Whole-genome sequencing reveals recent transmission of multidrug-resistant Mycobacterium tuberculosis CAS1-Kili strains in Lusaka, Zambia

Globally, tuberculosis (TB) is a major cause of death due to anti-microbial resistance. Mycobacte-rium tuberculosis CAS1-Kili strains that belong to Lineage 3 (Central Asian Strain, CAS) were previously implicated in the spread of multidrug-resistant (MDR)-TB in Lusaka, Zambia. Thus, we investigated recent transmission of those strains by whole genome sequencing (WGS) with Il-lumina MiSeq platform. Twelve MDR CAS1-Kili isolates clustered by traditional methods (MIRU-VNTR and spoligotyping) were used. Ninety-two percent of isolates belonged to a cluster (less than or equal to 12 SNPs) while 50% (6/12) were involved in recent transmission events as they differed by less than or equal to 5 SNPs. All the isolates had KatG Ser315Thr (isoniazid resistance), EmbB Met306 substitutions (ethambutol resistance), and several kinds of rpoB mutations (rifampicin resistance). WGS also revealed compensatory mutations including a novel deletion in embA regulatory region (-35A>del). Several strains shared the same combinations of drug-resistance associated muta-tions indicating transmission of MDR strains. Zambian strains belonged to the same clade with Tanzanian, Malawian, and European strains, although most of those were pan drug-susceptible. Hence, complimentary use of WGS to traditional epidemiological methods provides an in-depth insight on transmission and drug resistance patterns which can guide targeted control measures to stop the spread of MDR-TB.