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. 2023 Dec 19;61(12):e0074123.
doi: 10.1128/jcm.00741-23. Epub 2023 Nov 21.

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

Desiree Henares  1   2   3 , Stephanie W Lo  4   5 , Amaresh Perez-Argüello  1   2 , Alba Redin  1   2 , Pilar Ciruela  3   6 , Juan Jose Garcia-Garcia  3   7   8 , Pedro Brotons  1   2   3   9 , Jose Yuste  10   11 , Raquel Sá-Leão  12 , Carmen Muñoz-Almagro  1   2   3   9
Affiliations

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

Desiree Henares et al. J Clin Microbiol. .

Abstract

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.

Keywords: ONT; Pathogenwatch; WGS; in silico serotyping; pneumococci; validation.

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Conflict of interest statement

C.M.A. reports a research grant from Pfizer laboratories paid to Sant Joan de Déu foundation and related with the submitted work, as well as fees as speaker at conferences from MSD, Pfizer and Sanofi-Pasteur. J.Y. reports research grants from Pfizer and MSD unrelated to the submitted work, as well as participation in scientific advisory boards organized by Pfizer and MSD.

Figures

Fig 1
Fig 1
Workflow for pneumococcal serotyping pipelines.
See this image and copyright information in PMC

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