Nasopharyngeal Staphylococcus aureus colonization among HIV-infected children in Addis Ababa, Ethiopia: Antimicrobial susceptibility pattern and association with Streptococcus pneumoniae colonization

Background Staphylococcus aureus and Streptococcus pneumoniae are common inhabitants of the nasopharynx of children. HIV-infected children have higher risk of invasive diseases caused by these pathogens. With widespread use of pneumococcal conjugate vaccines and the emergence of methicillin-resistant S aureus , the interaction between S. aureus and S. pneumoniae is of a particular significance. We sought to determine the magnitude of colonization by methicillin-sensitive and -resistant S. aureus and colonization by S. pneumoniae ; associated risk factors and antimicrobial susceptibility pattern among HIV-Infected children in Addis Ababa, Ethiopia. Method A prospective observational study was conducted in 183 HIV-infected children at ALERT hospital Addis Ababa, Ethiopia from September 2016 to August 2018. S. aureus and S. pneumoniae were identified using standard bacteriological techniques, antimicrobial susceptibility testing was performed on S. aureus and screening for methicillin resistance was carried out by amplifying the mecA gene. Risk factors were analyzed by using binary logistic regression. Results The prevalence of nasopharyngeal S. aureus , MRSA and S. pneumoniae colonization were 27.3%, 2.7% and 43.2% respectively. Multivariable analysis indicated an inverse association between S. aureus and S. pneumoniae nasopharyngeal colonization (aOR, 0.49; CI, (0.24, 0.99); p= 0 . 046 ). The highest level of resistance in both methicillin sensitive S. aureus (MSSA) and MRSA was observed against tetracycline. Conclusions We found an inverse association between S. aureus and S. pneumoniae colonization among HIV-infected children. Continued assessment of the impact of pneumococcal conjugate vaccines and anti-retroviral therapy on nasopharyngeal bacterial ecology is warranted. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by core fund from the Armauer Hansen Research Institute ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Not Applicable The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study procedures were in accordance with the Helsinki Declaration. The study protocol was approved by the AHRI/ All Africa Leprosy Rehabilitation and Training Hospital (ALERT) Ethical Review Committee (AAERC) (PO/017/2015). Official permission letter was obtained from ALERT hospital. A written informed assent and consent was obtained from study participants, and parents or guardians of children respectively, before including them in the study. The study participant's right to refuse or not give nasopharyngeal samples without affecting their routine medical services was granted. Samples were coded to keep the confidentiality of the study participants' personal information. 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. Not Applicable 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). Not Applicable I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Not Applicable All relevant data are within the manuscript and its Supporting Information files.