Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.

Lusayda Sánchez-Corrales,Paula Alejandra Castaño Jiménez,Carlos Ernesto Maldonado-Londoño,Ruth Arali Martínez-Vega,Narmer Fernando Galeano-Vanegas,Johan Sebastián Hernández-Botero,Fernando Siller-López,Olga Lucía Tovar-Aguirre,Seyed Ehtesham Hasnain

doi:10.1371/journal.pone.0258402

Abstract

Mycobacterium tuberculosis (M. tuberculosis) was the pathogen responsible for the highest number of deaths from infectious diseases in the world, before the arrival of the COVID-19 pandemic. Whole genome sequencing (WGS) has contributed to the understanding of genetic diversity, the mechanisms involved in drug resistance and the transmission dynamics of this pathogen. The object of this study is to use WGS for the epidemiological and molecular characterization of M. tuberculosis clinical strains from Chinchiná, Caldas, a small town in Colombia with a high incidence of TB. Sputum samples were obtained during the first semester of 2020 from six patients and cultured in solid Löwenstein-Jensen medium. DNA extraction was obtained from positive culture samples and WGS was performed with the Illumina HiSeq 2500 platform for subsequent bioinformatic analysis. M. tuberculosis isolates were typified as Euro-American lineage 4 with a predominance of the Harlem and LAM sublineages. All samples were proven sensitive to antituberculosis drugs by genomic analysis, although no phenotype antimicrobial tests were performed on the samples, unreported mutations were identified that could require further analysis. The present study provides preliminary data for the construction of a genomic database line and the follow-up of lineages in this region.

Highlights

M. tuberculosis (MTB) is considered one of the most lethal pathogens, with a toll of 1 billion people suffering tuberculosis (TB)-related deaths in the last two centuries
The aim of this study is to explore the potential use of whole genome sequencing (WGS) in the context of routine surveillance, describing the epidemiological and molecular characteristics of circulating M. tuberculosis strains from Chinchina, Caldas using minimal sequencing and computational resources
The analysis showed that all isolates belong to the Euro-American lineage (Lineage 4), divided in LAM and Harlem sublineages (Fig 2)

Summary

Introduction

M. tuberculosis (MTB) is considered one of the most lethal pathogens, with a toll of 1 billion people suffering tuberculosis (TB)-related deaths in the last two centuries. The World Health Organization (WHO) in their annual report of 2019 depicted an estimate of 10 million new cases and 1.7 million deaths per year [1], making MTB the deadliest single infectious agent before the arrival of SARS-CoV-2. In Caldas, a department located in the center of the country, TB is considered endemic causing 34 new cases and 2.31 deaths per 100,000 habitants at its peak in 2017, making this malady a primary public health concern in the region due to the progressive aging of the population, emerging immunosuppressive treatments, sociodemographic and comorbidities conditions. The development of local capacities bioinformatic analysis and the reduction on overall genome sequencing costs make whole genome sequencing (WGS) an increasingly accessible alternative for molecular epidemiologic studies [3]. With the genetic information obtained by WGS compared to other analysis, drug resistance profiles can be predicted for most of the current antibiotic treatment, enabling a wide monitoring of drug resistance

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