Résumé
Background Tuberculosis remains a pressing public health issue in Lebanon. The aim of this study was wholegenome-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.