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Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia.
Sánchez-Corrales, Lusayda; Tovar-Aguirre, Olga Lucía; Galeano-Vanegas, Narmer Fernando; Castaño Jiménez, Paula Alejandra; Martínez-Vega, Ruth Arali; Maldonado-Londoño, Carlos Ernesto; Hernández-Botero, Johan Sebastián; Siller-López, Fernando.
  • Sánchez-Corrales L; Maestría en Investigación en Enfermedades Infecciosas, Universidad de Santander, Bucaramanga, Santander, Colombia.
  • Tovar-Aguirre OL; Programa de Bacteriología, Universidad Católica de Manizales, Manizales, Caldas, Colombia.
  • Galeano-Vanegas NF; Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Manizales, Caldas, Colombia.
  • Castaño Jiménez PA; Departamento de Biotecnología, BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia.
  • Martínez-Vega RA; Programa de Bacteriología, Universidad Católica de Manizales, Manizales, Caldas, Colombia.
  • Maldonado-Londoño CE; Facultad de Salud, Universidad de Santander, Bucaramanga, Santander, Colombia.
  • Hernández-Botero JS; Centro Nacional de Investigaciones de Café -Cenicafé, Manizales, Caldas, Colombia.
  • Siller-López F; Grupo de Investigación Médica, Escuela de Medicina, Universidad de Manizales, Manizales, Caldas, Colombia.
PLoS One ; 16(10): e0258402, 2021.
Article in English | MEDLINE | ID: covidwho-1456096
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Tuberculosis, Multidrug-Resistant / Drug Resistance, Multiple, Bacterial / Whole Genome Sequencing / Genotype / Mycobacterium tuberculosis Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: South America / Colombia Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article Affiliation country: Journal.pone.0258402

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Tuberculosis, Multidrug-Resistant / Drug Resistance, Multiple, Bacterial / Whole Genome Sequencing / Genotype / Mycobacterium tuberculosis Type of study: Cohort study / Observational study / Prognostic study / Randomized controlled trials Limits: Adult / Aged / Female / Humans / Male / Middle aged Country/Region as subject: South America / Colombia Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article Affiliation country: Journal.pone.0258402