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

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.

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

“…The potential of WGS to provide a quick and comprehensive view of the genotype and reliable prediction of the lineages has been extensively reported [ 5 , 7 , 14 , 40 ]; thus, its application in surveillance programs is necessary. The Euro-American lineage (lineage 4) presents a variable distribution in Argentina with a predominance of M and Ra strains [ 41 ], for Brazil, lineage 4 varies between 25–99% [ 13 , 42 , 43 ], for Colombia, between 85–99% [ 44 – 46 ], for Mexico between 69–98% [ 47 , 48 ] and for Peru around 90% [ 12 , 49 , 50 ]. Ecuador is not an exception, in fact, all the samples analyzed by us belong to the Euro-American lineage.…”

A precision overview of genomic resistance screening in isolates ofMycobacterium tuberculosisusing web-based bioinformatics tools

“…Moreover, in recent times, the World Health Organisation (WHO) publishes updates of guidelines for TB treatment including drug-susceptible, single drugresistant, multidrug-resistant (MDR-TB) and extensively drug-resistant TB (XDR-TB) (23) which has allowed to improve the pipelines within the web-based tools. Despite the improvements in the WGS protocols for TB diagnosis that simultaneously allows, species differentiation, detection of drug resistance-associated mutations, and phylogenetic/clustering analyses to guide contact investigations (30)(31)(32), analysis of genomic sequencing data remains an obstacle to the routine use of WGS technology in clinical tuberculosis. This is mainly because it requires bioinformatics expertise, highperformance computing, funding, and training that are not readily available in most clinical laboratories (24,33)..…”

“…Genomic DNA was extracted from 88 isolates of Mycobacterium tuberculosis grown in Lowenstein-Jensen medium by two different protocols. In 21 isolates the DNA was extracted by the CTAB method (30,31) while for others 67 were obtained by the PureLink DNA Mini Kit (Fisher Scientific, Pennsylvania, USA) according to manufacturer instructions. Each extracted DNA was quantified by a Qubit 4.0 fluorometer (Invitrogen, Carlsbad, CA, USA.).…”

Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates from Diabetic and Non-Diabetic Patients with Pulmonary Tuberculosis

“…A more granular analysis of the WGS to identify genetic features of the pan-genomes of the isolates from DM vs. non-DM TB patients may reveal features associated with DM or non-DM patients. Table 5 shows studies determining lineages and spoligotypes distributed across the world and specifically in India [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 ]. An overview of various studies conducted in different regions around the world to determine the predominant lineages and spoligotypes of Mycobacterium tuberculosis , offers valuable insights into the distribution and diversity of the strains in different populations, and also raises several points for critical discussion.…”