Characterisation of nasal immunity and its association with pneumococcal carriage in people Living with HIV on anti-retroviral therapy

Abstract

Background
Streptococcus pneumoniae carriage is a prerequisite for invasive pneumococcal disease (IPD) transmission, and is a reservoir for the emergence of antimicrobial resistance. People Living with HIV (PLHIV) on long-term suppressive antiretroviral therapy (ART) have higher pneumococcal colonisation prevalence than HIV-uninfected adults or PLHIV on early ART. The mechanisms behind this susceptibility remain unclear. This thesis investigated nasopharyngeal pneumococcal carriage dynamics in PLHIV on ART>1y relative to PLHIV on ART<3m and HIV-uninfected adults and evaluated the alterations in the nasal mucosa immune landscape associated with susceptibility to pneumococcal carriage.

Methods
Three groups of volunteers between the ages of 18 and 45 were recruited, comprising of 65 asymptomatic HIV-uninfected adults, 65 People Living with HIV (PLHIV) on antiretroviral therapy (ART) for less than 3 months (<3m) and 65 PLHIV on ART for greater than 1 year (>1y). Cells from the inferior turbinate of the nasal mucosa, nasal lining fluid, nasopharyngeal swabs (NP) and peripheral blood were collected from every participant in a longitudinal study that followed up the participants weekly for 17 weeks. Standard microbiological culture, multiplex immunoassays, flow cytometry-based immunophenotyping, and single cell RNA sequencing were used to identify the presence or absence of S. pneumoniae, measure cytokine in nasal lining fluid, identify cell abundance and phenotype, and to measure the transcriptional landscape, respectively.

Results
PLHIV on ART>1y had higher acquisition and slower clearance of pneumococci than HIV-uninfected adults. The high carriage prevalence was primarily driven by non-PCV-13 (NVT) serotypes. Moreover, there was incomplete reconstitution of HIV-driven nasal immunity in PLHIV on ART>1y. This was supported by persistent neutrophilic inflammation characterised by high abundance of activated neutrophils, high levels of myeloperoxidase (MPO), upregulation of reactive oxygen species (ROS) genes, interleukins, and GM-CSF signaling genes. Furthermore, neutrophils uniquely exhibited an induction of apoptotic pathways characterised by upregulation of senescence associated secretory phenotype (SASP) in PLHIV on ART>1yr.

Conclusion
The data from this thesis demonstrates that PLHIV on ART>1y have impaired bacterial clearance mechanisms in the nasal mucosa, and this likely contribute to increased susceptibility to pneumococcal carriage.

Date of Award	14 May 2025
Original language	English
Awarding Institution	Liverpool School of Tropical Medicine
Supervisor	Daniela Ferreira (Supervisor), Kondwani Jambo (Supervisor) & Benjamin Kumwenda (Supervisor)