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Microbiology (Bacteria (Others (Mycobacterium (Mycobacterium Tuberculosis,…
Microbiology
Bacteria
Gram +
Bacilli
Aerobic
Listeria
Intracellular ROD - ingestion of unpasteurized dairy products and cold deli meat / transPLACENTAL / vaginal
Grows at refrigerated temps
Forms ROCKET TAILS via actin polymerization = intracellular movement and cell to cell spread -> tumbling motility.
Amnionitis, septicemia, spont abortion, neonatal meningitis
Ampicillin
Bacillus
Bacillis anthracis
Anthrax toxin - polypeptide capsule (D-glutamate).
MEDUSA HEAD appearance.
Cutaneuous anthrax
Painless papule surrounded by vesicles - black eschar.
LF (map kinase) and EF (cAMP)
Pulmonary anthrax - inhalation of spores. Known has wool sorter's disease. -> pulmonary hemorrhage, mediastinitis and shock
Treat with fluroquinilones and then doxycycline
Bacillus cereus.
Food poisoning -> spores in rice. CEREULIDE = preformed toxin. -> watery diarrhea x 8-18 hours.
Corynebacterium
Resp droplet transmission. Causes diphtheria via exotoxin encoded by B prophage ( inhibits protein synthesis via ADP ribosylation of EF2 (elongation factor 2)
Pseudomembrane pharyngitis (grey-white) with lymphadenopathy myocarditis and arrhythmias.
Metachromatic granules and + Elek test for toxin. Black colonies on cystine tellurite agar (Loeffler media)
TOXOID vaccine prevents diphtheria. -> IMMIGRANTS not vaccinated
Anaerobic
Clostridium (spore forming)
C tetani
Tetanospasmin - exotoxin ceasing tetanus - proteases that cleave SNARE proteins for neurotransmitters. Block release of GABA and glycine from RENSHAW cells.
Causes spastic paralysis, truisms, rises sardonicus , opisthotonos.
Prevent with tetanus TOXOID vaccine. Treat with diazepam
Clinical diagnosis
C botulinum
Heat labile toxin that inhibits ACh release at NM junction.
Adults = preformed toxin - babies = spores
Treat with antitoxin
Diplopia, dysarthria, dysphagia, dyspnea. Descending flaccid paralysis
C perfringes.
A toxin (lecithinase / a phospholipase that can cause myonecrosis and hemolysis.
Spores survive in undercooked food, heat labile enterotoxin -> Food poisoning.
Treat with IV penicillin B
C difficile
Toxin A an enterotoxin binds to brush border of gut and alters fluid secretion. Toxin B cytotoxin disrupts cystokeletal via actin depol. -> pseudomembranous colitis. / toxin megacolon
2º to clines or amp / ppi.
Diagnosed by 1/2 toxins by antigen detection or PCR.
Treat with metronidazole / oral Vanco / fidaxomicin or fecal microbiota transplant
Propionibacterium
Cocci
Catalase +
Staphylococcus(clusters)
Coagulase -
Novobiocin -
Staph saprophytic(clusters)
Normal flora of female genital tract and perineum.
2nd most common cause of UTI in woman.
Novobiocin + - mannitol -
Staph epidermis
Normal flora of skin
Infects prosthetic devices and IV catheters by biofilm.
Start vancomycin
Coagulase + mannitol +
Staph Aureus
Virulence: Protein A ( Fc-IgG)
Causes - inflammatory disease. Pneumonia after influenza virus
Toxin mediated disease: TSST1 - scalded skin syndrome, rapid onset food poisoning. Superantigen that binds to MHC 2 - desquamation.
MRSA : Resistant because of altered penicillin binding protein.
Food poisoning due to injection of preformed toixin. Enterotoxin is heat stable.
Catalase -
Streptococcus
Alpha hemolysis
Optochin resistant / bile soluble -
Viridans strep (mutans and mitis)
Normal flora of oropharynx that causes dental caries.
Can cause subacute bacterial endocarditis (dextran)
Optochin sensitive / bile soluble +
Strep pneumonia (lancet shaped)
Virulence: Encapsulated and IgA protease
Common cause of meningitis, otitis media, bacterial pneumonia, sinusitis.
Rusty sputum, sepsis in patients with sickle cell disease.
Beta hemolysis
Bacitracin sensitive -
Group B Strep agalactiae
Colonizes vagina causing pneumonia, meningitis, and sepsis.
Produces CAMP Factor enlarging hemolysis
Bacitracin sensitive +
Group A strep Strep pyogenes (chains)
Pyogenic
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Toxigenic
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Immunologic
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Pyrrolidonyl arylamidase (PYR) + . Hyaluronic acid capsule which inhibits phagocytosis. Antibodies to M protein.
ASO titer or anti-DNase B antibodies = recent infection
Gamma (no) hemolysis
Growth in 6.5 % NaCl -
Nonenterococcus
S bovis (colonizes gut)
can cause bacteria and subacute endocarditis. -associated with colon cancer
Growth in 6.5 % NaCl +
Group D enterococcus (E faecium / E faecalis)
Normal colonic flora that are PenG resistant
Cause UTI, biliary pathology, subacute endocarditis
PYR + and VRE - GROWS ON Hypertonic solution
Branching Filaments
Aerobic
Nocardia
Acid fast
pulm infections in immunocompromised - mimics TB but no PPD/ cut infections after trauma in immunocompetent patients. / BRAIN ABSCESSES. -> can spread to CNS
TMP/SMX
Anaerobic
Actinomyces
Not acid fast
Oral/facial abscesses that drain through sinus tracts. Associated with dental carries / yellow shofar granules .Can cause PID with IUDs.
treat with penicillin
Cervicofacial actinomycetes - upper jaw / mandible , slowly progressing with no pain.
Pulmonary actinomyces. Aspiration (alcoholism increases risk).
Gram -
Dilococci
Aerobic
Maltose -
N gonorrhoeae
Contains lipxooligosaccharides with endotoxin activity
-> intracellular in neutrophils.
Grows on chocolate agar / VPN agar / Thayer Martin.
no vaccine due to antigenic variation of pills.
Causes gonorrhoea, knee septic arthritis, neonatal conjunctivitis , PID, Fitz -hugh- Curtis syndrome -> liver capsule inflammation -> violin string adhesions
Erythromycin eye ointment to prevent neonatal blindness
Ceftriaxone + azithromycin (possible chlamydial confection)
Produces IgA protease
Moraxella
Maltose +
N meningitides
Polysaccharide capsule -> virulence
Vaccine - not for type B
Transmitted via resp and oral secretions
meningococcemia with petechial and gangrene toes.
WATERHOUSE FRIDERICHSEN Syndrome -> adrenal insufficiency DIC and shock - adrenal gland failure.
Rifampin, ciprofloxacin, ceftriaxone prophylaxis in close contacts.
Produces IgA protease
Coccobacilli
H influenza
Unencapsulated strains are most common mucosal infections - OM, conjunctivitis, bronchitis.
IgA protease
Chocolate agar container factor V (Nad+) and (hematin). Can also grow with Staph Aureus
Causes epiglottitis, meningitis (type B), OM and pneumonia, septic arthritis
Amox +- clan, ceftriaxone for meningits, rifampin for close contacts.
Vaccine contains type B capsular polysaccharide (cpolyribosylribitol phosphate) conjugated to diphtheria toxoid. Given between 2-18 months.
COPD exacerbations
Pasteurella
Brucella
Bordetella pertussis
Virulence = pertussis toxin (Disables G1) and tracheal cytotoxin. Transmitted by responses droplets. Increases in CAMP which leads to lymphocytosis.
catarrhal - low grade feels - coryza
paroxysmal - intense cough followed by inspiratory whoop/ posttussive vomiting
convalescent - recovery of chronic cough.
Prevented by Tdap / DTap vaccines.
Francisella tularensis
Comma-shaped rods
Oxidase +
Campylobacter jejuni (grows in 42ºC)
Bloody diarrhea in children
Undercooked contaminated poultry or meat, unpasteurized milk.
Infected animals
Common antecedent to GBS and reactive arthritis.
Vibrio cholera (grows in alkaline media)
Endemic to developing countries. RICE WATER diarrhea via Fibrae -> cholera enterotoxin that activates Gs. Increase CAMP. Needs like inoculum.
Contaminated water or uncooked raw shellfish (oysters). Need oral rehydration. + electrolytes
Stool microscopy = no leukocytes / erythrocytes = mucous seen.
Helicobacter pylori (produces urease)
Flagellated TRIPLE + catalase +, oxidase + urease +. Can use urea breath test or fecal antigen test. Alkaline environment helps H pylori survive acidic mucosa.
Antrum of stomach - gastritis and DUODENAL peptic ulcers-> RF for PUD, gastric adenocarcinoma, MALT lymphoma.
triple therapy; Amox (metronidazole if allergies). Clarithromycin, PPI.
Decrease in somatostatin delta cells in antrum -> decrease in duodenal carb.
Bacilli (rod)
Lactose -
Oxidase -
H2S on TSI agar -
Shigella
Humans - Cell to cell - no hematogenous.
Endotoxin - SHIGA TOXIN
Small inoculum needed.
bloody. diarrhea.
No vaccine.
Four F's. FINGERS - FLIES - FOOD- FECES
Invasine of M cells is key
Uses actin filaments / polymerization to spread
Hemolytic ureic syndrome - S dysenteriae.
Yersinia
Transmitted from pet faces (puppies)/ milk / pork
Diarrhea / pseudo appendicitis -> RLQ pain due to mesenteric adenitis (lymph) and terminal ileitis
Black Death / bubonic plague : Rats / prairie dog fleas.
Swollen lymph nodes -> DIC
Aminoglycosides + tetracycline
H2S on TSI agar +
Salmonella
S typhi
Humans, disseminate hematogenously, Produces H2S. Produces flagella. CARRIER IS GALLBLADDER
Endotoxin Vi capsule -> MONOYTES react.
High large inoculum - inactivated by gastric acids (acid labile)
Constipations -> Diarrhea (pea soup)
Vaccine = live attenuated / IM = Vi capsular polysaccharide
Typhoid fever - rose spots on abdominal,
Ceftriaxone or fluorine
Other spp except for Typhi
Humans and animals can can disseminate hematogenously.
H2S and Flaggela
Diarrhea
No vaccine
Poultry, eggs, pets and TURTLES are common
Can cause osteomyelitis and endocarditis.
Proteus
Oxidase +
Pseudomonas
Produces pyocyanin - blue green pigment with grape like door.
Endotoxin - exotoxin A (inactivates Elongation factor 2), phospholipase C and pyocynin.
Pneumonia, sepsis, ecthyma gangrenosum , UTI, diabetes, drug use, osteomyeltits , otitis external, Skin infections (hot tub folliculitis
Ecthyma gangrenosum - necrotic cutaneous lesion - seen in immunocompromised
Treatment: CAMPFIRE
Carbapenems
Aminoglycosides
Monobactams
Polymyxins
Fluoroquinolones (cipro/levo)
3rd gen cephalosporins
Extended spectrum penicillins
Wound infections in burn victims.
Legionella pneumophila
Gram stains poorly - use silver stain. Grows on charcoal yeast extract with iron and cysteine. Detected by presence of antigen in urine . Labs =
Hyponatremia
.
Transmission - aerosol from environmental water - aircon / hot water tanks. -no person to person
treat with macrolide or quinolone.
Legionnaires disease - unilateral pneumonia, fever, GI and CNS symptoms. SMOKERS and chronic lung disease.
Pontiac = mild flu like syndrome.
Lactose +
Fast
Klebsiella
Lobar pneumonia in alcoholics and diabetes when aspirated
Caused by abundant polysaccharide capsules
Dark red currant jelly sputum
Nosocomial UTIS
Abscess in lungs and liver
E Coli
EIEC
Invades intestinal mucosa and causes necrosis
ETEC
Heat labile and heat stable enterotoxin - travellers diarrhea.
EPEC
No toxin - adheres to surface - flattens villi prevents absorption. Child diarrhea.
EHEC
O157:H7 is common serotype.
Undercooked meat, raw leafy veggies.
Shiga like toxin causes hemolytic ureic syndrome - anemia, thrombocytopenia, and acute renal failure due to microthrombia. Schistocytes -> platelet consumption and decreased renal blood flow.
Toxin alone causes necrosis and inflammation
No orbital - hemorrhagic hamburgers hemolytic uraemia syndrome.
MacConkey Agar
Virulence factors: Fibrae - cystitis and pyelnephritis (P-Pili), K capsule pneumonia, neonatal meningitis, LPS endotoxin - septic shock - LIPID A
Enterobacter
Slow
Citrobacter
Serratia
Spirochetes
Leptospira Interrogans
Hook shaped found in water with animal urine.
Leptospirosis - flu symptoms , myalgia of calves, jaundice, photophobia with conjunctival suffusion (erythema without exudate). Prevalent in surgeries in tropics)
Weil disease: Icterohemorrhagic leptospirosis: Severe form with jaundice and aoztemia from liver and kidney dysfunction - fever, hemorrhage and anemia.
Borrelia burgdorferi (Lyme disease)
Ixodes tick natural reservoir is mouse and important to tick life cycle. Northeastern US - new Hampshire / conneticut.
Stage 1 - early localized - erythema migrant (Bulls eye config) - pathognomonic
Stage 2- early disseminated - secondary lesions, carditis / heart block, bells palsy, migratory myalgia / transient arthritis.
Stage 3 - Late disseminated encephalopathies - chronic arthritis. Large joints. - Memory difficulty - not visualized on microscopy.
Treat with doxy, amor, cefuroxime in pregnant women and children (prophylaxis)
Treponema Pallidum (syphilis)
Primary: Painless chancre - dark field microscopy to visualize trepnomes in fluid of chancre. VDRL + in 80%
Secondary: Disseminated . constitutional symptoms. maculupapular rash . Condylomata lata, patchy hair loss . VDRL / RPR . Confirm diagnosis with FTA-ABS
Tertiary: Gummas - aortitis - neurosyphilis , tabes dorsalis (posterior column), argyl robertson pupil. Broad base ataxia, + Romberg, Charcot joint, stroke no HTN.
Congenital: Facial abnormalities: Rhagades - linear scars are concern of mouth . Snuffles, saddle nose, notches (hutchinson teeth) / mulberry molars and short maxillae. Saber shins / CN VII deafness. Treat in early pregnancy.
VDRL positives: Viral EBV, hepatitis, drugs, rheumatic fever, lupus and leprosy.
Jarisch Herxheimer reaction - flu like reaction after abx - due to killed spirochetes
Gram variable
Garderella vaginalis
Others
Rickettsia rickettsia (Rocky Mountain spotted fever)
R typhi (typhus)
R prowazekii (typhus)
Ehrlichia
Anaplasma
Coxiella burnettii
Chlamydiae
Chlamydia trachomatis
Chlamydophila pneumonia / psittaci
Mycoplasma pneumonia
Mycobacterium
Mycobacterium Tuberculosis
PPD + if current infection, PPD - if no infection in sarcoidosis or HIV infection.
Interferon y has fewer FP than BCG vaccination.
Caseating granulomas with central necrosis + LANGHANS Gian cells are characteristic of 2º tuberculosis
Ghon complex = mid/ lower lobes.
Ranke complex = calcification tuberculin +
2º tuberculosis = fibrocaseous aviary lesion - usually upper lobes b/c oxygenated better.
Potts disease = vertebrae involved.
Treatment = Rifampin, isonazide (causes to lose acid fastness), pyrazinamide, ethambutol.
Cord factor creates serpentine cord appearance in virulent M tuberculosis strains - actives macrophages and induces TNF -a sulfotides, inhibit phagolysosomal fusion. (causes wasting too). Macrophages display mycobacterial antigens on MHCII
M avian / intracellular - causes disseminated diseases in AIDS - resistant to multiple drugs - prophylaxis with rzithro.
M scrofulaceum - cervi lymphadenitis in children
M marinum - hand infection in aquarium handlers.
M leprae (Leprosy / Hansen disease) (acid fast bacilli)
glove and stocking loss of sensation
diagnosis: Skin biopsy/ tissue PCR
reservoir in US armadillos.
Lepromatous - diffusely over skin with lion like facies communicable - low cell mediated immunity with HUMORAL Th2 response.- can be fatal
Treat: Dapsone + rifampin + clofazimine (2-5 years)
Tuberculoid: Few Hypoesthetic hairless skin plaques - high cell mediated immunity with Th1 immune response
Treat: Dapsone / daxone + rifampin (6 months)
ANTIBIOTICS
CELL - WALL SYNTHESIS
Penicillin
Penicillin G /V
Resistance by penicillinase
GRAM + / GRAM - COCI
D-Ala D - Ala analog. Blocks transpeptidase cross linking of peptidoglycan in cell wall
Penicillinase sensitive penicillins (amoxicillin, ampicillin, aminopenicillins
Extended spectrum penicillin - H influenza / H pylori / E Coli/ Salmonella/ Shigella
Penicillinase resistant penicillins( Dicloxacillin, nafcillin, oxacillin)
Bulky R group blocks access of B Lactamase to B lactam ring
S aureus
Antipseudomonal penicillins: Pip / ticarcillin
Pseudomonas spp / gram - rods.
B- lactase inhibitors: Clavulanic - added to penicillin antibiotics to protect antibiotic
Cepalosoporins
B-lactam that inhibit cell wall synthesis but less susceptible to penicillinases.
1st gen: Cefazolin/cephalexin - gram + cocci. . Preent S aureus wound infections
2nd gen: Cefaclor, cefoxitin, cefuroxime - gram + cocci.
3rd gen: Ceftriaxone , cefotaxime, cefpodoxime , ceftazidime - gram - infections- Crosses blood brain barrier
4th gen - cefepime . Gram - organisms with increase activity against Pseudomonas and gram + organisms
5th gen Ceftaroline - broad gram + and gram - organism coverage. MRSA
Resistance: Structural change in penicillin binding proteins - transpeptidases
Carbapenems: Imipenem, meropenem, erapenem, doripenem: Broad spectrum b-lactamase resistant carbapenem.
Gram + cocci, gram - rods/ anaerobes
Monobactams: Aztreonam: Less susceptible to B - lactamases - prevents peptidoglycan cross linking by binding to penicillin binding protein 3 - gram - rods only. No activity against Gram + rods or anaerobes.
Vancomycin: Inhibits cell wall peptidoglycan formation by binding D-ala D-ala portion of cell wall precursors .
Gram + bug only.
PROTEIN SYNTHESIS
30 S inhibitors
Aminoglycosides; Gent, Neo, Tobra, Strepto MYCIN
Gram - rod
Tetracyclines: Tetra, doxy, mino CYCLINE
Borrelia burgdorferi, M pneumona. Reickettsia, Chlamydia
Glycylcylines: Tigercycline: Gram -, broad spectrum anaerobic, gram + coverage. MRSA / VRE
50 S inhibitors
Chloramphenicol: Blocks peptidyltransferase at 50S ribosomal unit. Meningitis and Rocky Mountied spotted fever
Clinda: Anaerobic infections
Oxazolidinones: Linezolid - Gram + species including MRSA and VRE
Macrolide: Azithromycin , clarithromycin, erythromycin: Atypical pneumonia's, gram + Cocci.
FOLIC ACID SYNTHESIS
Sulfamethoxazole (SMX) - Gram + gram -, simple UTI
Dapsone: Leprosy
Trimethoprim: Inhibits dihydrofolate reductase. (TMP)
Fluoroquinolones: Cipro, levo, FLOXACIN
Inhibit enzymes topoisomerase DNA Gyrase .
Gram - RODS of urinary and GI tract
Daptomycin: lipoprotein that disrupts cell membranes of gram + cocci . S aureus skin infections
Metronidazole: Forms toxin free radical metabolites in the bacterial cell that damage DNA. Gardia, entamoeba, trichomna, gardnerella vaginalis, anaerobes
Parasites
Protozoa
Gastrointestinal
Entamoeba histolytica
Cryptosporidium
Giardia lamblia
CNS
Toxoplasma gondii
Naegleria fowleri
Trypanosoma brucei
Hematologic
Plasmodium
Vivax/ovale
Falciparum
Malariae
Babesia
Other
Trypanosoma Cruzi
Leishmania Donavani
Trichomonas vaginalis
Nematodes / roundworms
Intestinal
Enterbius vermicularis (pinworm)
Ascaris lumbricoides (giant roundworm)
Strongyloides stercoralis (threadworm)
Ancylostoma duodenale / Necator americanus (hookworm)
Trichinella spiralis
Trichuris trichina (whipworm)
Tissue
Toxocara canis
Onchocerca volvulus
Loa loa
Wuchereria bancrofti
Cestodes (tapeworms)
Taenia solium
Diphyllobothrium latum
Echnococcus granulosus
Trematodes (flukes)
Schistosoma
Clonorchis sinensis
Ectoparasites
Sarcoptes scabiei
Pediculus humanus/ phthirus pubis
Fungi
Systemic
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Coccidioidomycosis
Para-coccidioidomycosis
Cutaneous
Tinea
Capitis
Corporis
Cruris
Pedis
Unguium
Pityriasis / versicolor
Opportunisitc
Candida albicans
Aspergillus fumigaturs
Cryptococcus neoformans
Mucor / Rhizopus
Other
Pneumocystis Jirovecii
Sporothrix Schenckii
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