Whole-genome phylogenetic analysis of Mycobacterium avium complex from clinical respiratory samples

Abstract

The Mycobacterium avium complex (MAC) is a common causative agent causing nontuberculous mycobacterial (NTM) pulmonary disease worldwide. Whole-genome sequencing was performed on a total of 203 retrospective MAC isolates from respiratory specimens. Phylogenomic analysis identified eight subspecies and species. M. avium subspecies hominissuis (MAH) was the overwhelmingly dominant species (148/203, 72.9%). The other seven identified species were M. intracellulare subsp. yongonense (18/203, 8.9%), M. intracellulare subsp. chimaera (10/203, 4.9%), M. colombiense (11/203, 5.4%), M. paraintracellulare (6/203, 3%), M. marseillense (5/203, 2.5%), M. intracellulare (3/203, 1.5%), and M. avium subspecies paratuberculosis (2/203, 1%). Significant genetic clustering was observed among MAH isolates. Notably, a large cluster (<12 SNPs) of 76 MAH isolates bearing the same sequence type was observed. The presence of closely related isolates within hospital settings raises concerns about transmission routes with environmental sources potentially playing a significant role. Based on susceptibility breakpoints that are available for clarithromycin, amikacin, linezolid, and moxifloxacin, low rates of clarithromycin (0.5%, 1/203) and amikacin (1.5%, 3/203) phenotypic resistance were observed. While linezolid and moxifloxacin resistance were 25.6% (52/2030) and 46.3% (94/203), respectively. Drug resistance-associated loci were searched for mutations linked to phenotypic drug resistance. Of the entire cohort, only one isolate was found to have a A2059G 23S rRNA (rrl) gene mutation responsible for macrolide resistance.

Importance: Mycobacterium avium complex (MAC) infections are increasingly challenging to manage due to their complex species diversity and varied resistance patterns. This study underscores the genetic diversity within MAC, identifying at least eight species and subspecies among 203 clinical isolates, with M. avium subsp. hominissuis (MAH) being most prevalent at 72.9%. Notably, genetic clustering was observed within MAH and M. intracellulare subsp. chimaera, suggesting potential transmission routes within healthcare settings. Clarithromycin and amikacin resistance was found to be uncommon, aligning with the rarity of resistance-associated genetic mutations. These findings emphasize the need for enhanced infection control measures and routine susceptibility testing to tailor antibiotic therapies effectively.

Keywords: Mycobacterium aviumcomplex (MAC); antibiotic resistance; environmental sampling; nontuberculous mycobacteria (NTM); phylogenetic analysis; transmission dynamics; whole-genome sequencing (WGS).

FIG 1

Core-SNP phylogenetic tree of 203 Mycobacterium avium complex (MAC) genomes analyzed in this study. Metadata displayed includes SNP counts, multi-locus sequence type (ST), hospital location, collection date (month/year), and identified resistance mutations. SNP counts are derived from core-SNPs obtained through intra-species genome alignments. Different species and subspecies are represented by distinct colors. New MLSTs were assigned arbitrarily in this study to indicate unique allelic Profiles. Profiles marked with an asterisk (*) indicate MLST profiles that have imperfect matches to existing alleles in the Mycobacteria spp. PubMLST typing database. GenBank accession numbers for reference assemblies are included in parentheses. All isolates sequenced in this study are labeled with the prefix "mv."