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

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 invol...

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Autores principales:	Lusayda Sánchez-Corrales, Olga Lucía Tovar-Aguirre, Narmer Fernando Galeano-Vanegas, Paula Alejandra Castaño Jiménez, Ruth Arali Martínez-Vega, Carlos Ernesto Maldonado-Londoño, Johan Sebastián Hernández-Botero, Fernando Siller-López
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8e0e7a78837146ab95323e3759c8cfed
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spelling	oai:doaj.org-article:8e0e7a78837146ab95323e3759c8cfed2021-11-25T05:54:12ZPhylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.1932-620310.1371/journal.pone.0258402https://doaj.org/article/8e0e7a78837146ab95323e3759c8cfed2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0258402https://doaj.org/toc/1932-6203Mycobacterium 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.Lusayda Sánchez-CorralesOlga Lucía Tovar-AguirreNarmer Fernando Galeano-VanegasPaula Alejandra Castaño JiménezRuth Arali Martínez-VegaCarlos Ernesto Maldonado-LondoñoJohan Sebastián Hernández-BoteroFernando Siller-LópezPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0258402 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lusayda Sánchez-Corrales Olga Lucía Tovar-Aguirre Narmer Fernando Galeano-Vanegas Paula Alejandra Castaño Jiménez Ruth Arali Martínez-Vega Carlos Ernesto Maldonado-Londoño Johan Sebastián Hernández-Botero Fernando Siller-López Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
description	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.
format	article
author	Lusayda Sánchez-Corrales Olga Lucía Tovar-Aguirre Narmer Fernando Galeano-Vanegas Paula Alejandra Castaño Jiménez Ruth Arali Martínez-Vega Carlos Ernesto Maldonado-Londoño Johan Sebastián Hernández-Botero Fernando Siller-López
author_facet	Lusayda Sánchez-Corrales Olga Lucía Tovar-Aguirre Narmer Fernando Galeano-Vanegas Paula Alejandra Castaño Jiménez Ruth Arali Martínez-Vega Carlos Ernesto Maldonado-Londoño Johan Sebastián Hernández-Botero Fernando Siller-López
author_sort	Lusayda Sánchez-Corrales
title	Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
title_short	Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
title_full	Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
title_fullStr	Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
title_full_unstemmed	Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
title_sort	phylogenomic analysis and mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of caldas, colombia.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/8e0e7a78837146ab95323e3759c8cfed
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Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.

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