Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data

Author:

Cheng Hsueh-Chien Raymond1ORCID,Belman Sophie21ORCID,Salje Henrik3ORCID,Dagan Ron4ORCID,Bentley Stephen D.1

Affiliation:

1. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

2. Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain

3. Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK

4. Gunzburger Chair for Study of Infectious Diseases, The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel

Abstract

Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country. This article contains data hosted by Microreact.

Funder

Bill and Melinda Gates Foundation

Wellcome Trust

Publisher

Microbiology Society

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