Poster Presentation Lancefield International Symposium for Streptococci and Streptococcal Diseases 2025

Genomic insights into horizontal transfer of macrolide resistance among Streptococcus pneumoniae via mobile integrative conjugative elements following azithromycin mass drug administration in Malawi (#75)

Akuzike Kalizang'oma 1 2 3 4 , Jia Mun Chan 3 , Khumbo Kalua 5 6 , Farouck Bonomali 1 , Comfort Brown 1 , Jacqueline Msefula 1 , David Chaima 2 , Lyson Samikwa 2 , Harry Meleke 2 , John D Hart 7 , Alison Craik 8 , Chrispin Chaguza 9 10 11 12 , Rory Cave 3 , Jennifer Cornick 1 13 , Brenda Kwambana 1 2 3 4 14 , Stephen D Bentley 9 , Thandie Mwalukomo 15 , Dorothee Van Breevoort 16 , Robin Bailey 7 , Ana Belén Ibarz-Pavón 1 17 , Todd D Swarthout 1 3 , Neil French 17 , Robert S Heyderman 3 4
  1. Malawi Liverpool Wellcome Programme, Blantyre, Malawi
  2. Department of Pathology, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
  3. Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
  4. NIHR Global Health Research Group of Vaccines to Prevent Respiratory Pathogens and AMR, Division of Infection and Immunity, University College London, London, United Kingdom
  5. Department of Surgery, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
  6. Blantyre Institute for Community Outreach, Blantyre, Malawi
  7. Clinical Research Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
  8. Department of Infectious Diseases, Royal Free Hospital, London, United Kingdom
  9. Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
  10. Darwin College, University of Cambridge, Silver Street, Cambridge, United Kingdom
  11. Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
  12. Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, United States
  13. Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
  14. Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
  15. Department of Medicine, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
  16. Department of Family Medicine, School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
  17. Institute of Global Health, University of Liverpool, Liverpool, United Kingdom

Background
The MORDOR azithromycin mass drug administration (MDA) cluster-randomised trial conducted in sub-Saharan Africa (2014–2018) demonstrated a 13.5% reduction in mortality in communities receiving biannual azithromycin versus placebo. However, the impact of MDA on the dissemination of macrolide resistance via mobile integrative conjugative elements (ICEs) in Streptococcus pneumoniae remains poorly understood. We investigated potential horizontal gene transfer (HGT) of ICEs among pneumococci across a previous MDA trial site.

Methods
We performed longitudinal, geographically weighted sampling of children aged 1–9 years in the Malawi MORDOR trial site at baseline (2015), 6-months post-MDA (2017), and 3.5-years post-MDA (2021). Whole-genome sequencing was conducted on 495 prospective and 392 historical pneumococcal isolates from trial clusters. Global pneumococcal sequence clusters (GPSCs), sequence types (STs), antimicrobial resistance (AMR) genes, ICEs and their sequence diversity were analysed.

Results
Complete ICEs were identified in 53% (169/318) of macrolide-resistant isolates using ICEFinder. The most prevalent ICE family was Tn2010 (~20 kb), which carries macrolide resistance genes mefA and tetracycline resistance gene tet, and was detected in 135 isolates. Despite extensive Tn2010 diversity, several sequences clustered by similarity and identical ICEs were found in pneumococcal isolates from distinct genetic backgrounds, including vaccine-type (VT) serotype 6A (GPSC180-ST9549) and non-vaccine-type (NVT) serotype 15A (GPSC5-ST172).

Conclusion
The presence of identical ICEs in strains from diverse genetic backgrounds and serotypes suggests HGT, which could limit antibiotic options in disease caused by NVTs acquiring these elements. High-resolution genomic surveillance is essential to track ICE movement across lineages to inform future vaccine interventions.