Microbiology chapters
Mycobacterium tuberculosis
The TB bacillus: its acid-fast wall and slow growth, how it spreads and causes primary and secondary (post-primary) TB, the Ghon complex and caseating granulomas, latent TB, laboratory diagnosis (smear, GeneXpert, culture), tuberculin and interferon-gamma tests, BCG vaccine, atypical mycobacteria and leprosy.
- M. tuberculosis is a slow-growing (doubling about 18 hours), obligate aerobe, acid-fast bacillus whose mycolic acid-rich wall resists Gram staining and drying; cord factor is a key virulence factor; it spreads by droplet nuclei and survives inside macrophages, controlled by Th1 cells and IFN-γ that form caseating granulomas (epithelioid cells, Langhans giant cells).
- Primary TB (first infection, often children): Ghon focus (lower part of upper lobe or upper part of lower lobe, subpleural) + hilar node = Ghon complex; usually heals (calcified), sometimes progresses (miliary TB, meningitis in children); secondary (post-primary) TB is reactivation or reinfection with apical cavitation (high oxygen) and infectious sputum; latent TB has no symptoms and no spread but can reactivate (HIV, diabetes, malnutrition, steroids, old age).
- Diagnosis: sputum ZN/auramine smear, GeneXpert MTB/RIF (rapid DNA test that also detects rifampicin resistance), culture on Löwenstein-Jensen (weeks) or liquid MGIT (gold standard, gives sensitivity); the Mantoux test and IGRA show infection, not active disease; BCG (live attenuated M. bovis) given at birth protects children against TB meningitis and miliary TB.
On this page
The organism
| Feature | Details |
|---|---|
| Shape and stain | Thin, slightly curved rods; acid-fast (Ziehl-Neelsen: red bacilli on blue background); not seen well on Gram stain |
| Wall | Rich in mycolic acid (waxes): resists drying, acids, alkalis and many disinfectants; makes it acid-fast |
| Virulence factors | Cord factor (trehalose dimycolate: serpentine cords in culture; inhibits neutrophils, damages mitochondria, triggers TNF), sulfatides (block phagosome-lysosome fusion), wax D (adjuvant), tuberculoproteins (cause the tuberculin reaction) |
| Oxygen | Obligate aerobe (favours the well-aerated apices of the lungs in reactivation) |
| Growth | Very slow (generation time about 15–20 hours); colonies on LJ in 2–8 weeks: rough, buff, dry ("breadcrumb"); niacin positive, nitrate reductase positive |
| Resistance | Survives in dried sputum for weeks; killed by sunlight (UV), pasteurisation, heat, 5% phenol |
| Toxin | None: damage is from the immune response (type IV hypersensitivity) |
Other members of the M. tuberculosis complex: M. bovis (unpasteurised milk: intestinal and cervical node TB; source of BCG), M. africanum.
Transmission and risk factors
- Airborne droplet nuclei from people with active pulmonary TB (especially smear-positive and cavitary disease), coughing, sneezing, talking.
- Close, prolonged, indoor contact; crowding, poor ventilation.
- Risk of disease after infection: HIV (the strongest risk factor), diabetes, malnutrition, silicosis, smoking, steroids and TNF-α inhibitors, chronic kidney disease, cancer, young children and the elderly, alcohol and drug misuse.
- Pakistan has one of the highest TB burdens in the world, so TB must always be considered in chronic cough, fever, weight loss and lymphadenopathy.
Pathogenesis
- Inhaled bacilli reach the alveoli and are taken up by alveolar macrophages, where they multiply (they block phagosome-lysosome fusion).
- Bacilli spread via lymphatics to hilar nodes and through the blood to many organs (seeding of apices, kidneys, bones, meninges).
- After 3–8 weeks, cell-mediated immunity develops: macrophages present antigen (MHC II, IL-12) → CD4 Th1 cells → IFN-γ → activated macrophages (epithelioid cells) kill bacilli; TNF helps form and maintain granulomas.
- Granuloma (tubercle): central caseous necrosis surrounded by epithelioid macrophages, Langhans giant cells (horseshoe nuclei), lymphocytes and fibroblasts. The tuberculin skin test becomes positive (type IV hypersensitivity).
- In most people the infection is contained (latent TB). If immunity is weak, it progresses.
People taking TNF-α inhibitors (infliximab, adalimumab) can reactivate latent TB because TNF keeps granulomas intact; screen before treatment.
Forms of TB
Primary TB (first infection; common in children)
- Ghon focus: small area of caseating inflammation, usually subpleural, in the lower part of the upper lobe or upper part of the lower lobe (mid-zones, where most air goes).
- Ghon complex = Ghon focus + enlarged caseous hilar lymph nodes (+ lymphangitis between them; sometimes called the primary complex). When healed and calcified: Ranke complex.
- Usually heals with fibrosis and calcification; dormant bacilli may remain.
- Progressive primary TB (young children, HIV, malnutrition): pneumonia, cavitation, pleural effusion, enlarged nodes compressing bronchi (collapse), miliary TB, TB meningitis.
Secondary (post-primary) TB (adults)
- Reactivation of latent bacilli (most cases) or reinfection.
- Starts in the apex of the upper lobe (Simon focus: apical seeding from primary bacteraemia; Assmann focus: infraclavicular). High oxygen tension favours the obligate aerobe.
- Caseation and cavitation (cavities connect to bronchi → infectious sputum), fibrosis, haemoptysis (Rasmussen aneurysm in a cavity wall).
- Little hilar node involvement (immunity is already present).
- Symptoms: chronic cough over 2–3 weeks, haemoptysis, fever (evening), night sweats, weight loss, anorexia.
Miliary TB
Haematogenous spread: numerous tiny (millet-seed, 1–2 mm) granulomas in lungs, liver, spleen, kidneys, bone marrow, meninges; chest X-ray shows fine nodules throughout; choroid tubercles in the eye. Common in young children and immunosuppressed adults.
Extrapulmonary TB
| Site | Notes |
|---|---|
| Lymph nodes (commonest extrapulmonary site) | Cervical (scrofula), matted nodes, cold abscess, discharging sinuses |
| Pleura | Exudative, lymphocytic effusion; raised adenosine deaminase (ADA) |
| TB meningitis | Basal meningitis, cranial nerve palsies, hydrocephalus; CSF: high protein, low glucose, lymphocytes, cobweb clot; treat with steroids plus prolonged anti-TB drugs |
| Spine (Pott disease) | Thoracolumbar; destroys vertebral bodies and the disc, anterior wedging → gibbus (kyphosis), psoas cold abscess, paraplegia |
| Abdomen | Ileocaecal (strictures, mass), peritoneal (ascites, "doughy" abdomen); M. bovis from milk |
| Genitourinary | Sterile pyuria, haematuria; infertility (fallopian tubes, epididymis) |
| Pericardium | Constrictive pericarditis |
| Adrenals | Addison disease |
| Skin | Lupus vulgaris |
Laboratory diagnosis
| Test | Details |
|---|---|
| Sputum smear microscopy | Ziehl-Neelsen (or fluorescent auramine-rhodamine, more sensitive); needs about 5,000–10,000 bacilli/mL; two samples (one early morning); cheap and quick; does not separate TB from other mycobacteria or show drug resistance |
| GeneXpert MTB/RIF (Ultra) | Automated real-time PCR: detects M. tuberculosis DNA and rifampicin resistance (a marker for MDR-TB) in about 2 hours; more sensitive than smear; recommended first test in Pakistan's TB programme and for HIV and children |
| Culture | Gold standard; Löwenstein-Jensen (2–8 weeks) or liquid MGIT (1–3 weeks); allows drug sensitivity testing; needs biosafety level 3 |
| Line probe assay | Rapid detection of resistance to rifampicin, isoniazid and second-line drugs |
| Histology | Caseating granulomas with AFB in biopsies (nodes, pleura) |
| Chest X-ray | Upper lobe infiltrates and cavities (post-primary), hilar nodes (primary), miliary pattern, effusion |
| Fluids | Adenosine deaminase (ADA) in pleural, peritoneal and pericardial fluid; lymphocytic exudate |
| Urine LAM antigen | Helps diagnose TB in advanced HIV |
Tests for infection (not for active disease)
- Tuberculin skin test (Mantoux): 5 TU of PPD injected intradermally on the forearm; induration (not redness) read at 48–72 hours (type IV hypersensitivity).
- Positive: 10 mm or more in most people; 5 mm or more in HIV, close contacts, immunosuppressed; 15 mm or more in people with no risk factors (in many guidelines).
- False positives: BCG vaccination, atypical mycobacteria.
- False negatives: HIV, malnutrition, measles, miliary TB, steroids, very young age, old age, sarcoidosis, recent live vaccines, technical errors.
- Interferon-γ release assays (IGRA, QuantiFERON, T-SPOT): blood T cells release IFN-γ in response to TB-specific antigens (ESAT-6, CFP-10); not affected by BCG.
A positive Mantoux or IGRA shows infection (past or present), not active disease; a negative one does not rule out TB.
Prevention
- BCG vaccine: live attenuated M. bovis (bacille Calmette-Guérin); given intradermally at birth in Pakistan's EPI schedule (left upper arm); forms a papule, then a small ulcer and scar. Protects children against severe forms (TB meningitis, miliary TB); protection against adult pulmonary TB is variable. Contraindicated in symptomatic HIV and other immunosuppression (risk of disseminated BCG).
- Case finding and treatment (DOTS) of infectious people: the most important control measure.
- Contact tracing and TB preventive therapy (isoniazid for 6 months, or rifapentine-isoniazid) for child contacts under 5 and people with HIV.
- Infection control: ventilation, masks, cough etiquette, isolation of smear-positive patients.
- Pasteurisation of milk (M. bovis).
Treatment regimens and drug adverse effects are covered in anti-TB drugs.
MDR-TB: resistant to isoniazid and rifampicin. XDR-TB: MDR-TB plus resistance to fluoroquinolones and at least one other key second-line drug (bedaquiline or linezolid in current definitions).
Atypical (non-tuberculous) mycobacteria
| Organism | Disease |
|---|---|
| M. avium-intracellulare complex (MAC) | Disseminated infection in AIDS (CD4 < 50); lung disease in older adults with lung damage; cervical nodes in children |
| M. kansasii | TB-like lung disease |
| M. scrofulaceum | Cervical lymphadenitis in children |
| M. marinum | "Fish tank granuloma" (skin) |
| M. ulcerans | Buruli ulcer |
| M. fortuitum, M. chelonae, M. abscessus | Rapid growers: wound, surgical site and injection infections |
They are found in soil and water, are not spread person to person, and are often resistant to standard anti-TB drugs.
Mycobacterium leprae (leprosy)
- Cannot be grown in artificial media (mouse footpad, nine-banded armadillo); doubling time about 12–14 days; prefers cooler body parts (skin, peripheral nerves, nose, testes).
- Weakly acid-fast (decolourised with 5% sulphuric acid).
- Spread mainly by nasal droplets from untreated lepromatous patients; long incubation (years).
| Feature | Tuberculoid | Lepromatous |
|---|---|---|
| Immunity | Strong cell-mediated (Th1) | Weak CMI (Th2) |
| Bacilli | Few (paucibacillary) | Many (multibacillary; "globi") |
| Lesions | Few, well-defined, hypopigmented anaesthetic patches; thickened nerves | Many symmetrical nodules, leonine facies, loss of eyebrows, nasal collapse |
| Lepromin test | Positive | Negative |
| Infectivity | Low | High |
Between them lie borderline forms. Treatment: multidrug therapy (dapsone, rifampicin, clofazimine). Reactions: type 1 (reversal) and type 2 (erythema nodosum leprosum).
Expect: acid-fast wall and mycolic acid, cord factor, obligate aerobe and apical disease, Th1/IFN-γ and caseating granulomas, Ghon focus and complex, primary vs secondary TB, miliary TB, commonest extrapulmonary site, TB meningitis CSF, Pott disease, diagnostic tests (ZN, GeneXpert with rifampicin resistance, LJ culture as gold standard), Mantoux technique, reading and false negatives, IGRA vs BCG, BCG strain and protection, MDR/XDR-TB definitions, MAC in AIDS, and tuberculoid vs lepromatous leprosy.
Quick revision
- Acid-fast (mycolic acid); cord factor; obligate aerobe; slow growth.
- Granuloma: Th1, IFN-γ, epithelioid cells, Langhans cells, caseation.
- Ghon focus + hilar node = Ghon complex (primary). Apical cavity = post-primary.
- Commonest extrapulmonary: lymph nodes. Pott disease: vertebrae + disc, gibbus, psoas abscess.
- GeneXpert: TB DNA + rifampicin resistance in 2 hours. Culture (LJ) is gold standard.
- Mantoux: 48–72 h, induration; infection not disease; false negative in HIV, malnutrition, measles.
- BCG: live M. bovis at birth; protects against TB meningitis and miliary TB.
- Leprosy: tuberculoid (lepromin +) vs lepromatous (lepromin −, many bacilli).
Written by The House Job from standard microbiology references (Levinson's Review of Medical Microbiology and Immunology).
FAQ
What is the Ghon complex?
The combination of the Ghon focus (a small subpleural area of caseating inflammation in the lung) and the caseous hilar lymph nodes, seen in primary TB.
Why does post-primary TB favour the lung apices?
M. tuberculosis is an obligate aerobe, and the apices have the highest oxygen tension.
What does GeneXpert detect?
DNA of Mycobacterium tuberculosis and mutations causing rifampicin resistance, within about two hours.
What does a positive Mantoux test mean?
That the person has been infected with TB (or vaccinated with BCG, or exposed to atypical mycobacteria); it does not by itself mean active disease.