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

• DOI: 10.1371/journal.pone.0258402
• Publication Date: 2021-10-08T13:18:00Z
• Authors: Lusayda Sánchez-C...; Olga Lucía Tovar-...; Narmer Fernando G...; Paula Alejandra C...; Ruth Arali Martín...; Carlos Ernesto Ma...; Johan Sebastián H...; Fernando Siller-L...
• Keywords: Adult; Male; 0301 basic medicine; Genotype; Whole Genome Sequencing; SARS-CoV-2; Science; Q; R; COVID-19; Mycobacterium tuberculosis; Colombia; Middle Aged; 3. Good health; 03 medical and health sciences; Drug Resistance, Multiple, Bacterial; Tuberculosis, Multidrug-Resistant; Medicine; Humans; Female; Phylogeny; Research Article; Aged; Retrospective Studies

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