Population structure and genetic diversity of Mycobacterium tuberculosis in Ecuador

Abstract

Tuberculosis (TB) is a significant public health problem in Ecuador with an incidence of 43 per 100,000 inhabitants and an estimated multidrug-resistant-TB prevalence in all TB cases of 9%. Genotyping of Mycobacterium tuberculosis (MTBC) is important to understand regional transmission dynamics. This study aims to describe the main MTBC lineages and sublineages circulating in the country. A representative sample of 373 MTBC strains from 22 provinces of Ecuador, with data comprising geographic origin and drug susceptibility, were genotyped using 24 loci-MIRU-VNTR. For strains with an ambiguous sublineage designation, the lineage was confirmed by Regions of Difference analysis or by Whole Genome Sequencing. We show that lineage 4 is predominant in Ecuador (98.3% of the strains). Only 4 strains belong to lineages 2-sublineage Beijing and two strains to lineage 3-sublineage Delhi. Lineage 4 strains included sublineages LAM (45.7%), Haarlem (31.8%), S (13.1%), X (4.6%), Ghana (0.6%) and NEW (0.3%). The LAM sublineage showed the strongest association with antibiotic resistance. The X and S sublineages were found predominantly in the Coastal and the Andean regions respectively and the reason for the high prevalence of these strains in Ecuador should be addressed in future studies. Our database constitutes a tool for MIRU-VNTR pattern comparison of M. tuberculosis isolates for national and international epidemiologic studies and phylogenetic purposes.

Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru

“…Our results establish that the LAM family was dominant among the Peruvian XDR-TB strains analysed, which is consistent with that evidenced in neighbouring South American countries 67 – 72 . However, it disagrees with a previous study also carried out on Peruvian XDR-TB strains in which it was established that the dominant family was Haarlem 12 .…”

Molecular Epidemiology and Genetic Diversity of Multidrug-Resistant Mycobacterium tuberculosis Isolates in Bangladesh

“…EAI and CAS lineages among MDR-TB strains were also reported by our previous studies ( 18 , 20 ), as well as by neighboring countries, such as India ( 30 ), Nepal ( 23 ), and Myanmar ( 19 ). Studies from Latin American countries have reported the LAM lineage, which is strongly associated with drug resistance and MDR-TB ( 31 , 32 ). However, a report from Brazil has shown a high proportion of T and H lineages among MDR-TB isolates ( 13 ).…”

Distribution of Mycobacterium tuberculosis lineages in South America

“…This dispersion is how the LAM sublineage appears in cities with high population concentrations, promoting a more severe disease due to its high mutation rate. In turn, a new mutation from this sublineage has been reported, giving rise to a new RD Rio strain that appears in the population of Rio de Janeiro with a clinical picture that has with high bacillary loads (Moraes et al, 2017); lineage 4 sublineages such as Haarlem and T are directly related to their stability and transmissibility in urban areas and the S sublineage in rural areas, especially in indigenous communities (Díaz Acosta et al, 2019;Garzon-Chavez et al, 2020). The Beijing sublineage is unique due to its high level of virulence, reduced inflammatory response and predisposition to antibiotic resistance.…”

“…At present, its distribution in South America is not total, not because of its level of transmission and prevalence but because of the scarce genotyping studies in the countries where it is not reported (Cerezo-Cortés et al, 2019). For the circulating sublineages belonging to lineages 1, 3 and 6, since they have a low prevalence, it is not possible to determine their specific level of influence in a population area, except for their increased variability as complex outbreaks and new routes of infection (Garzon-Chavez et al, 2020).…”

“…Soto Cabezas et al, 2020 reported that almost half of the XDR-TB cases analyzed (48%) had no previous anti-TB treatment, which highlights the need to evaluate TB control programs. For bordering countries, both Ecuador and Chile have reported an increase in Beijing sublineage strains, making Ecuador and Colombia additional areas identified as critical or hotspots for the prevalence of lineage 2 (Garzon-Chavez et al, 2020;Lagos et al, 2016).…”