Medical Microbiology - UTIs/STIs and GI System Infections/Diseases

Dental Caries

• Gram-positive cocci (Streptococcus mutans), Gram-positive rods (Lactobacillus);
also Bifidobacterium.
• Virulence: fermentation of sugars = acid production → enamel demineralization;
strong biofilm (dental plaque).
• Key features: cavities, plaque accumulation; sugar-dependent.
• Diagnosis: clinical examination.
• Treatment: fluoride, restoration, dental hygiene.
• Notes: low pH drives the entire pathology

Endodontic Infections (Pulpitis → Necrosis)

• Polymicrobial anaerobes (Streptococcus viridans – Gram+ cocci; Fusobacterium &
Prevotella – Gram– rods; Actinomyces – Gram+ rods).
• Virulence: deep tissue invasion via proteolytic enzymes and fermentation acids.
• Key features: reversible (cold sensivity) vs irreversible pulpitis (spontaneous,
intense pain); necrosis leads to abscess.
• Diagnosis: clinical exam + X-ray.
• Treatment: root canal; drainage if abscess present.
• Notes: complications = cellulitis of Ludwig’s angina (spread deeper spaces)

Periodontal Diseases

• Gram-negative anaerobes (Porphyromonas, Tannerella, Prevotella) +
Aggregatibacter (Gram– coccobacillus).
• Virulence: proteases, LPS inflammation, mature biofilm.
• Key features: gingivitis (reversible) → periodontitis (tissue destruction).
• Diagnosis: probing depth, bone loss.
• Treatment: scaling, root planing, hygiene; sometimes antibiotics.
• Notes: smoking is the strongest risk factor. Also can lead to cellulitis or abscesses
(deeper tissues)

Campylobacter jejuni

• Gram-negative curved rod; microaerophilic.
• Reservoir and transmission: zoonosis = undercooked poultry.
• Virulence: cytolethal distending toxin (CDT toxin); mucosal invasion (flagella -
motility and adhesins = enterocytes attachment).
• Key features: fever, abdominal cramps, watery → bloody diarrhea (inflammatory
diarrhea)
• Diagnosis: stool PCR or culture at 42°C (quickly!)
• Treatment: supportive, hydration. Severe = antibiotics.
• Notes: associated with Guillain–Barré syndrome

Salmonella enterica (Non-typhoidal)

• Gram-negative motile rod.
• Reservoir and transmission: zoonosis = poultry, eggs, reptiles and livestock.
• Virulence: mucosal invasion; survival inside macrophages. SPIs 1-2. LPS.
• Key features: fever, watery diarrhea; mucus or bloody.
• Diagnosis: stool PCR/culture. Blood culture.
• Treatment: supportive (self-limited). Avoid antibiotics = prolong fecal carriage.
• Notes: antibiotics only for severe/high-risk cases. High bacterial load to infect (10 5)

Shigella spp.

• Gram-negative non-motile rod.
• Reservoir and transmission: human, fecal-oral route
• Virulence: Shiga toxin (in S. dysenteriae) → protein synthesis inhibition. Invasion
plasmid (M cells) and actin-based intracellular motility.
• Key features: bloody, mucoid diarrhea (dysentery); tenesmus.
• Diagnosis: stool PCR/culture + toxin detection.
• Treatment: Antibiotics = shorten duration of symptoms.
• Notes: highly contagious; low infectious dose; outbreaks. HUS risk. Acid resistance

Pathogenic E. coli

• Gram-negative rod (ETEC, EPEC, EIEC, EAEC, STEC).
• Reservoir and transmission: depend on pathotype (water, foodborne, toxins, oral-
fecal…)
• Virulence: LT/ST toxins (ETEC), attaching-effacing lesions (EPEC), Shiga toxin
(STEC), invasion like Shigella (EIEC) and biofilm formation (EAEC).
• Key features: watery diarrhea (ETEC/EPEC) vs bloody (EIEC/STEC). Chronic
diarrhea (EAEC/ EPEC). Travel’s diarrhea = ETEC // HUS risk = STEC.
• Diagnosis: stool PCR + Shiga toxin test.
• Treatment: oral or IV rehydration. Antibiotics only for severe ETEC/EIEC.
• Notes: avoid antibiotics in STEC due to HUS risk.

Clostridium perfringens (foodborne)

• Gram-positive anaerobic spore-former.
• Reservoir and transmission: soil, animal intestine, raw meat, poultry. Foodborne.
• Virulence: enterotoxin (CPE) produced during sporulation.
• Key features: watery diarrhea (8–16h), no fever.
• Diagnosis: clinical ± stool toxin.
• Treatment: supportive. Antibiotics not required (short disease / self-limited)
• Notes: linked to reheated meat dishes. Bacterium does not invade mucosa = not
produce systemic toxins = short duration of the disease

Vibrio cholerae

• Gram-negative curved rod.
• Reservoir and transmission: brackish and coastal waters, water and food
contaminated with fecal matter.
• Virulence: CTXφ bacteriophage → cholera toxin → ↑cAMP → massive water loss.
Non-invasive bacterium = colonizes via TCP pili (toxin).
• Key features: profuse ‘rice-water’ stools; dehydration.
• Diagnosis: stool PCR/culture.
• Treatment: Immediate oral or IV rehydration. Antibiotics = shorten duration.
• Notes: water sanitation essential. Life-threatening. Endemic. Oral cholera vaccine for
prevention

Yersinia enterocolitica

• Gram-negative rod. Facultative intracellular pathogen.
• Reservoir and transmission: pig, zoonosis.
• Virulence: Yops proteins (plasmid encode proteins) → immune evasion.
• Key features: pseudoappendicitis (targets Peyer’s patches) + diarrhea.
• Diagnosis: stool PCR/culture.
• Treatment: self-limited, hydration. Antibiotics in severe cases.
• Notes: grows at refrigeration temperatures. Several days to see symptoms.
Complications: reactive arthritis an sepsis in iron-overloaded patients

Bacillus cereus

• Gram-positive spore-forming rod.
• Reservoir and transmission: cooked food, rice. Foodborne (toxin or bacterium).
• Virulence: emetic toxin (cereulide/toxin) and diarrheal enterotoxins (bacterium).
• Key features: emetic (1–6h, rice) vs diarrheal (8–16h).
• Diagnosis: clinical.
• Treatment: self-limited. Not necessary antibiotics.
• Notes: toxin preformed in emetic type

Staphylococcus aureus (food poisoning)

• Gram-positive cocci; heat-stable enterotoxins.
• Reservoir and transmission: animals = food = zoonosis. Creamy foods.
• Virulence: preformed enterotoxins.
• Key features: rapid vomiting (1–6h), mild diarrhea, no fever.
• Diagnosis: clinical.
• Treatment: Hydration. Not necessary antibiotics.
• Notes: poor food handling. No tissue invasion (toxin only)

Clostridioides difficile

• Gram-positive anaerobic spore-former.
• Reservoir and transmission: normal gut microbiota.
• Virulence: toxins A & B causing colitis.
• Key features: antibiotic-associated diarrhea; pseudomembranes.
• Diagnosis: Stool PCR + toxin EIA.
• Treatment: oral vancomycin, or similar. Fecal microbiota transplant if recurrent.
• Notes: spores resist disinfectants

Listeria monocytogenes

• Gram-positive motile rod. Facultative intracellular pathogen (macrophages).
• Reservoir and transmission: ready-to-eat food, foodborne.
• Virulence: intracellular survival (listeriolysin); actin-based motility (ActA),
internalins = epithelial invasion.
• Key features: severe disease in pregnancy/elderly/neonates.
• Diagnosis: blood/CSF culture.
• Treatment: Antibiotics = ampicillin or combined.
• Notes: avoid soft cheeses in pregnancy. It can grow at refrigerator temperatures

Enteric Viruses (Rotavirus, Norovirus, Adenovirus 40/41, Astrovirus)

• RNA viruses (except adenovirus = dsDNA).
• Virulence: epithelial destruction → malabsorption.
• Key features: vomiting + watery diarrhea.
• Diagnosis: stool PCR.
• Notes: rotavirus vaccine prevents severe cases. Norovirus = low infection dose and
resistant to disinfectants = outbreaks

Protozoa (Giardia, Cryptosporidium, Entamoeba)

• Type: protozoa, parasites.
• Virulence: attachment (Giardia), chlorine resistance (Crypto), tissue invasion
(Entamoeba).
• Key features: Giardia → steatorrhea; Crypto → watery diarrhea; Entamoeba →
dysentery.
• Diagnosis: stool antigen/PCR; acid-fast stain for Crypto.
• Notes: waterborne; travel-related

Asymptomatic Bacteriuria

•Definition: ≥10⁵ CFU/mL without symptoms.

•Treatment: indicated only in pregnancy or before urologic procedures.

•Diagnosis: urine culture.

•Notes: do NOT treat healthy non-pregnant adults.

Cystitis (Lower UTI)

•Typical microorganisms: E. coli (most common), S. saprophyticus, Proteus, Klebsiella.

•Key features: dysuria, frequency, urgency; suprapubic pain; no fever.

•Diagnosis: urine dipstick, urine culture if needed.

•Treatment: oral antibiotics (short course).

•Prevention:
hydration, post-coital urination.

Pyelonephritis (Upper UTI)

•Typical microorganisms: E. coli, Klebsiella, Proteus.

•Key features: fever, chills, flank pain, CVA tenderness.

•Diagnosis: urine culture; blood cultures if severe.

•Treatment: systemic antibiotics (oral or IV depending on severity).

•Prevention: treat lower UTIs promptly.

Complicated UTIs

• Risk factors: structural abnormalities, catheters, diabetes, male sex, obstruction.

•Typical microorganisms: broad spectrum including Pseudomonas, Enterococcus

•Diagnosis: urine culture mandatory.

•Treatment:
systemic broad-spectrum initially; adjust after culture.

Catheter Associated UTIs

•Typical microorganisms: Pseudomonas, Proteus, Enterococcus, Enterobacterales

•Key features: biofilm on catheter surface.

•Diagnosis: urine culture after catheter change.

•Treatment: remove/replace catheter + systemic antibiotics.

•Prevention: minimize catheter use; aseptic insertion.

Prostatitis

•Typical microorganisms: E. coli, also Enterobacterales and Enterococcus spp.

•Key features: Inflammation/infection of the prostate. Acute: fever, perineal pain, dysuria and
urinary retention. Chronic: pelvic discomfort, recurrent.

•Diagnosis: Urine culture, clinical. Clinical exam: tender prostate (acute), avoid prostate massage.

•Treatment: Long antibiotics courses.

•Notes: Less common than cystitis. Important factor: age

Vulvovaginal Candidiasis

• Typical microorganisms: Yeast (Candida albicans).
• Key features: Vulvar itching, thick white discharge (“cottage cheese”), erythema.
• Diagnosis: Microscopy of discharge. Culture if necessary.
• Treatment: Antifungal therapy (topical or systemic azole-class). Supportive care.
• Prevention: Avoid unnecessary antibiotics; glucose control in diabetics. In men candida produce
balance is.

Gonorrhea

• Typical microorganisms: Neisseria gonorrhoeae (Gram-negative diplococcus).
• Key features: Men: urethritis, purulent urethral discharge, dysuria. Women: cervicitis, often
asymptomatic. Can also affect other body parts depending on sexual contact: proctitis, pharyngitis.
• Diagnosis: NAAT (gold standard). Culture if needed (differentiated medium).
• Treatment: Systemic antibacterial therapy (beta-lactam class). Treat partners.
• Prevention: Safer sex, screening in high-risk groups.
• Notes: Can infect neonates = ophthalmia neonatorum. A major global STI with high rates of
resistance

Chlamydia (Serovars D–K)

• Typical microorganisms: Chlamydia trachomatis (obligate intracellular bacterium).
• Key features: Often asymptomatic (women). Cervicitis, urethritis, possible PID. Produce discharge,
pelvic discomfort (women) and dysuria.
• Diagnosis: NAAT on urine or cervical/vaginal swabs.
• Treatment: Antibacterial therapy (tetracycline-class or macrolide-class). Partner treatment.
• Prevention: Screen sexually active young individuals; safer sex. Pregnacy!
• Notes: Also produce postpartum endometriosis and conjunctivitis in newborns.

Trichomoniasis

• Typical microorganisms: Protozoan (Trichomonas vaginalis). Motile = flagellated.
• Key features: Frothy yellow-green discharge, pruritus, strawberry cervix (hemorrhages).
• Diagnosis: Wet mount microscopy; NAAT (most sensitive). Check pH (really acidic).
• Treatment: Antiprotozoal therapy (nitroimidazole-class). Treat partners.
• Prevention: Safer sex; partner treatment.

Bacterial Vaginosis

• Typical microorganisms: Polymicrobial imbalance: Gardnerella vaginalis + anaerobes (loss of
lactobacilli).
• Key features: Thin gray discharge, fishy odor, pH > 4.5, clue cells.
• Diagnosis: Amsel criteria (positive in almost 3 test): clue cells, positive whiff test, thin discharge
and higher pH.
• Treatment: Antibacterial therapy (nitroimidazole-class or alternative).
• Prevention: Avoid vaginal douching; sexual health counseling

Genital Herpes (HSV-1/HSV-2)

• Typical microorganisms: Herpes simplex virus (enveloped dsDNA virus).
• Key features: Painful grouped vesicles → shallow ulcers, recurrent episodes. HSV-1 = oral-genital
transmission. HSV-2 = classical cause of recurrent genital disease.
• Diagnosis: PCR from lesion swab. Serology if necessary.
• Treatment: Antiviral therapy. Supportive care.
• Prevention: Avoid sexual contact during outbreaks; consider suppressive therapy. Latency!

Syphilis

• Typical microorganisms: Treponema pallidum (spirochete).
• Key features: Primary: painless chancre. Secondary: rash, condyloma lata. Systemic symptoms.
Tertiary/Latent: neurologic/cardiac disease. Gummas (skin).
• Diagnosis: Non-treponemal + treponemal tests.
• Treatment: Antibacterial therapy (beta-lactam class).
• Prevention: Screening, safer sex, prenatal care

Chancroid

• Typical microorganisms: Haemophilus ducreyi (Gram-negative coccobacillus).
• Key features: Painful genital ulcers, irregular and purulent base. Tender inguinal
lymphadenopathy.
• Diagnosis: Clinical + exclusion of other ulcerative STIs.
• Treatment: Antibacterial therapy (macrolide or beta-lactam classes).

• Prevention: Safer sex practices. Rare in high-income countries

Lymphogranuloma Venereum (LGV)

• Typical microorganisms: Chlamydia trachomatis L1–L3 (obligate intracellular).
• Key features: Small painless ulcer → painful inguinal lymphadenitis (“buboes”). Proctocolitis.
• Diagnosis: NAAT with serovar identification.
• Treatment: Antibacterial therapy (tetracycline-class).
• Prevention: Prevention in MSM communities; safer sex

Donovanosis

• Typical microorganisms: Klebsiella granulomatis (Gram-negative).
• Key features: Chronic beefy-red ulcers that bleed easily.
• Diagnosis: Tissue smear with Donovan bodies.
• Treatment: Antibacterial therapy (macrolide-class).
• Prevention: Safer sex, early diagnosis. Endemic tropical regions

Human Papillomavirus (HPV)

• Typical microorganisms: Non-enveloped circular dsDNA virus.
• Key features: Genital warts (types 6/11), cervical dysplasia (16/18). It can also affect anogenital
and oropharyngeal mucosa.
• Diagnosis: Pap smear, HPV DNA testing.
• Treatment: Local treatments for warts; lesion removal. No antiviral cure.
• Prevention: HPV vaccination; screening programs. Vaccine (children = before first sex)

HIV, HBV, HCV

• Typical microorganisms: HIV: retrovirus. HBV: enveloped DNA hepadnavirus. HCV: RNA
flavivirus.
• Key features: HIV: acute syndrome → chronic → AIDS. HBV/HCV: chronic hepatitis risk.
• Diagnosis: Serology + PCR depending on virus.
• Treatment: Antiretroviral therapy (HIV); antivirals for HBV/HCV. Supportive care.
• Prevention: Condom use; vaccination (HBV); harm reduction.

Molluscum Contagiosum

• Typical microorganisms: Poxvirus (large dsDNA virus).
• Key features: Umbilicated pearly papules on genital/perineal region. No pain. Self-limited.
• Diagnosis: Clinical diagnosis.
• Treatment: Supportive care; local removal if needed.
• Prevention: Avoid direct skin contact; hygiene

Pubic Lice (Pediculosis pubis)

• Typical microorganisms: Ectoparasite: Pthirus pubis.
• Key features: Intense genital itching; visible lice/nits.

• Diagnosis: Clinical inspection.
• Treatment: Topical pediculicides.
• Prevention: Avoid sharing bedding/clothing; partner treatment

Scabies

• Typical microorganisms: Mite: Sarcoptes scabiei.
• Key features: Burrows, papules, intense nocturnal itching.
• Diagnosis: Clinical diagnosis; skin scraping.
• Treatment: Topical or oral antiparasitic therapy.
• Prevention: Treat household/sexual contacts; hygiene.