirrow’s  agar  
species   • Campy’s  agar  
    • Morphology:   • Microaerophilic     • No  toxin   • Duodenal  ulcers   • Bismuth,  ampicillin,  metronidazole  and     • Peptic  ulcer  disease  
Helicobacter   curved  gram-­‐ • Urease-­‐positive   • Chronic  gastritis   tetracycline   • Gastric  carcinoma  
pylori   negative  rods  with       • Clarithromycin  and  omeprazole   • MALT  lymphoma  
a  tuft  of  polar   • Both  regimens  reduce  duodenal  ulcer  
flagella   relapse  
  • Colon   • Part  of  the  normal   • Anaerobic  (O2     • Does  not  contain   • Abscesses  in  the   • Metronidazole  –  DOC  for  anaerobic   • Gram-­‐stain   • Infection  occurs  when  the  
Bacteriodes     flora  of  the   inhibits  its   lipid  A   gastrointestinal  tract,   infections   • Anaerobic  culture   organism  enters  the  
fragilis   intestine   growth)   pelvis  and  lungs   • Clindamycin     peritoneal  cavity  
• Most  common   • Gram-­‐negative   • Brain  abscesses   • Chloramphenicol   • Hence,  if  the  anatomy  of  
colonic  flora   rod   (chloramphenicol  is  ideal   • Chloramphenicol  is  static,  but  -­‐cidal  to   the  GI  tract  is  altered  
  • Non-­‐spore   because  it  is  lipophilic)   the  following:   (surgery,  trauma,  
former     o Neisseria  meningitidis   perforation)  
• Polysaccharide   o Bacteroides  fragilis    
capsule   o Streptococcus  pneumonia  
  o Haemophilus  influenza  
o NBSH  –  No  Boyfriend  Since  
Highschool  
  • Soil,  Water,   • Medical  devices   • Obligate   • Motile  (polar   • Exotoxin  A   • Burn  infections   • MDR,  XDR  strains   • Culture:  greenish,   • Common  etiology  for  
Pseudomonas   Plants,   • Hands  of  healthcare   aerobe  (does   flagella)   (similar  to   • Endocarditis  in  IV  drug   • SEE  ANTIPSEUDOMONAL  LIST  GIVEN  BY   metallic  colonies   infection  in  neutropenic  
aeruginosa     Animals,   workers   not  ferment)   • Hemolysins   diphtheria  toxin):   users   DR.  CALDERON   on  blood  agar,   patients.  
Intestinal     • Non-­‐lactose   • Collagenase   inhibits  protein   • Necrotizing  pneumonia  –   • Antimicrobials  are  the  mainstay  of   with  fruity  odor   • Produces  pigments  when  
Flora,  Skin   fermenter   • Elastase   synthesis  by   fleur  de  lys  morphology   therapy.     (grape-­‐like  odor)   cultured:    
• Oxidase-­‐ • Fibrinolysin   blocking  EF2   on  histopath   • Meningitis:  Ceftazidime  is  the   • Cetrimide   o pyocyanin  (blue  
positive   • Phopholipase  C   • Sepsis  (in  the   antibiotic  of  choice   medium   pigment)  
  • DNAse   immunocompromised);   • Eye  infections     o pyoverdin  (green  
• Antiphagocytic   ecthyma  gangrenosum   o Treat  small  superficial  ulcers  with     pigment)  
capsule   • Malignant  otitis  externa   topical  therapy  (eg,  ophthalmic     • Nosocomial  organisms  
  • UTI  (catheter-­‐related)   aminoglycoside  solution  rather  than     similar  to  Pseudomonas:  
  • Diabetic  osteomyelitis   an  ointment)  every  30-­‐60  minutes     o Acinetobacter  
• Typhlitis,  Shanghai  fever   o When  perforation  is  imminent,     baumannii  
• It  is  the  most  common   subconjunctival  (or  subtenon)     o Elizabethkingia  
pathogen  isolated  from   administration  is  preferred       meningosepticum  
patients  who  have  been   o Management  of  endophthalmitis   o Burkholderia  cepacia  
hospitalized  longer  than  1   requires  aggressive  antibiotic  therapy    
week,  and  it  is  a  frequent   (parenteral,  topical,  subconjunctival    
cause  of  nosocomial   [or  subtenon],  and,  often,  
infections.   intraocular)  
 

  12  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   PREVENTION  
GRAM  NEGATIVE  BACILLI  ZOONOTIC  
  • Wild  rodents   • Flea  bite   • Facultative   • Fraction  1  (F1):  this   • Pesticins:  kills   • Bubonic  plague   • Streptomycin  or   • Gram  strain     • Facultative  intracellular  
Yersinia  pestis   • City  rats   • Contact  with   anaerobe   capsular  antigen  is   other  bacteria   o Regional  lymph  nodes   gentamicin   o Gram-­‐negative  rods   parasite  
• Squirrels  and   infected  animal   • Virulence   antiphagocytic     (including  E.   (usually  groin)  swell,  and   • Doxycycline   with  bipolar  staining     • Yersinia  can  accept  plasmids  
prairie  dogs   tissue   factors  are   • V  and  W  proteins   coli)   become  red,  hot  and   • Killed  vaccine  is   o The  ends  of  these  rod   in  E.  coli,  and  shares  many  
in  the  U.S   • Inhaled   temperature   • Non-­‐motile   • Intracellular   tender  (called  a  bubo);     effective  only  for  a  few   shaped  bacteria  take   antigens  with  enteric  bacteria  
aerosolized   sensitive:  only   o
• Requires  calcium  at  37 C.   murine  toxin:   o High  fever   months   up  stain  more  than   • Subcutaneuos  hemorrhage  
organisms:   expressed  at   If  insufficient  calcium,  Y.   lethal  to  mice   o Conjunctivitis     • Attenuated  vaccine  is   the  center     result  in  a  blackish  skin  
o
human  to   37 C   pestis  alters  its     • Septicemic  plague   more  effective  but  also   o Closed  safety  pin   discoloration,  giving  the  name  
human   (temperature   metabolism  and  protein     o Bacteria  survive  in   has  more  side  effects   appearance   “Black  Death”  
transmission   inside   production.  This  trait     macrophages     • Blood  culture   • Yersinia  is  named  in  honor  of  
occurs  during   macrophages)   assists  with  its   o Spread  to  blood  and     • Culture  bubo  aspirate   Alexander  Yersin,  who  
epidemics   • Virulence  is   intracellular  state.   organs   • Serology   successfully  isolated  the  
  plasmid-­‐ • The  virulence  of  this   o Death  occurs  in  75%  in   • Rapid  diagnositic  test:   bacteria  in  1894  during  the  
  mediated   bacterium  results  from   untreated   antibody  against  F1   pandemic  that  began  in  China  
  the  32  Y  pestis   • Pneumonic  plague   (capsular  antigen)   in  the  1860s.  
  chromosomal  genes  and   o During  epidemics,   • Plague  was  first  described  in  
two  Y  pestis  –specific   pneumonia  occurs  as   the  Old  Testament  and  has  
plasmids,  constituting  the   bacteria  are  spread  from   persisted  into  the  modern  
only  new  genetic  material   person  to  person  by   era.  Plague  has  caused  large-­‐
acquired  since  its   aerosolized  respiratory   scale  epidemics,  thereby  
evolution  from  its   secretion:  100%  in   changing  the  course  of  history  
predecessor.  These   untreated   in  many  nations.    
acquired  genetic  changes     • The  first  pandemic  was  
have  allowed  the     believed  to  have  started  in  
pathogen  to  colonize  fleas   Africa  and  killed  100  million  
and  to  use  them  as   people  over  a  span  of  60  
vectors  for  transmission.   years.  In  the  Middle  Ages,  
• The  bacteria  elaborate  a   plague  killed  approximately  
lipopolysaccharide   one  fourth  of  Europe's  
endotoxin,  coagulase,  and   population.  The  pandemic  
a  fibrinolysin,  which  are   that  began  in  China  in  the  
the  principal  factors  in  the   1860s  spread  to  Hong  Kong  in  
pathogenesis  of  plague.   the  1890s  and  was  
subsequently  spread  by  rats  
transported  on  ships  to  Africa,  
Asia,  California,  and  port  cities  
of  South  America.  In  the  early  
twentieth  century,  plague  
epidemics  accounted  for  
about  10  million  deaths  in  
India.  As  reported  in  National  
Geographic,  mass  graves  of  
plague  victims  were  recently  
discovered  in  an  area  of  
Venice  called  "Quarantine  
 
Island."  
 
 
 
 

  13  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TREATMENT  AND  
RESERVOIR   TRANS-­‐MISSION   METABOLISM   VIRULENCE  FACTORS   TOXINS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   PREVENTION  
  • Rabbits  and   • Bite  of  tick,   • Obligate   • Capsule  anti-­‐phagocytic     • Tularemia   • Gentamicin  or   • Culture   • The  diagnosis  of  tularemia  is  
Francisella   squirrels   deerfly  or   aerobe   • Non-­‐motile   • Ulceroglandular   streptomycin  (DOC)   o Very  dangerous  due   usually  based  on  serology  
tularensis   • Ticks  can   infected   • Requires   • The  ability  of  F  tularensis   o At  the  site  of  tick  bite  or  • Doxycycline   to  its  high  infectivity     results.    
serve  as  a   animals   cysteine   to  impair  phagocyte   direct  contact  with   • Attenuated  vaccine:   o Requires  addition  of   • Tests  vary  from  antibody  
reservoir   • Direct  contact     function  and  survive  in   contaminated  rabbit,  an   only  for  high-­‐risk   cysteine  to  blood  agar   detection  (using  latex  
  with  infected     infected  cells  is  central  to   ulcer  devcelops,  with   individuals   media   agglutination  or  enzyme-­‐
  animal  tissue     its  virulence.  This   swelling  of  focal  lymph     • Skin  test   linked  immunosorbent  assay  
  (usually  rabbit)   intracellular  life  cycle  has   nodes     • Measure  rise  in  IgG   [ELISA]  testing)  to  the  
• Inhaled   been  shown  to  be  related   • Pneumonic   antibody  titer  (IgM  is   examination  of  a  range  of  
aerosolized   to  the  tightly  regulated   o Inhalation,  or  through  the   not  very  good)   polymerase  chain  reaction  
organisms   expression  of  a  series  of   blood       (PCR)  assay  products.  
• Ingestion  of   genes.   • Oculoglandular     • An  agglutination  titer  greater  
contaminated     o Direct  inoculation  into   than  1:160  is  considered  
meat  or  water     eyes   presumptively  positive,  and  
• Easily   • Typhoidal   treatment  may  be  started  if  
transmitted  to   o Ingestion  results  in   this  result  is  obtained.  A  
lab  personnel   gastrointestinal  symptoms     second  titer,  demonstrating  a  
(abdominal  pain)  and   4-­‐fold  increase  after  2  weeks,  
fever   confirms  the  diagnosis.  
Brucella   • Direct  contact   • Obligate   • Capsule     • Brucellosis:   • Pasteurization  of  milk   • Culture  blood,  bone   • Brucella  ovis  
  • Goats   with   aerobe   • Non-­‐motile   • Undulating  fever   • Treat  with  combination   marrow  (best  yield),   o Non-­‐pathogenic  to  man  
Brucella   (meeee!)   contaminated   • Aerobic  gram-­‐ • Tropism  for  erythritol,  a   o Fever  peaks  in  the   of  Doxycycline  and  one   liver,  or  lymph  nodes   • Although  Brucella  infection  is  
meltitensis   livestock  or   negative   sugar  found  in  animal   evening,  and  returns  to   other  drug  (gentamicin,   • Serologic  tests   primarily  controlled  through  
(highest   aborted   coccobacilli     placentas   normal  by  morning   streptomycin,  or   • Skin  test:  Indicates   cell-­‐mediated  immunity  
pathogenicity)   placentas   • Possess  a   • Erythritol  is  a  four-­‐carbon   • Weakness   rifampin).   exposure  only   rather  than  antibody  activity,  
  • Ingestion  of   unique  ability   sugar  preferentially   • Loss  of  appetite   • All  cattle  are  immunized     some  immunity  to  reinfection  
  • Cattle   infected  milk   to  invade  both   utilized  by  Brucella  spp.   • Includes  abortions  in   with  a  living  attenuated     is  provided  by  serum  
Brucella   products   phagocytic  and   The  presence  of  erythritol   animals   strain  of  Brucella   immunoglobulin  (Ig).    
abortus   • Aerosolization   nonphagocytic   in  the  placentas  of  goats,   abortus   • Initially,  IgM  levels  rise,  
  in  laboratory  or   cells     cows,  and  pigs  has  been     followed  by  IgG  titers.  IgM  
  • Pigs   possibly  due  to   • Survive  in  the   used  to  explain  the     may  remain  in  the  serum  in  
Brucella  suis   bioterrorism   intracellular   localization  of  Brucella  to   low  levels  for  several  months,  
    environment   these  sites  and  the   whereas  IgG  eventually  
  • Dogs     by  finding  ways   subsequent  accumulation   declines.  Persistently  elevated  
Brucella  canis   to  avoid  the   of  large  amounts  of   IgG  titers  or  second  rises  in  
immune   bacteria,  eventually   IgG  usually  indicate  chronic  or  
system.   leading  to  abortion.   relapsed  infection.  IgA  
  [Microbes  Infect.  2013   antibodies  are  elaborated  late  
  Jun;15(6-­‐7):440-­‐9]   and  also  may  persist  for  very  
  long  intervals.  
  • Part  of  the   • Bite  from  dog   • Facultative   • Capsule     • Wound  infections  (following   • Penicillin  G   • Culture  specimen  on   • Not  a  facultative  intracellular  
Pasteurella   normal  flora   or  cat   anaerobe   • Non-­‐motile   dog  or  cat  bites)   • Doxycycline   standard  laboratory   organism  
multocida   of  domestic     o May  progress  to  infection   • Third  generation   media   • Human  bite  infection-­‐  
and  wild     of  nearby  bones  and  joints   cephalosporin   Eikenella  corrodens  
animals    
 
 
 

  14  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   VIRULENCE   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   FACTORS   PREVENTION  
MISCELLANEOUS    
  • Humans   • Direct  contact   • LIFE  CYCLE   • Resistant  to   • Trachoma   • Genital  and  eye   • Gram-­‐stain  of  genital  secretions  will  not   • Gram-­‐negative,  but  lacks  
Chlamydia   • Primarily  affects   o Elementary  body   lysozyme  (since   o Serotypes  A,  B,  &  C   infections:   show  gram-­‐negative  organisms   peptidoglycan  layer  and  
trachomatis   the  eyes,   (EB):  dense   their  cell  wall   o Causes  scarring  of  the  inside   o Doxycycline  (use   • Culture   muramic  acid    
  genitals,  lungs   spherule  that   lacks  muramic   of  the  eyelid,  resulting  in   only  for  adults   o Can  NOT  be  grown  artificial  media.     • Trachoma  is  seen  in  
• Poor  hygiene  for   infects  cells   acid)   redirection  of  the  eyelashes   o Erythromycin   o Can  classically  be  grown  in  chick  yolk   underdeveloped  countries,  and  
trachoma   Initial  (reticulate)   • Prevents   onto  the  corneal  surface  à   (especially  for   sacs:  More  commonly  chlamydia  is   transmission  occurs  due  to  poor  
  body   phagosome  –   corneal  scarring  and   infants  and   cultured  in  certain  cell  lines  (McCoy   hygiene  
  o After  EB  enters   lysosome  fusion   blindness   pregnant  women)   cells  for  example)   • Presence  of  chlamydial  
  cell,  it  transforms   • Non-­‐motile   • Inclusion  conjunctivitis     o Azithromycin   • Immunofluorescent  slide  test  place   inclusions  or  elementary  bodies  
  into  an  Initial   • No  pili   o Serotypes  D  through  K     infected  genital  or  ocular  secretions  on  a   on  Giemsa-­‐stained  smears  of  
  body  (larger,   • No  exotoxins   o Opthalmia  neonatorum     slide  and  stain  with  fluorescein-­‐ the  conjunctivae  or  
    osmotically     • Infant  pneumonia     conjugated  anti-­‐chlamydial  antibody   nasopharynx  confirms  the  
  fragile,  can     • Urethritis,  cervicitis  and  pelvic     • Serologic:  Examine  blood  for  elevated   diagnosis  
A-­‐C:  trachoma   produce  via     inflammatory  disease  (PID)  in     titers  of  antichlamydial  antibodies  with   • Interesting  risk  factors:  
D-­‐K:  genital,  neonatal   binary  fission,     women       compliment  fixation  and   o Certain  cytokine  
L1-­‐3:  LGV   requires  ATP   • Nongonococcal  urethritis,     immunofluorescence  tests.   polymorphisms  –  These  have  
    from  the  host)     epididymitis  and  prostatitis  in     • Lymphogranuloma  venereum   been  associated  with  severe  
    o The  initial  body   men   o Serologic  test   disease  and  risk  of  tubal  
    transform  back   • Complications  of  chlamydial   • For  inclusion  conjunctivitis  (ophthalmia   factor  infertility  
    into  EB,  which   genital  tract  infection:   neonatorum)   o Certain  variants  in  Toll-­‐like  
    leaves  the  cell  to   o Sterility,  ectopic  pregnancy   o Scraping  from  the  surface  of  the   receptor  1  and  4  genes  –  
    infect  the  other   and  chronic  pain  may  occur   conjunctiva  will  show  intracytoplasmic   These  predispose  to  infection  
    cells   after  pelvic  inflammatory   inclusion  bodies  within  conjunctival   Having  been  a  foster  child  
  disease   epithelial  cells  (Halberstaedter-­‐ (males  only)  
  • Reiter’s  syndrome   Prowazek  inclusions).  The  inclusion    
  o Triad  of  conjunctivitis,   bodies  contain  glycogen  and  thus,  stain    
  urethritis,  and  arthritis   of  iodine  or  Giemsa  
  • Fitz-­‐Hugh-­‐Curtis  Syndrome:   • Urethritis:  most  commonly  diagnosed  by  
  perihepatitis     polymerase  chain  reaction  of  urethral  
  • Lymphogranuloma  venereum   swab  or  urine  sample  
(LGV)   • Frei  test,  which  is  rarely  used,  is  similar  to  
o Serotypes  L1,  L2  &  L3     the  PPD  skin  test  for  tuberculosis    
  • Birds,   • Bird  feces  dry   • Life  cycle  is  similar     • Psittacosis   • Doxycycline   • Serologic   • History  of  occupational  
Chlamydophila   poultry   out,  fecal   to  Chlamydia   o A  viral-­‐like  atypical   • Erythromycin   o Examine  blood  for  elevated  titers  of   exposure  to  birds  
psittaci   particles  are   trachomatis   pneumonia,  with  fever  and     antibodies    compliment  fixation  and   • This  bacterium  can  infect  
inhaled,  infecting   dry,  non-­‐productive  cough     immunofluorescence  tests   parrots,  parakeets,  canaries,  
the  lungs   o Similar  to  Mycoplasma     • According  to  case  definitions  from  the   and  other  avian  species  (eg,  
• An  occupational   pneumonia)   CDC  (2000),  a  confirmed  case  involves   turkeys,  pigeons,  ducks).    
disease  of  zoo   one  of  the  following  criteria:   • Another  term  for  this  infection  
and  pet-­‐shop   o Isolation  of  the  organism  by  culture   is  ornithosis,  which  describes  
employees,   o Compatible  clinical  illness  with  a  4-­‐fold   the  infection  caused  by  
poultry  farmers,   rise  (to  a  reciprocal  titer  of  32  or   nonpsittacine  birds.  
and  ranchers.     greater  by  paired  sera  collected  at  least   • Psittacosis  is  found  worldwide.  
• Human-­‐to-­‐ 2  weeks  apart)  in  CF  or  MIF  antibodies   The  incidence  seems  to  be  
human   against  C  psittaci     increasing  in  developed  
transmission  is   o Detection  of  an  IgM  titer  of  16  or   countries,  which  is  correlated  to  
rare.   greater  against  C  psittaci  by  MIF   the  import  of  exotic  birds.  
  15  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 

MICRO-­‐   VIRULENCE   TREATMENT  AND  

RESERVOIR   TRANSMISSION   METABOLISM   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   FACTORS   PREVENTION  
  • Humans   • Respiratory   • Life  cycle  is     • Atypical  pneumonia   • Macrolides  (first-­‐ • Serologic  (Gold  Standard)   • Accelerated  atherosclerosis  
Chlamydophila   (spread   route   similar  to   o Viral  like  atypical   line  antibiotics)   o Examine  blood  for  elevated  titers  of   • Culture  for  C.  pneumoniae  is  technically  
pneumoniae   from   Chlamydia   pneumonia  (similar  to   • Doxycycline   antibodies  with  compliment  fixation  and   complex  and  time  consuming.  When  
human  to   trachomatis   Mycoplasma)  in  young   • Erthromycin   immunofluorescence  test.       compared  to  serology  and  PCR,  it  also  has  
human)   adults     o Criteria  for  infection  include  a  single  IgM  titer   low  sensitivity  and  is  mainly  used  in  research  
≥1:16  or  a  4-­‐fold  increase  in  IgG  titer.   labs  
• Intracytoplasmic  inclusion  bodies  do  not  stain   • The  Film  Array  Respiratory  Panel  is  a  
with  iodine   multiplex  PCR,  which  detects  common  
• The  Infectious  Diseases  Society  of  America  and   respiratory  pathogens  in  nasopharyngeal  
American  Society  of  Microbiology  currently   specimens.  In  2012,  the  US  Food  and  Drug  
recommend  serologic  testing  or  polymerase   Administration  (FDA)  approved  the  addition  
chain  reaction  (PCR)  for  the  diagnosis  of  C   of  2  corona  viruses  and  3  bacteria  to  the  
pneumoniae.  Despite  evident  drawbacks,   Panel,  including  C  pneumoniae,  Bordetella  
serology  is  still  considered  the  gold  standard.   pertussis,  and  Mycoplasma  pneumonia.  The  
• Real-­‐time  PCR  assays  of  pharyngeal  swab,   Film  Array  Panel  can  now  detect  17  viruses  
bronchoalveolar  lavage,  sputum  or  tissue  can  be   and  3  bacteria  from  a  single  sample.  
used  to  detect  C  pneumoniae-­‐specific  DNA.   Reported  sensitivity  and  specificity  were  both  
Because  of  the  complexity  of  these  tests,   100%  for  C  pneumoniae  but  the  sample  size  
widespread  implementation  had  been  limited   was  small  and  fewer  than  10  samples  were  
until  recent  years.   positive  in  the  study.  
  • Dogs   • Wood  tick:  In       • Rocky  mountain  spotted   • Doxycycline   • Clinical  exam    
Rickettsia  rickettsii   • Rabbits       western  U.S   fever:     • Chloramphenicol   • Direct  immunofluorescent  exam  of  skin  biopsy  
• Wild   Dermacentor   o Fever     from  rash  site  
rodents   andersoni   o Conjunctival  injection     • Serology  
• Dog  tick:  In   (redness)     • Well-­‐Felix  reaction  
Eastern  U.S   o Severe  headache     o Positive  OX-­‐19  
Dermacentor   o Rash  on  wrists,  ankles,   o Positive  OX-­‐2  
variabilis   soles  and  palms  initially,  
become  generalized  
later  
  • House   • Mites  (which  live       • Rickettsial  Pox:     • Doxycycline   • Well-­‐Felix  reaction  negative    
Rickettsia  akari   mice   on  the  house   o Vesicular  rash  similar  to   • Chloramphenicol  
mice)   chicken  pox.  
o Resolves  over  2  weeks  
  • Humans   • Human  body       • Epidemic  Louse-­‐borne   • Doxycycline   • Well-­‐Felix  reaction   • Epidemic  typhus  is  caused  by  Rickettsia  
Rickettsia  prowazekii   • Flying   louse  (Pediculus   typhus   • Chloramphenicol   o Positive  OX-­‐19   prowazekii  and  transmitted  by  human  body  
squirrels   humanus  var.   o Abrupt  onset  of  fever   • Eradicate  human   • Serology   lice.    
  corporis)   and  headache   lice     • For  centuries,  it  has  been  associated  with  
  o Rash,  which  spares  the       overcrowding,  cold  weather,  and  poor  
  palms,  soles,  and  face       hygiene.    
  o Delirium/stupor       • Brill-­‐Zinsser  disease  is  a  recurrent  form  of  
  o Gangrene  of  hands  or       epidemic  typhus  that  is  unrelated  to  louse  
  feet       infestation  and  develops  sporadically  years  
  • Brill-­‐Zinsser  Disease:       after  the  primary  illness.  Clinical  features  are  
o Reactivation  of   similar  to,  but  milder  than,  those  of  epidemic  
Rickettsia  prowazekii   typhus.  
o Mild  symptoms  
o NO  rash  
  16  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 
 

MICRO-­‐   TREATMENT  AND  

RESERVOIR   TRANSMISSION   METABOLISM   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   PREVENTION  
  • Rats   • Rat  flea         • Endemic  (or  murine)  typhus   • Doxycycline   • Well-­‐Felix  reaction    
Rickettsia   • Small   (Xenosylla  cheopsis)   o Fever   • Chloramphenicol   o Positive  OX-­‐19  
Typhi   Rodents   o Headache    
      o Rash  
  • Rats   • Mite  larvae         • Scrub  typhus:     • Doxycycline   • Well-­‐Felix  reaction    
Orientia   • Shrew   (chiggers)   o Fever  and  headache   • Chloramphenicol   o Positive  OX-­‐K  
tsutsugamushi   • Mongooses   o Eschar  (scab)  at  bite  site    
• Birds   o Followed  by  a  rash    
  • Humans     • Body  louse   • Not  an  obligate     • Trench  Fever   • Doxycycline   • Serology    
Bartonella  quintana   intracellular   o Fever,  headache  and  back  pain.     • Chloramphericol   • PCR  
parasite   o Last  for  5days  recurs  at  5  day   • Azithromycin    
interval    
• Bacteremia,  endocarditis,  and  
baciliary  angiomatosis  
  • Cats   • Cat  bite  or  scratch   • Not  an  obligate               • Cat-­‐scratch  disease   • Azithromycin   • Serology   • Bacillary  angiomatosis  is  a  
Bartonella  henselae   intracellular   • Baciliary  angiomatosis   • Doxycycline   • PCR   differential  diagnosis  for  
parasite   • Bacteremia       Kaposi’s  sarcoma  
• Endocarditis,  “culture  negative”      
  • Cattle   • No  anthropod  vector   • Can  grow  at  pH     • Q  fever   • Doxycycline   • Complement  fixation  test   • This  is  the  only  rickettsial  
Coxiella  burnetii   • Sheep   required.     4.5  within   o Fever,  headache  &  viral-­‐like   • Erythromycin   demonstrating  a  rise  in   disease  without  a  skin  rash.  
• Goats   • Direct  airborne   phagolysosomes   pneumonia.     • Pasteurize  milk  at   antibody  
o
transmission  of   • Has  an  endospore   o No  rash!   60 C   • PCR  
endospore  from  cow   form   • Complications:      
hide  or  dried  placenta,     o Hepatitis    
or  via  consumption  of     o Endocarditis  
endospore-­‐
contaminated  
unpasteurized  cowmilk    
  • Deer   • Ticks       • Clusters  of  Ehrlichia   • Human  ehrlichiosis   • Doxycycline   • Rise  in  acute  and  convalescent   • Ehrlichiosis  is  an  infection  of  
Ehrlichia  chaffeensis   • Dogs     multiply  in  host   o Similar  to  rocky  mountain   • Rifampin     antibody  liters   white  blood  cells  that  affects  
  • Coyotes   monocyte  vacuoles   spotted  fever,  but  rash  is  rare   • Resistant  to   • Characteristic  ehrlichial   various  mammals,  including  
Anaplasma     (phagosomes)  to  form   chloramphericol   inclusion  bodies  are   mice,  cattle,  dogs,  deer,  
phogocytophilum   • Deer   large,  mulberry-­‐   sometimes  seen  in  leukocytes   horses,  sheep,  goats,  and  
  • White-­‐footed   shaped  aggregates     on  blood  smears   humans  
Ehrlichia  ewingii   mouse   called  morulae   • PCR   • The  primary  target  cell  for  
        human  monocytic  erlochiosis  
      (HME)  is  the  macrophage,  and  
the  primary  target  for  human  
granulocytic  anaplasmosis  
(HGA)  is  the  granulocyte.    
• Intracellular  infection  is  
established  within  
phagosomes,  most  often  
found  in  macrophages  in  the  
liver,  spleen,  lymph  nodes,  
bone  marrow,  lung,  kidney,  
 
and  CNS.  
 
 
 

  17  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   VIRULENCE   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   FACTORS   PREVENTION  
  • Humans  only   • Sexual     • Microaerophilic     • Motile   • Syphilis   • Penicillin  G   • Jarisch-­‐Herxheimer  reaction:  
Treponema   • Morphology:  thick  rigid   o Primary:  painless  chancre     • Erythromycin     acute  worsening  of  symptoms  
pallidum   spirals   o Second  stage:  Rash  on  palms  and  soles   • Doxycycline   after  Penicillin  is  started  
pallidum   • Highly  sensitive  to   § Condylomata  lata:  painless,  wart-­‐like     • Between  1905  and  1910,  
  elevated  temperatures   lesion  which  occurs  in  warm,  moist     Schaudinn  and  Hoffman  
    places  (vulva  or  scrotum)   identified  T.  pallidum  as  the  
  § CNS,  eyes,  bones,  kidneys  and/or   cause  of  syphilis,  and  
joints  can  be  involved   Wasserman  described  a  
o Latent:  25%  may  relapse  back  to  the     diagnostic  test  for  the  long-­‐
secondary  stage   • Cultaneuos  lesions  examined   recognized  infection.  
o Tertiary  (33%)   by  dark  field  microscopy,   Pathogenic  treponemes  are  
§ Gummas  of  skin  and  bone   immunofluorescence,  ELISA,   associated  with  the  following  
§ Cardiovascular  syphilis  (aortitis)   or  silverstain   4  diseases:  
§ Neurosyphilis:  Agryll-­‐Robertson  pupil   • Non-­‐specific  treponemal  tests   o Venereal  syphilis    
• Congenital  syphilis   o VDRL   § by  T  pallidum  pallidum  
o Contacted  transplacentally  (MCC  of   o RPR   o Yaws  
death  is  pulmonary  hemorrhage)       • Specific  treponemal  test   § by  T  pallidum  pertenue  
o According  to  a  Centers  for  Disease   o FTA-­‐ABS   o Endemic  syphilis  (bejel)  
Control  and  Prevention  report,   o MHA-­‐TP   § by  T  pallidum  endemicum    
untreated  syphilis,  especially  early   • VDRL  and  FTA-­‐ABS  are  positive   o Pinta  
syphilis,  during  pregnancy  can  lead  to     § by  T  carateum  
deafness,  neurologic  impairment,  bone    
deformities,  stillbirth,  and  neonatal  
death  
Borrelia   • White-­‐footed   • Vector  =  Ixodes   • Microaerophilic     • LYME  DISEASE   • Doxycycline  (DOC)   • Largest  medically  important  
burgdorferi   mouse     ticks   o Early  localized  stage  (stage  1)     • Amoxicilin   bacterium  (size)  
• White-­‐tailed  deer   • Ixodes  scapularis:   § Erythema  chronicum  migrans  (ECM)   • Ceftriaxone  for    
  East  &  Midwest   o Early  disseminated  stage  (stage  2)   neurologic  disease    
  • Ixodes  pacificus:   § Multiple  smaller  ECM      
  West  coast   § Neurologic:  aseptic  meningitis,      
  • Together  with   cranial  nerve  palsies  (Bell’s  palsy),      
  Babesia  microti   and  peripheral  neuropathy        
    § Cardiac:  transient  heart  block  or     • Elevated  levels  of  antibodies    
  myocarditis     against  Borellia  burgdorferi  
  § Brief  attacks  of  arthritis  of  large   ban  be  detected  by  ELISA  
joints  (knee)   • Western  immunoblotting  
o Late  stage  (stage  3):    
§ Chronic  arthritis      
§ Acrodermatitis  chronica  atrophicans  
§ Encephalopathy  
 
 
 
 
 
 
 
 

  18  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   VIRULENCE   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   FACTORS   PREVENTION  
  • Zoonotic  (dogs,   • Direct  contact   • AEROBIC  –  the     • Leptospiremic  phase   • Penicillin  G   • First  week   • The  traditional  system  
Leptospira   cats,  livestock,   with  infected   other  spirochetes   o Organisms  in  blood  and  CSF   • Doxycycline  for   o Culture  blood  or  cerebral  spinal  fluid  (on  lab  media,  or  by   divided  the  genus  into  
interorgans   and  wild   urine  or  animal   are   o S/SX:  high  spiking  temperature,   chemo-­‐ inoculation  into  animals   2  species  
  animals)   tissue     microaerophiles   headache  and  severe  muscle  aches   prophylaxis   o Pathogenic  
  • History  of   • Organism   • Spiral  shaped,   (thighs  and  lower  back)     Leptospira  
23  serogroups   wading  in  flood   penetrate   with  hooks  on   • Immune  phase     interrogans  
rd
250  serovars   water  (in  3   broken  skin   both  ends  (“ice   o Correlates  with  emergence  of  IgM     o Nonpathogenic  
    world  setting)   (i.e.  on  feet)   tongs”)  à   o Involves  recurrence  of  the  above     Leptospira  biflexa.    
    • History  of   and  mucous   Shepherd’s  crook   symptoms,  often  with     • These  species  were  
    exposure  to   membranes   appearance   meningismus  (neck  pain)   • Second  week  to  months   divided  further  into  
    animals   (swallowing   • Two  axial  flagella   • WEIL’S  DISEASE   o Culture  urine     serogroups,  serovars,  
(butcher)     urine-­‐ wrap  around  and   o Most  severe  case  of  leptospirosis   • Rarely,  dark  field  microscopy  is  successful  (not   and  strains  based  on  
  contaminated   run  along  the   with  renal  failure,  hepatitis  (and   recommended)   shared  antigens.  L  
  water)     length  of  the   jaundice),  mental  status  changes,   • Antibody  based  ELISA  to  detect  Leptospira  antigens  in  the   interrogans  included  
organism  under   and  hemorrhage  in  many  organs.     urine   more  than  250  
the  outer   o ECG  abnormalities  are  common   • Polymerase  Chain  Reaction  (PCR)  to  detect  bacterial  DNA  in   serovars.  
membrane   during  the  leptospiremic  phase  of   serum,  CSF  and  urine    
(oeriplasmic   Weil  syndrome.     • Microscopic  agglutination  testing  (MAT)      
flagella)   o In  severe  cases,  congestive  heart   o The  criterion  standard  for  serologic  identification  of    
  failure  and  cardiogenic  shock  may   leptospires    
  occur.   o Available  only  at  reference  laboratories  
  • 40%  of  total   • Aerobic   • Mycosides   • No   • Tuberculosis   • First  line  drugs:   • Acid-­‐fast  stain  of  specimen  (carbolfuchsin  primary  stain;   • Mycolic  acids  are  also  
Mycobactrium   cell  dry  weight   • Catalase-­‐ • Cord  factor:  only   exotoxin   o Primary  tuberculosis:   o Isoniazid   methylene  blue  secondary  stain)   found  in  Nocardia  
tuberculosis   is  lipid     positive     found  in  virulent   nor   § Asymptomatic   (INH)   • RAPID  CULTURE:   (which  also  is  acid  fast)  
• Composed  of   • Slow  growth   strain  (May  be   endotoxin   § Overt  disease,  involving  the   o Rifampin   o Bactec  radiometric  culture   • Purified  Protein  
mycolic  acids   rate   responsible  for   lungs  or  other  organs   o Pyrazinamide   o A  liquid  broth  in  a  bottle,  with  radioactive  palmitate  as  a   Derivative  (PPD)  Test    
• Thin  rods     release  of  tumor   o Reactivation  or  secondary   o Ethambutol     carbon  source.  Mycobacteria  grow  and  use  the  carbon,   o Measure  zone  of  
• Non-­‐motile     necrosis  factor   tuberculosis:   o Streptomycin   allowing  early  detection  (in  1-­‐2  weeks)  even  before   unduration:  Positive  
• Facultative     • Sulfatides:  inhibit   1.  Pulmonary     colonies  can  be  seen.   reaction  
intracellular     phagosome-­‐ 2.  Pleural  or  pericardial     • PPD  skin  test   § >5mm  (immune-­‐
growth:  M.     lysosome  fusion   3.  Lymph  node  infection     • Chest  X-­‐ray   compromised  
tuberculosis     • Wax  D:  acts  as  an   4.  Kidney   • PCR  and  DNA  probes   host)  
can  survive  and   adjuvant   5.  Sketetal   • Mycobacterium  Tb  Direct  Test  (MTDT):  amplifies  ribosomal   § >10  mm  (have  
multiply  in   • Iron  siderophore   6.  Joints   RNA  in  respiratory  secretions,  allowing  rapid  identification  of   chronic  disease  or  
macrophages   (mycobactin)   7.  Central  Nervous  System   M.  tuberculosis   risk  factors  for  
    8.  Miliary  Tuberculosis   • QuantiFERON-­‐TB   exposure  to  TB)  
      o Blood  test  that  measures  interferon  gamma  levels   § >15mm  (all  others)  
    produced  in  whole  blood  in  response  to  addition  of  specific   o A  positive  reaction  
  tuberculosis  antigens  has  been  approved  by  the  FDA.   does  not  mean  active  
o An  advantage  of  this  test  is  the  relative  specificity  for   disease.  
Mycobacterium  tuberculosis;  it  is  not  positive  in  patient  in   o Can  get  false  
previous  BCG  vaccination,  (MMWR,  Recommendation  and   negative  in  patients  
Reports,  2005)   with  AIDS  or  
• Luciferase  Reporter  Mycobacteriophage  (LRP)  Assays     malnourished  
o Can  detect  Mycobacterium  tuberculosis  and  characterize   individuals  
mycobacterial  drug  susceptibility  patterns  within  24  to  48    
h  in  positive  cultures  (luciferase  is  an  enzyme  obtained    

 
from  fireflies)  

  19  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   VIRULENCE   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   FACTORS   PREVENTION  
  • Humans   • Catalase-­‐positive   • Non-­‐motile     • Leprosy     • Rifampin   • Can  NOT  be  grown  on  artificial   • Lepromin  skin  test  
Mycobacterium   • Armadillos   • Grows  best  at  low   • Facultative   o The  most  common  cause  of   • Dapsone   lab  media:  can  only  be   o Although  not  useful  for  diagnosis,  it  allows  
leprae     temperature   intracellular   crippling  of  the  hand   • Clofazimine   cultured  in  certain  animals,   positioning  of  patients  on  the  immunologic  
  • Phenolase-­‐positve:   growth   • Lepromatous  leprosy  (LL)     such  as  mice  foot  pads,   spectrum  
  converts  DOPA  into     o Low  cell-­‐mediated  immunity     armadillos  or  monkeys   • Also  known  as  Hansen  disease,  named  after  G.A.  
  a  pigmented     o Organisms  found  everywhere     • Skin  or  nerve  biopsy  will  reveal   Hansen,  who  is  credited  with  the  1873  discovery  
  product  (used  for     (organs  and  blood)     acid-­‐fast  bacilli  (lepromatous)   of  M  leprae.  
diagnosis)     o Skin,  nerves,  eyes  and  testes   or  granulomas  (tubercoloid)     • Classification  of  leprosy  (2  classifications)  
    involved  bilaterally:  multiple  skin     o Ridley-­‐Jopling  system  
  lumps  and  bumps,  leonine  facies,   § 5-­‐category  
  saddle  nose,  peripheral   § Depending  on  the  host  response  to  the  
  neuropathy,  digit  absorption,   organism,  leprosy  can  manifest  clinically  
blindness  and  infertility  in  men   along  a  spectrum  bounded  by  the  
(from  testicular  damage)   tuberculoid  and  lepromatous  forms  of  the  
• Tubercoloid  leprosy  (TL)   disease.    
o Intact-­‐cell  mediated  immunity   § Most  patients  fall  into  the  intermediate  
o Difficult  to  isolate  M.  leprae  from   classifications,  which  include  borderline  
skin  or  blood   tuberculoid  leprosy,  midborderline  leprosy,  
o Skin  and  nerves  involved:  1  or  2   and  borderline  lepromatous  leprosy.    
superficial  unilateral  lesions     § The  classification  of  the  disease  typically  
    changes  as  it  evolves  during  its  progression  
• Damage  in  the  following  nerves  is     or  management.    
associated  with  characteristic     § The  Ridley-­‐Jopling  system  is  used  globally  
impairments  in  leprosy   and  forms  the  basis  of  clinical  studies  of  
o Ulnar  and  median  -­‐  clawed  hand   leprosy.  It  may  also  be  more  useful  in  guiding  
o Posterior  tibial  -­‐  Plantar   treatment  regimens  and  assessing  risk  of  
insensitivity  and  clawed  toes   acute  complications.    
o Common  peroneal  -­‐  Foot  drop   § Physical  findings  in  each  subtype  are  
o Radial  cutaneous,  facial,  and   presented  in  the  Clinical  section.  
greater  auricular  nerves  (may  also   o WHO  standard  (simpler  and  more  commonly  
be  involved)   used)  
  § Classified  according  to  the  number  of  lesions  
and  the  presence  of  bacilli  on  a  skin  smear  
§ This  method  is  useful  in  countries  where  
biopsy  analysis  in  unavailable.  
• Paucibacillary  
o Leprosy  is  characterized  by  5  or  fewer  lesions  
with  absence  of  organisms  on  smear.    
o Generally  includes  the  tuberculoid  and  
borderline  lepromatous  categories  from  the  
Ridley-­‐Jopling  system.  
• Multibacillary  
o Leprosy  is  marked  by  6  or  more  lesions  with  
possible  visualization  of  bacilli  on  smear.    
o Lepromatous  leprosy,  borderline  lepromatous  
leprosy,  and  midborderline  leprosy  on  the  
Ridley-­‐Jopling  scale  are  included  in  the  
 
multibacillary  leprosy  category.  
 

  20  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   PREVENTION  
  • No  cell  wall   • Requires  STEROL   • Protein  P1  adhsesin   • Community-­‐acquired   • Tracheobronchitis   • Macrolides   • Cold  agglutinins   • Chest  X-­‐ray  will  show  patchy  infiltrates  that  
Mycoplasma   • Pleomorphic:  can   for  membrane   o Adheres  to   respiratory  disease   • Walking  pneumonia  (also  called   (azithromycin,   • Complement  fixation  test   look  worse  than  physical  examples  and  
pneumoniae     appear  round  to   formation  à   epithelial  cells  of   toxin  (CARDS)   atypical  pneumonia):     clarithromycin)   clinical  symptoms  suggest  
  oblong  shaped   bacteria  do  not   the  respiratory   o Exotoxin  that  is   o Fever  with  a  dry   • Tetracyclines   • Disease  usually  occurs  in  children,  
The  smallest   • Smallest  bacteria   normally  contain   tract   believed  to  play  a   o Non-­‐productive  hacking  cough   (doxycycline)   adolescents  and  young  adults  
free-­‐living   capable  of   sterols   o Mediates   major  role  in  the     • Quinolones   • CHILD  5-­‐15  YEARS  OLD  WITH  
organisms   growth  &   • Aerobic  (the   attachment,   damage  to  the     (ciprofloxacin,   PNEUMONIA?  THINK  MYCOPLASMA!  
  reproduction   other   followed  by   respiratory     levofloxacin)   Children  with  sickle  cell  disease  and  
  outside  a  living   mycoplasmas  are   induction  of   epithelium  that     • Penicillin  and     functional  asplenia  may  be  at  greater  risk  
cell  (smaller  that   facultative   ciliostasis,  local   occurs  during  acute     cephalosporins   • Culture   for  severe  respiratory  tract  disease  
some  viruses:  1-­‐2   anaerobes)   inflammation   infection.       do  NOT  work  as   o Takes  2-­‐3  weeks  (Eaton’s    
microns)     that  consists   o An  ADP-­‐ribosylating   mycoplasma  does   agent)   • Although  scientists  have  isolated  at  least  
• Motile  (glides)     primarily  of   and  vacuolating   not  have  a  cell   o Requires  cholesterol  and   17  species  of  Mycoplasma  from  humans,  4  
    perivascular  and   cytotoxin  similar  to   wall   nucleic  acids   types  of  organisms  are  responsible  for  
    peribronchial   pertussis  toxin     o Add  penicillin  to  inhibit   most  clinically  significant  infections  that  
    infiltration  of   • Evidence  from  animal     growth  of  contaminating   may  come  to  the  attention  of  practicing  
    mononuclear   models  of  M.     bacteria   physicians.  These  species  are:  
leukocytes,  and   pneumoniae  infection     o Dome-­‐shape  colonies  with   o Mycoplasma  pneumoniae    
tissue  destruction   have  proven  that   “fried  egg”  appearance  or   o Mycoplasma  homini  
that  may  be   recombinant  CARDS   “mulberry”  appearance   o Mycoplasma  genitalium  
mediated  by   toxin  results  in   (in  the  case  of   o Ureaplasma  species.  
liberation  of   significant  pulmonary   Mycoplasma  pneumoniae)    
hydrogen   inflammation,  release   • Rapid  identification  Test:    
peroxide   of  proinflammatory   o Sputum  can  be  tested    
cytokines,  and  airway   with  DNA  probes  (nucleic    
dysfunction.  [PLoS   acid  hybridization)    
One.  2009.   o PCR  sputum  samples.    
4(10):e7562]  
  • Normal  flora  of   • Gram-­‐positive       • Actinomycosis   • Penicillin  G   • Examine  tissue  or  pus  from   • Yellow  “sulfur  granules”  
Actinomyces   the  mouth  and  GI   rod;    filamentous   o Subacute,  chronic,  cellulitic   • Surgery   infection  site,  and  look  for   o Microcolonies  of  Actinomyces  and  
israelii   tract   bacterium   invasion  of  the  soft  tissues     “sulfur  granules”   cellular  debris  
• Anaerobic   that  causes  the  formation  of     • Anaerobic  culture   • All  species  of  Actinomyces  are  normal  
bacteria  (ABC!)   external  sinus  tracts  that       commensal  inhabitants  of  the  oral  and  
• Grow  as   discharge  sulfur  granules.         buccal  cavities  in  humans  and  certain  other  
branching  chains   o This  process  spreads     mammals.    
or  beaded   unimpeded  by  traditional     • They  cannot  be  classified  as  symbiotic  
filaments   anatomic  barriers  after  the   organisms  because  they  do  not  have  a  
  endogenous  oral  commensal   mutually  beneficial  relationship  with  their  
  organisms  invade  the  tissues   host.  They  are  not  true  parasites  because  
  of  the  face  and  neck.   they  usually  do  not  cause  harm  to  the  host;  
o May  also  spread  to  the   however,  they  definitely  assume  a  parasitic  
pulmonary  and  GI  systems.   role  when  they  result  in  an  infection  with  
• Eroding  abscesses  of  the  mouth,   an  inflammatory  tissue  response.  
lung  or  gastrointestinal  tract,   • Does  not  appear  to  be  an  opportunistic  
classified  as:   infection  because  actinomycosis  is  not  
o Cervicofacial  actinomycosis   common  in  patients  who  are  
o Thoracic  actinomycosis   immunosuppressed  or  in  patients  with  
o Abdominal  actinomycosis   AIDS  
 

  21  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
MICRO-­‐   TREATMENT  AND  
RESERVOIR   TRANSMISSION   METABOLISM   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   DIAGNOSIS   NOTES  
ORGANISM   PREVENTION  
  • Never  part  of  the   • Gram-­‐positive       • Pneumonia   • Thrimethoprim/sulfa • Nocardia  infection  usually  occurs  in  
Nocardia   normal  flora   rods   • Formation  of  abscesses  in  the   methozole   immunocompromised  patients  
asteroides   • Respiratory   • Partially  acid-­‐ lung,  kidney,  and  central      
transmission   fast:  due  to   nervous  system   • SNAP    
• Members  of  the   mycolic  acids  in     o Sulfa  à  Nocardia    
genus  Nocardia   the  cell  wall                      Actinomyces  ß    
are  aerobic   • Aerobic     Penicillin  
 
actinomycetes   • Grow  as   • Gram-­‐stain  
that  are   branching  chains   • Modified  acid-­‐fast  stain:  
ubiquitous   or  beaded   Decolorized  with  1%  
saprophytes  in   filaments   sulfuric  acid  instead  of  
soil,  decaying     acid  alcohol.      
organic  matter,   • Nocardia  are  typically  
and  fresh  and  salt   weakly  acid-­‐fast  after  
water.     traditional  staining  and  
positive  on  modified  acid-­‐
fast  staining,  but  this  is  
not  invariable.  
• Aerobic  culture  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  22  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 
VIRUS  
 
DNA  VIRUSES   RNA  VIRUSES  
 

           
 
                                                                     
 
NOTES:  
 
 
 
 
 
 
 
 
  23  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 

VIRUS   TAXONOMY/MORPHOLOGY   TRANSMISION   CLINICAL   TREATMENT     SEROLOGY  

HEPATITIS  
  • Picornaviridae   • Fecal-­‐oral   • Acute  viral  hepatitis     • Pooled  immune  serum  globulin   • Anti-­‐HAV  IgM    –  Active  disease  
Hepatitis  A   • Positive  (+)  single-­‐stranded  RNA   o Fever   • Supportive  care   • Anti-­‐HAV  IgG  –  Old:  No  active  disease  against  repeated  infection  
• No  envelope  (naked)   o Jaundice   • HAV  vaccine    
• Icosahedal  capsid   o Painful  enlarged  liver    
  • Hepadnaviridae     • Blood  transfusion   • Acute  viral  hepatitis   • Prevention:  Hepatitis  B  recombinant   • HBsAg  –  Disease  (acute  or  chronic)  
Hepatitis  B   • Double-­‐stranded  circular  DNA   • Needlestick  injury   • Fulminant  haepatitis   vaccine     • Anti-­‐HbsAg  –  immunity  provides  protection  against  repeated  infection  
• Enveloped   • Sexual   o Severe  acute  hepatitis  and  rapid   • Screen  blood  to  remove  HBV   • IgM  anti-­‐HBcAg  –  New  infection  
Icosahedal  capsid   • Across  the  placenta   destruction  of  liver   contaminated  blood  to  the  donor  pool   • HBeAg  –  high  infectivity  
• Dane  particle  (intact  virus)  includes:     • Perinatally   • Chronic  hepatitis  (10%)   • Treatment  options   • Anti-­‐  HBeAg  –    Low  infectivity  
o Envelope     o Asymptomatic  carrier   o Interferons  
o Capsid-­‐  associated  proteins     o Chonic  persistent  hepatitis   § Interferon  alfa  
o Capsid     o Chronic  active  hepatitis   § Pegylated-­‐interfron  alfa)    
o Core  (DNA+protein  enzymes)   • Coinfection  or  superinfection  with   o Nucleoside  analogs  
o Hepatis  B  surface  antigen  (HBsAg),     hepatitis  Delta  virus  (HDV)   § Lamivudine  
o Envelope   • Complications:  primary   § Adefovir  
o Capsid-­‐associated  proteins   hepatocellular  carcinoma,  cirrhosis   § Entecavir  
o Heptitis  B  core  antigen  (HBcAg)     § Telbivudine  
• Double-­‐stranded  DNA   • Lamivudine    
• DNA  polymerase  enzyme   o Antiretroviral  drug  
• Capsid     o Also  used  in  HIV    
  o A  reverse  transcriptase  inhibitor   • Hepatitis  B  antigen  (HBeAg):  soluble  component  of  the  core,  which  is  
because  HBV  also  expresses  reverse   marker  for  active  disease  
transcriptase  
  • Flavivirus   • Blood  transfusion   • Acute  viral  hepatitis   • Treatment:  combination  therapy  with   • Screening  anti-­‐HCV  antibodies  
Hepatitis  C   • Single-­‐stranded  RNA   • Needlestick  injury   o Up  to  85%  develop  chronic  
hepatitis  
interferon  and  ribavirin    
• Enveloped  icosachedral  capsid   • Sexually  
  • Across  the  placenta   o 20%  will  develop  cirrhosis    
o Increased  risk  of  developing      
primary  hepatocellular  
carcinoma  (especially  with  
alcoholism)  
  • Incomplete  RNA  virus-­‐only  infective   • Blood  transfusion   • Coinfection:  HBV  and  HDV  are   • Control  of  HBV  infection  is  currently   • Serology  is  not  very  helpful,  since  detectable  titers  of  IgM  and  IgG  anti-­‐HDV  
Hepatitis  D   with  the  help  of  hepatitis  B  virus   • Needlestick  injury   acquired  at  the  same  time,  and   the  only  way  to  protect  against  HDV   are  present  only  fleetingly  
  • Helical  nucleocapsid  that  requires  the   • Sexual   caused  an  acute  hepatitis.  
Complementation   hepatitis  B  envelope  (HBsAg)  to  be   • Across  the  placenta   • Anti-­‐HBV  antibodies  help  cure  
with  HBV   infectious     infections  
        • Superinfection  
      o HDV  infects  a  patient  with  
      chronic  hepatitis  B  who  can  not  
      manufacture  Anti-­‐HBsAg  
antibodies  
• Complications:  
o Fulminany  hepatitis  
o B.  Cirrhosis  
  • Hepeviridae   • Fecal-­‐oral   • Hepatitis  (like  hepatitis  A)      
Hepatitis  E   • Single-­‐stranded  RNA   • High  mortality  in  pregnant  women  
 
• No  envelope  (naked)  

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
DNA  VIRUSES  
1.  HERPESVIRIDAE  
  • Double-­‐stranded  DNA   • Direct  contact  of  mucous   • Gingivostomatitis     • Acyclovir   • Tzanck  smear  reveals  multinucleated  giant  
HSV  1  AND  2   • Enveloped   membranes     o Reactivation  of  Gingivostomatitis  occurs  immunocompromised   • Valacyclovir   cells  with  intranuclear  inclusions  
• Icosahedral  symmetry   • Viral  shedding  usually  occurs  in   individuals     • Famciclovir   • Viral  culture  
  the  presence  of  obvious  herpetic   • Herpetic  keratitis     • Trifluridine  eye  drops:  for  corneal   • Polymerase  chain  reaction  
    lesions,  but  viral  shedding  can   o TEMPORAL  lobe  encephalitis:  infection  (most  cases  are   infection   • Serology  
    also  occur  when  there  no  visible   reactivation  of  latent  HSV-­‐1)  of  the  brain  results  in  cell  death     • Direct  Fluorescent  Antibodies  (DFA)  Ulcer  
    lesions   and  brain  tissue  swelling  ,  manifested  as  fever,  headache  and     base  scrapings  can  be  tested  with  
    • Sexually  transmitted   neurologic  abnormalities     antibodies  will  latch  onto  HSV  if  present  &  
    • HSV  travels  up  sensory  nerve  fibers   • Genital  herpes     will  fluoresce  
to  the  sensory  nerve  ganglia,   o Painful  group  local  vesicles  on  the  cervix,  or  on  the  external    
where  it  replicates  then  returns   genitalia  of  men  and  women.  Often  associated  with  fever  and    
along  the  sensory  nerve  fibers  to   viral  symptoms.  These  vesicles  usually  do  not  scar.    
produce  skin  lesions   o Reactivation  of  genital  herpes  similar  eruption  of  vesicles,  but    
(NEUROTROPISM,  LATENCY)   less  painful  and  vesicles  last  for  few  more  days  
  • Neonatal  herpes  
  o Acquired  during  the  passage  of  a  fetus  through  an  infected  
  birth  canal.    
  o The  risk  of  transmission  is  highest  when  a  primary  genital  
  infection  is  present  during  delivery  (One  of  the  TORCHES  
Organism)  
• Herpetic  whitlow  
• Disseminated  herpes  infection  of  organs  
      • Aerosolized  respiratory  secretions   • Varicella  (chicken  pox)   • Acyclovir   • Vesicles  are  described  as  few  drops  on  the  
VARICELLA-­‐       • Contact  with  ruptured  vesicles   o 2  week  incubation  period   • Valacyclovir   top  of  a  rose  petal  (a  red  base  with  fluid  
ZOSTER  VIRUS       • Zoster:  reactivation  of  VZV  from   o Fever  and  headache   • Famciclovir   filled  vesicle  on  top)  
(VZV)       dorsal  root  ganglion   o Rashes:  vesicles  first  erupts  on  the  trunk  and  face,  and  spread   • Varicella  vaccine   • Lesions  appear  in  all  stages  of  development  
    • Risk  factors  for  severe  varicella  in   to  involve  the  entire  body  (including  mucous  membranes).   • Zoster  immune  globulin   (erupting  papules,  active  vesicles,  crusting  
    neonates  are  as  follows:   Vesicles  erupt  in  crops,  so  one  crop  forms  as  another  crop     lesions)  at  a  single  time  à  differentiates  
    o The  first  month  of  life:  A   scabs  over.  Patients  are  infectious  until  all  their  lesions  scab     varicella  from  other  pediatric  rashes  
    neonate’s  first  month  of  life  is  a   over.     • Tzanck  smear  reveals  multinucleated  giant  
susceptible  period  for  severe   o Pneumonia  or  encephalitis  can  occur  in  immunocompromised   cells  
varicella,  especially  if  the  mother   patients      
is  seronegative.     • Zoster  (shingles)    
o Early  delivery:  Delivery  before  28   o Painful  eruption  of  vesicles  isolated  to  a  single  dermatome    
weeks’  gestation  also  renders  a   distribution.  The  vesicles  dry  up  and  form  crusts,  which    
baby  susceptible  because   disappear  in  about  3  weeks.    
transplacental  transfer  of   o Pain  in  the  dermatomal  distribution  can  last  for  months  in  the  
immunoglobulin  G  (IgG)   elderly.  
antibodies  occurs  after  this  time   • Herpes  zoster  ophthalmicus  
o Vesicles  on  one  side  of  the  forehead  and  on  tip  of  the  nose  (the  
dermatomal  distribution  of  the  first  division  of  cranial  nerve  V)  
may  be  associated  with  severe  corneal  involvement  that  
(similar  to  HSV)  can  lead  to  blindness  
• Although  most  varicella  infection  confers  life-­‐long  immunity,  
varicella  clinical  reinfections  among  healthy  children  have  been  
 
described  [Pediatrics.  2002  Jun.  109(6):1068-­‐73.]  

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
DNA  VIRUSES  
  • Virus  present  in  milk,  saliva,  urine  &   • Asymptomatic  infection  (latent  phase)   • Ganciclovir   • CMV  shell  viral  culture  
CYTOMEGALO-­‐ tears   • Congenital  disease  (TORCHES)   • Foscarnet   o Blood  buffy  coat  (WBC)  is  cultured  
VIRUS  (CMV)   • Transmission  occurs  with  prolonged   • CMV  mononucleosis  (heterophil-­‐negative)   • Cidofovir   overnight.  The  cells  are  then  centrifuged.    
exposure,  such  as  between  children  in   • Reactivation  in  immunocompromised  patients   • Formivirsen   o This  breaks  up  the  white  blood  cells,  
households  or  day  care  center   o Pneumonia   • Healthy  people  who  are  infected  with   releasing  CMV  antigens,  which  are  
• Sexual  transmission   o Retinitis  (MCC  of  blindness  in  HIV)   CMV  but  who  have  no  symptoms   detected  with  monoclonal  antibodies  
o Esophagitis   usually  do  not  require  medical   • CMV  has  been  detected  via  culture  (human  
o Disseminated  DIsease   treatment.   fibroblast),  serologies,  antigen  assays,  
  • Antiviral  treatment  is  used  for   polymerase  chain  reaction  (PCR),  and  
 
immunocompromised  individuals  who   cytopathology.    
• Double-­‐stranded  
linear  DNA   have  eye  infections  or  life-­‐threatening   • In  the  transplant  population,  antigen  assays  
illnesses  due  to  CMV.   or  PCR  is  used  (sometimes  in  conjunction  
• Enveloped  
Icoshedral  symmetry   • DOC  for  prevention  of  CMV  disease  in   with  cytopathology)  for  diagnosis  and  
solid-­‐organ  transplant  patients  is   treatment  determinations.  
valganciclovir  [Lancet.  2005  Jun  18-­‐24.   • Histology  
365(9477):2105-­‐15]   o Reveals  enlarged  (Cytomegalic)  cells  with  
• Currently,  no  vaccine  available     intranuclear  and  cytoplasmic  inclusion  
  bodies.  
o The  pathologic  hallmark  of  CMV  
infection  is  an  enlarged  cell  with  viral  
inclusion  bodies.  
• CMV  early  antigens  can  be  detected  in  
WBC’s.  These  antigens  are  an  early  marker  
for  infection  in  bone  marrow  transplant  
patients  
• PCR  testing  for  CMV  DNA  
  • Double-­‐stranded   • Intimate  contact  from  asymptomatic   • Infectious  mononucleosis   • Supportive     • Elevated  heterophileantibodies    
EPSTEIN-­‐BARR   linear  DNA   shedders  of  EBV   o S/SX:  Fever,  sore  throat,  severe  lethargy,  enlarged  lymph   • Differential  white  blood  cells  count  will  
VIRUS  (EBV)   • Enveloped   • Infects  human  B-­‐cells  à  transforms   nodes  and  spleen  (generalized)   show  elevated  “atypical  lymphocytes”  à  
• Icoshedral  symmetry   them  (Receptor:  CD  21)   o Infectious  mononucleosis  was  first  described  by  Sprunt  and   Downey  cells  
  • Immune  response  to  EBV  infection  is   Evans  in  the  Bulletin  of  the  Johns  Hopkins  Hospital  in  1920.   • Serology:  IgM  against  the  viral  capsids  
fever  à  occurs  because  of  cytokine   • Associated  with  Burkitt’s  B-­‐cell  lymphoma  (MCC  lymphoma   antigens  (VCA)    
release  consequent  to  B-­‐lymphocyte   in  children)    
invasion  by  EBV.      
• Lymphocytosis  observed  in  the  RES  is  
caused  by  a  proliferation  of  EBV-­‐
infected  B  lymphocytes.    
• Pharyngitis  observed  in  EBV  infectious  
mononucleosis  is  caused  by  the  
proliferation  of  EBV-­‐infected  B  
lymphocytes  in  the  lymphatic  tissue  of  
the  oropharynx.  
  • Double-­‐stranded   • Transmitted  by  saliva   • Roseola  (exanthum  subitum)   • Supportive   • Clinical  diagnosis  
HUMAN   linear  DNA   o High  fever  lasting  3-­‐5  days,  which  resolves,  and  is  followed  
HERPESVIRUS  6   • Enveloped   by  a  rash:  located  mostly  on  trunk,  which  lasts  just  a  day  or  
(HHV-­‐6)   • Icoshedral     two  
 
 
 
 
 

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 

VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
DNA  VIRUSES  
  • Double-­‐stranded   • Sexual  transmission,  especially   • Appears  to  be  the  cause  of  Kaposi’s  sarcoma   • HAART  is  an  integral  part  of  successful  Kaposi  sarcoma   • CD4  lymphocyte  counts  and  plasma  HIV  viral-­‐load  
HHV-­‐8   linear  DNA   with  MSM  practice   • Kaposi’s  sarcoma     therapy.     studies  should  be  performed  for  patients  with  
• Enveloped   o A  spindle-­‐cell  tumor  thought  to  be  derived  from   • HAART  may  be  tried  as  the  sole  modality  in   HIV  infection.  
• Icoshedral     endothelial  cell  lineage;  carries  a  variable  clinical  course   nonvisceral  disease.  For  visceral  disease,  
  ranging  from  minimal  mucocutaneous  disease  to   chemotherapy  may  be  added.  
  extensive  organ  involvement.     • The  following  local  therapies  can  be  used  for  palliation  
  o Categorized  into  4  types:   of  locally  advanced  symptomatic  disease  or  in  
  § Epidemic  of  AIDS-­‐related   individuals  who  have  cosmetically  unacceptable  
§ Immunocompromised     lesions:  
§ Classic,  or  sporadic     o Radiation  therapy    
§ Endemic  (African)     o Cryotherapy    
• AIDS-­‐related  Kaposi  sarcoma,  unlike  other  forms  of  the   o Laser  therapy    
disease,  tends  to  have  an  aggressive  clinical  course.  It  is   o Surgical  excision    
the  most  common  presentation  of  Kaposi  sarcoma.   o Intralesional  vinca  alkaloid  therapy    
o Topical  retinoids    
• Immunomodulation  with  interferon-­‐alfa  has  clinical  
activity  in  Kaposi  sarcoma  that  may  be  mediated  by  its  
antiangiogenic,  antiviral,  and  immunomodulatory  
properties.  
  • Complex  coat:   • Smallpox  is  a  high-­‐priority   • Smallpox   • Vaccine:  an  avirulent  pox  vaccine  was  developed  that   • No  animal  reservoirs  
2.  POXVIRIDAE   large,  brick-­‐ (category  A)  agent  for   o Causes  skin  lesions  and  death.     included  immunity  to  virulent  pox  virus   o Virologists  have  speculated  that  it  evolved  from  
shaped  virus   bioterrorism,  defined  as  follows  by   o This  disease  has  been  eradicated  from  the  earth.     an  African  rodent  poxvirus  10  millennia  ago.    
(making  it   the  CDC:   o Histopathology:  Guarnieri  bodies   o Because  of  the  absence  of  an  animal  vector,  
cytoplasmic  in   o Easily  disseminated  or   • Molluscum  contagiosum   communities  had  to  reach  a  critical  population  
location)   transmitted  from  person  to   o Small  white  bumps  with  a  central  dimple  (like  a  wart).     (estimated  at  200,000  around  3000  B.C.)  before  
• Double-­‐stranded   person     o Often  found  in  the  genital  region.     endemic  smallpox  could  be  established.  
linear  DNA   o High  mortality  rate  and  potential   o Histopathology:  Henderson-­‐Peterson  bodies   • Codes  for  DNA  and  RNA  polymerase  
• The  only  DNA   for  significant  public  health    
virus  to  replicate   effect  
in  cytoplasm   o Probable  instigator  of  panic  and  
social  disruption    
• Special  actions  required  for  public  
health  preparedness  
 
 
 
 
 
 
 
 
 
 
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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
DNA  VIRUSES  
2.  POXVIRIDAE  
  • Naked     • Human  papilloma  virus  (HPV)  causes  warts  (over  50  viral   • Methods  of  wart  removal   • Second  smallest  DNA  virus  
PAPOVAVIRIDAE   icosahedral   strains)   o Liquid  nitrogen  (freeze  them  off)    [Best  Method]   • HPV  is  oncogenic  because  of  E6  and  E7  genes  that  
  • Double-­‐stranded   Common  warts   Types  1,  2,  4  &  7   o Surgical   code  for  suppressors  of  human  tumor  suppressor  
circular  DNA   Genital  warts   Types  6,  11,  16,  18   o Electrosurgery  (laser  ablation)   genes.  
• Replicates  in   condylomata  acuminata   and  others   o Podophyllin:  for  genital  warts   • Condylomata  lata  –  syphilis  
nucleus   Laryngeal  warts   Types  6,  11   • Many  warts  resolves  spontaneously  in  1-­‐2  years   • Condylomata  acuminata  –  genital  warts,  okay?  
• Koilocytes   Penile,  vulvar,  cervical,  anal  CA   Type  16,  18,  31,  33   • Relapses  are  common  after  treatment,  because  HPV   • In  genital  intraepithelial  neoplasia,  it  is  essential  
  • About  50%  of  men  who  are  homosexual  and  have  anal   DNA  is  found  in  normal  appearing  tissue  around  the   to  determine  the  extent  of  disease  through  
  squamous  cell  carcinoma  (SCC)  have  a  history  of   wart   careful  inspection  and  colposcopy.  
    anorectal  warts     • Laboratory  studies  that  may  be  considered  
  • BK  Polyomavirus     include  the  following:  
  o Causes  kidney  disease  in  renal  transplant  patients,     o Cervical  cytologic  testing  with  the  Papanicolaou  
hemorrhagic  cystitis  in  bone  marrow  transplant   (Pap)  test  to  screen  for  cervical  neoplasia  
patients,  and  mild  respiratory  illness  in  children   (guidelines  for  cervical  cancer  screening  now  
• JC  polyomavirus   include  a  delay  in  the  initiation  of  screening  
o Progressive  multifocal  leukoencephalopathy,   and  longer  intervals  between  subsequent  
characterized  by  degenerative  central  nervous  system   screens  
white  matter  disease   o HPV  DNA  testing  (eg,  with  Hybrid  Capture  II  or  
polymerase  chain  reaction  [PCR]  assay)  for  
detection  of  HPV  and  posttreatment  follow-­‐up  
of  cervical  intraepithelial  neoplasia    
o The  acetic  acid  test:  This  test  can  be  used  in  
conjunction  with  colposcopy  to  examine  
cervical  lesions;  however,  it  is  reserved  for  
suspicious  lesions  and  should  not  be  used  for  
routine  screening  
  • Naked     • Childhood  upper  respiratory  tract  infections   • Illness  is  self-­‐limited   • Pharyngo-­‐conjunctival  fevel  
ADENOVIRIDAE   icosahedral   o Rhinitis  
• Double-­‐stranded   o Sore  throat    
circular  DNA   o Fever  
• Replicates  in   o Conjunctivitis  
nucleus   • Epidemic  keratoconjunctivitis  (pink  eye)  
• Epidemic  diarrheal  illness  in  infants  and  children  
  • Naked     • Erythema  infectiosum  (fifth  disease):  affects  children   • Illness  is  self-­‐limited   • Smallest  DNA  virus  
PARVOVIRIDAE   icosahedral   between  the  ages  of  4  to  12   • I.V.  immunoglobulin  can  be  used  with  aplastic  crisis  
  • Double-­‐stranded   • Fever  +  “Slapped  cheek”  rash  
PARVOVIRUS  B-­‐19   linear  DNA  virus   • Transient  aplastic  anemia  crisis  
    (negative   o Occurs  when  the  Parvovirus  stops  the  production  of  
stranded)   red  blood  cells  in  the  boone  marrow  
• Replicates  in  
nucleus  
 
 
 
 
 

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
RNA  VIRUSES  
1.  ORTHOMYXOVIRIDAE  
  • Negative  (-­‐)   • Hemagglutinin  (HA)  glycoprotein   • Influenza   • Vaccine  contraindicated  in  egg  allergies  (vaccine  grown  in  eggs)   • Antigenic  drift  
INFLUENZA  A   single-­‐stranded   o Binds  to  red  blood  cells  and  cells  of  the   o Fever   • Prevention  of  influenza  is  the  most  effective  management   o Small  mutations,  resulting  in  minor  changes  in  
(Human  and   RNA   upper  respiratory  tract   o Sore  throat   strategy.  Influenza  A  and  B  vaccine  is  administered  each  year   the  antigenicity  of  HA  or  NA.    
animal  strain)   Segmented  (7-­‐8)   o HA  is  then  cleaved  into  pieces  (HA1  &  HA2)   o Myalgias   before  flu  season.  The  CDC  analyzes  the  vaccine  subtypes  each   o This  results  in  epidemics  of  the  common  flu  
    genome   by  host  cell  proteases,  which  allows  HA  to   o Frontal  or  retro-­‐orbital  headache   year  and  makes  any  necessary  changes  on  the  basis  of  worldwide   • Antigenic  shift    
INFLUENZA  B   • Lipid  containing   activate  fusion.     o Nasal  discharge   trends.   o (occurs  with  Influenza  A)  
(Human  only   envelope   o The  viral  RNA  in  then  dumped  into  these   o Weakness  and  severe  fatigue   • Traditionally,  the  vaccine  is  trivalent  (ie,  designed  to  provide   o genomic  reassortment  
strain)   • Helical   cells   o Cough  and  other  respiratory   protection  against  3  viral  subtypes,  generally  an  A-­‐H1,  an  A-­‐H3,   o Major  changes  of  the  HA  or  NA  (including  
  symmetry   • Neuraminidase  (NA)  glycoprotein   symptoms   and  a  B).     acquisition  of  animal  HA  or  NA).  This  results  in  
INFLUENZA  C   • Replicates  in   o Breaks  down  neuraminic  acid,  an   o Tachycardia   • The  first  quadrivalent  vaccines,  which  also  provide  coverage   devastating  influenza  pandemics  
(Human  only   the  nucleus   important  component  of  mucin   o Watery  eyes   against  a  second  influenza  B  subtype,  were  approved  in  2012  and   • New  avian  influenza  H5N1  has  infected  hundreds  of  
strain)   (Retroviruses   • The  hemagglutinin  and  neuraminidase   • Complications     were  made  available  for  the  2013-­‐2014  flu  season.   people  and  represents  a  great  risk  of  starting  a  
are  the  only   variants  are  used  to  identify  influenza  A  virus   o Secondary  bacterial  pneumonias     human  pandemic.  
other  type  of   subtypes.     in  the  elderly     • Amantadine  and  Rimantidine  (used  in  parkinsonism)  prevent  viral   • Mortality  is  highest  in  infants  and  the  elderly.    
RNA  viruses  that   o For  example,  influenza  A  subtype  H3N2   o in  children  who  use  aspirin,  get   uncoating  of  influenza  A   • The  2012-­‐2013  season  was  notable  for  widespread  
replicate  in  the   expresses  hemagglutinin  3  and   liver  and  brain  disease   • Zanamivir  (inhaled)  &  Oseltamivir  (oral)  are  neuraminidase   disease  and  a  higher  death  rate  than  was  reported  
nucleus)   neuraminidase  2.  Reye’s  syndrome   Increased  mortality  in  the  elderly   inhibitors.  Can  shorten  course  of  influenza  A  and  B   in  previous  years.  In  addition,  the  predominant  
o The  most  common  subtypes  of  human   and  in  those  underlying   influenza  virus  subtype  was  an  H3N2,  in  contrast  to  
influenza  virus  identified  to  date  contain   pulmonary  and  cardiac  disease   dominance  by  H1N1  subtypes  in  recent  past  years.  
only  hemagglutinins  1,  2,  and  3  and   • Year  1918  -­‐  the  Spanish  flu  (though  cases  appeared  
neuraminidases  1  and  2.     earlier  in  the  United  States  and  elsewhere  in  
o H3N2  and  H1N1  are  the  most  common   Europe),  this  pandemic  killed  an  estimated  20-­‐50  
prevailing  influenza  A  subtypes  that  infect   million  persons  [Emerg  Infect  Dis.  2006  Jan.  12(1):9-­‐
humans.     14.]  
o Each  year,  the  trivalent  vaccine  used  
worldwide  contains  influenza  A  strains  
from  H1N1  and  H3N2,  along  with  an  
influenza  B  strain.  
• Because  the  viral  RNA  polymerase  lacks  
error-­‐checking  mechanisms,  the  year-­‐to-­‐
year  antigenic  drift  is  sufficient  to  ensure  
that  there  is  a  significant  susceptible  host  
population  each  year.    
• However,  the  segmented  genome  also  has  
the  potential  to  allow  reassortment  of  
genome  segments  from  different  strains  of  
influenza  in  a  coinfected  host.  
 
 
 
 
 
 
 
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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
RNA  VIRUSES  
2.  PARAMYXOVIRIDAE  
  • Negative  (-­‐)  single   • HA,  but  no  NA   • Measles     • Treatment  of  measles  is  essentially  supportive  care,  as  follows:   • Although  the  diagnosis  of  measles  is  usually  
MEASLES   stranded  RNA   • F-­‐protein  (fusion  protein)  –  leads  to   o One  of  the  most  contagious  infectious   o Maintenance  of  good  hydration  and  replacement  of  fluids  lost   determined  from  the  classic  clinical  picture,  
(RUBEOLA)   • Unsegmented   formations  of  multinucleated  giant  cells   diseases,  with  at  least  a  90%   through  diarrhea  or  emesis   laboratory  identification  and  confirmation  of  the  
• Lipid  containing     secondary  infection  rate  in   o IV  rehydration  may  be  necessary  if  dehydration  is  severe   diagnosis  are  necessary  for  public  health  and  
envelope     susceptible  domestic  contacts.     o Vitamin  A  supplementation  should  be  considered       outbreak  control.  Laboratory  confirmation  is  
• Helical  symmetry       o Despite  being  considered  primarily  a   • Post-­‐exposure  prophylaxis  should  be  considered  in  unvaccinated   achieved  by  means  of  the  following:  
• Replicates  in     childhood  illness,  measles  can  affect   contacts;  timely  tracing  of  contacts  should  be  a  priority.     o Serologic  testing  for  measles-­‐specific  IgM  or  IgG  
cytoplasm   people  of  all  ages.   • Patients  should  receive  regular  follow-­‐up  care  with  a  primary   titers  
o Prodrome:  high  fever,  hacking  cough   care  physician  for  surveillance  of  complications  arising  from  the   o Isolation  of  the  virus    
and  conjunctivitis     infection.   • Reverse-­‐transcriptase  polymerase  chain  reaction  
o Koplik’s  spots:  small  red-­‐based  blue-­‐ • WHO  recommends  vitamin  A  supplementation  for  all  children   (RT-­‐PCR)  evaluation  
white  centered  lesions  in  the  mouth   diagnosed  with  measles,  regardless  of  their  country  of   • Biopsy  of  rash  or  Koplik’s  spots  reveals  
o Rash:  from  head,  then  to  neck  and    
residence,  based  on  their  age, as  follows:   multinucleated  giant  cells  
torso,  then  to  feet.  As  the  rash   o Infants  younger  than  6  months:  50,000  IU/day  PO  for  2  doses   • Warthin-­‐Finkeldey  bodies  (multinucleated  giant  
spreads,  it  coaleces   o Age  6-­‐11  months:  100,000  IU/day  PO  for  2  doses     cells  in  measles)  
o Complications   o Older  than  1  year:  200,000  IU/day  PO  for  2  doses      
§ Pneumonia,  eye  damage,   • Children  with  clinical  signs  of  vitamin  A  deficiency    
myocarditis  and  encephalitis   o The  first  2  doses  as  appropriate  for  age,  then  a  third  age-­‐  
§ 20%  risk  of  fetal  death  if  acquired   specific  dose  given  2-­‐4  weeks  later  
by  a  pregnant  women  early  in  her   • Prevention:  MMR  vaccine:  
pregnancy          1.  Measles  (live  attenuated)  
• Subacute  Sclerosing  Panencephalitis:          2.  Mumps  
slow  form  of  encephalitis  that  occurs          3.  Rubella  
many  years  after  a  measles  infection  
(Damson  disease)  
  • Negative  (-­‐)  single   • Glycoproteins  with  combined  HA  and  NA   • Upper  respiratory  tract  infection  in   • Supportive:  racemic  epinephrine   • Isolation  and  identification  of  the  virus  in  cell  
PARA-­‐ stranded  RNA   activity   adults:  bronchitis,  pharyngitis,  rhinitis   • Antiviral  agents  are  of  uncertain  benefit   culture  or  direct  detection  of  the  virus  in  respiratory  
INFLUENZA  1   • Unsegmented   • F-­‐protein  (Fusion  protein):  results  in   • Viral  pneumonia:  in  children  elderly  and   • Antibiotics  are  used  only  if  bacterial  complications  (e.g.  otitis   secretions  by  means  of  immunofluorescent  assay,  
AND  2   • Lipid  containing   multinucleated  giant  cells  (called  syncytial   immunocompromised   and  sinusitis)  develop.   enzyme-­‐linked  immunosorbent  assay  (ELISA),  or  
envelope   cells)   • Croup     polymerase  chain  reaction  (PCR)  assay    
• Helical  symmetry     • Human  PIVs  are  common  community-­‐ o Children  develop  a  barking  cough  due     • Demonstration  of  a  significant  rise  in  specific  
• Replicates  in   acquired  respiratory  pathogens  without   to  infection  and  swelling  (narrowing)   immunoglobulin  G  (IgG)  antibodies  between  
cytoplasm   ethnic,  socioeconomic,  gender,  age,  or   of  the  larynx  à  STEEPLE  SIGN   appropriately  collected  paired  serum  specimens  or  
  geographic  boundaries.     HUMAN   Most  commonly   in  specific  immunoglobulin  M  (IgM)  antibodies  in  a  
• Many  factors  have  been  found  that   PIV-­‐1   associated  with  croup   single  serum  specimen  
predispose  individuals  to  these  infections,   HUMAN   Also  associated  with  croup  
including  the  following:   PIV-­‐2  
o Malnutrition     Second  only  to  RSV  as  a  
o Overcrowding     HUMAN   cause  of  pneumonia  and  
o Vitamin  A  deficiency     PIV-­‐3   bronchiolitis  in  infants  and  
o Lack  of  breastfeeding     young  children  
o Environmental  smoke  or  toxins   Detected  in  patients  less  
HUMAN   often,  perhaps  because  
PIV-­‐4   HPIV-­‐4  causes  less  severe  
 
disease.  
 
 
 

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
RNA  VIRUSES  
  • Negative  (-­‐)   • F-­‐protein     • Most  common  cause  of  pneumonia  in   •      Palivizumab   • Specific  diagnostic  tests  for  confirming  RSV  infection  include  the  following:  
RESPIRATORY   single  stranded   • NO  HA  nor  NA   infants  less  6  months  of  age   o Monoclonal  antibody  against  RSV   o Culture    
SYNCYTIAL  VIRUS   RNA   glycoproteins   • Acute  otitis  media  occurs  in  up  to  33%   that  is  produced  a  recombinant   o Antigen-­‐revealing  techniques    
(RSV)   • Unsegmented     of  children  with  RSV  illness   DNA.  It  is  given  intramuscularly.   o Polymerase  chain  reaction  (PCR)  assay    
  • Lipid  containing       • Ribavirin   o Molecular  probes  
The  leading  cause  of   envelope     o Primarily  reserved  for  patients    

lower  respiratory   • Helical  symmetry     with  significant  underlying  risk   The  American  Academy  of  Pediatrics  has  released  updated  guidelines  addressing  palivizumab  
tract  infections   • Replicates  in   factors  and  severe  acute  RSV   prophylaxis  for  respiratory  syncytial  virus  (RSV).  
(LRTIs)  in  infants  and   cytoplasm   disease  (eg,  transplant  recipients)   o According  to  the  updated  recommendations,  palivizumab  prophylaxis  for  RSV  should  be  limited  
young  children.   to  infants  born  before  29  weeks'  gestation  and  to  infants  with  chronic  illness  such  as  congenital  
    heart  disease  or  chronic  lung  disease.  Other  recommendations  include  the  following:  
    § Give  infants  who  qualify  for  prophylaxis  in  the  first  year  of  life  no  more  than  five  monthly  
doses  of  palivizumab  (15  mg/kg  per  dose)  during  the  RSV  season  
§ In  the  second  year  of  life,  palivizumab  prophylaxis  is  recommended  only  for  children  who  
needed  supplemental  oxygen  for  28  days  or  more  after  birth  and  who  continue  to  need  
medical  intervention  (supplemental  oxygen,  chronic  corticosteroid,  or  diuretic  therapy).    
§ Clinicians  may  consider  prophylaxis  for  children  younger  than  24  months  if  they  will  be  
profoundly  immunocompromised  during  the  RSV  season.  
  • Negative  (-­‐)   • Glycoproteins  with   • Mumps   • Conservative,  supportive  medical  care   • Mumps  is  a  clinical  diagnosis.  
MUMPS   single  stranded   combined  HA  and  NA   o Acute,  self-­‐limited,  systemic  viral   is  indicated  for  patients  with  mumps.   • Only  one  antigenic  type.  Therefore,  the  vaccine  is  protective.  
(RUBULAVIRUS)   RNA   activity   illness  characterized  by  the  swelling   No  antiviral  agent  is  indicated  for  viral    
• Unsegmented   • F-­‐protein   of  one  or  more  of  the  salivary   illness,  as  mumps  is  a  self-­‐limited    
• Lipid  containing     glands,  typically  the  parotid  glands.     disease.  
envelope     o The  illness  is  caused  by  the  RNA   • Current  evidence  suggests  that  
• Helical  symmetry       virus,  Rubulavirus   patients  diagnosed  with  mumps  
• Replicates  in   • Parotid  gland  swelling  (painful)   should  be  isolated  for  5  days  from  the  
cytoplasm   • Testicular  inflammation  (very  painful)   onset  of  symptoms.  
• Meningitis  Encephalitis   • Prevention:  MMR  vaccine  
3.  TOGAVIRIDAE  
  • Enveloped  virus   • The  virus  attaches  to   • Rubella  (German  mesles/3  day   • Prevention:  MMR  vaccine   • A  clinical  diagnosis  of  rubella  may  be  difficult  to  make  because  many  exanthematic  diseases  
RUBELLA   with  an   and  invades  the   measles)       may  mimic  rubella  infection.    
  icosahedral   respiratory  epithelium.   o Fever,  lymphadenopathy  and  mild   • As  many  as  50%  of  rubella  infections  may  be  subclinical;  therefore,  laboratory  studies  are  
Derived  from  a  Latin   nucleocapsid  and   It  then  spreads   flu-­‐like  symptoms   important  to  confirm  the  diagnosis  of  acute  rubella  infection.  
term  meaning  "little   one  ss-­‐positive-­‐ hematogenously   o Rash:  from  forehead  to  face  to  torso   • Laboratory  diagnosis  of  rubella:  
red."   RNA   (primary  viremia)  to   to  extremities  (lasts  3  days)   o (1)  Serologic  testing  
regional  and  distant   • The  major  complication  of  rubella  is  its   § Demonstrating  the  presence  of  rubella-­‐specific  immunoglobulin  M  (IgM)  antibody  in  a  
lymphatics  and   teratogenic  effects  when  pregnant   single  serum  sample  or    
replicates  in  the   women  contract  the  disease,   § Observation  of  a  significant  (>4-­‐fold)  rise  in  rubella-­‐specific  immunoglobulin  G  (IgG)  
reticuloendothelial   especially  in  the  early  weeks  of   antibody  titer  between  the  acute  and  convalescent  serum  specimens  drawn  2-­‐3  weeks  
system.  This  is   gestation.   apart.  
followed  by  a   • Congenital  defects   False-­‐positive  rubella  IgM  test  results  have  been  reported  in  persons  with  other  viral  
secondary  viremia  that   o Occurs  when  a  women  in  her  first   infections  (eg,  acute  EBV,  CMV,  parvovirus  B19  infection)  and  in  the  presence  of  rheumatoid  
occurs  6-­‐20  days  after   trimester  of  pregnancy  gets   factor  (RF).  
infection.   exposed.  The  fetus  may  develop   o (2)  Viral  culture  
defects  of  the  heart,  eyes,  or  central   • The  “R”  in  TORCHES  
nervous  system  
 
 

  31  
NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
VIRUS   MORPHOLOGY   VIRULENCE   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
FACTORS  
RNA  VIRUSES  
4.  FLAVIVIRIDAE  
  • Positive  (+)  single-­‐   • Yellow  fever:  hepatitis  with  (jaundice),  Fever,  Backache   • Prevention:  mosquito   • Viral  culture  
YELLOW  FEVER   stranded  RNA   • Dengue  fever:  “Break  bone  fever”   control   • Serology  
VIRUS     • Nonsegmented  RNA     • “Painful  fever”:  High  fever  along  with   • Vaccination  required   • With  repeat  infections,  individuals  are  at  higher  risk  
  • Icosahedral   o Headaches     when  travelling  to  and   of  developing  the  hemorrhagic  form  of  dengue  
DENGUE  VIRUS   symmetry   o Muscle  aches   from  endemic  countries   fever  
  • Replicates  the   o Joint  aches     • West  Nile:  Serology  is  much  more  sensitive  that  
ST.  LOUIS   cytoplasm   o Backache     PCR,  although  because  of  cross-­‐reactions  with  
ENCEPHALITIS   • Enveloped     • Dengue  hemorrhagic  fever:  hemorrhage,  thrombocytopenia  and  septic  shock     other  flaviviruses,  it  is  less  specific  
  • Vector  =  mosquito   • St.  Louis,  Japanese,  West  Nile  encephalitis:  encephalitis  and  fever      
JAPANESE  B   o Aedes:  yellow   • Hepatitis  C  virus:  see  Hepatitides      
ENCEPHALITIS   fever  and  dengue   • West  Nile:  fever  and  encephalitis  or  myelitis  that  produces  flaccid  paralysis    
  fever    
HEPATITIS  C  VIRUS   o Culex:  St.  Louis,    
  Japanese,  and    
WEST  NILE  VIRUS   West  Nile    
  encephalitis  
5.  PICORNAVIRIDAE  
  • Positive  (+)  single-­‐   • Inapparent,  asymptomatic  infection   • Salk  vaccine  F   • Transmission:  Fecal-­‐oral  
POLIOVIRUS   stranded  RNA   • Abortive  poliomyelitis   o Formalin-­‐kilied  polio   • The  chance  of  developing  paralytic  poliomyelitis  
    • Naked  icosahedral   o Most  common  clinical  form;  mild,  febrile  illness  with  headache,  sore  throat,  nausea,  and  vomiting.     virus   increase  as  one  gets  older.  
    symmetry   • Nonparalytic  poliomyelitis   o Injected  subcutaneously     • Since  the  World  Health  Assembly  in  May  1988  
    • Replication  occurs  in   o Aseptic  meningitis   • Oral  polio  vaccine     resolved  to  eradicate  poliomyelitis,  the  estimated  
    the  cytoplasm   • Paralytic  poliomyelitis   o Developed  by  Sabin     global  incidence  of  polio  has  decreased  by  more  
      o Virus  destroys  the  anterior  horn  cells  in  the  spinal  cord  à  flaccid  paralysis;  permanent  motor  nerve   o Attenuated  (non-­‐ than  99%,  and  3  World  Health  Organization  (WHO)  
      damage   virulent)  polio  virus  is   regions  (the  Americas,  the  Western  Pacific,  and  
ingested     Europe)  have  been  certified  as  polio-­‐free.  
      • “Cold”  rashes,  viral  meningitis      
COXSACKIE  A     • Herpangina      
COXSACKIE  B     o Fever,  sore  throat  and  small  red-­‐  based  vesicle  over  the  back  of  the  patient’s  throat      
      • Hand  Foot  and  Mouth  Disease      
      o Occurs  in  children  less  than  5      
      o Vesicles  erupt  on  hands,  foot  and  mouth,  which  are  highly  contagious      
      • Viral  meningitis      
      • Myocarditis/pericarditis:  arrhythmia,  cardiomyopathy,  heart  failure      
• Pleurodynia:  fever  and  sharp  pleuritic  chest  pain    
ECHOVIRUSES       • “Cold”,  rashes,  viral  meningitis        
(ENTERIC,     • Pericarditis      
CYTOPATHIC,  
HUMAN  ORPHAN)  
      • Common  colds      
RHINOVIRUS     • Replicates  better  at  33°C  than  at  37°C  à  they  affect  primarily  the  nose  and  conjunctiva  rather  than  the    
113  SEROTYPES   lower  respiratory  tract.    
    • Acid-­‐labile  à  killed  by  gastric  acid  when  swallowed  à  they  do  not  infect  the  gastrointestinal  tract,    
    unlike  the  enteroviruses.  
 
• Host  range  is  limited  to  humans  and  chimpanzees  

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VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
RNA  VIRUSES  
6.  CALICIVIRIDAE  
  • Positive  (+)  single   • Highly  contagious,  with  infection   • Viral  gastroenteritis   • Supportive   • Immune  electron  microscopy  
NORWALK  VIRUS  ;   stranded  RNA   requiring  fever  than  10  virions   o Explosive,  but  self-­‐limited   o Immune  serum  is  used  to  aggregate  virus  in  stool  samples  to  
  • Naked  icosahedral   (ID50  =  10  virions),  leading  to   o Fever,  Abdominal  pain,  Vomiting,  Diarrhea   aid  detection    
New  name:   symmetry   disease  in  50%  of  inoculated     • Antigen  detection  immunoassay  
NOROVIRUS   • Replication  occurs   individuals.     • Incubation  period:  approximately  1-­‐2  days,   o Has  high  sensitivity  but  low  specificity  because  of  reactivity  
The  most  common   in  the  cytoplasm   • Extremely  stable  in  the   • Symptoms:  typically  last  1-­‐3  days  (or  longer  in   with  antigenic  variants  and  homologous  viruses    
cause  of  epidemic   • Fecal-­‐oral   environment  and  resists  freezing   immunocompromised  individuals)     • Nucleic  acid  amplification  
nonbacterial   transmission   temperatures,  heat  (up  to  60°C),   • Viral  shedding:  up  to  3  wks  after  infection   o Highly  sensitive  and  specific  
gastroenteritis  in  the   disinfection  with  chlorine,  acidic   o Serum  antibody  titers  can  be  detected  within  2  weeks  of  
world   conditions,  vinegar,  alcohol,   illness  
antiseptic  hand  solutions,  and   o During  norovirus  infection,  immunoglobulin  M  (IgM)  to  
high  sugar  concentrations   norovirus  has  been  found  to  be  more  specific  than  IgG.  
7.  REOVIRIDAE  
  • Double-­‐stranded     • Viral  gastroenteritis   • Intravenous  fluids   • Rotavirus  may  be  identifies  by  the  following  means:  
ROTAVIRUS   RNA   o Causes  profound  dehydration   • New  oral  rotavirus  vaccine   •  enxyme  immuno  assay  (most  common)  
    • Segmented  (11   o Most  common  finding:  Hyperactive  bowel  sounds   o Appears  safe  and  effective  in   •  latex  agglutination  
    segments)  genome   • Especially  in  infants   infants   •  electron  microscopy  
• Naked  icosahedral   o Fever,  abdominal  pain,  vomiting  and  diarrhea   o Currently  2  FDA-­‐approved   •  culture  
symmetry     • No  blood,  No  pus  in  diarrhea   rotavirus  vaccines  to  protect  
• Fecal-­‐oral   • A  major  cause  of  infant  death  in  underdeveloped   against  rotavirus  gastroenteritis    
transmission   countries  and  the  most  common  cause  of  diarrhea  in   o RotaTeq:    aged  6-­‐32  weeks  
infants  less  than  3  years  of  age   o Rotarix:  aged  6-­‐24  weeks  
8.  CORONAVIRIDAE  
  • Positive  (+)  single-­‐ • After  establishment  of  infection,   • Upper  respiratory  tract  infection  (“common  cold”)   • No  vaccine  currently  exists  for  MERS,   • According  to  guidelines  from  the  Centers  for  Disease  Control  and  
CORONAVIRUS   stranded  RNA   SARS-­‐CoV  causes  tissue  damage   • Severe  acute  respiratory  syndrome  (SARS)   and  no  specific  treatment  has  been   Prevention  (CDC),  the  laboratory  diagnosis  of  SARS-­‐CoV  infection  
• Nonsegmented   by:   o Serious,  potentially  life-­‐threatening  viral  infection   recommended.   is  established  on  the  basis  of  detection  of  any  of  the  following  
• Helical  symmetry   o Direct  lytic  effects  on  host   caused  by  a  previously  unrecognized  virus  from  the   • Management  is  currently  supportive.   with  a  validated  test,  with  confirmation  in  a  reference  
• Enveloped   cells   Coronaviridae  family,  the  SARS-­‐associated  coronavirus   laboratory:  
• Replication  in  the   o Indirect  consequences   (SARS-­‐CoV)   o Serum  antibodies  to  SARS-­‐CoV  in  a  single  serum  specimen  
cytoplasm   resulting  from  the  host   o The  clinical  course  generally  follows  a  typical  pattern.     o A  4-­‐fold  or  greater  increase  in  SARS-­‐CoV  antibody  titer  
immune  response   § Stage  1  is  a  flulike  prodrome  that  begins  2-­‐7  days   between  acute-­‐  and  convalescent-­‐phase  serum  specimens  
o Induction  of  apoptosis     after  incubation,  lasts  3-­‐7  days,  and  is  characterized   tested  in  parallel    
§ SARS-­‐CoV–3a  and  –7a   by  the  following:   o Negative  SARS-­‐CoV  antibody  test  result  on  acute-­‐phase  serum  
proteins  have  been   − Fever  (>100.4°F  [38°C]),  Chills,  Headache     and  positive  SARS-­‐CoV  antibody  test  result  on  convalescent-­‐
demonstrated  to  be   − Fatigue,  Myalgias,  Malaise,  Anorexia   phase  serum  tested  in  parallel    
inducers  of  apoptosis  in   • Middle  East  respiratory  syndrome  (MERS)   o Isolation  in  cell  culture  of  SARS-­‐CoV  from  a  clinical  specimen,  
various  cell  lines   o A  respiratory  disease  caused  by  a  newly  recognized   with  confirmation  using  a  test  validated  by  the  CDC    
• Autopsies  demonstrated   coronavirus  (MERS-­‐CoV)   o Detection  of  SARS-­‐CoV  RNA  via  reverse  transcriptase  
changes  that  were  confined   o First  reported  in  2012  in  Saudi  Arabia  and  is  thus  far   polymerase  chain  reaction  (RT-­‐PCR)  assay  validated  by  the  
mostly  to  pulmonary  tissue,   linked  to  countries  in  or  near  the  Arabian  Peninsula   CDC,  with  confirmation  in  a  reference  laboratory,  from  (1)  two  
where  diffuse  alveolar  damage   (United  Arab  Emirates  [UAE],  Qatar,  Oman,  Jordan,   clinical  specimens  from  different  sources  or  (2)  two  clinical  
was  the  most  prominent  feature.     Kuwait,  Yemen,  and  Lebanon).     specimens  collected  from  the  same  source  on  2  different  days  
o As  of  May  2014,  two  cases  had  been  reported  in  the   • The  recommended  algorithm  for  detection  of  MERS-­‐CoV  
United  States,  both  in  men  who  had  recently  returned   includes  testing  using  rRT-­‐PCR.    
from  Saudi  Arabia.    [MMWR  Morb  Mortal  Wkly  Rep.   o Serologic  testing  is  available  for  the  evaluation  of  MERS-­‐CoV  
2015  Jan  30.  64  (3):61-­‐2]   infection  or  exposure  
 

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VIRUS   MORPHOLOGY   VIRULENCE  FACTORS   CLINICAL  SYNDROMES   TREATMENT  &  PREVENTION   DIAGNOSIS  
RNA  VIRUSES  
9.  RHABDOVIRIDAE  
  • Bullet  shaped   • Highly  neurotropic  virus  that  evades  immune   • Incubation  period  (asymptomatic)   • NO  TREATMENT   • Microscopic  examination    
RABIES  VIRUS   • Negative  (-­‐)  single-­‐stranded   surveillance  by  its  sequestration  in  the  nervous   • Prodromal  period   • Vaccination  of  animals   o Negri  bodies  at  the  central  nervous  system  
RNA   system     o The  virus  enters  the  CNS.     • If  bitten  by  possible  rabid   § These  are  collections  of  virions  in  the  cytoplasm  where  
• Nonsegmented   • Upon  inoculation,  it  enters  the  peripheral  nerves.     o The  duration  of  this  period  is  2-­‐10  days.     animal,  there  are  three   replication  occurs  
• Helical  nucleocapsid  is  coiled   • A  prolonged  incubation  follows,  the  length  of   o Nonspecific  symptoms  and  signs   possibilities:   o Viral  cultures  and  PCR  
into  a  bullet  shape     which  depends  on  the  size  of  the  inoculum  and  its   develop.     o Capture  animal:  observe  for   § Saliva  
• Replication  in  the  cytoplasm   proximity  to  the  CNS.   o Paresthesia,  pain,  or  intense  itching  at   10  days   − Results  of  saliva  culture  for  rabies  virus  are  positive  in  low  
• Zoonotic  (all  warm  blooded   • Amplification  occurs  until  bare  nucleocapsids  spill   the  inoculation  site  is  pathognomonic   o Destroy  animal:  examine  for   yield  within  2  weeks  of  illness  onset    
animals):  dogs,  cats,  skunks,   into  the  myoneural  junction  and  enter  motor  and   for  rabies  and  occurs  in  50%  of  cases   Negri  bodies   § Cerebrospinal  fluid  
coyotes,  foxes,  raccoons,  and   sensory  axons.     during  this  phase;  this  may  be  the   • Treat  immediately  (if  you  can   − After  the  first  week  of  illness,  80%  monocytosis  is  
bats  are  reservoirs  in  the  U.S.   • At  this  point,  prophylactic  therapy  becomes  futile,   individual’s  only  presenting  sign.   not  capture  the  animal,  or  the   observed;  protein  and  glucose  test  results  are  normal    
• Transmitted  via  an  animal   and  rabies  can  be  expected  to  follow  its  fatal   • Acute  neurologic  period:  associated  with   animal  is  found  to  have  a   § Brain  tissue  
bite   course,  with  a  mortality  rate  of  100%.   objective  signs  of  developing  CNS   rabies):   − Often  postmortem  
• The  rabies  virus  travels  along  these  axons  at  a  rate   disease.     o Clean  wound   − Staining  with  immunohistochemical  or  florescent  antibody  
of  12-­‐24  mm/d  to  enter  the  spinal  ganglion.       o Passive  immunization  with   staining  is  definitive.    
• Its  multiplication  in  the  ganglion  is  heralded  by  the   • Furious  rabies  may  develop  during  this   rabies  immune  globulin   − Negri  bodies  are  pathognomonic  (cytoplasmic  inclusion  
onset  of  pain  or  paresthesia  at  the  site  of  the   period:  patients  develop  agitation,   o Active  immunization  with   bodies  reflective  of  accumulated  virions  within  rabies-­‐
inoculum,  which  is  the  first  clinical  symptom  and  a   hyperactivity,  restlessness,  thrashing,   killed  rabies  virus  vaccine   infected  neurons).    
hallmark  finding.     biting,  confusion,  or  hallucinations.   − They  are  found  in  the  horn  of  Ammon  of  the  hippocampus  
• From  here,  the  rabies  virus  spreads  quickly,  at  a   • Paralytic  rabies  (dumb  rabies  or   and  cerebral  cortex  
rate  of  200-­‐400  mm/d,  into  the  CNS,  and  spread  is   apathetic  rabies)  à  patient  is  relatively  
marked  by  rapidly  progressive  encephalitis.     quiet  compared  with  a  person  with  the  
• Thereafter,  the  virus  spreads  to  the  periphery  and   furious  form  
salivary  glands.  
10.  RETROVIRIDAE  
  • Enveloped  virus  with  two   • FUSION  PROTEIN  (gp41)     • PHASE  0  –  INFECTION:  HIV  acquired   • Highly  active  antiretroviral   • Presumptive  diagnosis  
HUMAN   copies  (diploid)  of  a  single-­‐ o Transmembrane  protein  which  is  linked  to  a   through  sexual  intercourse,  blood,  or   therapy  (HAART)   o Detection  of  antibodies  by  ELISA.    
IMMUNO-­‐ stranded,  positive-­‐polarity   surface  protein  and  SU  (ATTACHMENT  PROTEIN,   perinatally     o Two  nucleoside  inhibitors   o There  are  some  false-­‐positive  results  with  this  test  
DEFICIENCY   RNA  genome   gp120)     • PHASE  1  -­‐  WINDOW  PERIOD:  rapid  viral   (zidovudine  and  lamivudine)     • Definitive  diagnosis  à  Western  blot  analysis  
VIRUS   • Most  complex  of  the  known   • CA  (p24)   replication  but  HIV  test  is  negative     o Protease  inhibitor  (indinavir)    
  retroviruses     o Cone-­‐shaped,  icosahedral  core  containing  the   • PHASE  2  –  SEROCONVERSION:  peak  of   • Grown  in  culture  from  clinical  specimens  
HIV   • Many  serotypes     major  capsid  protein   viral  load,  positive  HIV  test,  mild  flu-­‐like   • Polymerase  chain  reaction  (PCR)  
      • MA  (p17)   illness,  lasting  1-­‐2  weeks     o Very  sensitive  and  specific  
    o Directs  entry  of  the  double-­‐stranded  DNA  provirus   • PHASE  3  -­‐  LATENT  PERIOD:   o To  detect  HIV  DNA  within  infected  cells  
    into  the  nucleus,  and  is  later  essential  for  the   asymptomatic,  CD4  goes  down,  lasts  1-­‐15   o Some  individuals  who  do  not  have  detectable  antibodies  have  
process  of  virus  assembly.     years     been  shown  by  this  test  to  be  infected.    
o There  are  two  identical  copies  of  the  positive   • PHASE  4  -­‐  EARLY  SYMPTOMATIC:  CD4   o Amount  of  viral  RNA  in  the  plasma  (i.e.,  the  viral  load)  can  also  
sense,  single-­‐stranded  RNA  genome  in  the  capsid   500  to  200,  lasts  5  years,  mild   be  determined  using  PCR-­‐based  assays.    
(that  is,  unlike  other  viruses,  retroviruses  are   mucocutaneous,  dermatologic  and    
diploid).   hematologic  illnesses    
• The  RNA  is  tightly  complexed  with  a  basic  protein,   • PHASE  5  –  AIDS:  CD4  <200,  lasts  2  years,  
NC  (p7),  in  a  nucleocapsid  structure  that  differs  in   AIDS-­‐defining  illnesses  develop    
morphology  among  the  different  retrovirus  genera.    
 
 
 

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MYCOLOGY  
 
NAME   RESERVOIR   MORPHOLOGY   CLINICAL  SYNDROME   TREATMENT   DIAGNOSIS   NOTES   ANATOMIC  LOCATION  
  • Naturally  found  on  the   • “Spaghetti  and  meat   • Tinea/Pityriasis  versicolor     • Dandruff  shampoo   • Potassium  hydroxide  (KOH)  prep     SUPERFICIAL  (SKIN)  
Malassezia  furfur   skin  surfaces  of  many   balls”   o A  common,  benign,  superficial   (containing   o Reveals  short,  curved,  unbranched  
  animals,  including   • Dimorphic,  lipophilic   cutaneous  fungal  infection     selenium  sulfide)   hyphae  with  spherical  yeast  cells  
AN-­‐AN   humans.     fungi   o Usually  characterized  by   • Topical  imidazole   (look  like  “spaghetti  and  
AP-­‐AP   • Isolated  in  18%  of     hypopigmented  or  hyperpigmented   meatballs”)  
    infants  and  90-­‐100%  of   macules  and  patches  on  the  chest  and   • Extremely  difficult  to  propagate  in  
adults.   the  back.     laboratory  culture  and  is  culturable  
o In  patients  with  a  predisposition,  tinea   only  in  media  enriched  with  C12-­‐  to  
versicolor  may  chronically  recur.  The   C14-­‐sized  fatty  acids.  
fungal  infection  is  localized  to  the  
stratum  corneum.  
  • Depending  on  the   • Dermatophytosis   • Topical  imidazole   • KOH   • Secretes  the  enzyme  keratinase,   CUTANEOUS  
DERMATOPHYTES   particular  species   o Tinea  corporis  (body):  “ringworm”   • Oral  griseofuivin  is   o Branched  hyphae   which  digests  keratin  
  • Soil  (geophilic)   o Tinea  cruRis  (groin):  “jock  itch”   used  for  tinea   o Wood’s  lamp:  certain  species  of   • For  atypical  presentations  of  
Microsporum     Animals    (zoophilic)   o Tinea  pedis  (feet):  “athlete’s  foot”   unguium  and  tinea   Microsporum  will  fluoresce  under   tinea  corporis,  further  evaluation  
Trichopyton     Human   o Tinea  capitis  (scalp)   capitis   ultraviolet  light   for  HIV  infection  and/or  an  
Epidermophyton   (anthropophilic)   o Tinea  unguium  (nail):  Onychomycosis   • Oral  terbinafine   • A  fungal  culture,  which  is  often  used   immunocompromised  state  
floccosum   • Infections  due  to     as  an  adjunct  to  KOH  for  diagnosis,  is   should  be  considered.  
    zoophilic  or  geophilic   more  specific  than  KOH  for  detecting    
dermatophytes  may   a  dermatophyte  infection.  
produce  a  more   • Therefore,  if  the  clinical  suspicion  is  
intense  inflammatory   high  yet  the  KOH  result  is  negative,  a  
response  than  those   fungal  culture  should  be  obtained.  
caused  by   • If  the  above  clinical  evaluations  are  
 

anthropophilic   inconclusive,  a  polymerase  chain  

microbes   reaction  (PCR)  assay  for  fungal  
deoxyribonucleic  acid  (DNA)  
identification  can  be  used.  
  • Found  on  rose  thorns     • Suppurating  subcutaneous  nodules  that   • Itraconazole   • Dimorphic   • Primary  pulmonary  infection   SUBCUTANEOUS  
Sporothrix  schenkii   progress  proximally  along  lymphatic   • Fluconazole   o Culture  at  25ºC  will  grow   (pulmonary  sporotrichosis)  is  
channels  (lymphocutaneous   • Oral  potassium   branching  hyphae   rare,  as  is  direct  inoculation  into  
sporotrichosis)   iodide   o Culture  at  37ºC  will  grow  yeast   tendons,  bursae,  or  joints.    
  cells   • Osteoarticular  sporotrichosis    
  • Definitive  diagnosis  of  sporotrichosis   caused  by  direct  inoculation  or  
at  any  site  requires  the  isolation  of  S.   hematogenous  seeding.    
schenckii  in  a  specimen  culture  from   • In  rare  cases,  disseminated  S  
a  normally  sterile  body  site.   schenckii  infection  (disseminated  
• The  organism  can  be  recovered  with   sporotrichosis)  occurs,  
fungal  culture  from  sputum,  pus,   characterized  by  disseminated  
subcutaneous  tissue  biopsy,  synovial   cutaneous  lesions  and  
fluid,  synovial  biopsy,  bone  drainage   involvement  of  multiple  visceral  
or  biopsy,  and  cerebrospinal  fluid   organs;  this  occurs  most  
 
(CSF).   commonly  in  persons  with  AIDS.  
 

 
 

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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
ANATOMIC  
NAME   RESERVOIR   MORPHOLOGY   CLINICAL  SYNDROME   TREATMENT   DIAGNOSIS   NOTES   LOCATION  
  • Desert  areas  of  the   • Dimorphic   • Coccidiodomycosis   • Amphotericin  B   • Biopsy  of  affected  tissue  (lung,  skin,  etc)   • Common  oppurtunisitc   SYSTEMIC  
Coccidioides   southwestern  United   o Mycelial  forms  with   • Asymtomatic  (in  most  persons)   • Itraconazole   • Silver  stain  or  KOH  prep   infection  in  AIDS  patients  
immitis   States  and  northern   spores  at  25ºC   • Pneumonia     • Fluconazole   • Culture  on  Sabouraud’s  agar   from  the  southwest  
Mexico   o Yeast  forms  at  37ºC   • Disseminated:  can  affect  the  lungs,  skin  ,  bones  and  meninges     • Serology   United  States  
• Respiratory       • Skin  test   • SPHERULES  WITH  
transmission   ENDOSPORES  
  • Mississippi  valley     • Dimorphic   • Histoplasmosis   • Itraconazole   • Lung  biopsy,  Silver  stain  specimen   • Can  survive   SYSTEMIC  
Histoplasma   • Present  in  bird  and   o Mycelial  forms  with   o Asymptomatic  (in  most  persons)   • Amphotericin  B  (in   • Culture  on  Sabouraud’s  agar  will  reveal   intracellularly  within  
o o
capsulatum   bat  droppings   spores  at  25ºC   o Pneumonia:  lesions  calcify,  which  can  be  seen  on  chest  X-­‐ray   immune-­‐ hyphae  at  25 C  and  yeast  at  37 C   macrophages  
• Respiratory   o Yeast  forms  at  37ºC   (may  look  similar  to  PTB)   compromised   • Serology   • YEASTS  WITHIN  
transmission     o Disseminated:  can  occur  in  almost  any  organ,  especially  in  lung,   patients)   • Skin  test  (test  for  exposure  only)   MACROPHAGES  
spleen,  or  liver     • Urine  antigen  test    
    • Dimorphic:   • Blastomycosis     • Itraconazole   • Biopsy  of  affected  tissue(lung,  skin,  etc)   • BROAD-­‐BASED  BUD   SYSTEMIC  
Blastomyces   o Mycelial  forms  with   o Asymptomatic  (uncommon)   • Ketoconazole   • Silver  stain  specimen  
dermatitidis   spores  at  25ºC   o Pneumonia:  lesion  rarely  calcifies   • Amphotericin  B     • Culture  on  Sabouraud’s  agar  
o Yeast  forms  at  37ºC   o Disseminated  (most  common):  present  with  weight  loss,  night     • Serology  
  sweats,  lung  involvement  and  skin  ulcers     • Skin  test  (test  for  exposure  only)  
  o Cutaneuos:  skin  ulcer     • Sputum  specimens  processed  with  10%  
  • Blastomycosis  is  usually  localized  to  the  lungs  and  may  present  with:     potassium  hydroxide,  cytology  smears,  
  o A  self-­‐limited  flulike  illness  with  fever,  chills,  myalgia,  headache,     or  a  fungal  stain    
  and  a  nonproductive  cough       • Enzyme  immunoassay  (EIA)  techniques  
  o An  acute  illness  resembling  bacterial  pneumonia,  with  high  fever,     on  sputum,  tissue,  or  bronchoscopic  
chills,  a  productive  cough,  and  pleuritic  chest  pain;  mucopurulent   specimens  
or  purulent  sputum      
o Chronic  illness,  with  low-­‐grade  fever,  a  productive  cough,  fatigue,    
night  sweats,  and  weight  loss      
o Rapidly  progressive,  and  severe  disease,  eg,  multilobar  
pneumonia  or  ARDS,  with  fever,  shortness  of  breath,  tachypnea,  
hypoxemia,  and  finally  hemodynamic  collapse  
  • Pigeon  droppings   • Polysaccharide   • Cryptococcus   • Amphotericin  B  and   • India-­‐ink  stain  of  cerebrospinal  fluid   • Most  cases  occur  in   SYSTEMIC  
Cryptococcus   capsule   o Subacute  or  chronic  meningitis   flucytosine  (is   (CSF):  observe  encapsulated  yeast   immunocompromised  
neoformans   • Yeast  form  only  (Not   o Pneumonia:  usually  self-­‐limited  and  asymptomatic   superior  to   • Cryptococcal  antigen  test  of  CSF:   person  
dimorphic)   o Skin  lesions:  look  like  acne   amphotericin  B   detects  polysaccharide  antigens   • MCC  of  
    alone)   • Fungal  culture   meningoencephalitis  in  
    HIV  
• YEAST  WITH  A  HALO  
  • Normal  flora  of  the   • Pseudohyphae  and   • Candidiasis  in  a  normal  host   • The  choice  of   • KOH  stain  of  specimen   • YEAST  WITH   CUTANEOUS  or  
Candida   skin,  mouth  and   yeast   o Oral  thrush   antifungal  agent   • Silver  stain  of  specimen   PSEUDOHYPHAE   SYSTEMIC  
albicans   gastrointrointestinal   o Vulvovaginal  candidiasis   depends  on  the   • Blood  culture:  growth  must  be   (normal  host,  
tract   o Cutaneous   area  involved  and   respected   or  
o Diaper  rash   its  severity.     • Blood  assay  for  beta-­‐D-­‐glucan   opportunistic)  
o Rash  in  the  skin  folds  of  obese  individuals    
• Candidiasis  in  an  immunocompromised  host      
o Thrush,  vaginitis  and/or  cutaneous,  plus:      
§ Esophageal        
§ Disseminated  candidiasis:  acquired  by  very  sick  hospitalized      
patients,  resulting  in  multi-­‐organ  system  failure      
§ Chronic  mucocutaneous  candidiasis    
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NAME:  __________________________________________________________                                    SECTION:  _______________________                                              TOPNOTCH  MICROBIOLOGY  TABLE  (UPDATED  MAY  2017)  
 
 

ANATOMIC  
NAME   RESERVOIR   MORPHOLOGY   CLINICAL  SYNDROME   TREATMENT   DIAGNOSIS   NOTES   LOCATION  
  • Ubiquitous   • Branching  septated   • Aspergillosis   • Corticosteroid:   • Allergic  brochopulmonary   • Rarely  found  in  individuals  who  are   OPPORTUNISTIC  
Aspergillius   • Aspergillus  may  cause  a  broad   hyphae  (acute  angles,   o Allergic  bronchopulmonary   Allergic   aspergillosis   immunocompetent  
O
fumigatus   spectrum  of  disease  in  the  human   45 )   aspergillosis  (IgE  mediated)     bronchopulmonary   o High  level  of  IgE  (IgE  level  >  1000   • The  FDA  has  approved  an  
  host,  ranging  from   § Asthma  type  reaction  with   aspergillosis   IU/dL)   intravenous  formulation  of  the  
Aspergillius  flavus   hypersensitivity  reactions  to   shortness  of  breath  and  high   • Removal  via  thoracic   o Sputum  culture   triazole  antifungal  posaconazole  
  direct  angioinvasion.     fever   surgery:   o Wheezing  patient  and  chest  X-­‐ (Noxafil),  which  is  indicated  for  the  
Aspergillius  niger   • Aspergillus  primarily  affects  the   o Asperigilloma  (Fungus  ball):   Aspergilloma:     ray  with  fleeting  infiltrates   prophylaxis  of  invasive  Aspergillus  
    lungs,  causing  the  following  four   associated  with  hemoptysis   • Voriconazole,   o Increased  level  of  eosinophils   and  Candida  infections  in  severely  
main  syndromes:   (blood  cough)   possibly  caspofungin:   o Skin  test:  immediate   immunocompromised  adults  who  
o Allergic  bronchopulmonary   o Invasive  aspergillosis   Invasive  aspergillosis   hypersensitivity  reaction   are  at  high  risk  of  developing  these  
aspergillosis  (ABPA)   § Necrotizing  pneumonia.     (very  high  mortality)   • Aspergilloma:  diagnose  with  chest   infections.  
o Chronic  necrotizing  Aspergillus   § May  disseminate  to  other     X-­‐ray  or  CT  scan   • Aflatoxins  contaminate  peanuts,  
pneumonia  (or  chronic   organs  in  immune-­‐   • Invasive  aspergillosis:  sputum   grains,  and  rice  
necrotizing  pulmonary   compromised  patients     examination  and  culture  
aspergillosis  [CNPA])     • Aflatoxin  consumption  (produced  
o Aspergilloma     by  Aspergillus  flavus  )  can  cause  
o Invasive  aspergillosis   liver  damage  and  live  cancer  
  • Saprophytic  molds   • Broad,  non-­‐septated,   • Mucormycosis   •    Amphotericin  B     • Biopsy   • The  disease  is  rapidly  fatal   OPPORTUNISTIC  
Rhizopus   branching  hyphae   • Rhinocerebral  (associated  with   •    Surgery   • Black  nasal  discharge  
o
  (right  angles,  90 )   diabetes):  starts  on  nasal  mucosa    
Rhizomucor   and  invades  the  sinus  and  orbit  
  • Pulmonary  mucormycosis  
Mucor  
 
Pneumocystis   • Unicellular  fungi  found  in  the   • The  organism  is  found   • Pneumocystis  jirovecii  pneumonia   • TMP-­‐SMX   • A  lactic  dehydrogenase  (LDH)  study   • The  taxonomic  classification  of  the    
jirovecii   respiratory  tracts  of  many   in  3  distinct   (PJP)   is  performed  as  part  of  the  initial   Pneumocystis  genus  was  debated  for  
mammals  and  humans   morphologic  stages,  as   o Occurs  when  both  cellular   workup   some  time.  It  was  initially  mistaken  for  
follows:   immunity  and  humoral  immunity   o LDH  levels  are  usually  elevated   a  trypanosome  and  then  later  for  a  
o Trophozoite   are  defective.     (>220  U/L)  in  patients  with  P   protozoan.    
(trophic  form),  in   • Once  inhaled,  the  trophic  form  of   jiroveci  pneumonia  (PJP).     • In  the  1980s,  biochemical  analysis  of  
which  it  often  exists   Pneumocystis  organisms  attach  to   o They  are  elevated  in  90%  of   the  nucleic  acid  composition  of  
in  clusters     the  alveoli.     patients  with  PJP  who  are   Pneumocystis  rRNA  and  mitochondrial  
o Sporozoite   • Multiple  host  immune  defects  allow   infected  with  HIV.     DNA  identified  the  organism  as  a  
(precystic  form)   for  uncontrolled  replication  of   o The  study  has  a  high  sensitivity   unicellular  fungus  rather  than  a  
o Cyst,  which  contains   Pneumocystis  organisms  and   (78%-­‐100%);  its  specificity  is   protozoan.    
several  intracystic   development  of  illness.     much  lower  because  other   • Subsequent  genomic  sequence  
bodies  (spores)     • Activated  alveolar  macrophages   disease  processes  can  result  in   analysis  of  multiple  genes  including  
  without  CD4+  cells  are  unable  to   an  elevated  LDH  level.  [Clin   elongation  factor  3,  a  component  of  
eradicate  Pneumocystis  organisms.     Invest  Med.  1992  Aug.  15(4):309-­‐ fungi  protein  synthesis  not  found  in  
• Increased  alveolar-­‐capillary   17.   protozoa,  further  supported  this  
permeability  is  visible  on  electron   • Quantitative  PCR  for  pneumocystis   notion.  
microscopy.   may  become  useful  in  distinguishing  
between  colonization  and  active  
infection,  but  these  assays  are  not  
yet  available  for  routine  clinical  use.  
 

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