Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Investigating genomic changes in circulating pneumococci following pneumococcal vaccine introduction in Lao PDR (#111)

Laura K Boelsen 1 , John D Hart 1 2 , Ashleigh C Wee-Hee 1 , Leena Spry 1 , Casey L Pell 1 , Belinda D Ortika 1 , Stephanie W Lo 3 , Keoudomphone Vilivong 4 , Toukta Bounkhoun 4 , Laddaphone Bounvilay 4 , Valin Chanthalaunglath 4 , Nar Kingkeooudom 4 , Stephen D Bentley 3 , Elizabeth Ashley 4 , Mayfong Mayxay 4 5 6 , Fiona M Russell 1 2 , Catherine Satzke 1 2 7
  1. Infection and Immunity, Murdoch Children's Research Institte, Parkville, VIC, Australia
  2. Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
  3. Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
  4. Lao-Oxford-Mahosot Hospital-Welcome Trust Research Unit (LOMWRU), Mahosot Hospital, Vientiane, Lao PDR
  5. Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
  6. Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
  7. Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC, Australia

Streptococcus pneumoniae (the pneumococcus) is a significant cause of disease and death in children under five years of age globally. Effective paediatric vaccines targeting a subset of pneumococcal capsular polysaccharide types (serotypes) have been available for over two decades. Pneumococci circulating within a population significantly change after vaccine introduction with reductions in vaccine serotypes, and often replacement with non-vaccine serotypes. Vaccine serotypes frequently carry more antimicrobial resistance (AMR) and virulence determinants leading to declines in AMR and disease. However, little is known about the effects of pneumococcal vaccination on AMR and virulence in Asia, where AMR, antimicrobial use and disease burden are high. Lao PDR was among the first Asian countries to introduce pneumococcal vaccine in 2013. Here we examine changes to circulating pneumococci following vaccine introduction in Lao PDR.

Nasopharyngeal samples (n=1,631) were collected from children with pneumonia presenting to Mahosot Hospital in Vientiene, Lao PDR between 2013 and 2020. Pneumococci were isolated following molecular screening and culture on selective media. Pneumococcal isolates (n=473) were sequenced (2x150 bp) using the NovaSeq platform (Illumina). Genomes were assembled (de novo; Shovill) and annotated (Prokka). Serotype was determined using (SeroBA and PneumoCaT) and genetic lineage determined using Global Pneumococcal Sequence Cluster classification (PopPUNK with the Global Pneumococcal Sequencing project reference database (version 6)). AMR determinants were characterised using CDC-developed pipeline and virulence determinants examined using Virulence Finder Database (ABRicate).

Data analysis is in progress to thoroughly examine changes in serotype, genetic lineage, AMR determinants and virulence determinants after vaccine introduction in Lao PDR. Preliminary analyses show that vaccine serotypes had more AMR and virulence determinants compared with non-vaccine types (both p<0.05). Over time there were fewer vaccine serotypes and circulating AMR determinants (both p<0.05), but no net change in virulence determinants. These results will provide some of the first data from the region on the impacts of pneumococcal vaccine on circulating pneumococci and will help inform future vaccine strategies.