Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population

Abstract

Mycobacterium abscessus comprises three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. These closely related strains are typically multi-drug-resistant and can cause difficult-to-treat infections. Dominant clusters of isolates with increased pathogenic potential have been demonstrated in pulmonary infections in the global cystic fibrosis (CF) population. An investigation was performed on isolates cultured from an Asian, predominantly non-CF population to explore the phylogenomic relationships within our population and compare it to global M. abscessus isolates. Whole-genome-sequencing was performed on M. abscessus isolates between 2017 and 2019. Bioinformatic analysis was performed to determine multi-locus-sequence-type, to establish the phylogenetic relationships between isolates, and to identify virulence and resistance determinants in these isolates. A total of 210 isolates were included, of which 68.5 % (144/210) were respiratory samples. These isolates consisted of 140 (66.6 %) M. abscessus subsp. massiliense, 67 (31.9 %) M. abscessus subsp. abscessus, and three (1.4 %) M. abscessus subsp. bolletii. Dominant sequence-types in our population were similar to those of global CF isolates, but SNP differences in our population were comparatively wider despite the isolates being from the same geographical region. ESX (ESAT-6 secretory) cluster three appeared to occur most commonly in ST4 and ST6 M. abscessus subsp. massiliense, but other virulence factors did not demonstrate an association with isolate subspecies or sample source. We demonstrate that although similar predominant sequence-types are seen in our patient population, cross-transmission is absent. The risk of patient-to-patient transmission appears to be largely limited to the vulnerable CF population, indicating infection from environmental sources remains more common than human-to-human transmission. Resistance and virulence factors are largely consistent across the subspecies with the exception of clarithromycin susceptibility and ESX-3.

Keywords: Mycobacterium abscessus complex; Mycobacterium bolletii; Mycobacterium massiliense; genomic epidemiology; whole genome sequencing.

Fig. 1.

Core SNP phylogenetic tree of 210 isolates of Mycobacterium abscessus . The metadata includes specimen source, resistance determinants, virulence factors and multi-locus sequence type (ST). The black branch labels belong to M. abscessus subsp. massiliense, the purple labels to M. abscessus subsp. bolletii and the orange labels to M. abscessus subsp. massiliense. Two isolates marked with red asterisks were from cystic fibrosis (CF) patients. glp; glycopeptidolipid, ESX; ESAT-6 secretion system. The bootstrap values are indicated on the nodes.

Fig. 2.

MIC distribution of tested antimicrobials stratified by subspecies. The figures beneath the histograms indicate the number of isolates with a particular MIC, with the right-most figure indicating no inhibition within the tested MIC range. Blank results indicate MICs outside of the tested ranged. MICs presented in mg l⁻¹; AMK: Amikacin; CFX: Cefoxitin; CIP: Ciprofloxacin; DOX: Doxycycline; IMI: Imipenem; LZD: Linezolid; MOX: Moxifloxacin; SXT: Co-trimoxazole; TOB: Tobramycin; MIN: Minocycline; TIG: Tigecycline; CFZ: Clofazimine; BDQ: Bedaquiline; ERV: Eravacycline; RFB: Rifabutin; Mab: Mycobacterium abscessus subsp. abscessus; Mma: Mycobacterium abscessus subsp. massiliense .