Whole-Genome Sequencing-Based Characterisation of Clinically Relevant Mycobacterium abscessus Complex Isolates from...

Mycobacterium abscessus complex is a rapidly growing non-tuberculous mycobacterium(NTM) associated with difficult-to-treat pulmonary and extrapulmonary infections. Clinical management is complicated by intrinsic antimicrobial resistance, inducible macrolide resistance, and genomic heterogeneity. This study characterised five clinical pulmonary M. abscessus isolates from India using whole-genome sequencing (WGS)-based genomic, phylogenetic, and antimicrobial resistance analysis.

Five clinical isolates recovered from pulmonary specimens were sequenced using the Illumina NovaSeq platform (Illumina, Inc., San Diego, California, United States) with paired-end 151 bp chemistry. Reads were quality filtered using fastp v1.0.1. Reference-guided alignment and consensus generation were performed using Burrows-Wheeler Aligner (BWA)-Maximal Exact Match (MEM) and SAMtools-based workflows. Genome annotation was conducted using Prokka v1.14.6, functional annotation using eggNOG-mapper, variant analysis using Genome Analysis Toolkit (GATK) HaplotypeCaller and SnpEff, and antimicrobial resistance gene detection using the Comprehensive Antibiotic Resistance Database (CARD). Phenotypic antimicrobial susceptibility findings and GenoType NTM-drug resistance (DR) Line Probe Assay Version 1.0 results (Bruker Corporation, Billerica, Massachusetts, United States) were used to support the interpretation of macrolide resistance-associated findings.

The isolates generated 0.92-1.24 Gb of high-quality sequencing data, with Q30 values exceeding 95%. Genome coverage at ≥30× depth exceeded 91%, and average sequencing depth ranged from 44.16× to 149.59×. Annotation identified 4,457-4,751 coding sequences, 45-48 tRNA genes, three rRNA genes, and one tmRNA gene per isolate. Reference alignment ranged from 24.86% to 64.22%, supporting isolate-level genomic heterogeneity. MAB β-lactamase (blaMab) gene was detected in all isolates, while erm(41) was detected only in LIN.

WGS-enabled isolate-level characterisation of pulmonary M. abscessus isolates from India demonstrated conserved genomic features with measurable heterogeneity. blaMab supports intrinsic β-lactam resistance, while erm(41) in LIN was consistent with an inducible macrolide resistance pattern supported by available phenotypic antimicrobial susceptibility testing.