Snapshot based on whole-genome sequencing revealing the species and antimicrobial susceptibility profiles of Mycobacterium tuberculosis complex recovered at a major tertiary care center in Lebanon.

BACKGROUND: Tuberculosis remains a pressing public health issue in Lebanon. The aim of this study was whole-genome-based determination of species and sub-species and antibiotic susceptibility profiles of Mycobacterium tuberculosis complex (MTBC) isolates recovered from a major tertiary care center in Lebanon. METHODS: A total of 48 clinical MTBC isolates were identified and characterized through whole genome sequence using Illumina MiSeq. RESULTS: Genomic analysis revealed that 39/48 (81.25%) of the clinical isolates were M. tuberculosis and 9/48 (18.75%) were Mycobacterium bovis. M. tuberculosis was distributed over four lineages, Indo-Oceanic L1 (n = 3/39; 7.6%), East-Asian L2 (n = 1/39; 2.5%), East-African Indian L3 (n = 5/39; 12.8%) and Euro-American L4 (n = 30/39; 76.9%). Sub-lineage L4.8 (Euro-American, mainly T), comprising 8/39 of the isolates (20.5%) was predominant, followed by sub-lineages L3 (East-African Indian, n = 5/39 isolates; 12.8%), L4.2.2.2 (Euro-American (Ural), n = 4/39 isolates; 10.2%) and L4.6.5 (Euro American, n = 4/39 isolates; 10.2%). The nine M. bovis isolates were clustered into two separate clades, designated as unknown 2 (n = 2/9, 22.2%) and unknown 3 (n = 7/9, 77.8%). Further genome-wide single nucleotide polymorphism (SNP) analyses identified two possible transmission clusters, each comprising isolates differing by < 12 SNPs, consistent with recent transmission events. In silico antimycobacterial susceptibility profiling against 13 drugs showed uniform susceptibility among 24/39 (61.53%) M. tuberculosis isolates while the M. bovis isolates were susceptible to all the antimycobacterial drugs except pyrazinamide. CONCLUSIONS: This study characterized the molecular features, clustering patterns, and resistance profiles of human MTBC isolates, and identified the lineages and sub-lineages of M. tuberculosis along with their prevalence. Unexpectedly, our findings also revealed the presence of M. bovis, which is often misidentified due to the limited availability of facilities for molecular typing and characterization of MTBC isolates. This identification helps improve the detection of the causative agents of tuberculosis and assess the zoonotic contribution. CLINICAL TRIAL: Not applicable.