Journal Article

Whole Genome Sequencing of Mycobacterium tuberculosis under routine conditions in a high-burden area of multidrug-resistant tuberculosis in Peru

Huamán, Teresa, Moore, David A. J., Puyén, Zully M., Ruiz-Nizama, Nathaly, Santos-Lázaro, David, Asto, Belisa, Vigo, Aiko N., Cotrina, Vidia V., Alarcón, Miriam J.

2024

Overview

Whole Genome Sequencing (WGS) is a promising tool in the global fight against tuberculosis (TB). The aim of this study was to evaluate the use of WGS in routine conditions for detection of drug resistance markers and transmission clusters in a multidrug-resistant TB hot-spot area in Peru. For this, 140 drug-resistant Mycobacterium tuberculosis strains from Lima and Callao were prospectively selected and processed through routine (GenoType MTBDR sl and BACTEC MGIT) and WGS workflows, simultaneously. Resistance was determined in accordance with the World Health Organization mutation catalogue. Agreements between WGS and BACTEC results were calculated for rifampicin, isoniazid, pyrazinamide, moxifloxacin, levofloxacin, amikacin and capreomycin. Transmission clusters were determined using different cut-off values of Single Nucleotide Polymorphism differences. 100% (140/140) of strains had valid WGS results for 13 anti-TB drugs. However, the availability of final, definitive phenotypic BACTEC MGIT results varied by drug with 10–17% of invalid results for the seven compared drugs. The median time to obtain results of WGS for the complete set of drugs was 11.5 days, compared to 28.6–52.6 days for the routine workflow. Overall categorical agreement by WGS and BACTEC MGIT for the compared drugs was 96.5%. Kappa index was good (0.65≤k≤1.00), except for moxifloxacin, but the sensitivity and specificity values were high for all cases. 97.9% (137/140) of strains were characterized with only one sublineage (134 belonging to “lineage 4” and 3 to “lineage 2”), and 2.1% (3/140) were mixed strains presenting two different sublineages. Clustering rates of 3.6% (5/140), 17.9% (25/140) and 22.1% (31/140) were obtained for 5, 10 and 12 SNP cut-off values, respectively. In conclusion, routine WGS has a high diagnostic accuracy to detect resistance against key current anti-TB drugs, allowing results to be obtained through a single analysis and helping to cut quickly the chain of transmission of drug-resistant TB in Peru.

• Publisher: Public Library of Science
• Subject: Agreements / Amikacin / Antibiotics / Antitubercular agents / Antitubercular Agents - pharmacology / Antitubercular Agents - therapeutic use / Biology and Life Sciences / Capreomycin / Clustering / Clusters / Disease transmission / DNA sequencing / Drug resistance / Drug resistance in microorganisms / Drug Resistance, Multiple, Bacterial - genetics / Drugs / Female / Gene polymorphism / Gene sequencing / Genetic aspects / Genome, Bacterial / Genomes / Genomics / Humans / Isoniazid / Laboratories / Levofloxacin / Male / Medicine and Health Sciences / Microbial Sensitivity Tests / Moxifloxacin / Multidrug resistance / Mutation / Mycobacterium tuberculosis / Mycobacterium tuberculosis - drug effects / Mycobacterium tuberculosis - genetics / Mycobacterium tuberculosis - isolation & purification / Nucleotide sequencing / Nucleotides / People and places / Peru - epidemiology / Polymorphism / Polymorphism, Single Nucleotide / Pyrazinamide / Rifampin / Single nucleotide polymorphisms / Single-nucleotide polymorphism / Strains (organisms) / Tuberculosis / Tuberculosis, Multidrug-Resistant - drug therapy / Tuberculosis, Multidrug-Resistant - epidemiology / Tuberculosis, Multidrug-Resistant - microbiology / Whole genome sequencing / Whole Genome Sequencing - methods / Workflow