An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data

Disratthakit, Areeya; Toyo-Oka, Licht; Thawong, Penpitcha; Paiboonsiri, Pundharika; Wichukjinda, Nuanjun; Ajawatanawong, Pravech; Thipkrua, Natthakan; Suthum, Krairerk; Palittapongarnpim, Prasit; Tokunaga, Katsushi; Mahasirimongkol, Surakameth

doi:10.1016/j.meegid.2019.104152

Cited by 7 publications

(5 citation statements)

References 28 publications

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“…Multiple gVCF files were aggregated and combined into one GVCF file using GATK GenotypeGVCFs. Only the single nucleotide polymorphisms (SNPs) from VCF output were extracted using SelectVariants tool and filtered using VariantFiltration (23). The snpEff software (v4.2) was used for variant annotation (24).…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto - Beijing genotype

Srilohasin

Prammananan

Faksri

et al. 2020

Emerging Microbes & Infections

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Tuberculosis disease (TB), caused by Mycobacterium tuberculosis , is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With ≤ 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the fadD14 gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient M. tuberculosis strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within desA3 (Rv3230c) , large deletions in the plcB, plcA, and ppe38 gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type.

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Section: Bioinformatics Analysismentioning

confidence: 99%

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto - Beijing genotype

Srilohasin

Prammananan

Faksri

et al. 2020

Emerging Microbes & Infections

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“…We applied variant calling methods by using the H37Rv reference genome (GenBank accession no. NC_00962.3) ( 12 ). We used an in-house Python script to determine the M. tuberculosis lineage on the basis of WGS data ( 13 ).…”

Section: Methodsmentioning

confidence: 99%

“…We constructed a phylogenetic tree by using the maximum-likelihood methods in MEGAX ( 14 ) and visualized the tree with the Interactive Tree of Life (iTOL) online tool, version 6.5.2 ( https://itol.embl.de ). We also analyzed pairwise single-nucleotide polymorphism (SNP) distances by using MEGA X and the frequency of pairwise SNP distances within sublineages ( 12 ). We used 2 SNP difference thresholds that have been used internationally to define clusters ( 15 – 17 ); the main analysis used a 12-SNP cutoff, which enabled inclusion of potentially related isolates, and the secondary analysis used a 5-SNP cutoff to identify highly related isolates.…”

Section: Methodsmentioning

confidence: 99%

Risk for Prison-to-Community Tuberculosis Transmission, Thailand, 2017–2020

Miyahara¹,

Piboonsiri²,

Chiyasirinroje³

et al. 2023

Emerg. Infect. Dis.

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To determine contributions of previously incarcerated persons to tuberculosis (TB) transmission in the community, we performed a healthcare facility–based cohort study of TB patients in Thailand during 2017–2020. We used whole-genome sequencing of Mycobacterium tuberculosis isolates from patients to identify genotypic clusters and assess the association between previous incarceration and TB transmission in the community. We identified 4 large genotype clusters ( > 10 TB patients/cluster); 28% (14/50) of the patients in those clusters were formerly incarcerated. Formerly incarcerated TB patients were more likely than nonincarcerated patients to be included in large clusters. TB patients within the large genotype clusters were geographically dispersed throughout Chiang Rai Province. Community TB transmission in the community was associated with the presence of formerly incarcerated individuals in Thailand. To reduce the risk for prison-to-community transmission, we recommend TB screening at the time of entry and exit from prisons and follow-up screening in the community.

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“…2015; Disratthakit et al . 2020). Smear microscopy, the traditional mainstay for testing TB, can detect and identify bacilli via combining culture (Ma et al .…”

Section: Introductionmentioning

confidence: 99%

“…Currently, the detection of Mycobacterium tuberculosis complex (MTBC) bacilli in samples of sputum expectorated by the patient is the dominating identification approach of TB (Bradley et al 2015;Disratthakit et al 2020). Smear microscopy, the traditional mainstay for testing TB, can detect and identify bacilli via combining culture (Ma et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Rapid detection of Mycobacterium tuberculosis based on antigen 85B via real-time recombinase polymerase amplification

Zhang

et al. 2021

Letters in Applied Microbiology

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Tuberculosis (TB), as a common infectious disease, still remains a severe challenge to public health. Due to the unsatisfied clinical needs of currently available diagnostic vehicles, it is desired to establish a new approach for universally detecting Mycobacterium tuberculosis. Herein, we designed a real‐time recombinase polymerase amplification (RPA) technology for identifying M. tuberculosis within 20 min at 39°C via custom‐designed oligonucleotide primers and probe, which could specifically target antigen 85B (Ag85B). Particularly, the primers F4‐R4 produced the fastest fluorescence signal with the probe among four pairs of designed primers in the RPA assays. The optimal primers/probe combination could effectively identify M. tuberculosis with the detection limit of 4·0 copies per μl, as it could not show a positive signal for the genomic DNA from other mycobacteria or pathogens. The Ag85B‐based RPA could determine the genomic DNA extracted from M. tuberculosis with high reliability (100%, 22/22). More importantly, when testing clinical sputum samples, the real‐time RPA displayed an admirable sensitivity (90%, 95% CI: 80·0‐96·0%) and specificity (98%, 95% CI: 89·0‐100·0%) compared to traditional smear microscopy, which was similar to the assay of Xpert MTB/RIF. This real‐time RPA based Ag85B provides a promising strategy for the rapid and universal diagnosis of TB.

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An optimized genomic VCF workflow for precise identification of Mycobacterium tuberculosis cluster from cross-platform whole genome sequencing data

Cited by 7 publications

References 28 publications

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto - Beijing genotype

Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto - Beijing genotype

Risk for Prison-to-Community Tuberculosis Transmission, Thailand, 2017–2020

Rapid detection of Mycobacterium tuberculosis based on antigen 85B via real-time recombinase polymerase amplification

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