Developing a Genotyping Scheme for Mycobacterium abscessus Complex Using Whole Genome Sequencing Data

Abstract

Mycobacterium abscessus complex is a rapid growing non-tuberculous mycobacteria (NTM) and a clinically significant pathogen capable of causing varying infections in humans. It is notoriously difficult to treat due to its inducible resistant state to clarithromycin and intrinsic resistant states to other drugs including rifampicin. Typing schemes for bacterial pathogens provide numerous applications including sourcing an outbreak, identifying cross contamination, chain of transmission and surveillance. However, they either lack or are limited for many NTMs including M. abscessus complex. The current publically available scheme on PubMLST has not been updated in several years and was only able to apply a sequence type to less than half of tested isolates. This project was aimed at creating a workflow for the development of a multi-locus sequence typing (MLST) scheme using whole genome data. A total of 104 genomes and 14 loci were used to build the scheme (including 3 type strains of each of the 3 subspecies). All 7 genes from the PubMLST scheme were incorporated namely, argH, cya, gnd, murC, pta, purH, and rpoB and were expanded by 6, 9, 12, 8, 12, 10, and 8 alleles, respectively. Another 7 novel genes were added including hsp65, erm(41), arr, rrs, rrl, gyrA, and gyrB with 9, 14, 20, 7, 25, 24, 22 alleles, respectively with 62 unique sequence types were identified among all isolates. This scheme can also differentiate M. abscessus complex to the subspecies level on the basis of 3 discriminatory genes and includes 6 genes related to antimicrobial resistance.

 

Supplementary information available online at: http://ojs.lib.umanitoba.ca/index.php/pmuser/article/view/682/699