A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches

dc.contributor.authorBogaerts, Bert
dc.contributor.authorDelcourt, Thomas
dc.contributor.authorSoetaert, Karine
dc.contributor.authorBoarbi, Samira
dc.contributor.authorCeyssens, Pieter-Jan
dc.contributor.authorWinand, Raf
dc.contributor.authorVan Braekel, Julien
dc.contributor.authorDe Keersmaecker, Sigrid C. J.
dc.contributor.authorRoosens, Nancy H.C.
dc.contributor.authorMarchal, Kathleen
dc.contributor.authorMathys, Vanessa
dc.contributor.authorVanneste, Kevin
dc.date.accessioned2022-04-28T07:45:35Z
dc.date.available2022-04-28T07:45:35Z
dc.date.issued2021-05-19
dc.description.abstractThe use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNPbased AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of .99% for all assays, except for spoligotyping, where sensitivity dropped to ;90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s).en_US
dc.description.departmentGeneticsen_US
dc.description.librarianam2022en_US
dc.description.sponsorshipThe PubMLST website (https://pubmlst.org/) was funded by the Wellcome Trust. The National Reference Center is partially supported by the Belgian Ministry of Social Affairs through a fund within the Health Insurance System.en_US
dc.description.urihttps://jcm.asm.orgen_US
dc.identifier.citationBogaerts, B., Delcourt, T., Soetaert, K., Boarbi, S., Ceyssens, P.-J., Winand, R., Van Braekel, J., De Keersmaecker, S.C.J., Roosens, N.H.C., Marchal, K., Mathys, V. & Vanneste, K. 2021. A bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approaches. Journal of Clinical Microbiology 59:e00202-21. https://DOI.org/ 10.1128/JCM.00202-21.en_US
dc.identifier.issn0095-1137 (print)
dc.identifier.issn1098-660X (online)
dc.identifier.other10.1128/JCM.00202-21
dc.identifier.urihttps://repository.up.ac.za/handle/2263/84927
dc.language.isoenen_US
dc.publisherAmerican Society for Microbiologyen_US
dc.rights© 2021 Bogaerts et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.en_US
dc.subjectValidationen_US
dc.subjectPublic healthen_US
dc.subjectNational reference centeren_US
dc.subjectMycobacterium tuberculosis (MTB)en_US
dc.subjectWhole genome sequencing (WGS)en_US
dc.subjectSingle nucleotide polymorphism (SNP)en_US
dc.subjectAntimicrobial resistance (AMR)en_US
dc.titleA bioinformatics whole-genome sequencing workflow for clinical Mycobacterium tuberculosis complex isolate analysis, validated using a reference collection extensively characterized with conventional methods and in silico approachesen_US
dc.typeArticleen_US

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