Medical Microbiology - Diseases of the Respiratory System, Eye, and Skin

Staphylococcus aureus

Gram-positive cocci in clusters; catalase+, coagulase+

Habitat: nasal cavity (main reservoir), skin

Virulence: Protein A, coagulase, hemolysins, leukocidins, exfoliative toxins, TSST-1, enterotoxins, PVL

Diseases: impetigo, folliculitis, abscesses, cellulitis, wound infections

Notes: MRSA = mecA → PBP2a → β-lactam resistance

Streptococcus pyogenes (GAS)

Gram-positive cocci in chains; catalase-, β-hemolytic

Habitat: skin and oropharynx

Virulence: M protein, streptolysins O/S, streptokinase, hyaluronidase, pyrogenic exotoxins

Diseases: impetigo, erysipelas, cellulitis, necrotizing fasciitis

Notes: rapid tissue spread; risk of post-infection sequelae

Staphylococcus epidermidis

Gram-positive cocci; catalase+, coagulase-

Habitat: major skin commensal

Virulence: biofilm formation, adhesins

Diseases: catheter/prosthesis infections, post-surgical infections

Notes: some strains carry mecA; common cause of device-related infections

Pseudomonas aeruginosa

Gram-negative aerobic rod; oxidase+

Habitat: water, moist skin, hospital environments

Virulence: Exotoxin A, pyocyanin, elastases, proteases, biofilm, efflux pumps

Diseases: hot-tub folliculitis, otitis externa, burn wound infections, chronic ulcers

Notes: green pigment, sweet odor; intrinsically multidrug resistant

Clostridium perfringens

Gram-positive anaerobic spore-forming rod

Habitat: soil, GI tract, deep contaminated wounds

Virulence: alpha toxin, rapid gas production

Diseases: gas gangrene, necrotizing soft tissue infections

Notes: medical emergency; very rapid progression

Candida albicans

Yeast; part of normal microbiota

Habitat: skin folds, mucosal surfaces

Virulence: yeast–hypha transition, adhesins, biofilm

Diseases: intertrigo, paronychia, oral thrush

Notes: thrives with moisture, diabetes, antibiotics

Malassezia spp.

Lipophilic yeast

Habitat: sebaceous areas (scalp, chest, face)

Virulence: lipid dependence, inflammatory potential

Diseases: tinea versicolor, seborrheic dermatitis

Notes: common commensal organism

Herpes Simplex Virus (HSV-1/2)

Family: Herpesviridae; enveloped linear dsDNA

Characteristics: latency in sensory ganglia; recurrent vesicles

Diseases: oral or genital herpes

Symptoms: painful grouped vesicles on erythematous base

Varicella-Zoster Virus (VZV)

Family: Herpesviridae; linear dsDNA

Diseases: chickenpox, shingles

Key signs: dermatomal pain; Hutchinson sign if trigeminal involvement

Human Papillomavirus (HPV)

Family: Papillomaviridae; circular dsDNA

Characteristics: infects keratinocytes; types 16/18 are oncogenic

Diseases: common warts, plantar warts, anogenital warts

Molluscum Contagiosum Virus

Family: Poxviridae; large dsDNA virus

Diseases: dome-shaped umbilicated papules

Notes: spread by contact/fomites; common and benign in children

Impetigo

Microbes: S. aureus, S. pyogenes

Features: honey-colored crusts, highly contagious

Treatment: topical if mild; oral if extensive

Folliculitis

Microbes: S. aureus; Pseudomonas (hot-tub)

Features: pustule at hair follicle

Treatment: topical agents; hygiene measures

Abscess / Furuncle

Microbes: S. aureus (including MRSA)

Features: painful, fluctuant nodule with pus; multiple lesions → carbuncle

Treatment: incision & drainage ± antibiotics

Erysipelas

Microbe: S. pyogenes

Features: raised, sharply demarcated, bright-red hot skin

Treatment: oral or IV antibiotics

Cellulitis

Microbes: S. pyogenes + S. aureus

Features: diffuse erythema, swelling, pain

Treatment: oral or IV antibiotics depending on severity

Necrotizing Fasciitis

Microbes: S. pyogenes, Clostridium, polymicrobial

Features: severe pain, rapid spread, necrosis, systemic toxicity, gas in tissues

Treatment: urgent surgery + IV therapy

Gas Gangrene / Myonecrosis

Microbe: Clostridium perfringens

Features: crepitus, gas in tissues, foul odor

Treatment: emergency surgery + IV antibiotics

Surgical Wound Infections

Microbes: S. aureus (MRSA common), S. epidermidis, Gram-negative rods

Features: delayed healing, purulent drainage

Diagnosis: deep wound swab/aspirate

Treatment: wound care, drainage, systemic antibiotics

Pressure Ulcer & Vascular Ulcer Infections

Microbes: polymicrobial (Enterococcus, Pseudomonas, Proteus, S. aureus, anaerobes)

Features: chronic non-healing wounds, foul odor, purulent exudate

Treatment: debridement, pressure relief, systemic antibiotics;

Streptococcus pneumoniae

Haemophilus influenzae (non-typeable)

Gram-negative coccobacillus

Habitat: upper respiratory tract, normal flora

Virulence: outer membrane proteins, IgA protease, biofilm

Diseases: COPD exacerbations, bronchitis, sinusitis, otitis media

Key features: bronchopneumonia, subacute course

Notes: NTHi not prevented by Hib vaccine

Moraxella catarrhalis

Gram-negative diplococcus

Habitat: URT, especially in children

Virulence: β-lactamase, adhesins, biofilm

Diseases: otitis media, sinusitis, COPD exacerbations

Key features: similar to H. influenzae

Notes: often penicillin-resistant

Staphylococcus aureus (Respiratory Context)

Gram-positive cocci in clusters; nasal colonizer

Virulence: PVL toxin, TSST-1, Protein A, hemolysins

Diseases: post-influenza pneumonia, necrotizing pneumonia, lung abscess

Key features: rapid deterioration after viral illness

Notes: MRSA requires non–beta-lactam therapy

Pseudomonas aeruginosa (Respiratory)

Gram-negative aerobic rod, oxidase+

Habitat: water systems, hospital devices

Virulence: Exotoxin A, elastase, biofilm, efflux pumps

Diseases: HAP/VAP, bronchiectasis infections

Key features: necrotizing pneumonia, green sputum

Notes: highly resistant; common in ventilated patients

Enterobacterales (Klebsiella, E. coli, Enterobacter)

Gram-negative rods

Habitat: gut microbiota; aspiration in vulnerable patients

Virulence: capsules (notably Klebsiella), endotoxin

Diseases: severe pneumonia in alcoholics/diabetics/aspiration risk

Key features: Klebsiella → currant jelly sputum, lobar consolidation

Notes: ESBL strains common

Mycoplasma pneumoniae

Atypical bacterium without a cell wall

Habitat: respiratory mucosa

Virulence: CARDS toxin, P1 adhesin

Diseases: atypical pneumonia in young adults

Key features: dry cough, interstitial infiltrates, extrapulmonary symptoms

Notes: β-lactams ineffective

Chlamydia pneumoniae

Obligate intracellular bacterium

Virulence: intracellular survival; EB/RB lifecycle

Diseases: prolonged atypical pneumonia, bronchitis

Key features: persistent dry cough for weeks

Notes: mild community-spread illness

Legionella pneumophila

Poorly staining gram-negative rod (needs silver stain)

Habitat: water systems, AC units, cooling towers

Virulence: intracellular replication in macrophages

Diseases: Legionnaires' disease (severe atypical pneumonia)

Key features: high fever, diarrhea, confusion, hyponatremia

Notes: urinary antigen test; spread via aerosols, not person-to-person

Influenza virus

Segmented (-)ssRNA

Causes: fever, myalgia, viral pneumonia; predisposes to bacterial superinfection

SARS-CoV-2

(+)ssRNA

Causes: mild URTI → severe pneumonia; diagnosis via PCR

RSV

Causes bronchiolitis in infants; wheezing, hypoxia

Human Metapneumovirus
RSV-like winter outbreaks

Parainfluenza

Causes croup; barking cough

Adenovirus

Causes pharyngitis, conjunctivitis

Common in children

Rhinovirus

Number 1 cause of common cold

Note: All damage respiratory epithelium, increasing bacterial risk.

Otitis Media (AOM)

Microbes: S. pneumoniae, H. influenzae, M. catarrhalis

Features: ear pain, fever, bulging TM

Diagnosis: clinical

Treatment: analgesia ± antibiotics

Prevention: pneumococcal vaccine, avoid smoke

Sinusitis

Microbes: post-viral; S. pneumoniae, H. influenzae, M. catarrhalis

Features: facial pressure, purulent discharge, symptoms >10 days

Treatment: supportive if viral; antibiotics if bacterial

Common Cold (Nasopharyngitis)

Microbes: rhinovirus (most common), adenovirus, influenza, parainfluenza

Features: congestion, rhinorrhea, mild sore throat, self-limited

Treatment: supportive

Pharyngitis

Microbes: most viral; GAS (Strep pyogenes)

Features: sore throat, fever; GAS → exudates + tender LN

Diagnosis: rapid strep test ± culture

Treatment: supportive (viral) or antibiotics (GAS)

Tonsillitis

Microbes: viral; H. influenzae, M. catarrhalis, S. pneumoniae, S. aureus

Features: enlarged painful tonsils, odynophagia

Treatment: supportive; antibiotics usually not needed

Laryngitis

Microbes: viral

Features: hoarseness, dry cough

Treatment: voice rest, hydration

Epiglottitis

Microbes: H. influenzae, S. pneumoniae, S. pyogenes, S. aureus

Features: fever, drooling, dysphagia; airway emergency

Treatment: airway management + IV antibiotics

Prevention: Hib vaccine

Diphtheria

Microbe: Corynebacterium diphtheriae

Features: gray pseudomembrane, “bull neck,” airway obstruction

Diagnosis: culture + toxigenicity testing

Treatment: diphtheria antitoxin + antibiotics

Prevention: DTaP/Tdap vaccine

Acute Bronchitis

Microbes: viral (influenza, RSV, parainfluenza)

Features: cough ± sputum; no pneumonia signs

Treatment: supportive

COPD Exacerbations

Microbes: H. influenzae, M. catarrhalis, S. pneumoniae

Features: increased dyspnea, cough, sputum purulence

Treatment: bronchodilators, steroids ± antibiotics

Bronchiolitis

Microbes: RSV (main), metapneumovirus, parainfluenza

Features: infants <2 yrs; wheezing, tachypnea, retractions

Treatment: supportive

Community-Acquired Pneumonia (CAP)

Microbes: S. pneumoniae, H. influenzae, Moraxella, atypicals, viruses

Features: fever, cough, dyspnea; focal findings

Diagnosis: CXR, sputum culture, blood cultures if severe

Treatment: oral or IV antibiotics

Viral Pneumonia

Microbes: influenza, SARS-CoV-2, RSV, metapneumovirus

Features: interstitial infiltrates; severe in risk groups

Diagnosis: PCR

Treatment: antivirals (influenza/COVID) or supportive

HAP / VAP

Microbes: Pseudomonas, Klebsiella, Enterobacterales, MRSA

Features: new infiltrate ≥48h after admission or intubation

Diagnosis: endotracheal aspirate or BAL cultures

Treatment: broad-spectrum IV → targeted therapy

Streptococcus pneumoniae

Gram-positive, lancet-shaped diplococci

Virulence: polysaccharide capsule, pneumolysin

Causes: bacterial conjunctivitis, keratitis

Clues: painful central corneal ulcer, hypopyon

Haemophilus influenzae (non-typeable)

Gram-negative coccobacillus

Virulence: IgA protease, mucosal adherence

Causes: purulent conjunctivitis

Clues: thick purulent discharge, common in children

Adenovirus

Non-enveloped dsDNA virus

Causes: viral conjunctivitis, keratoconjunctivitis

Clues: watery discharge, lymphadenopathy, very contagious

Herpes Simplex Virus Type 1 (HSV-1)

Enveloped dsDNA virus

Causes: herpetic keratitis, blepharoconjunctivitis

Clue: dendritic corneal ulcers on fluorescein

Varicella-Zoster Virus (VZV – HZO)

Reactivation of VZV in ophthalmic (V1) nerve

Causes: HZO, keratitis, conjunctivitis, uveitis

Clues: unilateral rash; Hutchinson sign → corneal involvement

Acanthamoeba spp.

Free-living amoeba

Causes: Acanthamoeba keratitis

Clues: severe pain out of proportion, ring infiltrate, contact lens + water exposure

Staphylococcus aureus

Common cause of conjunctivitis, blepharitis, keratitis, endophthalmitis

Often presents with purulent discharge or eyelid margin inflammation

Staphylococcus epidermidis

Normal skin flora

Major cause of post-operative endophthalmitis

Pseudomonas aeruginosa

Highly aggressive Gram-negative rod

Causes contact lens–associated keratitis and endophthalmitis

Can rapidly destroy the cornea

Candida spp.

Fungus causing fungal endophthalmitis

Conjunctivitis

Causes: adenovirus, S. aureus, S. pneumoniae, H. influenzae

Viral: watery discharge, gritty sensation

Bacterial: purulent discharge, worse in mornings

Allergic: intense itching

Blepharitis

Usually caused by S. aureus

Symptoms: red, swollen eyelids, crusting

Can be seborrheic, Demodex-related, or due to Meibomian gland dysfunction

Keratitis

Causes: Pseudomonas, S. aureus, S. pneumoniae, HSV-1

Symptoms: eye pain, photophobia, corneal opacity/ulcer

Strongly associated with contact lens misuse

Herpes Zoster Ophthalmicus (HZO)

VZV reactivation in ophthalmic (V1) nerve

Symptoms: unilateral rash, eye pain, photophobia

Hutchinson sign predicts corneal involvement

Endophthalmitis

Causes: S. epidermidis, S. aureus, Pseudomonas, Candida

Symptoms: sudden severe pain, redness, vision loss, hypopyon