Comprehensive Microbiology and Pathogen Review Notes

Major Bacterial Pathogens Classification

• Top Gram-Positive Cocci:

  • Staphylococci: Clusters; includes Staphylococcus aureus and Staphylococcus saprophyticus.

  • Streptococci: Chains or pairs, coagulase-negative; includes Lancefield Group A (Streptococcus pyogenes), Group B (Streptococcus agalactiae), Streptococcus pneumoniae (pneumococcus), and Streptococcus viridans group.

  • Enterococcus: Enterococcus faecalis and Enterococcus faecium.

• Top Gram-Negative Rods:

  • Respiratory: Haemophilus influenzae, Moraxella catarrhalis.

  • Enteric: Escherichia coli, Klebsiella.

  • Nonenteric: Pseudomonas aeruginosa.

• Top Atypical Pneumonia Pathogens:

  • Legionella (Gram-negative)

  • Mycoplasma (no Gram stain)

  • Chlamydophila (no Gram stain)

Urinary Tract Infections (UTIs)

• Etiology:

  • Escherichia coli: Primary cause in $75-90\%$ of isolates.

  • Staphylococcus saprophyticus: Causes $5-15\%$ of UTIs.

  • Other Enterobacteriaceae: Klebsiella, Proteus, Enterobacter, Citrobacter.

• Classification by Location:

  • Uncomplicated UTI (uUTI): Infection confined to the bladder (cystitis or urethritis) in afebrile women or men.

  • Complicated UTI (cUTI): Infection extending beyond the bladder, including acute pyelonephritis (flank pain, tenderness, fever, dysuria), febrile or bacteremic UTI, catheter-associated UTI (CAUTI), and prostatitis.

• Pathogen Characteristics:

  • Escherichia coli: Most abundant facultative anaerobe in the colon; classified into over $1000$ antigenic types using $O$ (cell wall), $H$ (flagella), and $K$ (capsule) antigens; endotoxin is its primary virulence factor.

• Proteus, Providencia, and Morganella: Urease-positive organisms (Proteus vulgaris, Proteus mirabilis, Providencia rettgeri, Morganella morganii); urease cleaves urea to elevate urine $\text{pH}$ and precipitate urinary stones; highly motile swarming bacteria.

• Enterococcus species: Opportunistic nosocomial pathogens residing in the colon; cause UTIs via catheterization or surgery, bacteremia, abdominal wound infections, and endocarditis.

• Staphylococcus saprophyticus: Coagulase-negative, Gram-positive coccus causing pyogenic UTIs in sexually active individuals; produces no exotoxins.

Fungal Infections

• Fungal Morphologies: Eukaryotic organisms existing as yeast, mold (hyphal networks), or dimorphic structures.

• Candida albicans:

  • Transitions between yeast and hyphal forms to mediate tissue invasion.

  • Transmitted via normal microbiome opportunism, sexual contact, or invasive procedures.

  • Causes thrush, infant diaper rash, vaginal yeast infections, catheter-associated UTIs, and disseminated candidiasis.

• Dermatophytes:

  • Includes Trichophyton, Microsporum, and Epidermophyton (formerly Tinea species).

  • Least invasive fungi; restricted to keratinized outer layers of skin, hair, and nails.

Respiratory Tract Infections

• Epidemiology: Respiratory illness accounts for $80\%$ of acute US morbidity, with $80\%$ of cases being viral.

• Upper Respiratory Tract Etiology:

  • Otitis Media & Acute Sinusitis: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis.

  • Pharyngitis: Streptococcus pyogenes (Group A Streptococcus), Adenovirus.

  • Common Cold: Rhinovirus, Coronavirus.

  • Epiglottitis: Haemophilus influenzae type B.

  • Croup & Laryngitis: Parainfluenza virus, Rhinovirus.

• Lower Respiratory Tract & Pneumonia:

  • Acute vs. Chronic: Acute pneumonia develops within $24-48\text{ hours}$; chronic pneumonia develops over $\ge 3\text{ weeks}$.

  • Community-Acquired Pneumonia (CAP): Defined as pneumonia in patients without hospital/care facility exposure in the preceding $14\text{ days}$. Most common causes are respiratory viruses, followed by Streptococcus pneumoniae.

  • Atypical Pneumonia: Subacute onset with nonproductive cough ("walking pneumonia") and chest X-rays showing more severe infiltration than physical exam findings; caused by Mycoplasma pneumoniae, Chlamydophila pneumoniae, Influenza, Adenovirus, Parainfluenza, and RSV.

• Opportunistic Non-Enteric Gram-Negative Rods:

  • Pseudomonas aeruginosa: Highly aggressive opportunist present in $10\%$ of normal skin/colon flora; grows in tap water and hot tubs; infects burns, wounds, cystic fibrosis lungs (ventilator-associated pneumonia), and the outer ear (otitis externa).

  • Burkholderia, Stenotrophomonas, Acinetobacter: Environmental/aquatic Gram-negative rods colonizing medical devices and skin; cause necrotizing pneumonia, UTIs, and bacteremia in immunocompromised or hospitalized patients.

Skin, Soft Tissue, and Systemic Pathogenesis

• Staphylococcus aureus:

  • Pyogenic Infections: Characterized by pus-forming abscesses with central necrosis and neutrophil infiltration; causes boils, impetigo, cellulitis, mastitis, osteomyelitis, septic arthritis, endocarditis, and necrotizing pneumonia.

  • Toxinoses: Mediated by toxins leading to gastroenteritis (food poisoning), Toxic Shock Syndrome (TSS), and Scalded Skin Syndrome.

• Streptococcus pyogenes (Group A):

  • Pyogenic: Pharyngitis, impetigo, erysipelas, cellulitis, pneumonia.

  • Post-Infectious Immune Sequelae: Rheumatic fever, glomerulonephritis.

  • Toxinoses: Scarlet fever, Streptococcal Toxic Shock Syndrome, necrotizing fasciitis.

• Streptococcus agalactiae (Group B / GBS):

  • Causes neonatal meningitis and bacteremia (transmitted during delivery), peripartum fever, and opportunistic soft tissue infections/diabetic foot ulcers.

• Viridans Streptococci (S. mutans, S. bovis, S. anginosus, S. mitis, S. salivarius):

  • Commensal oral flora; enter the bloodstream following mucosal trauma to serve as the principal cause of subacute endocarditis and dental caries.

• Clostridium perfringens:

  • Causes gas gangrene (myonecrosis and necrotizing fasciitis) and self-limiting food poisoning.

• Zoonotic Wound Pathogens:

  • Pasteurella multocida and Capnocytophaga: Transmitted via dog and cat bites (normal oral flora of pets); manifest as rapidly spreading cellulitis.