Dataset Information

Application of next-generation sequencing to detect variants of drug-resistant Mycobacterium tuberculosis: genotype-phenotype correlation.

ABSTRACT: BACKGROUND:Drug resistance in Mycobacterium tuberculosis (MTB) is a major health issue worldwide. Recently, next-generation sequencing (NGS) technology has begun to be used to detect resistance genes of MTB. We aimed to assess the clinical usefulness of Ion S5 NGS TB research panel for detecting MTB resistance in Korean tuberculosis patients. METHODS:Mycobacterium tuberculosis with various drug resistance profiles including susceptible strains (N?=?36) were isolated from clinical specimens. Nucleic acids were extracted from inactivated culture medium and underwent amplicon-based NGS to detect resistance variants in eight genes (gyrA, rpoB, pncA, katG, eis, rpsL, embB, and inhA). Data from previous studies using the same panel were merged to yield pooled sensitivity and specificity values for detecting drug resistance compared to phenotype-based methods. RESULTS:The sequencing reactions were successful for all samples. A total of 24 variants were considered to be related to resistance, and 6 of them were novel. Agreement between the phenotypic and genotypic results was excellent for isoniazid, rifampicin, and ethambutol, and was poor for streptomycin, amikacin, and kanamycin. The negative predictive values were greater than 97% for all drug classes, while the positive predictive values varied (44% to 100%). There was a possibility that common mutations could not be detected owing to the low coverage. CONCLUSIONS:We successfully applied NGS for genetic analysis of drug resistances in MTB, as well as for susceptible strains. We obtained lists of polymorphisms and possible polymorphisms, which could be used as a guide for future tests applying NGS in mycobacteriology laboratories. When analyzing the results of NGS, coverage analysis of each samples for each gene and benign polymorphisms not related to drug resistance should be considered.

SUBMITTER: Ko DH

PROVIDER: S-EPMC6317249 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Application of next-generation sequencing to detect variants of drug-resistant Mycobacterium tuberculosis: genotype-phenotype correlation.

Ko Dae-Hyun DH Lee Eun Jin EJ Lee Su-Kyung SK Kim Han-Sung HS Shin So Youn SY Hyun Jungwon J Kim Jae-Seok JS Song Wonkeun W Kim Hyun Soo HS

Annals of clinical microbiology and antimicrobials 20190103 1

<h4>Background</h4>Drug resistance in Mycobacterium tuberculosis (MTB) is a major health issue worldwide. Recently, next-generation sequencing (NGS) technology has begun to be used to detect resistance genes of MTB. We aimed to assess the clinical usefulness of Ion S5 NGS TB research panel for detecting MTB resistance in Korean tuberculosis patients.<h4>Methods</h4>Mycobacterium tuberculosis with various drug resistance profiles including susceptible strains (N = 36) were isolated from clinical ...[more]

PMID: 30606210

Similar Datasets

Project description:Although Mycobacterium tuberculosis isolates are consisted of several different lineages and the epidemiology analyses are usually assessed relative to a particular reference genome, M. tuberculosis H37Rv, which might introduce some biased results. Those analyses are essentially based genome sequence information of M. tuberculosis and could be performed in sillico in theory, with whole genome sequence (WGS) data available in the databases and obtained by next generation sequencers (NGSs). As an approach to establish higher resolution methods for such analyses, whole genome sequences of the M. tuberculosis complexes (MTBCs) strains available on databases were aligned to construct virtual reference genome sequences called the consensus sequence (CS), and evaluated its feasibility in in sillico epidemiological analyses.The consensus sequence (CS) was successfully constructed and utilized to perform phylogenetic analysis, evaluation of read mapping efficacy, which is crucial for detecting single nucleotide polymorphisms (SNPs), and various MTBC typing methods virtually including spoligotyping, VNTR, Long sequence polymorphism and Beijing typing. SNPs detected based on CS, in comparison with H37Rv, were utilized in concatemer-based phylogenetic analysis to determine their reliability relative to a phylogenetic tree based on whole genome alignment as the gold standard. Statistical comparison of phylogenic trees based on CS with that of H37Rv indicated the former showed always better results that that of later. SNP detection and concatenation with CS was advantageous because the frequency of crucial SNPs distinguishing among strain lineages was higher than those of H37Rv. The number of SNPs detected was lower with the consensus than with the H37Rv sequence, resulting in a significant reduction in computational time. Performance of each virtual typing was satisfactory and accorded with those published when those are available.These results indicated that virtual CS constructed from genome sequence data is an ideal approach as a reference for MTBC studies.

Dataset Information

Application of next-generation sequencing to detect variants of drug-resistant Mycobacterium tuberculosis: genotype-phenotype correlation.

Publications

Application of next-generation sequencing to detect variants of drug-resistant Mycobacterium tuberculosis: genotype-phenotype correlation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets