14.1 Specimens, Major Pathogens, and Disease States

14.1 Specimens, Major Pathogens, and Disease States

Quick Answer: Plant digested sputum or BAL for pulmonary TB and NTM, a dedicated mycobacterial blood culture for disseminated MAC, and tissue or aspirate (with a 30 °C set) for M. marinum, M. abscessus, and Nocardia. M. tuberculosis spreads person-to-person by airborne droplet nuclei and is a BSL-3 culture organism. MAC is environmental and disseminates in advanced AIDS. M. kansasii mimics pulmonary TB. M. abscessus is a rapid grower of CF lung and skin. M. marinum is fish-tank granuloma. Nocardia is a partially acid-fast branching Gram-positive filament with pulmonary and brain disease in immunocompromised hosts. M. gordonae is the tap-water contaminant.

Domain III (Mycobacteriology, Virology, Parasitology, Mycology) is 20–30% of the M examination. Official outline III.A Mycobacteriology and Nocardia spp. (content guideline revised 2025-09-25) is the acid-fast half of that domain. This section is the clinical map: which specimen to plant, which organism is a pathogen versus a water organism, and how the patient acquired disease. Growth rate, pigment, and cords are 14.2. Sequencing, MALDI inactivation, direct NAAT, and RIPE/MDR/XDR concepts are 14.3. Less-common mycobacteria listed as SM-only on the outline (M. leprae, M. haemophilum, M. scrofulaceum) are not M-tested content—do not spend exam time on their special media or AST.

Specimen sources the outline names

A mycobacteriology workup is only as good as the specimen. The M outline groups sources around lower respiratory, blood, and soft tissue. They are not interchangeable, and they do not all go to 37 °C on the same media.

First-morning sputum on three consecutive days remains the classic pulmonary TB collection because overnight secretions concentrate AFB. Induced sputum or BAL is used when the cough is dry. Gastric lavage appears in pediatric practice because young children swallow sputum; it is still a respiratory specimen conceptually. Do not use the NALC–NaOH digest as an excuse to skip a tissue grind: biopsies for Nocardia and rapid growers should also go to routine bacterial and fungal media, because those organisms often appear there first.

Blood for mycobacteria is a dedicated culture. MAC bacteremia in untreated advanced HIV is the scenario the exam loves: fever, wasting, anemia, and AFB from blood or bone marrow. A routine bacterial blood-culture instrument is not validated as an AFB recovery system.

Soft-tissue mycobacteria and Nocardia hide in nodules, ulcers, and surgical sites. Tell the bench the exposure: fish tank, seawater, tattoo, injection, soil-contaminated trauma, or transplant. That history chooses 30 °C incubation and a modified acid-fast stain, not just a 37 °C MGIT.

Mycobacterium tuberculosis: person-to-person droplet nuclei

M. tuberculosis (and the rest of the M. tuberculosis complex) is the only common mycobacterium that spreads person to person. Infectious particles are airborne droplet nuclei (about 1–5 µm) generated by coughing, singing, or aerosol-generating procedures. They remain suspended and reach alveoli. Fomites and casual surface contact are not the usual route. A smear-positive cavitary patient is the classic transmitter; latent TB infection is not contagious.

Clinically the exam splits latent infection (immune control, no symptoms, not infectious) from active pulmonary or extrapulmonary disease. Cavities, night sweats, weight loss, and hemoptysis are the pulmonary picture. Extrapulmonary TB (lymph node, bone, genitourinary tract, meningitis) still starts from a respiratory acquisition in most hosts. Culture manipulation of M. tuberculosis is a BSL-3 activity because a grown culture is a concentrated aerosol risk. Smear preparation from digested sputum is performed in a certified BSC with centrifuge safety cups; never sniff an AFB plate, and never work a mold-like buff colony from mycobacterial medium on the open bench.

MAC/MAI: environmental, AIDS-disseminated

M. avium complex (MAC), historically called M. avium–intracellulare (MAI), is acquired from water and soil, not from another patient’s cough. Person-to-person spread is not the epidemiology. Two disease states dominate:

1. Disseminated MAC in advanced AIDS (typically very low CD4 counts), with mycobacteremia, marrow involvement, and gastrointestinal disease.
2. Chronic pulmonary MAC in older adults with COPD or nodular bronchiectasis, and in cystic fibrosis, without HIV.

MAC is a slow-growing nonphotochromogen. A single respiratory isolate in a patient without compatible disease may be airway colonization or water contamination. Repeated isolation plus radiology and symptoms is what turns MAC into a pulmonary pathogen. Blood isolates in AIDS are not contaminants.

M. kansasii, M. abscessus group, and M. marinum

M. kansasii causes pulmonary disease that looks like TB: upper-lobe cavities, cough, and weight loss. It is a slow-growing photochromogen (pigment after light—details in 14.2). It is associated with municipal water but is treated as a true pathogen when the clinicoradiographic picture fits, not as a tap-water throwaway.

The M. abscessus group is a rapid grower (visible colonies in fewer than 7 days, often on routine bacterial media). It is a major nontuberculous mycobacterium of CF and other chronic lung disease, and it causes skin and soft-tissue infection after surgery, injection, or trauma. Isolation from CF sputum is clinically important because the organism can persist in damaged airways. Do not confuse it with MAC: time-to-colony is the first split.

M. marinum is fish-tank (or swimming-pool) granuloma. Traumatic inoculation in aquarium or seawater produces nodular or sporotrichoid lesions on cool extremities. The laboratory clue is growth at 30 °C with poor or no growth at 37 °C. If the skin specimen is incubated only at 37 °C, the culture can be falsely negative.

Nocardia and the tap-water contaminant

Nocardia spp. are aerobic actinomycetes, not mycobacteria. They appear as branching Gram-positive filaments, often beaded, that are partially acid-fast on a modified acid-fast stain (weak acid decolorizer) and negative or only faintly colored with standard mycobacterial acid-alcohol. Disease is pulmonary nocardiosis that can seed brain abscesses in immunocompromised hosts (transplant, high-dose steroids, chronic granulomatous disease). Traumatic cutaneous nocardiosis occurs in immunocompetent people. Colonies are dry and chalky and may show aerial hyphae on bacterial or fungal media over several days. A “partially AFB-positive filament from lung or brain” is Nocardia until the identification says otherwise.

M. gordonae is the common tap-water scotochromogen. It contaminates sputum cups, ice machines, bronchoscopes, and laboratory water. A single isolate from a patient without disease is not TB and is not MAC. Report it with clinical correlation; do not trigger BSL-3 public-health panic for a yellow-orange water organism.

Safety closes the loop: BSL-3 for TB culture. NTM and Nocardia are generally handled with BSL-2 practices once M. tuberculosis complex is excluded, but any unidentified AFB from a pulmonary specimen is treated as TB until the identification is known. That is why growth rate plus pigment (14.2) and molecular direct detection (14.3) decide containment, not just the final species name.