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

被引:40
|
作者
Jajou, Rana [1 ,2 ]
Kohl, Thomas A. [3 ,4 ]
Walker, Timothy [5 ]
Norman, Anders [6 ]
Cirillo, Daniela Maria [7 ]
Tagliani, Elisa [7 ]
Niemann, Stefan [3 ,8 ]
de Neeling, Albert [1 ]
Lillebaek, Troels [6 ,9 ]
Anthony, Richard M. [1 ]
van Soolingen, Dick [1 ]
机构
[1] Natl Inst Publ Hlth & Environm RIVM, TB Reference Lab, Bilthoven, Netherlands
[2] Natl Inst Publ Hlth & Environm RIVM, Ctr Epidemiol & Surveillance Infect Dis, Bilthoven, Netherlands
[3] Forsch Zentrum Borstel, Mol & Expt Mycobacteriol, Borstel, Germany
[4] German Ctr Infect Res, Borstel Site, Borstel, Germany
[5] Univ Oxford, John Radcliffe Hosp, Nuffield Dept Med, Oxford, England
[6] Statens Serum Inst, Int Reference Lab Mycobacteriol, Copenhagen, Denmark
[7] IRCCS San Raffaele Sci Inst, Div Immunol Transplantat & Infect Dis, Emerging Bacterial Pathogens Unit, Milan, Italy
[8] German Ctr Infect Res DZIF, Partner Site Hambur Lubeck Borstel Riems, Braunschweig, Germany
[9] Univ Copenhagen, Dept Publ Hlth, Global Hlth Sect, Copenhagen, Denmark
来源
EUROSURVEILLANCE | 2019年 / 24卷 / 50期
关键词
MYCOBACTERIUM-TUBERCULOSIS; RECENT TRANSMISSION; IDENTIFICATION; INFECTIONS; OUTBREAKS; TOOL;
D O I
10.2807/1560-7917.ES.2019.24.50.1900130
中图分类号
R51 [传染病];
学科分类号
100401 ;
摘要
Background: Whole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custombuilt analysis pipelines with little standardisation between them. Aim: To compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases. Methods: From 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. Results: The 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. Conclusion: Concordance 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.
引用
收藏
页码:8 / 17
页数:10
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