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Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

2023-12Artigo científico Acesso aberto
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dc.contributor.authorHenares, Desiree
dc.contributor.authorLo, Stephanie W.
dc.contributor.authorPerez-Argüello, Amaresh
dc.contributor.authorRedin, Alba
dc.contributor.authorCiruela, Pilar
dc.contributor.authorGarcia-Garcia, Juan Jose
dc.contributor.authorBrotons, Pedro
dc.contributor.authorYuste, Jose
dc.contributor.authorSá-Leão, Raquel
dc.contributor.authorMuñoz-Almagro, Carmen
dc.contributor.institutionInstituto de Tecnologia Química e Biológica António Xavier (ITQB)
dc.contributor.pblAmerican Society for Microbiology
dc.date.accessioned2024-04-02T23:46:45Z
dc.date.available2024-04-02T23:46:45Z
dc.date.issued2023-12
dc.descriptionFunding Information: C.M.A. reports a research grant from laboratories paid to Sant Joan de Déu foundation and related with the submitted work, as well as fees as speaker at conferences from MSD, and J.Y. reports research grants from and MSD unrelated to the submitted work, as well as participation in advisory boards organized by and MSD. Funding Information: This study has been funded in part by Fondo Europeo de Desarrollo Regional (FEDER) and the Ministry of Science and Innovation, Instituto de Salud Carlos III (ISCIII) through the project "PI19/00104" (Principal Investigator: C.M.A.), the predoctoral Contract for Training in Research into Health “FI17/00248” (Recipient: D.H.), and the grant “PID2020– 119298RB-I00“ (Recipient: J.Y.). CMA also received a research grant from laboratories and Fundación Godia paid to the Sant Joan de Déu foundation. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Publisher Copyright: © 2023 Henares et al.
dc.description.abstractWhole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of differentbioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by differentWGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine differentserotypes were identifiedby serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent872701
dc.identifier.doi10.1128/jcm.00741-23
dc.identifier.issn0095-1137
dc.identifier.otherPURE: 83536795
dc.identifier.otherPURE UUID: bdcc92c6-e556-48df-90ab-99ad445ccff4
dc.identifier.otherScopus: 85180411262
dc.identifier.otherPubMed: 38092657
dc.identifier.urihttp://hdl.handle.net/10362/165722
dc.identifier.urlhttps://www.scopus.com/pages/publications/85180411262
dc.language.isoeng
dc.peerreviewedyes
dc.subjectin silico serotyping
dc.subjectONT
dc.subjectPathogenwatch
dc.subjectpneumococci
dc.subjectvalidation
dc.subjectWGS
dc.subjectMicrobiology (medical)
dc.titleComparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniaeen
dc.typejournal article
degois.publication.issue12
degois.publication.titleJournal Of Clinical Microbiology
degois.publication.volume61
dspace.entity.typePublication
rcaap.rightsopenAccess

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