A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus sequence typing) using whole-genome sequencing data

Michelle Wuzinski; Aneta K Bak; Aaron Petkau; Walter H B Demczuk; Hafid Soualhine; Meenu Kaushal Sharma

doi:10.4103/ijmy.ijmy_106_19

A multilocus sequence typing scheme for Mycobacterium abscessus complex (MAB-multilocus sequence typing) using whole-genome sequencing data

Int J Mycobacteriol. 2019 Jul-Sep;8(3):273-280. doi: 10.4103/ijmy.ijmy_106_19.

Authors

Michelle Wuzinski¹, Aneta K Bak², Aaron Petkau³, Walter H B Demczuk⁴, Hafid Soualhine⁵, Meenu Kaushal Sharma⁵

Affiliations

¹ National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada; Department of Microbiology, University of Manitoba, Manitoba, Canada.
² Department of Microbiology, University of Manitoba, Manitoba, Canada.
³ Department of Bioinformatics, National Microbiology Laboratory, Public Health Agency of Canada, Manitoba, Canada.
⁴ Streptococcus and Sexually Transmitted Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Manitoba, Canada.
⁵ National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada; Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.

PMID: 31512604
DOI: 10.4103/ijmy.ijmy_106_19

Abstract

Background: Mycobacterium abscessus is a rapid growing nontuberculous mycobacteria (NTM) and a clinically significant pathogen capable of causing variable infections in humans that are difficult to treat and may require months of therapy/surgical interventions. Like other NTMs, M. abscessus can be associated with outbreaks leading to complex investigations and treatment of affected cases. Typing schemes for bacterial pathogens provide numerous applications; including identifying chain of transmission and tracking genomic evolution, are lacking or limited for many NTMs including M. abscessus.

Methods: We extended the existing scheme from PubMLST using whole-genome data for M. abscessus by extracting data for 15 genetic regions within the M. abscessus genome. A total of 168 whole genomes and 11 gene sequences were used to build this scheme (MAB-multilocus sequence typing [MLST]).

Results: All seven genes from the PubMLST scheme, namely argH, cya, gnd, murC, pta, purH, and rpoB, were expanded by 10, 14, 13, 10, 13, 10, and 9 alleles, respectively. Another eight novel genes were added including hsp 65, erm(41), arr, rrs, rrl, gyrA, gyrB, and recA with 16, 16, 25, 7, 32, 35, 29, and 15 alleles, respectively, with 85 unique sequence types identified among all isolates.

Conclusion: MAB-MLST can provide identification of M. abscessus complex to the subspecies level based on three genes and can provide antimicrobial resistance susceptibility prediction based on results from seven genes. MAB-MLST generated a total of 85 STs, resulting in subtyping of 90 additional isolates that could not be genotyped using PubMLST and yielding results comparable to whole-genome sequencing (WGS). Implementation of a Galaxy-based data analysis tool, MAB-MLST, that simplifies the WGS data and yet maintains a high discriminatory index that can aid in deciphering an outbreak has vast applicability for routine diagnostics.

Keywords: MAB-multilocus sequence typing; Mycobacterium abscessus; Nontuberculous mycobacteria; multilocus sequence typing; rapid growing mycobacteria.

MeSH terms

Bacterial Proteins / genetics
Bacterial Typing Techniques
DNA, Bacterial
Drug Resistance, Multiple, Bacterial / genetics
Genome, Bacterial
Genotype
Multilocus Sequence Typing*
Mycobacterium Infections, Nontuberculous / microbiology
Mycobacterium abscessus / classification*
Mycobacterium abscessus / genetics
Phylogeny
Sequence Analysis, DNA
Whole Genome Sequencing*

Substances

Bacterial Proteins
DNA, Bacterial