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 thisstudy was whole-genome-based determination of species and sub-species and antibioticsusceptibility profiles of Mycobacterium tuberculosis complex (MTBC) isolates recovered froma major tertiary care center in Lebanon.Methods. A total of 48 clinical MTBC isolates were identified and characterized through wholegenome 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 overfour lineages, Indo-Oceanic L1 (n = 3/39; 7.6%), East-Asian L2 (n = 1/39; 2.5%), East-AfricanIndian 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 bysub-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. bovisisolates were clustered into two separate clades, designated as unknown 2 (n=2/9, 22.2%) andunknown 3 (n=7/9, 77.8%). In silico antimycobacterial susceptibility profiling against 13 drugsshowed uniform susceptibility among 24/39 (61.53%) M. tuberculosis isolates while all the M.bovis isolates were uniformly susceptible to all the antimycobacterial drugs except pyrazinamide.Conclusions. This study revealed the molecular characteristics, clustering, and resistanceprofiles of human MTBC isolates and the lineages and sub-lineages of M. tuberculosis and theirprevalence. Our findings also helped identify M. bovis which is usually misidentified because ofthe lack of the needed facilities for the molecular typing and characterization of the MTBC isolates and which helps to better identify the causative agents of tuberculosis and determine thezoonotic contribution.