Elsevier

Tuberculosis

Volume 129, July 2021, 102106
Tuberculosis

Characterization of genetic diversity and clonal complexes by whole genome sequencing of Mycobacterium tuberculosis isolates from Jalisco, Mexico

https://doi.org/10.1016/j.tube.2021.102106Get rights and content

Abstract

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.

Introduction

In 2019, the World Health Organization (WHO) estimated over 10 million new cases and 1.4 million deaths associated with tuberculosis (TB), making it the infectious disease with the greatest impact on human health [1].

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has multiple advantages over traditional genotyping techniques (MIRU-VNTR and spoligotyping) since it allows a more robust classification into lineages and sublineages [2]. WGS genotyping also facilitates our understanding of the dynamics of the disease and enables implementation of measures focused on the containment of specific TB genotypes circulating within a given region [2,3]. Moreover, WGS has a greater power of discrimination and resolution of single nucleotide differences between clinical isolates. This information is extremely useful for the establishment of genetic relationships and formation of genomic clusters; i.e., cases derived from recent transmission [[4], [5], [6], [7]]. WGS can also be used as a rapid and highly sensitive tool for identification of polymorphisms in genes related to drug resistance, and to predict sensitivity against first and second line drugs [8,9].

The combination of information obtained by WGS has important advantages compared to traditional epidemiological investigation and genotyping methods because it allows a more accurate description of the etiology of TB and provides improved resolution of the transmission topology, enabling definition of the directionality, evolution of transmission and development of drug resistance [10,11].

In Mexico, TB has an incidence of 22 cases per 100,000 inhabitants [12], of which 2.5% present resistance to at least one drug. Moreover, the numbers of multidrug resistant (MDR-), and extensively drug resistant-tuberculosis (XDR-TB), are increasing annually [13], with the country ranking among the top five contributors of TB in the American continent [14]. The state of Jalisco, located in the western region of Mexico, has a low prevalence of TB; however, in recent years, it has presented growing numbers of TB, DR-TB and MDR-TB. In addition, the number of studies of the molecular epidemiology of TB are limited [[15], [16], [17]], and there has been no description of polymorphisms related to drug resistance, or description of genotypic characterization using WGS. The aim of this study was therefore to perform a WGS characterization (lineage identification, spoligotyping, identification of transmission cluster and prediction of drug resistance and SNPs associated) of TB strains circulating in the state of Jalisco, Mexico.

Section snippets

Setting, clinical isolates and phenotypic drug susceptibility testing

A random selection of tuberculosis isolates, taken from patients diagnosed with pulmonary TB by the Public Health Institute of Jalisco from 2013 to 2016, was cultured in LJ media and subjected to analysis. Phenotypic drug sensitivity testing (DST) against first-line drugs was performed using the fluorometric method (BACTEC, MGIT 960 Becton-Dickinson), adopting standard conditions: isoniazid (H) > 0.1 μg/mL, rifampin (R) 1.0 μg/mL, ethambutol (E) 5.0 μg/mL and streptomycin (S) 1.0 μg/mL.

Population characteristics

Of the 32 individuals included in the study, the predominant population was male, with 19 individuals (60%) in an age range of 30–59 years. The most frequent comorbidity was type 2 diabetes mellitus, which was observed in five individuals (16%). In terms of treatment type, 18 individuals (56%) were in primary treatment, while four (12%) were in re-treatment. The most observed resistances were isoniazid in seven (22%) isolates and pyrazinamide in four (12%) individuals. Only two individuals (6%)

Discussion

This is the first characterization, using WGS, of clinical TB isolates circulating in a state in western Mexico. The results showed a predominance of L4 and a significant diversity of sublineages, which is consistent with the reports of previous studies using WGS in Mexico [30] and traditional genotyping methods [15,17,[31], [32], [33], [34], [35], [36]]. A total of 87% of the isolates were included in L4; this high proportion could be explained by migratory events from the European

Credit author statement

Luis Alfredo Rendón Bautista: Conceptualization, Methodology, Software, investigation, Writing- Original draft preparation. Manuel Sandoval-Díaz3: Data curation and methodology, resources. Juan Carlos Villanueva-Arias: Data curation and methodology, resources. Natividad Ayala-Chavira: Data curation and methodology, resources. Ikuri Álvarez-Maya: Data duration, methodology, supervision, investigation, writing- Reviewing and Editing. Roberto Zenteno: Supervision, methodology, Writing- Reviewing

Funding sources

Ikuri Alvarez-Maya was supported with funds provided by CONACYT through grant No. PDCPN_2014_247879, Programa de Atención a Problemas Nacionales. Luis Alfredo Rendón Bautista was funded by CONACyT, No. 928282.

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