Review article| Volume 22, ISSUE 4, P911-925, December 2002

Diagnosis of nontuberculous mycobacterial infections

      Laboratory diagnosis of the nontuberculous mycobacteria (NTM) involves the detection, processing, and isolation of the NTM from clinical specimens. Recent laboratory developments have emphasized greater speed and accuracy of diagnosis, in part because of similar emphasis for the diagnosis of tuberculosis. This section discusses the methods of laboratory diagnosis of NTM using conventional biochemical and nutritional requirements, acid fast smear microscopy, high performance liquid chromatography (HPLC), antibiotic susceptibility testing, and newer genetic methods such as molecular probes, polymerase chain reaction restriction fragment length polymorphism analysis (PRA) and 16S rDNA sequence analysis. Diagnosing NTM disease clinically is frequently more complicated than isolating and identifying an organism in the laboratory. The diagnosis of NTM disease, more so than many infectious diseases, is dependent on interpreting the laboratory findings in a larger clinical context. There are currently at least 100 identified NTM species [
      • Brown-Elliott B.A
      • Griffith D.E
      • Wallace Jr., R.J
      Newly described or emerging human species of nontuberculous mycobacteria.
      ]. Clinicians are increasingly confronted by cultures yielding a variety of NTM species with variable potential for causing human disease and uncertain clinical significance. This article discusses how laboratory results are applied by clinicians, as well as some of the difficulties and controversies regarding the diagnosis of NTM disease after the laboratory work is completed.
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        • Brown-Elliott B.A
        • Griffith D.E
        • Wallace Jr., R.J
        Newly described or emerging human species of nontuberculous mycobacteria.
        Infect Dis Clin N Amer. 2002; 16: 187-220
        • Metchock B.G
        • Nolte F.S
        • Wallace Jr., R.J
        in: Murray P.R Manual of clinical microbiology. 7th edition. American Society for Microbiology, Washington, DC1999: 399-437
        • Kent P.T
        • Kubica G.P
        Public health mycobacteriology: a guide for the level III laboratory.
        Centers for Disease Control. US Department of Health and Human Services, Atlanta, GA1985
        • Wayne L.G
        • Kubica G.P
        in: Sneath P.H.A Bergey's manual of systematic bacteriology. Volume 2. Williams & Williams, Baltimore (MD)1986: 1435-1457
        • Wolinsky E
        State of the art: Nontuberculous mycobacteria and associated diseases.
        Am Rev Respir Dis. 1979; 119: 107-159
        • Wright P.W
        • Wallace Jr., R.J
        • Wright N.W
        • Brown B.A
        • Griffith D.E
        Sensitivity of fluorochrome microscopy for detection of Mycobacterium tuberculosis versus nontuberculous mycobacteria.
        J Clin Microbiol. 1998; 36: 1046-1049
        • National Committee for Clinical Laboratory Standards
        Susceptibility testing of mycobacteria, nocardia and other aerobic actinomycetes.
        2nd edition. Tentative Standard, Wayne (PA)2000
        • Wallace Jr., R.J
        • Glassroth J
        • Griffith D.E
        • et al.
        Supplement: American Thoracic Society: diagnosis and treatment of disease caused by nontuberculous mycobacteria.
        Am J Respir Crit Care Med. 1997; 156: S1-S25
        • Jost K.C
        • Dunbar D.F
        • Barth S.S
        • Headley V.L
        • Elliott L.B
        Identification of Mycobacterium tuberculosis and M. avium complex directly from smear-positive sputum specimens and BACTEC 12B cultures by high-performance liquid chromatography with fluorescence detection and computer-driven pattern recognition models.
        J Clin Microbiol. 1995; 33: 1270-1277
        • LeBrun L
        • Espinasse F
        • Poveda J.D
        • Vincent-Levy-Frebault V
        Evaluation of nonradioactive DNA probes for identification of mycobacteria.
        J Clin Microbiol. 1992; 30: 2476-2478
        • Tortoli E
        • Simonetti M.T
        • Lavinia F
        Evaluation of reformulated chemiluminescent DNA probe (AccuProbe) for culture identification of mycobacterium kansasii.
        J Clin Microbiol. 1996; 34: 2838-2840
        • Goto M
        • Oka S
        • Okuzumi K
        • Kimura S
        • Shimada K
        Evaluation of acridinium-ester-labeled DNA probes for identification of Mycobacterium tuberculosis and Mycobacterium avium-Mycobacterium intracellulare complex in culture.
        J Clin Microbiol. 1991; 29: 2473-2476
        • Chapin-Robertson K
        • Dahlberg S
        • Waycott S
        • Corrales J
        • Kontnick C
        • Edberg S.C
        Detection and identification of Mycobacterium directly from BACTEC bottles by using a DNA-rRNA probe.
        Diagn Microbiol Infect Dis. 1993; 17: 203-207
        • Somoskövi Á
        • Hotaling J.E
        • Fitzgerald M
        • et al.
        False-positive results for Mycobacterium celatum with the AccuProbe Mycobacterium tuberculosis complex assay.
        J Clin Microbiol. 2000; 38: 2743-2745
        • Park H
        • Jang H
        • Kim C
        • et al.
        Detection and identification of mycobacteria by amplification of the internal transcribed spacer regions with genus- and species-specific PCR primers.
        J Clin Microbiol. 2000; 38: 4080-4085
        • Plikaytis B.B
        • Plikaytis B.D
        • Yakrus M.A
        • et al.
        Differentiation of slowly growing Mycobacterium species, including Mycobacterium tuberculosis, by gene amplification and restriction fragment length polymorphism analysis.
        J Clin Microbiol. 1992; 30: 1815-1822
        • Telenti A
        • Marchesi F
        • Balz M
        • Bally F
        • Böttger E.C
        • Bodmer T
        Rapid identification of mycobacteria to the species level by polymerase chain reaction and restriction enzyme analysis.
        J Clin Microbiol. 1993; 31: 175-178
        • Steingrube V.A
        • Gibson J.L
        • Brown B.A
        • et al.
        PCR amplification and restriction endonuclease analysis of a 65-Kilodalton heat shock protein gene sequence for taxonomic separation of rapidly growing mycobacteria.
        J Clin Microbiol. 1995; 33: 149-153
        • Springer B
        • Stockman L
        • Teschner K
        • Roberts G.D
        • Böttger E.C
        Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods.
        J Clin Microbiol. 1996; 34: 296-303
        • Roth A
        • Reischl U
        • Streubel A
        • et al.
        Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S–23S rRNA gene spacer and restriction endonucleases.
        J Clin Microbiol. 2000; 38: 1094-1104
        • Kirschner P
        • Springer B
        • Vogel U
        • et al.
        Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory.
        J Clin Microbiol. 1993; 31: 2882-2889
        • Runyon E.H
        Anonymous mycobacteria in pulmonary disease.
        Med Clin North Am. 1959; 43: 273-290
        • Runyon E.H
        Identification of mycobacterial pathogens using colony characteristics.
        Am J Clin Pathol. 1970; 54: 578-586
        • Vincent Lévy-Frébault V
        • Portaels F
        Proposed minimal standards for the genus Mycobacterium and for description of new slowly growing Mycobacterium species.
        Int J Syst Bacteriol. 1992; 42: 315-323
        • Silcox V.A
        • Good R.C
        • Floyd M.M
        Identification of clinically significant Mycobacterium fortuitum complex isolates.
        J Clin Microbiol. 1981; 14: 686-691
        • Wallace Jr., R.J
        • Silcox V.A
        • Tsukamura M
        • Brown B.A
        • Kilburn J.O
        • Butler W.R
        • et al.
        Clinical significance, biochemical features, and susceptibility patterns of sporadic isolates of the Mycobacterium chelonae-like organism.
        J Clin Microbiol. 1993; 31: 3231-3239
        • Butler W.R
        • Floyd M.M
        • Silcox V
        • et al.
        Standardized method for HPLC identification of mycobacteria.
        Centers for Disease Control and Prevention. US Department of Health and Human Services, Atlanta (GA)1996
        • Wallace Jr., R.J
        • Brown B.A
        • Onyi G.O
        Susceptibilities of Mycobacterium fortuitum biovar fortuitum and the two subgroups of Mycobacterium chelonae to imipenem, cefmetazole, cefoxitin, and amoxicillin-clavulanic acid.
        Antimicrob Agents Chemother. 1991; 35: 773-775
        • Wilson R.W
        • Steingrube V.A
        • et al.
        Mycobacterium immunogenum sp. nov., a novel species related to Mycobacterium abscessus and associated with clinical disease, pseudo-outbreaks, and contaminated metalworking fluids: an international cooperative study on mycobacterial taxonomy.
        Int J Syst Evol Microbiol. 2001; 51: 1751-1764
        • Brown B.A
        • Springer B
        • Steingrube V.A
        • et al.
        Mycobacterium wolinskyi sp. Nov. and Mycobacterium goodii sp. Nov. two new rapidly growing species related to Mycobacterium smegmatis and associated with human wound infections: a cooperative study from the International Working Group on Mycobacterial Taxonomy.
        Intern J Syst Bacteriol. 1999; 49: 1493-1511
        • Wallace Jr., R.J
        • Swenson J.M
        • Silcox V.A
        • Good R.C
        Disk diffusion testing with polymyxin and amikacin for differentiation of Mycobacterium fortuitum and Mycobacterium chelonei.
        J Clin Microbiol. 1982; 16: 1003-1006
        • Wallace Jr., R.J
        • O'Brien R
        • Glassroth J
        • et al.
        Diagnosis and treatment of disease caused by nontuberculous mycobacteria.
        Am Rev Respir Dis. 1990; 142: 940-953
        • Swenson J.M
        • Wallace Jr., R.J
        • Silcox V.A
        • Thornsberry C
        Antimicrobial susceptibility of five subgroups of Mycobacterium fortuitum and Mycobacterium chelonae.
        Antimicrob Agents Chemother. 1985; 28: 807-811
        • Brown B.A
        • Wallace Jr., R.J
        • Onyi G.O
        • De Rosas V
        • Wallace III, R.J
        Activities of four macrolides, including clarithromycin, against Mycobacterium fortuitum, Mycobacterium chelonae, and M chelonae-like organisms.
        Antimicrob Agents Chemother. 1992; 36: 180-184
        • American Thoracic Society
        Diagnostic standards and classification of tuberculosis and other mycobacterial disease.
        Am Rev Respir Dis. 1980; 121: 343-358
        • Ahn C.H
        • McLarty J.W
        • Ahn S.S
        • et al.
        Diagnositc criteria for pulmonary disease caused by Mycobacterium kansasii and Mycobacterium avium intracellulare.
        Am Rev Respir Dis. 1982; 125: 388-391
        • Prince D.S
        • Peterson D.D
        • Steiner R.M
        • et al.
        Infection with Mycobacterium avium complex in patients without predisposing conditions.
        N Engl J Med. 1989; 321: 863-868
        • Erasmus J.J
        • McAdams H.P
        • Farrell M.A
        • et al.
        Pulmonary nontuberculous mycobacterial infection: radiologic manifestations.
        Radiographics. 1999; 19: 1487-1505
        • Hartman T.E
        • Swensen S.J
        • Williams D.E
        Mycobacterium avium-intracellulare complex: evaluation with CT.
        Radiology. 1993; 187: 23-26
        • Moore E.H
        Atypical mycobacterial infection in the lung: CT appearance.
        Radiology. 1993; 18: 777-782
        • Swensen S.J
        • Hartman T.E
        • Williams D.E
        Computed tomographic diagnosis of Mycobacterium avium-intracellulare complex in patients with bronchiectasis.
        Chest. 1994; 105: 49-52
        • Tanaka E
        • Amitani R
        • Niimi A
        • et al.
        Yield of computed tomography and bronchoscopy for the diagnosis of Mycobacterium avium complex pulmonary disease.
        Am J Respir Crit Care Med. 1997; 155: 2041-2046