Poster Presentation Lancefield International Symposium for Streptococci and Streptococcal Diseases 2025

High propensity for multidrug-resistant pneumococcal aerosol shedding among adults living with HIV in Malawi: A Microbial Diversity Analysis (#76)

Lusako L Sibale 1 , Joseph A Phiri 1 , Newton Kalata 1 , Tinashe K Nyazika 2 , Ndaona Mitole 1 , Victoria Dyster 3 , Chrispin Chaguza 4 , Stephanie W Lo 4 , Alice Kusakala 1 , Mercy Khwiya 1 , Gift Sagawa 1 , Todd D Swarthourt 5 , Neil French 6 , Ken Malisita 7 , Arox W Kamng'ona 8 , Robert S Heyderman 5 , Stephen D Bentley 4 , Brenda A Kwambana-Adams 1 , Kondwani C Jambo 1
  1. Malawi Liverpool Wellcome Programmre, BLANTYRE, Malawi
  2. Department of Biomedical Sciences and Physiology, School of Life Sciences, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
  3. Translation and Innovation Hub, Mitra Bio, London, UK
  4. Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
  5. NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, WC1E 6JF, London, UK
  6. Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, UK
  7. Lighthouse-Queens Elizabeth Hospital and Gateway Health Centre, Queens Elizabeth Hospital and Gateway Health Centre, Blantyre, Malawi
  8. School of Life Science and Allied Health Professions, Kamuzu University of Health Sciences, Kamuzu University of Health Sciences, Blantyre, Malawi

Background: Oral and nasopharyngeal colonisation in adults is essential for Streptococcus pneumoniae surveillance. However, despite high oral colonisation in adults, the microbial landscape and antimicrobial resistance (AMR) profiles of oral pneumococci remain underexplored. This is particularly relevant among adults living with HIV (ALHIV), where long-term cotrimoxazole prophylaxis exerts selective pressure on pneumococcal populations. This study employs whole plate sweep sequencing to compare pneumococcal diversity and AMR profiles between nasopharyngeal and oral pneumococci.

Methods: We analysed 29 paired nasopharyngeal swabs and aerosol (cough on agar plate) samples from 29 ALHIV on antiretroviral therapy (ART >1 year) via whole plate sweep sequencing for comparative microbial and AMR profiling. Additionally, 23,490 publicly available pneumococcal genomes from Global Pneumococcal Sequencing project were analysed for resistance associations.

Results: Aerosol exhibited greater microbial diversity, with unclassified species (median 35.4% vs 2.7%, p<0.001) and Streptococcus oralis (10.5% vs 1.5%, p=0.001). Nasopharyngeal samples were enriched for Streptococcus pneumoniae (85.4% vs 6.7%, p<0.001). Aerosol were dominated by serotypes 19C (20.5%), while the nasopharyngeal samples were dominated by serotypes 3 (14.8%). Non-matching serotypes were observed in 74% of paired samples (p=0.0035) with a trend of high multiple carriage in aerosol (57.9% vs 26.3%). Cotrimoxazole resistance was near-universal (98%), with aerosol pneumococci exhibiting higher penicillin resistance and multidrug resistance (MDR) (62% vs 31%, p=0.018). The genome-wide analysis confirmed cotrimoxazole resistance strongly correlated with penicillin resistance (OR=7.37, p<0.001) and MDR (OR=15.2, p<0.001).

Conclusion: Higher pneumococcal diversity in aerosol may reflect increased genetic exchange potential, contributing to MDR reservoir in PLHIV.