Whole genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand

Regmi, Sanjib Mani; Chaiprasert, Angkana; Kulawonganunchai, Supasak; Tongsima, Sissades; Coker, Olabisi Oluwabukola; Prammananan, Therdsak; Viratyosin, Wasna; Thaipisuttikul, Iyarit

doi:10.1007/s00438-015-1048-0

Cited by 19 publications

(16 citation statements)

References 71 publications

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“…Ocheretina and colleagues [ 36 ] determined that 6 of their 8 isolates had the same resistance mutation for isoniazid and rifampicin, and thus judged that the outbreak represented primary resistance. Regmi et al [ 35 ] employed the same method but only examined 4 of the 54 isolates in their MDR-TB outbreak in Thailand.…”

Section: Resultsmentioning

confidence: 99%

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hatherell

Colijn

Stagg

et al. 2016

BMC Med

127

129

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BackgroundWhole genome sequencing (WGS) is becoming an important part of epidemiological investigations of infectious diseases due to greater resolution and cost reductions compared to traditional typing approaches. Many public health and clinical teams will increasingly use WGS to investigate clusters of potential pathogen transmission, making it crucial to understand the benefits and assumptions of the analytical methods for investigating the data. We aimed to understand how different approaches affect inferences of transmission dynamics and outline limitations of the methods.MethodsWe comprehensively searched electronic databases for studies that presented methods used to interpret WGS data for investigating tuberculosis (TB) transmission. Two authors independently selected studies for inclusion and extracted data. Due to considerable methodological heterogeneity between studies, we present summary data with accompanying narrative synthesis rather than pooled analyses.ResultsTwenty-five studies met our inclusion criteria. Despite the range of interpretation tools, the usefulness of WGS data in understanding TB transmission often depends on the amount of genetic diversity in the setting. Where diversity is small, distinguishing re-infections from relapses may be impossible; interpretation may be aided by the use of epidemiological data, examining minor variants and deep sequencing. Conversely, when within-host diversity is large, due to genetic hitchhiking or co-infection of two dissimilar strains, it is critical to understand how it arose. Greater understanding of microevolution and mixed infection will enhance interpretation of WGS data.ConclusionsAs sequencing studies have sampled more intensely and integrated multiple sources of information, the understanding of TB transmission and diversity has grown, but there is still much to be learnt about the origins of diversity that will affect inferences from these data. Public health teams and researchers should combine epidemiological, clinical and WGS data to strengthen investigations of transmission.Electronic supplementary materialThe online version of this article (doi:10.1186/s12916-016-0566-x) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hatherell

Colijn

Stagg

et al. 2016

BMC Med

127

129

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“…The number of genes tentatively associated with drug resistance ranged from one (rifabutin, minocycline, trimethoprim/sulfamethoxazole, bedaquiline, clofazimine) to 19 (isoniazid) per individual drug. Notably, in only a small number of studies [30,34] were polymorphisms in genes associated with resistance to linezolid and para-aminosalicylic acid included in the analysis; in others no associations were reported because of a lack of available phenotypic data. For the same reason, it was not possible to analyse performance characteristics of WGS for detection of resistance to bedaquiline, clofazimine and trimethoprim/sulfamethoxazole [6].…”

Section: Drugs and Genes/regions Associated With Drug Resistancementioning

confidence: 99%

Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review

Papaventsis

Coppola

Kontsevaya

et al. 2017

Clinical Microbiology and Infection

109

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28We conducted a systematic review to determine the diagnostic accuracy of Whole Genome Sequencing (WGS) of M. 29tuberculosis for the detection of resistance to first and second line anti-tuberculosis (TB) drugs. 30 Methods 31The study was conducted according to the criteria of the Preferred Reporting Items for Systematic Reviews group. A 32 total of 20 publications were included. The sensitivity, specificity, PPV and NPV of WGS using phenotypic Drug 33 Susceptibility Testing (DST) methods as a gold standard were determined. 45tuberculosis complex drug resistance, future studies should include information on clinical outcomes.

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“…The M. tuberculosis complex has 8 main lineages (L1-8) (5), which vary in their geographic distribution and spread, with L1 (Indo-Oceanic) and L2 (East Asian) the predominant ones circulating in Thailand (6)(7)(8)(9)(10). The modern Beijing sublineage (L2.2.1; AAF3) has been continuously reported to be associated with clonal expansion of MDR-TB (6,7,11). In contrast, the "Manu-ancestor" or "proto-Beijing" genotype (spoligotype 523, lineage 2.1; (9)) has a lower prevalence (6,10), with few reports, including detection in the Chiba prefecture in Japan (12) and Guangxi province of Southern China (13).…”

Section: Introductionmentioning

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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Whole genome sequence analysis of multidrug-resistant Mycobacterium tuberculosis Beijing isolates from an outbreak in Thailand

Cited by 19 publications

References 71 publications

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review

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

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