Background Whole genome sequencing (WGS) has been proposed as a tool for diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic countries with important numbers of drug resistance are scarce. The goal of this study was to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic region in Mexico. Methods WGS analysis was performed in 81 tuberculosis positive clinical isolates with a known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were identified for each isolate; drug resistant genotypes were predicted and compared with the phenotypic profile. Genotypes and transmission clusters based on genetic distances were also characterized. Findings Prediction by WGS analysis of resistance against isoniazid, rifampicin, ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, enabling classification of eight and two clinical isolates as pre- and extreme drug-resistant cases, respectively. Lastly, four lineages were identified in the population (L1, L2, L3 and L4). The most frequent of these was L4, which included 90% (77) of the isolates. Six transmission clusters were identified; the most frequent was TC6, which included 13 isolates with a L4.1.1 and a predominantly multidrug-resistant condition. Conclusions The results illustrate the utility of WGS for establishing the potential for prediction of resistance against first and second line drugs in isolates of tuberculosis from the region. They also demonstrate the feasibility of this procedure for use as a tool to support the epidemiological surveillance of drug- and multidrug-resistant tuberculosis.

BackgroundMexico is one of the most important contributors of drug and multidrug-resistant tuberculosis in Latin America; however, knowledge of the genetic diversity of drug-resistant tuberculosis isolates is limited.MethodsIn this study, the genetic structure of 112 Mycobacterium tuberculosis strains from the southeastern Mexico was determined by spoligotyping and 24-loci MIRU-VNTRs.FindingsThe results show eight major lineages, the most of which was T1 (24%), followed by LAM (16%) and H (15%). A total of 29 (25%) isolates were identified as orphan. The most abundant SITs were SIT53/T1 and SIT42/LAM9 with 10 isolates each and SIT50/H3 with eight isolates. Fifty-two spoligotype patterns, twenty-seven clusters and ten clonal complexes were observed, demonstrating an important genetic diversity of drug and multidrug-resistant tuberculosis isolates in circulation and transmission level of these aggravated forms of tuberculosis. Being defined as orphan or as part of an orphan cluster, was a risk factor for multidrug resistant-tuberculosis (OR 2.5, IC 1.05–5.86 and OR 3.3, IC 1–11.03, respectively). Multiple correspondence analyses showed association of some clusters and SITs with specific geographical locations.ConclusionsOur study provides one of the most detailed description of the genetic structure of drug and multidrug-resistant tuberculosis strains in southeast Mexico, establishing for the first time a baseline of the genotypes observed in resistant isolates circulating, however further studies are required to better elucidate the genetic structure of tuberculosis in region and the factors that could be participating in their dispersion.

2Background: Whole genome sequencing (WGS) has been proposed as a tool for 3 diagnosing drug resistance in tuberculosis. However, reports of its effectiveness in endemic 4 countries with important numbers of drug resistance are scarce. The goal of this study was 5 to evaluate the effectiveness of this procedure in isolates from a tuberculosis endemic 6 region in Mexico. 7 Methods: WGS analysis was performed in 81 tuberculosis positive clinical isolates with a 8 known phenotypic profile of resistance against first-line drugs (isoniazid, rifampin, 9 ethambutol, pyrazinamide and streptomycin). Mutations related to drug resistance were 10 identified for each isolate; drug resistant genotypes were predicted and compared with the 11 phenotypic profile. Genotypes and transmission clusters based on genetic distances were 12 also characterized. 13 Findings:. Prediction by WGS analysis of resistance against isoniazid, rifampicin, 14ethambutol, pyrazinamide and streptomycin showed sensitivity values of 84%, 96%, 71%, 15 75% and 29%, while specificity values were 100%, 94%, 90%, 90% and 98%, respectively. 16Prediction of multidrug resistance showed a sensitivity of 89% and specificity of 97%. 17 Moreover, WGS analysis revealed polymorphisms related to second-line drug resistance, 18 enabling classification of eight and two clinical isolates as pre-and extreme drug-resistant 19 cases, respectively.20