Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing

James R. Knight; Eileen M. Dunne; E. Kim Mulholland; Sudipta Saha; Catherine Satzke; Adrienn Tothpal; Daniel M. Weinberger

doi:10.1099/mgen.0.000494

Volume 7, Issue 1

Research Article

Open Access

Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing

James R. Knight¹, Eileen M. Dunne^2,3, E. Kim Mulholland^2,3,4, Sudipta Saha⁵, Catherine Satzke^2,3,6, Adrienn Tothpal^5,7 and Daniel M. Weinberger⁵
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Affiliations: ¹ Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA ² Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia ³ Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia ⁴ Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK ⁵ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA ⁶ Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia ⁷ Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
*Correspondence: James R. Knight, [email protected]
Published: 23 December 2020 https://doi.org/10.1099/mgen.0.000494

Abstract

Serotyping of Streptococcus pneumoniae is a critical tool in the surveillance of the pathogen and in the development and evaluation of vaccines. Whole-genome DNA sequencing and analysis is becoming increasingly common and is an effective method for pneumococcal serotype identification of pure isolates. However, because of the complexities of the pneumococcal capsular loci, current analysis software requires samples to be pure (or nearly pure) and only contain a single pneumococcal serotype. We introduce a new software tool called SeroCall, which can identify and quantitate the serotypes present in samples, even when several serotypes are present. The sample preparation, library preparation and sequencing follow standard laboratory protocols. The software runs as fast as or faster than existing identification tools on typical computing servers and is freely available under an open source licence at https://github.com/knightjimr/serocall. Using samples with known concentrations of different serotypes as well as blinded samples, we were able to accurately quantify the abundance of different serotypes of pneumococcus in mixed cultures, with 100 % accuracy for detecting the major serotype and up to 86 % accuracy for detecting minor serotypes. We were also able to track changes in serotype frequency over time in an experimental setting. This approach could be applied in both epidemiological field studies of pneumococcal colonization and experimental laboratory studies, and could provide a cheaper and more efficient method for serotyping than alternative approaches.

Received: 18/02/2020
Accepted: 27/11/2020
Published Online: 23/12/2020

Keyword(s): pneumococcus , serotyping and whole genome sequencing

Funding

This study was supported by the:

National Institute of Allergy and Infectious Diseases (Award R01AI123208)
- Principle Award Recipient: DanielM Weinberger

This is an open-access article distributed under the terms of the Creative Commons Attribution License.

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Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing

M Gen 7, 000494 (2021); https://doi.org/10.1099/mgen.0.000494

/content/journal/mgen/10.1099/mgen.0.000494

Volume 7, Issue 1

Research Article

Open Access

Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing

Abstract

Funding

Supplementary material 1

Supplementary material 2

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