2026-08-25T13:21:11Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/169402024-10-31T11:48:30Zcom_20.500.12105_2052com_20.500.12105_2051col_20.500.12105_19609
Repisalud
author
Henares, Desiree
author
Lo, Stephanie W
author
Perez-Argüello, Amaresh
author
Redin, Alba
author
Ciruela, Pilar
author
Garcia-Garcia, Juan Jose
author
Brotons, Pedro
author
Yuste, Jose Enrique
author
Sá-Leão, Raquel
author
Muñoz-Almagro, Carmen
funder
Instituto de Salud Carlos III
funder
Ministerio de Economía y Competitividad (España)
funder
Pfizer
funder
Fundación Godia
2024-01-11T18:12:07Z
2024-01-11T18:12:07Z
2023-12-19
J Clin Microbiol. 2023 Dec 19;61(12):e0074123.
10.1128/jcm.00741-23
1098-660X
Journal of clinical microbiology
38092657
http://hdl.handle.net/20.500.12105/16940
Whole 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 different bioinformatics 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 different WGS-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 different serotypes were identified by 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.
eng
Pneumococci
WGS
ONT
in silico serotyping
Validation
Pathogenwatch
Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae
research article
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