作者
Rebecca A Gladstone, Stephanie W Lo, John A Lees, Nicholas J Croucher, Andries J Van Tonder, Jukka Corander, Andrew J Page, Pekka Marttinen, Leon J Bentley, Theresa J Ochoa, Pak Leung Ho, Mignon Du Plessis, Jennifer E Cornick, Brenda Kwambana-Adams, Rachel Benisty, Susan A Nzenze, Shabir A Madhi, Paulina A Hawkins, Dean B Everett, Martin Antonio, Ron Dagan, Keith P Klugman, Anne Von Gottberg, Lesley McGee, Robert F Breiman, Stephen D Bentley
发表日期
2019/5/1
期刊
EBioMedicine
卷号
43
页码范围
338-346
出版商
Elsevier
简介
Background
Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background.
Methods
Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage.
Findings
The …
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RA Gladstone, SW Lo, JA Lees, NJ Croucher… - EBioMedicine, 2019