A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools.

INTRODUCTION: Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen's kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. IMPORTANCE: Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.

Population structure and genetic diversity of Mycobacterium tuberculosis in Ecuador.

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.

Country-wide rapid screening for the Mycobacterium tuberculosis Beijing sublineage in Ecuador using a single-nucleotide polymorphism-polymerase chain reaction method.

Background: Strains of the Beijing sublineage of Mycobacterium tuberculosis have caused large outbreaks of tuberculosis, often involving multidrug resistance strains and this genetically highly conserved family of strains predominates in some geographic areas. For most of the countries of Latin America, no country-wide studies about the prevalence of the Beijing lineage are available. Methods: In this study, we determine the prevalence of the Beijing sublineage in Ecuador, using a large nation-wide sample of 991 isolates from the years 2014-2016 and with the strains, in case-related-proportional representation, emerging from most of the provinces of the country. The isolates were genotyped with asinglenucleotidespecific polymorphism (SNP) polymerase chain reaction for the Beijing sublineage. SNPpositive strains were confirmed as belonging to this lineage with 24 mycobacterial interspersed repetitive unitvariable number of tandem repeat and DNA sequencing. Results: We identified only four Beijing isolates in this collection of 991 strains and calculated a prevalence rate of 0.43%. Conclusions: Our study shows a limited dissemination of the Beijing strains in the Ecuadorian population. This in contrast with the neighbor countries of Peru and Colombia were locally a prevalence of up to 16% has been reported.

Prevalence, Drug Resistance, and Genotypic Diversity of the Mycobacterium tuberculosis Beijing Family in Ecuador.

The Beijing family, the most successful Mycobacterium tuberculosis lineage, is considered hypervirulent, associated with clustering and has a strong association with multidrug-resistant tuberculosis. The Beijing strains have spread worldwide and also to Latin America. Genotyping of a countrywide collection of 380 M. tuberculosis strains from Ecuador, with 24-loci mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR), revealed only six Beijing strains, but four of these were MDR-TB. There was no clustering as all six strains had very distinct MIRU-VNTR profiles that have not been reported in the rest of Latin America. Although active transmission for Beijing has been described for the neighboring countries Peru and Colombia, there is no evidence that Beijing strains in Ecuador are more frequently transmitted than other strains. Moreover, the low prevalence (1.6%) of the Beijing sublineage in Ecuador challenges the concept of hyperadaptability and transmissibility of the Beijing strains in our country.

Sensibilidad a drogas de primera línea frente a cepas de M. tuberculosis del CRN Micobacterias, Guayas, 2016 / Sensitivity to first-line drugs against strains of M. tuberculosis of the CRN Micobacterias, Guayas, 2016

Objetivo: Determinar el perfil de sensibilidad de Mycobacterium tuberculosis a drogas de primera línea en cepas que llegan de diferentes unidades de salud de la provincia del Guayas. Materiales y métodos. Se trabajó con 614 cepas de Mycobacterium tuberculosis, las cuales se le realizó las pruebas de sensibilidad a drogas de primera (rifampicina, isoniacida, estreptomicina y etambutol) por el por el método de proporciones (Rist, Canetti, Grosset) y pirazinamida evaluada por el método Wayne. Resultado: Se realizó perfil de sensibilidad a 614 cepas, de las cuales el 70 % (n=427) es sensible a todas las drogas, 20 % (n=124) presentó resistencia al menos a una droga, el restante corresponden a cepas MDR. TB-Monorresistente tiene mayor incidencia (n=83) que la MDR (n=12) en pacientes sin tratamiento previo. Por otro lado en pacientes antes tratado la TB-Monorresistente es menor a la MDR (n=41 y n=51 respectivamente). Conclusiones: el método de proporciones sigue siendo la técnica de referencia. Se observa mayor sensibilidad a drogas de primera línea en pacientes sin tratamiento previo. Es de importancia clínica llevar un correcto seguimiento a pacientes que presenten algún tipo de resistencia, pero es prioridad preventiva la no conversión de los pacientes sensibles a fin de evitar la diseminación de cepas resistentes.

Objective: Difine first line susceptibility drug profile of Mycobacterium tuberculosis, to diferent strain from Province Guayas health establishments. Material and Methods.614 Mycobacterium tuberculosis strain were analized by first line susceptibility drug test (rifampicin, isoniazid, streptomycin, ethambutol) used proportions method (Rist, Canetti, Grosset) and pyrazinamide Wayne´s methods. Results: 614 strain were studied, 70 % strains (n=427) result sensible, 20 % (n=124) have at least resistence one drug; the residue responds to MDR strains. The TB-Monoresistence haved more incidence (n=83) than MDR (n=12) in virgin treatments patients. Nevertheless; in previous treatment patients, the TB-Monoresistence is smaller than MDR (n=41 y n=51 respectively). Conclutions: The proportion method is the reference technique. The analize shown biggest sensibility in virgin treatment patients for first line drugs. Is very important have a correct control of resistant pactients, but is preventive priority the non conversion of sensibility patients to avoid dissemination resistance strain.