Towards standardization: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases
| Autor: | Daniela Maria Cirillo, Troels Lillebaek, Timothy M Walker, Dick van Soolingen, Elisa Tagliani, Albert J. de Neeling, Thomas Kohl, Rana Jajou, Stefan Niemann, Anders Norman, Richard M. Anthony |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
030106 microbiology Single-nucleotide polymorphism Computational biology Minisatellite Repeats Genome Polymorphism Single Nucleotide DNA sequencing 03 medical and health sciences Virology Disease Transmission Infectious SNP analysis pipelines Humans Netherlands Whole genome sequencing Molecular Epidemiology Molecular epidemiology biology Whole Genome Sequencing Research Public Health Environmental and Occupational Health Mycobacterium tuberculosis biology.organism_classification 030104 developmental biology Geography TB Mycobacterium tuberculosis complex tuberculosis Tandem Repeat Sequences international Epidemiological Monitoring Multilocus sequence typing epidemiology Multilocus Sequence Typing |
| Zdroj: | Eurosurveillance Jajou, R, Kohl, T A, Walker, T, Norman, A, Cirillo, D M, Tagliani, E, Niemann, S, de Neeling, A, Lillebaek, T, Anthony, R M & van Soolingen, D 2019, ' Towards standardisation : comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases ', Eurosurveillance, vol. 24, no. 50, pp. 8-17 . https://doi.org/10.2807/1560-7917.ES.2019.24.50.1900130 |
| DOI: | 10.2807/1560-7917.es.2019.24.50.1900130 |
| Popis: | Background Whole 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. 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. |
| Databáze: | OpenAIRE |
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