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Nontuberculous Mycobacterial Disease pp 15–59Cite as

Laboratory Diagnosis and Antimicrobial Susceptibility Testing of Nontuberculous Mycobacteria

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Part of the book series: Respiratory Medicine ((RM))

Abstract

This chapter discusses principles and methods for the laboratory identification of nontuberculous mycobacteria (NTM) beginning with biochemical and chemotaxonomic methods [high-performance liquid chromatography (HPLC), thin-layer chromatography (TLC), and gas-liquid chromatography (GLC)] which have widely been replaced by the more definitive molecular methods including commercial probe technology, gene sequencing, and more recently mass spectrometry (MS) using the matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF). The MALDI-TOF-MS currently remains non-validated or beyond the capability of many clinical laboratories to implement into the NTM identification algorithm. As with all molecular methodologies, the creation and maintenance of adequate databases are critical to the success of implementation of these techniques. Notably, only limited gene sequencing (i.e., 16S rRNA gene) has been addressed by the Clinical and Laboratory Standards Institute (CLSI), and strict cutoff values for other genes are currently not available.

Early methods of antimicrobial susceptibility testing (AST) including agar dilution and agar disk diffusion have been replaced by broth microdilution as recommended by the CLSI M24-A guidelines published in 2003, 2011, and, more recently, proposals for revisions for a 2017 document. The CLSI has determined MIC breakpoints for multiple antimicrobials used for treatment of NTM disease and advised specific reporting criteria.

Genomic relatedness/diversity of species and subspecies along with antimicrobial resistance and biological properties such as virulence and pathogenic potential by whole genome sequencing is emerging as an important tool in both the identification and antimicrobial susceptibility of NTM. Currently, however, due to its requirement for bioinformatics and ability to interpret and analyze the sequence data which are not available in most clinical laboratories, the whole genomic approach has only been implemented in specialized research laboratories.

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Acknowledgments

The author wishes to thank Richard J. Wallace, Jr. for his expert review of the chapter and Joanne Woodring for her excellent clerical skills.

This chapter is dedicated to my beloved husband, Clyde Elliott, and my dear mother Clifford Brown, who passed away during the preparation of this chapter. They provided constant support and encouragement to me throughout my years in the laboratory.

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  1. Department of Microbiology, Mycobacteria/Nocardia Research Laboratory, The University of Texas Health Science Center, Tyler, TX, USA

    Barbara A. Brown-Elliott

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Correspondence to Barbara A. Brown-Elliott .

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  1. Professor of Medicine, University of Texas Health Science Center, Tyler, TX, USA

    David E. Griffith

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Brown-Elliott, B.A. (2019). Laboratory Diagnosis and Antimicrobial Susceptibility Testing of Nontuberculous Mycobacteria. In: Griffith, D. (eds) Nontuberculous Mycobacterial Disease. Respiratory Medicine. Humana Press, Cham. https://doi.org/10.1007/978-3-319-93473-0_2

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