RSV and Rhinovirus asymptomatic upper airway infection increases pneumococcal carriage acquisition rates and density in adults whereas nasal inflammation is associated with bacterial shedding.

Nasopharyngeal pneumococcal colonisation is a necessary step for disease development and the primary reservoir of bacterial spread and transmission. Most epidemiological studies report the impact of co-infection with respiratory viruses upon disease rates and outcome, but their effect on pneumococcal carriage acquisition and bacterial load is scarcely described. Here, we used controlled human infection with pneumococcus to assess whether certain respiratory viruses alter susceptibility to pneumococcal colonisation and bacterial density. A total of 581 healthy adults were screened for presence of upper respiratory tract viral infection before intranasal pneumococcal challenge. We showed that RSV and Rhinovirus asymptomatic infection conferred a substantial increase in carriage rates (88% and 66% of colonised individuals in Rhinovirus and RSV infected groups, respectively, vs 49% in the virus negative group). The risk ratio of pneumococcal colonization in RSV infected group was 5.3 versus 2.03 in rhinovirus infected group (p= 0.035). Pneumococcal density was overall greater in virus positive subjects, although RSV infection alone had a major impact on pneumococcal density up to 9 days post challenge, with a substantial 2-log increase at D2 compared to virus negative group (median, 3.76 vs 1.79) (p= 0.02). We also studied rates and kinetics of bacterial shedding through the nose and oral route in a subset of challenged individuals. Nasal bacterial shedding was twice more frequent than cough-induced shedding (64% vs 32%, respectively). High levels of bacterial colonisation density and nasal inflammation was strongly correlated with increased odds of nasal shedding, as opposed to cough-shedding. Healthy adults can act as reservoir of transmission for pneumococcus, particularly when colonised with high density and have local inflammation, two key characteristics of pneumococcal colonisation in paediatrics and/or viral co-infection. Hence, vaccines targeting these respiratory pathogens have the dual potential of reducing transmission and disease burden due to their indirect benefit to off target pathogens. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The study was financially supported by the Bill and Melinda Gates Foundation (grant no. OPP1117728) and the UK Medical Research Council (grant no. M011569/1) awarded to D.M.F and S.B.G. and a Robert Austrian Research award awarded to E.M. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Studies were approved by North-West National Health Service Research Ethics Committee (14/NW/1460, 18/NW/0481, 19/NW/0586) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors