Unit 3: Major bacterial pathogens
Systemic Bacteriology notes · PTU syllabus (BMLS201-18)
On this page
Unit summary
Each important pathogen has typical morphology, culture and biochemistry that guide its laboratory diagnosis. This unit covers Staphylococcus, Streptococcus, Pneumococcus, Neisseria, Haemophilus, Corynebacterium, Enterobacteriaceae, Vibrio, Clostridium, mycobacteria, spirochaetes, Bordetella, Brucella, Mycoplasma and Ureaplasma.
After this unit you can
- Describe Gram-positive cocci and their diagnosis
- Describe Gram-negative cocci and bacilli
- Describe Clostridium, mycobacteria and spirochaetes
- Describe Bordetella, Brucella, Mycoplasma and Ureaplasma
PTU syllabus topics
- Morphological
- cultural and biochemical characteristics
- pathogenesis and laboratory diagnosis of Staphylococcus
- Streptococcus
- Pneumococcus
- Neisseria gonorrhoeae and N. meningitidis
- Haemophilus
- Corynebacterium
- Enterobacteriaceae (E. coli, Klebsiella, Proteus, Salmonella, Shigella)
- Vibrio
- Clostridium
- Mycobacterium tuberculosis complex/atypical mycobacteria/M. leprae
- spirochetes (Treponema, Borrelia, Leptospira)
- Bordetella
- Brucella
- Mycoplasma and Ureaplasma
Gram-positive cocci
Staphylococcus, Streptococcus, Pneumococcus
Gram-negative cocci
Neisseria
Gram-positive bacilli
Corynebacterium, Clostridium
Gram-negative bacilli
E. coli, Klebsiella, Salmonella, Vibrio
Acid-fast bacilli
Mycobacterium tuberculosis, M. leprae
Spirochaetes
Treponema, Leptospira, Borrelia
Topic 1
Staphylococcus
- Morphology
- Gram-positive cocci in grape-like clusters; non-motile
- Culture
- Golden-yellow colonies; β-haemolysis on blood agar; ferments mannitol (yellow on mannitol salt agar)
- Tests
- Catalase +, coagulase +, DNase +
- Diseases
- Boils, abscesses, wound infections, osteomyelitis, food poisoning (enterotoxin), toxic shock syndrome, MRSA hospital infections
- Diagnosis
- Gram stain of pus, culture, coagulase test, antibiotic sensitivity including cefoxitin disc for MRSA
- Coagulase-negative staphylococci: S. epidermidis (device infections, novobiocin sensitive) and S. saprophyticus (urinary infection in young women, novobiocin resistant).
Topic 2
Streptococcus and Pneumococcus
S. pyogenes (group A)
Gram-positive cocci in chains; β-haemolytic; bacitracin sensitive; catalase negative
Pharyngitis, impetigo, cellulitis; rheumatic fever and glomerulonephritis after infection (ASO titre)
S. agalactiae (group B)
β-haemolytic; CAMP test positive
Neonatal sepsis and meningitis
Viridans streptococci
α-haemolytic; optochin resistant
Infective endocarditis
S. pneumoniae
Lanceolate diplococci, capsulated; α-haemolytic draughtsman colonies; optochin sensitive; bile soluble
Pneumonia, meningitis, otitis media
- Enterococcus: grows in 6.5% NaCl and bile aesculin; causes urinary infections; often drug resistant (VRE).
Topic 3
Neisseria
Morphology
Gram-negative kidney-shaped diplococci, intracellular in pus cells
Same; capsulated
Culture
Thayer–Martin medium; 5–10% CO₂
Blood or chocolate agar; CO₂
Sugars
Glucose only
Glucose and maltose
Disease
Gonorrhoea, ophthalmia neonatorum
Meningitis, meningococcaemia
Specimen
Urethral or cervical discharge
CSF, blood
- Both are oxidase positive and fragile — transport promptly; avoid refrigeration.
Topic 4
Haemophilus
- H. influenzae: small Gram-negative coccobacilli; needs X factor (haemin) and V factor (NAD) — grows on chocolate agar; satellitism around S. aureus on blood agar. Type b capsule causes meningitis and epiglottitis in children (Hib vaccine). H. ducreyi causes chancroid.
Topic 5
Corynebacterium
- C. diphtheriae: Gram-positive club-shaped bacilli in Chinese-letter arrangement with metachromatic granules (Albert's stain). Culture on Loeffler's serum slope (rapid growth) and potassium tellurite agar (black colonies). Toxin (Elek's gel precipitation test or PCR) causes diphtheria with a grey pseudomembrane, myocarditis and neuritis.
Topic 6
Enterobacteriaceae
Escherichia coli
Lactose fermenter (pink on MacConkey); motile; indole +
Urinary infection (commonest cause), diarrhoea (ETEC, EHEC O157), neonatal meningitis, sepsis
Klebsiella pneumoniae
Mucoid lactose fermenter; non-motile; capsulated; urease +
Pneumonia, urinary and hospital infections; carbapenem resistance
Proteus
Non-lactose fermenter; swarming on blood agar; urease + strongly; H₂S +
Urinary infection, stones
Salmonella Typhi
Non-lactose fermenter; motile; H₂S + (small amount); black colonies on Wilson–Blair
Typhoid — blood culture in week 1, Widal test, stool and urine later
Shigella
Non-lactose fermenter; non-motile; no H₂S
Bacillary dysentery — stool culture on XLD or DCA
- Diagnosis of typhoid: blood culture is best in the first week; stool culture from the second to third week; Widal agglutinins rise from the second week (fourfold rise significant).
Topic 7
Vibrio
- V. cholerae: comma-shaped Gram-negative bacilli with darting motility; oxidase positive; grows at alkaline pH. Transport: Cary–Blair or VR medium; enrichment: alkaline peptone water; selective medium: TCBS (yellow colonies). Cholera toxin causes profuse rice-water stools. Serogroups O1 and O139 cause epidemics.
Topic 8
Clostridium
C. perfringens
Large Gram-positive bacilli, non-motile, capsulated; double zone haemolysis; Nagler's reaction (lecithinase)
Gas gangrene, food poisoning
C. tetani
Drumstick spores (terminal, round); swarming
Tetanus — diagnosis mainly clinical
C. botulinum
Subterminal spores; neurotoxin
Botulism — flaccid paralysis
C. difficile
Toxins A and B
Antibiotic-associated diarrhoea, pseudomembranous colitis — stool toxin or PCR
- All are anaerobic spore formers — culture in Robertson's cooked meat medium and anaerobic jars.
Topic 9
Mycobacteria
- Morphology
- Slender acid-fast bacilli; slow growing (generation 18 hours)
- Specimens
- Sputum (two samples), BAL, CSF, pus, urine
- Smear
- ZN or fluorescent (auramine) microscopy
- Culture
- Löwenstein–Jensen medium — rough, buff, dry colonies in 2–8 weeks; liquid culture (MGIT) faster
- Molecular tests
- CBNAAT (GeneXpert) and Truenat detect TB and rifampicin resistance within 2 hours
- Other tests
- Line probe assay for drug resistance; Mantoux test and IGRA show infection, not disease
- Atypical (non-tuberculous) mycobacteria: M. avium complex (HIV patients), M. fortuitum and M. chelonae (wound and injection site infections) — classified by Runyon groups.
- M. leprae: cannot be grown in culture media; grows in mouse footpad and armadillo; diagnosis by slit-skin smear with modified ZN (5% H₂SO₄) and bacterial index; causes leprosy.
Topic 10
Spirochaetes
Treponema pallidum
Dark-ground microscopy of chancre fluid; VDRL and RPR (non-specific); TPHA and FTA-ABS (specific)
Syphilis
Borrelia
Giemsa-stained blood smear during fever
Relapsing fever (B. recurrentis); Lyme disease (B. burgdorferi)
Leptospira
Dark-ground microscopy of blood or urine; culture in EMJH medium; IgM ELISA and microscopic agglutination test
Leptospirosis (Weil's disease) after contact with rat urine
Topic 11
Bordetella and Brucella
- Bordetella pertussis: small Gram-negative coccobacilli; collected by pernasal swab; grows on Bordet–Gengou or charcoal blood agar ("bisected pearl" colonies); PCR preferred; causes whooping cough.
- Brucella: small Gram-negative coccobacilli; zoonosis from cattle, goats and unpasteurised milk; causes undulant fever; diagnosis by blood culture (biphasic Castaneda medium, prolonged incubation), Standard agglutination test (titre 1:160 or more) and ELISA. Highly infectious in the lab — handle in BSL-3.
Topic 12
Mycoplasma and Ureaplasma
- Mycoplasma: smallest free-living bacteria; no cell wall (resistant to penicillin; not seen in Gram stain); fried-egg colonies on PPLO agar. M. pneumoniae causes atypical (walking) pneumonia — diagnosed by serology (IgM ELISA, cold agglutinins) and PCR.
- Ureaplasma urealyticum: hydrolyses urea; tiny colonies; associated with non-gonococcal urethritis and infertility.
Key terms
- Satellitism
- Growth of Haemophilus around S. aureus colonies
- Lactose fermenter
- Organism forming pink colonies on MacConkey agar
- Darting motility
- Rapid motility of Vibrio cholerae
- CBNAAT
- Cartridge-based nucleic acid amplification test for TB
- Fried-egg colony
- Typical Mycoplasma colony with dense centre
Quick revision
- S. aureus: coagulase +, mannitol +; CoNS; MRSA.
- Streptococci: haemolysis, bacitracin, optochin, bile solubility; Enterococcus.
- Neisseria: oxidase +, sugars; Haemophilus X and V; C. diphtheriae on Loeffler's and tellurite.
- Enterobacteriaceae on MacConkey; typhoid diagnosis by week; Vibrio on TCBS; Clostridia.
- TB: ZN, LJ, MGIT, CBNAAT; M. leprae; spirochaetes; Bordetella; Brucella; Mycoplasma; Ureaplasma.
Important exam questions
Practice questions written to the PTU exam pattern for this unit's syllabus: short answers (Section A style) and long answers (Sections B and C style).
Short-answer questions
- Q1.Name two tests that identify S. aureus.
- Q2.Distinguish S. pyogenes and S. pneumoniae.
- Q3.What is satellitism?
- Q4.Which medium is used for V. cholerae?
- Q5.What is the best specimen for typhoid in the first week?
- Q6.Why is Mycoplasma resistant to penicillin?
Long-answer questions
- Q1.Describe the laboratory diagnosis of Staphylococcus aureus infections.
- Q2.Describe the laboratory diagnosis of typhoid fever.
- Q3.Describe the laboratory diagnosis of tuberculosis.
- Q4.Describe the laboratory diagnosis of syphilis.
Stuck on this unit?
Message SBS on WhatsApp for help with Systemic Bacteriology, or to ask about studying B.Sc MLS at Synetic.