Whole genome sequencing (WGS) analysis in tuberculosis allows the prediction of drug-resistant phenotypes, identification of lineages, and to better understanding of the epidemiology and transmission chains. Nevertheless the procedure has been scarcely assessed in Mexico, in this work we analyze by WGS isolates of Mycobacterium tuberculosis circulating in Jalisco, Mexico.

Lineage and phylogenetic characterization, drug resistant prediction, “in silico” spoligotyping determination, were provided by WGS in 32 M. tuberculosis clinical isolates. Lineage 4 (L4), with 28 isolates (87%) and eleven sublineages was dominant. Forty SNPs and INDELs were found in genes related to first-, and second-line drugs. Eleven isolates were sensitive, seven (22%) were predicted to be resistant to isoniazid, two resistant to rifampicin (6%) and two (6%) were multidrug-resistant tuberuclosis. Spoligotyping shows that SIT 53 (19%) and SIT 119 (16%) were dominant. Four clonal transmission complexes were found.

This is the first molecular epidemiological description of TB isolates circulating in western Mexico, achieved through WGS. L4 was dominant and included a high diversity of sublineages. It was possible to track the transmission route of two clonal complexes. The WGS demonstrated to be of great utility and with further implications for clinical and epidemiological study of TB in the region.

结核病中的全基因组测序 (WGS) 分析可以预测耐药表型、鉴定谱系，并更好地了解流行病学和传播链。然而，该程序在墨西哥几乎没有进行过评估，在这项工作中，我们通过在墨西哥哈利斯科州流行的 WGS结核分枝杆菌分离株进行分析。

WGS 在 32 个结核分枝杆菌临床分离株中提供谱系和系统发育表征、耐药性预测、“计算机”spoligotyping 测定。谱系 4 (L4)，有 28 个分离株 (87%) 和 11 个亚谱系占主导地位。在与一线和二线药物相关的基因中发现了 40 个 SNP 和 INDEL。11 个分离株是敏感的，7 个（22%）预计对异烟肼耐药，2 个对利福平耐药（6%），2 个（6%）是耐多药结核病。Spoligotyping 显示 SIT 53 (19%) 和 SIT 119 (16%) 占主导地位。发现了四个克隆传播复合物。

这是通过 WGS 对墨西哥西部流行的 TB 分离株进行的第一次分子流行病学描述。L4 占主导地位，包括高度多样性的亚谱系。可以追踪两个克隆复合体的传播途径。WGS 被证明非常有用，并且对该地区的结核病临床和流行病学研究具有进一步的意义。