Whole genomic sequencing as a tool for diagnosis of drug and multidrug-resistance tuberculosis in an endemic region in Mexico

Abstract

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.

Prevalence and Molecular Characteristics Based on Whole Genome Sequencing of Mycobacterium tuberculosis Resistant to Four Anti-Tuberculosis Drugs from Southern Xinjiang, China

“…6,42 There was no isolate carried rrs mutation combined with rpsL mutation in this study, suggesting that mutations in rrs and rpsL genes were mutually exclusive. Mutations in rrs and rpsL genes accounted for 68.6% STR resistance, higher than the data from the tertiary care tuberculosis hospital in China 35 and Mexico, 43 but lower than that from other regions, 44,45 indicating that there were regional differences in the mutations associated with STR resistance and additional resistance mechanisms correlated with STR resistance, such as gidB which was reported to contribute 2.4% to 37.5% STR resistance. 42,44,[46][47][48] EMB resistance was mostly associated with mutations within the embB gene (codon 306 as the dominant).…”

Genomics epidemiology analysis reveals hidden signatures of drug resistance in Mycobacterium tuberculosis

“…Interestingly, the most common drug-resistance classes found among the diabetic-derived samples were MDR (n=16) and pre-MDR (n=13). We also expected that some of our samples would probably fit into the transmission clusters previously identified in Veracruz (18), but that was not the case.…”

A case report of transmission and disease caused by Mycobacterium caprae and Mycobacterium bovis in Lima, Peru

“…A total of 2139 patient with symptoms of TB presented to health posts in the regions of Callao and Lima South between December 2008 and January 2010. Sputum culture, microscopic observation drug susceptibility assay (MODS), serial smear microscopy, DNA extraction, Mycobacterial Interspersed Repetitive Units (MIRU) typing, Spoligotyping and whole genome sequencing were performed as previously described [ 15 – 18 ]. The dataset included three M. caprae isolates and one M. bovis isolate.…”