Procedures

This section covers the key analytic procedures in Mycobacteriology and the study of Nocardia species

Specimen Sources: The Foundation of Accurate Diagnosis

Importance: Selecting the correct specimen source is crucial for detecting these organisms. The suspected site of infection dictates the appropriate specimen
Examples: Lower respiratory tract (sputum, BAL), blood, soft tissue/skin, sterile body fluids (CSF, pleural fluid), bone marrow, urine, and tissue biopsies
Key Considerations: Sterility, adequate volume, prompt processing, and safety

Focus: Understanding the etiology, epidemiology, and transmission of major pathogens
Mycobacterium tuberculosis: Causes TB (pulmonary and extrapulmonary)
Mycobacterium avium complex (MAC): Causes pulmonary and disseminated infections
Mycobacterium kansasii: Causes pulmonary disease
Mycobacterium marinum: Causes skin infections (fish tank granuloma)
Mycobacterium abscessus: Causes skin/soft tissue and pulmonary infections
Nocardia spp.: Causes pulmonary, cutaneous, and disseminated infections

Acid-Fast Stain: A key characteristic due to mycolic acids in the cell wall
Colony Morphology: Observation of colony size, shape, color, and texture on solid media
Growth Characteristics: Growth rate (slow vs. rapid), temperature requirements, and biochemical tests
Common Contaminant: M. gordonae is a frequent contaminant, differentiated by its scotochromogenic properties
Less Common Pathogens: M. leprae (cannot be cultured), M. haemophilum (requires iron), M. scrofulaceum (causes scrofula)

Sequencing: Determines the precise nucleotide sequence of target genes (16S rRNA, rpoB, hsp65) for definitive identification
MALDI-TOF MS: Identifies organisms based on their unique protein profiles

Bypasses Culture: Detects Mycobacteria and Nocardia directly from clinical specimens
NAATs (PCR, qPCR, TMA, LAMP): Amplify specific DNA or RNA sequences
Hybridization Assays (DNA Microarrays, FISH): Use labeled probes to detect target sequences
Next-Generation Sequencing (NGS): Provides comprehensive detection and genetic information

M. tuberculosis: Combination therapy (INH, RIF, PZA, EMB) for 6 months, addressing MDR-TB and XDR-TB with second-line drugs
MAC: Macrolide-based regimens (clarithromycin/azithromycin, ethambutol, rifamycin)
M. kansasii: Rifampin-based regimens (INH, rifampin, ethambutol)
M. marinum: Tetracyclines, macrolides, fluoroquinolones, rifampin, or TMP/SMX
Rapid Growers (RGM): Highly variable, species-dependent, and guided by DST

Broth Microdilution: Quantitative method to determine MIC values
Critical Concentration: Qualitative method (primarily for M. tuberculosis) to assess growth at a specific drug concentration
Direct Detection of Resistance Markers: Molecular methods to identify specific genetic mutations associated with resistance (e.g., rpoB, katG, rrl)

Etiology: Identifying the causative agent
Transmission: Understanding how the organism spreads
Virulence Mechanisms:
- Cell wall components (mycolic acids)
- Intracellular survival within macrophages
- Biofilm formation
- Secretion systems
- Enzymes (catalase, superoxide dismutase)
Opportunistic Nature: Many species primarily affect immunocompromised individuals