Simplified version of important Microbiology points that you need in Medical School.

Facultative Intracellular Salmonella, Nesseria, Brucella, Mycobacterium, Listeria, Francisella, Legionella, Yersinia.

[Some Nasty Bugs May Live FacultativeLY.]

Obligate Intracellular Rickettsia, Chlamydia. Can’t make own ATP

[Stay inside (cells) when it is Really Cold.]

Bacterial Growth Lag Phase

                Initial Phase (only 1 lag phase)

                Detoxifying medium

                Turning on enzymes to utilize medium

                For exam, number of cells at the beginning equals number or cells at the end of lag phase.


Log Phase

                Rapid exponential growth

                Generation time = time it takes one cell to divide into two. This is determined during log phase.


Stationary Phase

                Nutrients used up.

                Toxic products like acids and alkalies begin to accumulate

                Number of new cells equals number of dying cells.

Special stains Congo red : Amyloid; apple-green birefringence in polarized light (because of ß-pleated sheets)

Giemsa’s : Borrelia, Plasmodium, chlamydia, Calymmatobacterium donovani & trypanosomes.


PAS (periodic acid-Schiff) : Stains glycogen, mucopolysaccharides; used to diagnose Whipple’s disease (malabsorption syndrome caused by Tropheryma whippelii)


Ziehl-Neelsen : Acid-fast bacteria (Nocardia is partially acid fast!)


India Ink : Cryptococcus neoformans.


Silver Stain: Fungi, PCP (Pneumocystis carinii pneumonia), Legionella

Special culture requirements  H. influenzae – Chocolate agar + factors V (NAD) & X (hematin)


 N. gonorrhea – Thayer-Martin Medium


 B. pertussis – Bordet-Gengou (potato) agar


 C. diphtheriae – Tellurite plate, Loeffler’s medium, blood agar


 M. tuberculosis –  Lowenstein – Jensen agar


 Lactose fermenting enterics –  Pink colonies on MacConkey’s agar (Klebsiella, Enterobacteriaceae & E. coli)


 Legionella – Charcoal yeast extract agar buffered with increased iron and cysteine


 Fungi – Sabouraud’s agar

The four sisters “Ella” worship in the “Cysteine” chapel Francisella, Brucella, Legionella, Pasteurella
Bacterial spores Gram + soil bugs ≈ spore formers (Bacillus anthracis, Clostridium perfringens , Clostridium tetani)

Must autoclave to kill spores!

Zoonotic organisms Brucella

Bacillus anthracis

Listeria monocytogenes

Salmonella enteritidis


Coxiella burnetii – Q-fever

Chlamydia psittaci

Francisella tularensis

Yersinia pestis

Enterobacteriaceae Toxins CALM:



E coLi



Lactose fermentation

                1) Non Lactose fermenters:

                                a)Non-motile, non-H2S producers: Shigella, Yersinia

                                b)Motile, H2S producers: Salmonella, Proteus


                2)Lactose fermenters: E. Coli, Klebsiella

Staphylococcus S. epidermidis

◦Coagulase(-), gram (+) cocci


◦Infections of catheters/shunts


S. saprophyticus

◦Coagulase(-), gram (+) cocci


◦“Honeymoon cystitis”


Urinary Tract Infections

◦E. coli, S. saprophyticus, K. pneumoniae, P. vulgaris.


S. aureus

◦Coagulase(+), gram (+), catalase(+), ß-hemolytic of blood agar, cocciin ‘grape’ clusters.

◦Gastroenteritis: 2-6 h onset, salty foods, custards.

◦Endocarditis: acute

◦Toxic Shock Syndrome: desquamating rash, fever, hypotension

◦Impetigo: bullous+ honey crusted lesions

◦Pneumonia: nosocomial, typical, acute

◦Osteomyelitis: #1 cause unless HbS mentioned



◦Gastroenteritis is self-limiting

◦Nafcillin/oxacillinare DOC

◦For MRSA: vancomycin

◦For VRSA: quinupristin/dalfopristin(Synercid®)

Group A Streptococcus S. pyogenes

◦Catalase(-), ß hemolytic, bacitracinsensitive, gram (+) cocci

◦Pharyngitis: abrupt onset, tonsillaranscesses

◦Scarlet fever: blanching, sandpaper rash, strawberry tongue

◦Impetigo: honey-crusted lesions

◦Rheumatic fever: after streptococcal pharyngitis, ↑ ASO titer

◦Acute glomerulonephritis (AGN): after streptococcal skin or throat infection, hypertension, edema, smoky urine.



◦ß lactamdrugs (macrolidesused in penicillin allergy)

Group B streptococcus S. agalactiae

◦Group B, ß-hemolytic, Bacitracinresistant, Hydrolyzes hippurate

◦Gram (+), catalase(-), CAMP test (+)

◦Neonatal meningitis and septicemia: #1 cause, especially in prolonged labors.



◦Ampicillinor penicillin (DOC)

◦Clindamycinor erythromycin for penicillin allergies

Streptococcus pneumoniae ◦Gram (+), catalase(-), αhemolytic, soluble in bile, Optochinsensitive, + Quellung‟sreaction

◦Pneumonia: typical, most common cause, rusty sputum (productive cough) & lobar pneumonia

◦Meningitis: many PMNs, ↓glucose, ↑ protein in CSF, most common adult cause.

◦Otitismedia and sinusitis: most common cause.


Typical pneumonia:

◦Bacterial pneumonia such as S. pneumoniaeelicits neutrophils; arachidonicacid metabolites (acute inflammatory mediators) cause pain & fever. Pneumococcusproduces lobar pneumonia with productive cough, grows on blood agar, and usually responds well to penicillin treatment.



◦Bacterial pneumonia àmacrolides

◦Adult meningitis àceftriaxoneor cefotaxime

◦Otitismedia and sinusitis àamoxicillin, erythromycin (for allergic)

Viridans streptococci (S. sanguis, S. mutans)

◦Gram (+), catalase(-), αhemolytic, Optochinresistant, bile insoluble

◦Plaque and dental caries(S. mutans)

◦Subacutebacterial endocarditis:preexisting damage to heart valves; follows dental work (S. sanguis)



◦Penicillin G with aminoglycosidesfor endocarditis

Enterococcus Enterococcus faecalis/faecium

◦Gram (+), catalase(-), variable hemolysis, hydrolyzes esculin

◦Urinary/biliarytract infections –elderly males after prostate treatment

◦Subacute bacterial endocarditis–elderly males, follows GI/GU surgery, preexisting heart valve damage



◦Some vancomycin-resistant strains have no reliable effective treatment.

◦VanA strains have UDP-N-acetylmuramylpentapeptidewith the terminal D-alanyl-D-alaninereplaced with D-alanyl-D-lactate (functions in cell wall synthesis but does NOT bind to vancomycin)

Bacillus Bacillus anthracis

◦Gram (+), spore forming aerobic rods

◦Contact with animal hides or postal worker; escharor life-threatening pneumonia (wool sorter‟s disease)

◦Treatment : ciprofloxacin or doxycycline


Bacillus cereus

◦Rapid onset gastroenteritis

◦Fried rice, Chinese restaurants

◦Treatment : self-limiting

Clostridium Clostridium tetani

◦Dirty puncture wound

◦Rigid paralysis

◦Treatment: TIG + metronidazole/penicillin; spasmolytic(diazepam)


Clostridium botulinum

◦Home-canned alkaline vegetables

◦Floppy baby syndrome

◦Reversible flaccid paralysis


Clostridium perfringens

◦Contaminated wound

◦Pain, edema, gas, fever, tachycardia

◦Food poisoning : reheated meats, noninflammatorydiarrhea

◦Treatment :

                Gangrene à clindamycin, penicillin

                Food poisoning à self-limiting


Clostridium difficile

◦Hospitalized patient on antibiotics (antibiotics over-use)

◦Develops colitis, diarrhea

◦Treatment : metronidazole(vancomycin)



TETanus is TETanic paralysis

BOTulinumis from bad BOTtles of food and honey

PERFringens PERForates a gangrenous leg

DIfficilecauses DIiarrhea(Treat with metronidazole)

Listeria Listeriamonocytogenes

◦Gram (+) rods, ß-hemolytic

◦Facultative intracellular

◦Foodborne(deli foods) àunpasteurized milk


◦Neonatal septicemia and meningitis(3rdmost common cause)

◦Meningitis in renal transplant or cancer patients(most common cause)


Treatment : ampicillin(+ gentamycinfor IC patients)

Corynebacterium diphtheriae ◦Gram (+), aerobic, non-spore forming rods

◦BULL NECK, myocarditis, nerve palsies

◦Gray pseudomembraneàairway obstruction

◦Toxin produced by lysogeny(ß-corynephage)

◦Toxin ribosylatesEF-2; heart, nerve damage

◦V-L shapes àtellurite

◦Metachromaticgranules àLoeffler‟s


Treatment :

◦Erythromycin and antitoxin


Mnemonic: (ABCDEFG)

ADP-ribosylation; ß-corynephage; CorynebacteriumDiphtheria; Elongation Factor-2; metachromatic Granules

Actinomyces Actinomycesisraelii

◦Patient with mycetomaon jawline or spread from IUD

◦Causes oral/facial abscesses with YELLOW sulfur granules that may drain through sinus tracts in skin (can cause 1 brain abscess)

◦Sulfur granules in pus grow anaerobic, gram (+), non-acid fast branching rods (resembling fungi)


Treatment :

◦Ampicillinor penicillin G and surgical drainage

Nocardia Nocardiaasteoidsand Nocardiabrasiliensis

◦Gram (+) filamentous bacilli, aerobic, PARTIALLY acid fast

◦Norcardiosis: Cavitarybronchopulmonarydisease, mycetomas(can cause multiple foci brain abscesses)


Treatment :

◦Sulfanomidesor TMP-SMZ


Mnemonic: (SNAP)

Sulfa for Nocardia; Actinomycesuse Penicillin

Mycobacterium Mycobacterium Tuberculosis

◦High risk patient (Low SES, HIV+, IV drug user)

◦Chronic cough, weight loss

◦Auraminerhodaminestaining, acid fast bacilli in sputum

◦Produce niacin, heat sensitive catalase

◦Positive DTH test (PPD)

◦Facultative intracellular


                -TB granulomas(Ghonfocus) + lobar & perihilarlymph node involvement

                -Reflects 1˚ infection/exposure


Mycobacterium leprae(leprosy)

◦Acid fast bacilli in punch biopsy

◦Immigrant patient with sensory loss in extremities

◦+ leprominskin test in Tuberculoidtype (TL) BUT NOT Lepromatousleprosy (LL)


Neisseria Neisseria meningitidis

◦Young adults with meningitis

◦Abrupt onset with signs of endotoxintoxicity


Oxidase(cytochromeC oxidase) test:

◦flood colony with phenylenediamine; in presence of oxidase, phenylenediamineturns black. Rapid test.

◦Major oxidase-negative gram –group is Enterobacteriaceae


Treatment :

◦Neonates & infants: Ampicillinand cefotaxime

◦Children & adults: cefotaximeor ceftriaxone


Neisseria gonorrhoeae

◦Sexually active patient

◦Urethral/vaginal discharge (leukorrhea)

◦Arthritis possible

◦Neonatal ophthalmia

◦Gram –diploccocusin neutrophils


Treatment : ceftriaxone

Pseudomonas Pseudomonas aeruginosa

◦Oxidase(+), aerobic rod

◦Blue-greenpigments, fruity odor

◦Burn infections –blue-greenpus, fruity odor

◦Typical pneumonia –CGD or CF

◦UTI –catheterized patients


Treatment :

◦Penicillin + aminoglycoside


Drug resistance (very common):

◦Intrinsic resistance (missing high affinity porinsome drugs enter through);

◦Plasmid mediated ß-lactamasesand acetylating enzymes.

Legionella Legionella pneumophila

◦Elderly smoker, heavy drinker, or IC

◦Exposure to aerosols of water (air conditioning)

◦Atypical pneumonia (legionnaires disease), Pontiac fiver

◦Associated with hyponatremia


Treatment :

◦Fluoroquinoloneor azithromycinor erythromycin with rifampinfor IC patients

Francisella Francisellatularensis

◦Patient with ulceroglandulardisease, atypical pneumonia, or gastrointestinal disease


◦Exposure to rabbits/ticks


Treatment : ◦streptomycin

Bordetella Bordetella Pertussis

◦Unvaccinated child (immigrant family or religious objections)

◦Cough with inspiratory“whoop” (3 stages):

                (1-2 wks) catarrhal : CONTAGIOUS

                (2-4 wks) paroxysmal : organism begin disappearing

                (>3 wks) convalescence : secondary complications



                DTaPlasts 5 –10 years (IgA)

                Immunity to actual pertussisis life long


Treatment :

◦Supportive care & Erythromycin (14 days)

Brucella Brucellaspecies

◦Patient with acute septicemia

◦Exposure to animals or unpasteurized dairy

◦California/Texas or travel to Mexico


Treatment :

◦Adults : rifampin& doxycycline(6 wks)

◦Children : rifampin& cotrimoxazole

Campylobacter Campylobacter jejuni

◦Patient with inflammatory diarrhea

◦Microaerophillic, oxidase+, grows at 42˚C

◦Ten or more stools/day, maybe frankly bloody

◦Complications àGBS & reactive arthritis


Treatment :

◦Mostly fluid and electrolyte replacement.

◦Erythromycin, fluoroquinolones, penicillin resistant.

Helicobacter Helicobacter pylori

◦Patient with gastritis, ulcers, stomach cancer

◦Microaerophillic, oxidase+, urease+

◦Reservoir – HUMANS


Treatment :

◦Omeprazole+ amoxicillin + clarothromycin

◦Treat for 10 –14 days

Escherichia Escherichia coli

◦Isolation of E. coli from stool is not significant.

◦Sorbito lMacConkey screen

◦Most E. coliferment sorbitol(Most EHEC do not –colorless)

◦Toxins ↑cAMP

                EPEC = P (pediatric)

                ETEC = T (traveller)

                EIEC = I (inflammatory)

                EHEC = H (hamburger; Hemolytic colitis and Hemolytic Uremic Syndrome)

Shigella Shigellaspecies

◦patient with acute bloody diarrhea + fever

◦Non-motile, non-H2S producer and non-lactose fermenters

◦Shigellasonnei(most common in U.S)

◦Shigelladysenteriae(most severe disease) –SHIGA TOXIN (neuro, cyto, entero)

Klebsiella Klebsiella pneumonia

◦Elderly patient with typical pneumonia: currant jelly sputum

◦UTI (catheterized associated)


◦IC or nosocomial

◦Oxidase(-), encapsulated, lactose fermenters

◦Treatment : 3rdgeneration cephalosporin


Klebsiella Granulomatis

◦Patient from Caribbean or New Guinea with subcutaneous genital nodules

◦Encapsulated, inside mononuclear cells

◦Treatment :TMP-SMX; tetracyclinesand erythromycin

Salmonella Salmonella typhi

◦Patient with fever, abdominal pain, rose spots

◦Travel to endemic area

◦Encapsulated, nonlactosefermenter, produces H2S and is motile.

◦Widaltest +

Treatment: Fluoroquinolones or 3rd gen cephalosporins


S. enteritidis, S. typhimurium

◦Enterocolitis–inflammatory, follows ingestion of poultry products or handling pet reptiles.

◦Septicemia –very young or elderly

◦Osteomyelitis–sickle cell disease


◦For gastroenteritis : self-limiting

◦For invasive disease : Ampicillin, TMP-SMX, Fluoroquinolonesor 3rdgen cephalosporins.

Yersinia Yersinia pestis–THE PLAGUE!

◦High fever, buboes (swelling of regional lymph nodes), conjunctivitis and pneumonia

◦Exposure to small rodents, desert Southwest

◦Bipolar staining (“safety pin”)

◦Treatment : aminoglycosides


Yersinia enterolitica

◦Patient with inflammatory diarrhea or pseudoappendicitis

◦Cold climates; Unpasteurized milk, pork

◦Non-lactose fermenters, non-H2S producers

◦Treatment: For IC – fluoroquinoloness or 3rd generation cephalosporins.

Proteus Proteus mirabilis/Proteus vulgaris

◦Patient with UTI or septicemia

◦Swarming motility on blood agar plate

◦Staghornrenal calculi (struvitestones)

◦Non-lactose fermenting, urease(+)

◦Treatment : fluoroquinolones, TMP-SMX, or 3rdgeneration cephalosporinsfor uncomplicated cases.


NOTE:Weil Felix test: Antigens of OX strains of Proteus vulgariscross-react with rickettsial organisms.

Gardnerella Gardnerella vaginalis:

◦Female patient with increased thin gray vaginal discharge and a “fishy” amine odor.

◦Post antibiotic or menses

◦Clue cells

◦Whiff test +

◦Treatment : Metronidazoleor clindamycin

Vibrio Vibrio Cholera:

-Patient with non-inflammatory diarrhea

-Rice water stool; Dehydration

-Travel to endemic area

-Curved rods, polar flagella, oxidase +


                1.fluid and electrolyte replacement

                2.Doxycyclineor ciprofloxacin shorten disease and reduce carriage.


Vibrio parahaemolyticus

-Consumption of undercooked or raw seafood

-Watery diarrhea with abd cramps- self limiting


Vibrio vulnificus

-Swimming in brackish water; shucking oysters or consuming undercooked or raw seafood

-causes gastroenteritis or cellulitis(treat with tetracycline)

Rickettsia Rickettsiarickettsii

◦Patient with influenza-like symptoms and petechialrash that begins on ankles and wrists and moves to trunk

◦Rocky mountain spotted fever (RMSF)

◦East coast mountainous areas (North Carolina)

◦Spring/Summer seasons

◦Outdoor exposure

◦Weil-Felix (+)


Treatment : ◦doxycycline

Coxiella Coxiellaburnetii

◦Patient with fever, pneumonia, granulomatoushepatitis

◦Q-fever and chronic Q-fever

◦Exposure to domestic animal breeding operation

◦Diagnosed serologically


Treatment :Doxycycline& erythromycin

Chlamydia Chlamydia trachomatis

◦Sexually active patient or neonate

◦Adult : urethritis, cervicitis, PID, inclusion conjunctivitis

◦Neonate : inclusion conjunctivitis/pneumonia

◦Immigrant from Africa/Asia, swollen genital lymphadenopathy

◦Cytoplasmicinclusion bodies in scrappings

◦Active reticulate bodies & inactive elementary bodies

Treatment : ◦Doxycycline& azithromycin


C. pneumonia

◦Atypical “walking” pneumonia

◦Sputum with intracytoplasmicinclusions

◦Prominent dry cough and hoarseness

◦Treatment : Macrolidesand tetracycline


C. psittaci(psittacosis / ornithosis)

◦Atypical pneumonia with hepatitis

◦Cough may be absent and when present non-productive at first then scant mucopurulent

◦Treatment : Doxycycline

Mycoplasma Mycoplasma pneumoniae

◦Young adult with atypical pneumonia

◦Mulberry-shaped colonies on media containing sterols

◦Positive cold agglutinin test

◦Treatment: erythromycin, azithromycin, & clarithromycin(NO CEPHALOSPORINS or PENICILLINS)


Ureaplasma urealyticum

◦Adult with urethritis, prostatitis, renal calculi

◦Alkaline urine; urease(+)

◦Treatment: erythromycin or tetracycline

Dimorphic Fungi Body Heat Changes Shape for the dimorphic fungi





Pseudohyphae(Candida albicans) •Hyphaewith constrictions at each septum
Spore types Conidia

                -Asexual spores; formed off hyphae; common; air-borne



                -“Buds” on yeasts (asexual budding daughter yeast cells)



                -Asexual spores formed by a “joint”


Spherules and Endospores(Coccidioides)

                -Spores inside the spherules in tissues

Malassezia furfur Normal skin flora (lipophilicyeast)

Patient with blotchy hypo-pigmentation of skin

KOH scrapping shows “spaghetti and meatballs” or “bacon and eggs” yeast clusters & short curved septate hyphae

Treatment : Topical selenium sulfide; recurs

Dermatophytes(group of fungi) Filamentous (monomorphic) fungi

Three genera:

                Trichophyton–skin, hair and nails

                Mircrosporum–hair and skin

                Epidermophyton–skin and nails


Patient with scaly, ringlikelesions (Tineas) of skin. May involve hair shaft or nails.

KOH scrapping shows athroconidiaand hyphae

Treatment :

Topical imidazoleor tolnafate

ID reaction (dermatophytID) = allergic response to circulating fungal antigens.

Sporothrix schenckii Subcutaneous mycoses

Patient with subcutaneous/lymphocutaneous mycetoma

Gardener, florist, basket weaver, or alcoholic rose-garden sleeper disease (homeless)

Cigar-shaped yeast in pus

Treatment : intraconazoleor amphotericinB

Histoplasma capsulatum Deep fungal infection; dimorphic fungi

Normal patient with acute pulmonary; IC patient with chronic pulmonary or disseminated infection (FUNGUS FLU)

States following drainages of Great Lakes to Gulf of Mexico

Exposure to bird or bat excrement

Sputum or blood cultures with mononuclear cells packed with yeast cells (tiny yeast inside macrophages)

Treatment: Ketoconazole, amphotericin B

Coccidioides immitis Deep fungal infection; dimorphic fungi

Normal patient with erythemanodosumor self-resolving pneumonia

IC patient with calcifying chronic pulmonary or disseminated infections

Pregnant female in 3rdtrimester, disseminated infection

Desert southwest

Sputum has spherules with endospores

Treatment : AmphotericinB

Blastomyces dermatitidis Deep fungal infection; dimorphic fungi

Normal patient with acute pulmonary symptoms

IC patient with chronic pulmonary or disseminated infection

North and South Carolina (otherwise coexists with Histoplasma)

Sputum has broad-based, budding yeasts with double, refractilecell walls.

Treatment : Amphotericin B

Aspergillus fumigatus Monomorphicfilamentous OPPORTUNISTICfungi

Patient with asthma allergies –growing mucous plugs in lung

Patient with cavitarylung lesions –fungus ball

Patient with burns –cellulitis, invasion

IC patient –pneumonia, meningitis

Septatehyphaebranch at acute angles

Treatment : Itraconazole or Amphotericin B

Candida albicans OPPORTUNISTICfungi

Forms germ tubes at 37˚C; pseudohyphae& true hyphaewhen invades tissues

Germ tube test demonstrates pseudohyphaeand hyphae

IC patient, overuse of antibiotics –thrush, spread down GIT, septicemia

IV drug abusers -endocarditis

Treatment :

                topical or oral imidazoles; nystatin

                Disseminated : AmphotericinB or fluconazole

Cryptococcus neoformans Encapsulated (monomorphic) yeast; OPPORTUNISTIC fungi

Pigeon breeder with acute pulmonary symptoms

Hodgkins/AIDS patient with meningitis

India Ink mount of CSF with encapsulated yeasts

Treatment : AmphotericinB + flucytosineuntil afebrile(minumum10 wks), then fluconazole

Mucor, Rhizopus, Absidia Ketoacidoticdiabetic or leukemic patient with rhinocerebralinfection

Biopsy with non-septateirregular-width hyphaebranching at 90˚ angles.

Treatment :

                High fatality rate (rapid growth and invasion)

                Debridenecrotic tissue & start AmphotericinB fast.

Pneumocystis jiroveci Obligate extracellular parasite

Premature infant or AIDS patient with atypical pneumonia

Biopsy with honeycomb exudates and silver-staining cysts

X-ray ground glass

Treatment :

                TMP-SMX for mild

                Dapsonefor moderate to severe

Bacterial Meningitis

Practice Microbiology questions for free