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Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases.

ABSTRACT: BackgroundWhole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custom-built analysis pipelines with little standardisation between them.AimTo compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases.MethodsFrom the Netherlands, 535 Mycobacterium tuberculosis complex (MTBC) strains from 2016 were included. Epidemiological information obtained from municipal health services was available for all mycobacterial interspersed repeat unit-variable number of tandem repeat (MIRU-VNTR) clustered cases. WGS data was analysed using five different pipelines: one core genome multilocus sequence typing (cgMLST) approach and four single nucleotide polymorphism (SNP)-based pipelines developed in Oxford, United Kingdom; Borstel, Germany; Bilthoven, the Netherlands and Copenhagen, Denmark. WGS clusters were defined using a maximum pairwise distance of 12 SNPs/alleles.ResultsThe cgMLST approach and Oxford pipeline clustered all epidemiologically linked cases, however, in the other three SNP-based pipelines one epidemiological link was missed due to insufficient coverage. In general, the genetic distances varied between pipelines, reflecting different clustering rates: the cgMLST approach clustered 92 cases, followed by 84, 83, 83 and 82 cases in the SNP-based pipelines from Copenhagen, Oxford, Borstel and Bilthoven respectively.ConclusionConcordance in ruling out epidemiological links was high between pipelines, which is an important step in the international validation of WGS data analysis. To increase accuracy in identifying TB transmission clusters, standardisation of crucial WGS criteria and creation of a reference database of representative MTBC sequences would be advisable.

SUBMITTER: Jajou R

PROVIDER: S-EPMC6918587 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases.

Jajou Rana R Kohl Thomas A TA Walker Timothy T Norman Anders A Cirillo Daniela Maria DM Tagliani Elisa E Niemann Stefan S de Neeling Albert A Lillebaek Troels T Anthony Richard M RM van Soolingen Dick D

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 20191201 50

BackgroundWhole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custom-built analysis pipelines with little standardisation between them.AimTo compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases.MethodsFrom the Netherlands, 535 <i>Mycobacterium tuberculosis</i> complex (MTBC) strains from 2016 were included. Epidemiological information obtaine ...[more]

PMID: 31847944

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Project description:Background:Smoking is known to increase the risk of tuberculosis (TB) infection, active TB disease, relapse following treatment and death from TB, but its significance is often underappreciated as a potentially reversible risk factor in public health and clinical TB practice in Canada. Objective:To review the current evidence on smoking and the risk of TB, describe a cluster investigation of local TB transmission related to smoking in Toronto, Ontario, and discuss the practical implications of smoking for TB elimination in Canada. Investigation and public health response:Three TB cases were identified at the same workplace over a two year period. All three strains matched on genotyping. Extensive interviews with the cases and workplace / building managers confirmed that the three cases did not work or socialize together. The only epidemiologic link identified was that all three were regular smokers and used the same location outside the building for smoke breaks. A building ventilation assessment confirmed that unfiltered air was not recirculated between floors. Based on the epidemiological and laboratory evidence, we determined that transmission likely occurred at the partly-sheltered smoking area outside of the worksite. We established and advertised an active case-finding clinic on-site to all workers who frequented smoking areas near the building. Of 60 individuals screened with tuberculin skin testing (TST), no additional active TB cases were identified. One Canadianborn person was found to be TST positive. We also offered TB education sessions to all staff in the building, and used the opportunity to promote smoking cessation for interested individuals. Conclusion:This cluster shows compelling evidence for smoking-related transmission of TB in Toronto. The World Health Organization has called for integration of anti-smoking efforts as a key strategy toward TB elimination. Opportunities to integrate smoking and TB work in Canada include assessment for smoking-related transmission during contact investigations, routine use of smoking cessation supports for contacts and others with latent tuberculosis infection as well as those with active TB, and public health outreach.

Dataset Information

Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases.

Publications

Towards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases.

Similar Datasets

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