Comparing Two <i>Mycobacterium tuberculosis</i> Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments

Ryoo, Sungweon; Lee, Jeong-Soo; Oh, Jee Youn; Kim, Byeong Ki; Young, Kimball; Kim, Je Hyeong; Shin, Chol; Lee, Seung Heon

doi:10.4046/trd.2017.0091

Cited by 4 publications

(3 citation statements)

References 14 publications

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“…Strain harvest and DNA extraction were performed as previously described [ 11 ]. The library was prepared using the Ion Xpress™ Plus Library Kit for the AB Library Builder™ System, according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

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Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing

Kim

Lee

et al. 2021

Antibiotics

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Whole-genome sequencing (WGS) is promising for the quality control of laboratory facilities for Mycobacterium tuberculosis (MTB) strains. We describe the clinical and laboratory characteristics of false positive versus true positive MTB cultures based on WGS, which were experienced in a real clinical setting. Strain harvest and DNA extraction from seven isolates from pre-extensive drug-resistant (pre-XDR) TB patients transferred to the Korea University Ansan Hospital were performed, and epidemiologic links and clinical information, including the phenotypic drug susceptibility test (pDST), were investigated. WGS was performed using Ion GeneStudio with an ION530tm chip (average sequencing depth, ~100-fold). In the phylogenetic tree, identical and different strains were distributed separately. Five of the seven isolates were identical; the remaining two isolates differed from the others. The images of the referred pre-XDR-TB patients with false positive MTB that were analyzed were of regions close to old TB scars. Further, the results of WGS gene mutation analysis for ethambutol, streptomycin, and fluoroquinolone resistance in all six patients were not concordant with the pDST results. WGS and clinical information were useful in differentiating laboratory cross-contamination from true positive TB, thereby avoiding the unnecessary treatment of false positive patients and delay in treating true positive TB patients, with reliable genotypic drug resistance results.

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Section: Methodsmentioning

confidence: 99%

“…Whole-genome sequencing (WGS) shows promise in the quality control of Mycobacterium tuberculosis (MTB) laboratory cultures because it is faster and more accurate than other common methods [ 8 ] and can be applied to the identification of highly homologous strains, as well as to gene mutations for drug resistance [ 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing

Kim

Lee

et al. 2021

Antibiotics

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“…To date, WGS has been applied to MTB in the Republic of Korea in very small numbers; one study compared nine different strains of MTB between populations in the Republic of Korea, which found different lineages between TB from Chinese migrants and native Koreans. 18 WGS has also been applied to investigate false positive results due to laboratory contamination. 19 However, there have been no studies comparing genotypic predictions and phenotypic susceptibilities in MTB samples from the Republic of Korea to date.…”

Section: Introductionmentioning

confidence: 99%

A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea

Lee

Ferran

Witney

et al. 2023

JAC-Antimicrobial Resistance

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Background WGS has significant potential to help tackle the major public health problem of TB. The Republic of Korea has the third highest rates of TB of all Organisation for Economic Cooperation and Development countries but there has been very limited use of WGS in TB to date. Objectives A retrospective comparison of Mycobacterium tuberculosis (MTB) clinical isolates from 2015 to 2017 from two centres in the Republic of Korea using WGS to compare phenotypic drug susceptibility testing (pDST) and WGS drug susceptibility predictions (WGS-DSP). Methods Fifty-seven MTB isolates had DNA extracted and were sequenced using the Illumina HiSeq platform. The WGS analysis was performed using bwa mem, bcftools and IQ-Tree; resistance markers were identified using TB profiler. Phenotypic susceptibilities were carried out at the Supranational TB reference laboratory (Korean Institute of Tuberculosis). Results For first-line antituberculous drugs concordance for rifampicin, isoniazid, pyrazinamide and ethambutol was 98.25%, 92.98%, 87.72% and 85.96%, respectively. The sensitivity of WGS-DSP compared with pDST for rifampicin, isoniazid, pyrazinamide and ethambutol was 97.30%, 92.11%, 78.95% and 95.65%, respectively. The specificity for these first-line antituberculous drugs was 100%, 94.74%, 92.11% and 79.41%, respectively. The sensitivity and specificity for second-line drugs ranged from 66.67% to 100%, and from 82.98% to 100%, respectively. Conclusions This study confirms the potential role for WGS in drug susceptibility prediction, which would reduce turnaround times. However, further larger studies are needed to ensure current databases of drug resistance mutations are reflective of the TB present in the Republic of Korea.

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Comparative gene analysis of beer tolerant and sensitive Lactobacillus brevis

Zhao

Siegumfeldt

2023

Food Sci. Technol

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Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments

Cited by 4 publications

References 14 publications

Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing

Cross-Contamination versus Outbreak: Pre-XDR Mycobacterial Strains Confirmed by Whole-Genome Sequencing

A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea

Comparative gene analysis of beer tolerant and sensitive Lactobacillus brevis

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