Microbiology flowchart.pdf

Principes du monde microbien

1. Gram%&%
Diplococci%
(Neisseria)%
Maltose%%
fermenter%
N.#meningi)dis#
Maltose%%
Nonferm,%ox%+%
N.#gonorrheae#Coccoid%Rod%
H.#influenzae#
Pasteurella#
Brucella#
Bordetella#
pertussis##
Rod%
Lactose%%
fermenter%
Indole#;,#ox#;#Klebsiella#
Indole#+,#cat+#E.#Coli#
Enterobacter#
Lactose%%
Nonfermenter%
Oxidase%&%
Shigella#
Salmonella#
Proteus#
Oxidase%+%
Pseudomonas#
H.#pylori#
Comma%Shaped%
Oxidase%+%
Grows&at&42°#
Campylobacter#jejuni#
Grows&in&alkaline&media#
Vibrio#cholerae#
Glucose%fermenters%
Intes4nal&flora&
Lobar%pneumonia%in&alcoholics&and&
diabe4cs&when&aspirated.&&“Red%currant%
jelly”%sputum&due&to&capsule.&
Nosocomial&UTI&(3
rd
&leading&cause);&viscous&
colonies&
Neisseria&grows&on&Thayer&Marin/VPN%
[Vancomycin&inhibits&gram&+,&Polymyxin&
inhibits&other&gram&–’s.&Nysta4n&inhibits&fungi]&
Chocolate%agar%with&X&(hema4n)&&&V&(NAD+),&
can&also&be&grown&with&S.&aureus&which&
provides&factor&V&
CAPSULE&[Type&B&has&conjugate&vaccine],&IgA&
protease&&
Can&undergo&Transforma4on&(uptake&of&
naked&DNA)&
Aerosol&transmission&
Bordet&Gengou%(potato)&agar&
Pertussis%Exotoxin%overac4vates&
adenylate&cyclaet&by&disabling&Gi,&
impairing&phagocytosis&to&permit&survival&
of&microbe&
CAPSULE,&Vaccine&(none&for&type&B)&
TransmiXed&via&respiratory&&&oral&
secre4ons&
Meningi4s&in&Children&
Meningi4s&in&Adults&(#1%in%teens)&
Waterhouse[Friderichsen&Syndrome&
Rx:&Penicillin/CeQriaxone,&
Chloramphenicol,&Rifampin&prophylaxis&
Neisseria:&
• Faculta4ve&Intracellular&
• IgA&protease&
• Transforma4on&(takes&up&naked&DNA&from&
cell&lysis)&
• C5[9&deficiency!&recurrent&Neisseria&
bacteremia&
No&capsule,&no&vaccine&due&to&rapid&
an4genic&varia4on&of&pilus&proteins)&
STD&
Gonorrhea&(Creamy,%purulent%discharge),&
Sep4c&arthri4s&(migratory&arthri4s&with&an&
asymmetric&paXern)&
Rare&cause&of&osteomyli4s&
Neonatal%ConjuncRviRs%(prevent&with&
erythromycin&ointment),&PID,&Fitz[Hugh[
Cur4s&Syndrome&
Sterile%pyuria%and%–%urine%cultures%suggest&
N.&gonorrhoeae&or&Chlamydia&
Rx:&CeQriaxone&(+&azithro/erythro&for&
possible&chlamydia&coinfec4on)&
CAPSULE,&&Urease%+%(may&
cause&struvite&stones)&
(pink&on&
MacConkey&due&to&
acid&produc4on)&
E.&Coli&also&grows&on&eosin[
methylene&blue&(EMB)&as&colonies&
with&green&metallic&sheen&
CAPSULE,&Catalase+&("&infec4on&in&CGD)&
EHEC;%Enterohemorhagic&(inc.&0157:H7&undercooked&
meat)&
• Shiga&like%exotoxin%inac4vates&60S&by&removing&
adenine&from&rRNA.&&Enhances&cytokine&release&
causing&HUS.&&Does&not&invade&cells&(unlike&
shigella)&
ETEC;%Enterotoxigenic&(Traveler’s%Diarrhea)&&
• Heat[labile&(LT)&"cAMP&!&"&Cl[&secre4on&in&gut&
&&H2O&efflux&
• Heat[stable&(ST)&"cGMP!&#NaCL&resorp4on&in&
gut&
EIEC;%Enteroinvasive[&invades&colonic&mucosa,&causing&
necrosis&and&inflamma4on;&similar&to&Shigella&
EPEC;%Pediatric%no&toxin&produced.&&Adheres&to&apical&
surface,&flaXens&villi,&prevents&absorp4on&
&
Intes4nal&flora,&colonizes&in&vagina&
#1&cause&of&UTI&(fibriae)&
Nosocomial&UTI&(catheteriza4on)&
Pneumonia&
Neonatal&meningi4s&(K%Capsule)&
Sepsis&(LPS%endotoxin)&
Rx:%Ampicillin,&Amoxicillin&&
Shiga%Exotoxin%inac4vates&60S&ribosome&by&removing&
adenine&from&rRNA.&&GI&damage&!&dysentery.&&&
ST&also&enhances&cytokine&release&causing&HUS.&&
Cell[cell&transmission,&invades&colonic&mucosa&&&
causes&PMN&infiltra4on&
Human&&and&primate&reservoir&&
Faculta4ve&intracellular&
CAPSULE,&Flagella&(2&an4genic&variants),&produces&H
2
S%
Can&disseminate&hematogenously&,&invades&colonic&
mucosa&&&causes&monocyRc%response%
Animal&reservoir,&poultry,&meat,&eggs&
Bacillary%Dysentery%%
Reiter’s&Reac4ve&arthri4s&may&follow&
(Conjunc4vi4s,&urethri4s,&arthri4s)&&
Rx:&Ampicillin,&amoxicillin,&trimethoprim&
An4bio4cs&shorten&dura4on&of&fecal&
excre4on&&
Salmonella#typhi!"Typhoid&Fever&(rose&spots&on&
abdomen,&fever,&headache,&diarrhea;&can&remain&
in&gallbladder&and&cause&a&carrier&state)&
Reiter’s%Syndrome%may&follow&GI&food&poisoning&
OsteomyeliRs%in%Sickle%Cell%
Rx:&Ampicillin,&amoxicillin,&trimethoprim&&
An4bio4cs&prolong&dura4on&of&fecal&excre4on&&
Urease&+&(hydrolyze&urea&to&ammonia&[!&&
urine&alkalinza4on;&staghorn&struvite&stones)&
Mo4lity&causes&“swarming”&on&agar&
UTI&associated&with&catheteriza4on,&urine&
has&ammonia&scent.&&
Rx:&Ampicillin,&amoxicillin,&cephalosporins&
Recurrent&RTI&in&CF%paRents,&can&be&associated&with&respiratory&therapy&
equipment&
Burn%wounds,&nosocomial&pneumonia,&sepsis,&external&o44s&
Osteomyeli4s&&&malignant&o44s&externa&in&DM,&IV&drug&users&
Bacterial&endocardi4s&in&IV&drug&users&(tricuspid&valve),&2
nd
&to&S.&aureus&&
Hot%tub%folliculiRs%
UTI:&blue[green&pigment&and&fruity&odor,&usually&nosocomial&&&drug&resistant&&
Ecthyma%gangrenosum[&rapidly&progressive,&necro4c&cutaneous&lesions,&
usually&in&IC&
Rx:&Aminoglycoside&+&Piperacillin,&4carcilllin,&cefepime,&imipenem,&
meropenem&
Obligate&aerobe&
Produces&blue&green%pigment%
Exotoxin%A%inac4vated&EF[2&
causing&host&cell&death&
Silver&stain&
Urease,%catalase,%&%oxidase%+%
Curved&Rod&
Gastri4s&and&PUD&(especially&duodenal;&present&in&~70%&gastric&
ulcers&&&nearly&100%&duodenal&ulcers)&
Type%B%chronic%gastriRs%(antrum)!&"risk&of&adenocarcinoma&&&
MALT&lymphoma.&&Use&urease&breath&test&or&fecal&an4gen&test&
Rx:&[prazoles,&clarithromycin&+&amoxicillin&or&metronidazole&&
Comma&or&S&shaped%
Bloody%diarrhea%(especially&in&children)&
Fecal[oral&transmission.&&Ass.&w/&puppies,&livestock,&undercooked&meat&
Common&antecedent&to&GBS%and%Reiter’s%
Can&lead&to&autoimmune&aXack&of&peripheral&myelin&due&to&molecular&
mimicry.&&Destruc4on&of&Schwann&cells!&symmetric&ascending&muscle&
weakness,&CSF&protein&with&normal&cell&count.&"protein[[>&papilledema&
Grows&in&alkaline&media&
Endemic&to&developing&coun4es,&infected&seafood&&
Cholera&exotoxin&(encoded&on&lysogenized&phage)&
overac4vates&adenylate&cyclase&by&permanently%acRvaRng%Gs&
!&"&Cl
[
&secre4on&in&gut&&&H
2
O&efflux&&
Voluminous&“rice&water”&
diarrhea&
Prompt&rehydra4on&is&
necessary&
Inac4vated/killed&vaccine&
MeningiRs&in&unvaccinated&children&
6mos[6years(Rx:%cetriaxone,&rifampin&prophylaxis)&
EpigloaRs:&“thumb&sign”&
ORRs%Media%
Bronchopneumonia&in&adults/elderly&
Rx%mucosal%infecRons:&Amoxicillin&+&clavulanate&
2
nd
"genera*on"cephalosporin,"chloramphenicol""
Pasteurella"multocida:&Cat&or&dog&bite!&
celluliRs&&&osteomyeli4s&&
&
Faculta4ve&intracellular&
Infects&macros%and%monos%
Phase&varia4on&of&O%anRgen%
Vaccina4on&for&animals&
Unpasteurized&dairy,&animal&birthing&!&
brucellosis/undulant%fever%(headache,&cyclic&
fever,&chills,&arthralgia;&chronic&cases&have&cyclic&
bouts&of&malodourous%sweaRng%and&depression)&
Whooping%Cough:%child&coughs&on&
expira4on&and&whoops&on&inspira4on&
100&day&cough&in&adults&
Rx:&erythromycin,&cotrim&if&allergy&%
CHRONIC GRANULOMATOUS DISEASE (XLR)
• Defective NADPH oxidase which uses O
2
as
substrate ! # ROS.
• " Susceptibility to catalase + organisms
• Phagocytes in CGD patients can use H
2
O
2

generated by invading organisms and
convert is to ROS. If organism is catalase +,
it will be able to neutralize its own H
2
O
2.

• " infections with: Pseudomonas, Listeria,
Aspergillus, Candida, E. coli, S. aureus,
Serratia.
• Diagnosis: abnormal dihydrohodamine (flow
cytometry) test. Nitroblue tetrazolium due
reduction test is -.

2. Gram%+%%
Cocci%
Catalase%+% Staphylococcus,
Coagulate%+%
S.,aureus,
Coagulase%–%
Urease%+%
Novobiocin%Sensi7ve%
S.,epidermidis,
Novobiocin%Resistant%
S.,saprophy3cus,,
Catalase%9% Streptococcus,
alpha%/par7al%
hemolysis%
Capsule%(+quelling)%
Optochin%Sensi7ve%
S.,Pneumoniae,
No%capsule%
Optochin%Resistant%Viridans,,
Beta/comlete%
hemolysis%
(clear)% GAS%
Bacitracin%Sensi7ve%
S.,pyogenes,
GBS%
Bactracin%Resistant%S.,agalac3ae,
No%Hemolysis%
GDS%
Enterococcus%
Growth%in%bile%and%6.5%%
NaCl% E.,Faecalis,
GDS,%Nonenterococcus%
Growth%in%only%bile,%not%
salt%
S.,Bovis,
Rod%(bacilli)%
Clostridium,
C.,tetani,
C.,Botulinum,
C.,Perfringens,
C.,Difficile,,
Listeria,
Bacillus,
Mycobacterium,
Branching%
filaments%
NOT%acid%fast,%
anarobe%
Ac3nomyces,
Acid%fast,%
aerobe% Nocardia,
Catalase%degrades%H2O2%before%it%can%be%converted%
to%microbicidal%products%by%myeloperoxidase.%People%
with%chronic%granulomatous%disease%(NADPH%
oxidase%deficiency)%have%recurrent%infecHons%with%
catalase%+%organisms.%%
Examples:%Pseudomonas,*Listeria,*Aspergillus,*
Candida,*E.*coli,*S.*aureus,*Serra3a.*%
%
MRSA%(altered%PBP)M%nosocomial%infecHons%(esp.%wound)%
MC%Cause%of%Osteomyeli7s%%
Acute%Endocardi7s;%Tricuspid%valve%if%IV%drug%user.%%
[Acute4*rapid*onset,*large*vegeta3ons*on*normal*valve]%%%
ImpeHgo,%CelluliHs,%MCC%Mas77s%(Rx%dicloxacillin)%
Rx:%Nafcillin,%oxacillin,%dicloxacillin.%%Cefazolin%(1
st
%gen)%used%
prior%to%surgery%to%prevent%wound%infecHon.%Vancomycin%for%
MRSA%
Tetanospasmin%Exotoxin%leaves%SNARE!%%
No%release%of%GABA%&%Glycine%from%Renshaw%
cells%in%spinal%cord%!%Spas7c%Paralysis%
Rx:%anHtoxin,%vaccine%booster,%diazepam%
%
SporeMforming.%Honey,%canned%food%(bulging%cans)%
Preformed,%HL%exotoxin%(coded%on%lysogenized%phage)cleaves%
SNARE%&%prevents%release%of%ACH%!%Flaccid%paralysis%
Rx:%anHtoxin%
Obligate%anaerobes:%
%lack%catalase%and/or%SOD,%
suscepHble%to%oxidaHve%
damage.%%FoulMsmelling,%
difficult%to%culture,%produce%
CO
2
and%H
2
%in%Hssue)%
SporeMforming,%found%in%soil%
Alpha%toxinM%lecithinase%(PL)%that%degrades%
Hssue%&%cell%membranes%
Double%hemolysis%on%blood%agar%
Gas%gangrene,%watery%diarrhea%
TraumaHc%open%wound%
infecHon%
Rx:%Clindamycin%
Watery%diarrhea%&%
pseudomembranous%coli7s%
caused%by%anHbioHc%use%
(clindamycin,%ampicillin,%cephs;%
also%Ppis’)%Dx%by%toxins%in%stool.%%
Rx:%oral%metronidazole,%
vancomycin%if%refractory,%fecal%
transplant%%
Toxin%A%(enterotoxin):%binds%to%the%
brushborder%of%the%gut%
Toxin%B%(cytotoxin):%cytoskeletal%
disrupHon%via%acHn%depolymerizaHon%!%
pseudomembrnanous%coliHs%
FacultaHve%intracellular,%BMhemolyHc,%cat+%
Unpasteurized%dairy%&%deli%meat,%transplacental,%ver7cal%transmission%.%
Form%“rocket%tails”%(via%acHn%polymerizaHon)%that%allow%them%to%move%through%the%cytoplasm%and%into%the%
cell%membrane,%thereby%avoiding%an7body.%CharacterisHc%tumbling%moHlity;%
only%gram9posi7ve%organism%to%produce%LPS%endotoxin.%Lipid*A*induces*TNF*&*IL41,*O*an3gen.%%
AmnioniHs,%SepHciemia,%Spontaenous%aborHon..%%Neonatal%meningi7s.%MeningiHs%in%IC.%%Mild%GastroenteriHs%
in%healthy%individuals%(selfMlimited).%Granulomatosis%infanHsepHca%Rx:%Ampicillin%
%%
SporeMforming%aerobe%found%in%soil%
Bacillus%anthracis%produces%Edema%factor%that%mimics%
adenylate%cyclase%!%edematous%borders%of%black%eshar%in%
cutaneous%anthrax.%%
• ONLY%bacteria%with%a%polypep7de%capsule%(D9
glutamate)%
B.,AnthracisM%%
• Cutaneous%Anthrax:%boilMlike%lesion!%ulcer%with%black%eschar;%
painless,%necroHc.%May%progress%to%bacteremia%&%death%(rare).%%%
• Pulmonary%Anthrax%is%due%to%inhalaHon%of%spore%!%flulike%
symptoms%that%rapidly%progress%to%fever,%pulmonary%
hemorrhage,%mediasHniHs,%&%shock%
B.,cereusM%food%poisoning%(rice).%%Nausea%and%vomiHng%within%1M5%
hours%is%caused%by%cereulide%(preformed%toxin)%
Acid9fast%]ZeihlMNeelsen%
(carbol%fuchsin)%stain]%
Obligate%aerobe%
M.,tuberculosis:%Lowenstein4Jensen*Agar.%TB%(fever,%night%sweats,%weight%loss,%hemoptysis!%vertebral%osteomyeliHs%!%Poe’s).%%Cord%factor%in%
virulent%strains%inhibits%macrophage%maturaHon%and%induces%release%of%TNFMa.%%Sulfa7des%(surface%glycolipids)%inhibit%phagolysosomal%fusion%
• Rx:%Isoniazid%prophylaxis.%+%Rifampin,%Pyrazinamide,%Ethambutol%for%Tx%
M.,kanasii:%pulmonary%TBMlike%
M.,aviumFintracellulare:%disseminated%nonMTB%disease%in%AIDS%(<50%CD4);%oien%drugMresistant.%%ProphylaxisM%azythromycin%
• Rx:Azithromycin%prophylaxis.%%TxM%azithro/clarithro%+%ethamputol%+/M%rifabuHn%or%ciprofloxacin%
M.,leprae:%infects%skin%and%superficial%nerves!%“glove%and%stocking”%loss%of%sensaHon.%%Cannot%be%grown%in%vitro.%%Armadillo%reservoir.%
• LepromatousM%presents%diffusely%over%the%skin%with%leonine%(lion)%facies.%%Communicable,%low%CMI%with%strong%humoral%Th2%response%
• TuberculoidM%limited%to%a%few%hairless%plagues.%%High%CMI%with%Th1%response%
• Rx:%dapson%and%rifampin%for%6%months.%Clofazimine%for%2M5%years%if%lepromatous.%%
Obligate%anaerobe.%Oral%flora.%%
A.%Israelii%!%yellow%“sulfur”%granules%
composed%of%filaments%of%bacteria%
%
Oral/facial%abscess%that%drains%through%sinus%tract%
Rx:%penicillin%
Pulmonary%infecHon%in%IC%&%cutaneous%infecHons%aier%trauma%in%IC%
"InfecHons%if%#%granulocytes.%%Caseous%necrosis.%%
Rx:%sulfonamides%
Obligate%aerobe.%Urease%+,%Soil.%%
Colonizes%the%gut%
Bacteremia%(may%be%1
st
%presentaHon%
of%colon%cancer)%
Subacute%Endocardi7s%in%colon%
cancer%pa7ents%
Rx:%penicillin%prophylaxis%
Normal%colonic%flora,%
Pen%G%resistant.%
UTI%
Biliary%tract%infecHon%
Subacute%endocardidits%%
Colonizes%vagina,%causes%pneumonia,%meningiHs,%and%sepsis%mainly%in%babies.%%
CAMP%Factor%enlarges%the%area%of%hemolysis%formed%by%S.%aureus%
Screen%pregnant%women%at%35M37%weeks%!%intrapartum%penicillin%prophylaxis.%%
Streptolysin%O%Exotoxin%degrades%cell%membrane.,%encoded%
on%lysogenized%phage%%ASO%an7bodies%used%to%diagnose%
rheumaHc%fever%&%detect%recent%infecHon.%%
AnHbodies%to%M%protein%(prevents%phago)%enhance%host%
defenses%but%can%give%rise%to%RF.%
Superan7gen%crosslinks%B%region%of%TCR%to%MHCII%on%APCs.%%
Can%acHvate%any%TMcell%leading%to%massive%release%of%
cytokines.%%
Pyogenic%%
• pharyngiHs,%celluliHs,%impeHgo%
Toxigenic%%
• Scarlet%fever%(red,%sandpaperMlike%
rash%with%fever%and%sore%throat),%
TSLS,%necroHzing%fasciiHs%
Immunologic%
• Rheuma7c%fever%(Joints,%CardiHs,%
Nodules,%Erythema%marginatum,%
Syndelam%Choria),%acute%
glomerulonephriHs%%
Rx:%Penicillin%prophylazis%and%treatment%
Normal%Oropharynx%%flora%
Dental%caries%(s.%mutans)%%
Subacute%endocardi7s%at%damaged%valves%(S.,sanguinis;%
makes%dextrans%which%bind%to%fibrinMplatelet%aggregates)%
[Subacute:*small*vega3ons*on*abnormal*valve;*sequela*of*
dental*procedures.*Gradual*onset]*
CAPSULE,%IgA%protease%
TransformaHon%
MC%Cause%of:%
• MeningiHs%
• OHHs%media%
• Pneumonia%%
• SinusiHs%%
Rx:%penicillin/cephalosporin%
(systemic,%pneumonia).%%
Vancomycin%(meningitsi)%
2
nd
%MCC%UTI%
Normal%skin%flora;%contaminates%
blood%cultures.%%
Infects%prostheHc%valves%and%IV%
catheters%by%producing%adherent%
biofilms.%
OsteomyeliHs%in%prostheHc%joint%
replacement%
%
Coagulase%and%toxins%form%fibrin%
clot%around%self%!%abscess%
Yellow%Pigment%
Protein%A%(VF)%binds%FcMIgG%&inhibits%C’%
acHvaHon.%
TSST91%SuperanHgen%(binds%MHCII%and%TCR%
leading%to%release%of%IFNMy%and%ILM2)!%Toxic%
Shock%(fever,%rash,%shock;%linked%to%vaginal%or%
nasal%tampons).%%%
Exfolia7ve%toxin!%SSSS.%%
Enterotoxin%!%food%poisoning%%
%
Asplenic%pa7ents%&%paHents%without%B9cells%
(XL%Bruton’s%BTK)%risk%infecHons%with%
encapsulated%bacteria:%
• S.%pneumonia,%H.%influenza%type%B,%
Neisseria%meningiHs,%E.%coli,%Salmonella,%
Klebsiella%pneumoniae,%GBS.%Also%
Giargia%(no%IgA),%enteroviral%
encephaliHs,%poliovirus%if%BMcell%
deficient.%Autosplenectomy%has%
occurred%when%HowellMJolly%bodies%are%
present%in%Sickle%Cell%paHent.%%
Agranulocy7c%paHents%risk%infecHons%with:%
• Staph,%burkholderia%cepacia,%serraHa,%
nocardia,%candida,%aspergillus%
Complement%Deficient%(Factor%D,%Properdin,%
C5MC9)%%paHents%risk%infecHons%with:%
• Neisseria%%
%