Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland

Populations affected by humanitarian crises likely experience high burdens of pneumococcal disease. Streptococcus pneumoniae carriage estimates are essential to understand pneumococcal transmission dynamics and the potential impact of pneumococcal conjugate vaccines (PCV). Over 100 million people are forcibly displaced worldwide, yet here we present only the second pneumococcal carriage estimates for a displaced population. In October 2019, we conducted a cross-sectional survey among internally displaced people (IDP) living in Digaale, a permanent IDP camp in Somaliland where PCV has not been implemented. We collected nasopharyngeal swab samples from 453 residents which were assessed for presence of pneumococci and serotyped using DNA microarray. We found that pneumococcal carriage prevalence was 36% (95%CI 31 – 40) in all ages, and 70% (95%CI 64 – 76) in children under 5. The three most common serotypes were vaccine serotypes 6B, 19F, and 23. We estimated that the serotypes included in the 10-valent PNEUMOSIL vaccine were carried by 41% (95%CI 33 – 49) of all pneumococcal carriers and extrapolated that they caused 52% (95%CI 35 – 72) of invasive pneumococcal disease. We found some evidence that pneumococcal carriage was associated with recent respiratory symptoms, the total number of physical contacts made, and with malnutrition in children under 5. Through linking with a nested contact survey we projected that pneumococcal exposure of children under 2 was predominantly due to contact with children aged 2-5 (39%; 95%CI 32 – 48) and 6-14 (25%; 95%CI 18 – 33). These findings suggest considerable potential for direct and indirect protection against pneumococcal disease in Digaale through PCV use in children and potentially adolescents. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by Elrha's Research for Health in Humanitarian Crises (R2HC) Programme, which aims to improve health outcomes by strengthening the evidence base for public health interventions in humanitarian crises. The R2HC programme is funded by the UK Government (DFID), the Wellcome Trust, and the UK National Institute for Health Research (NIHR). SF acknowledges a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant: 208812/Z/17/Z). In addition, RME acknowledges an NIHR (grant: NIHR200908) for the Health Protection Research Unit in Modelling and Economics at LSHTM. MCRI was supported by the Victorian Government's Operational Infrastructure Support Program. The views expressed in this publication are those of the author(s) and not necessarily those of the NIHR or the UK Department of Health and Social Care. ### 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: Research Ethical Committee of the London School of Hygiene and Tropical Medicine gave ethical approval for this work (16577). Research Ethics Committee of the Republic of Somaliland Ministry of Health Development gave ethical approval for this work (2/13075/2019). 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