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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.

BackgroundStaphylococcus aureusandStreptococcus pneumoniaeare 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-resistantS aureus, the interaction between S.aureusandS. pneumoniaeis of a particular significance. We sought to determine the magnitude of colonization by methicillin-sensitive and -resistant S.aureusand colonization byS. pneumoniae; associated risk factors and antimicrobial susceptibility pattern among HIV-Infected children in Addis Ababa, Ethiopia.MethodA prospective observational study was conducted in 183 HIV-infected children at ALERT hospital Addis Ababa, Ethiopia from September 2016 to August 2018. S.aureusandS. pneumoniaewere identified using standard bacteriological techniques, antimicrobial susceptibility testing was performed on S.aureusand screening for methicillin resistance was carried out by amplifying themecAgene. Risk factors were analyzed by using binary logistic regression.ResultsThe prevalence of nasopharyngealS. aureus, MRSA andS. pneumoniaecolonization were 27.3%, 2.7% and 43.2% respectively. Multivariable analysis indicated an inverse association betweenS. aureusand S.pneumoniaenasopharyngeal colonization (aOR, 0.49; CI, (0.24, 0.99);p= 0.046). The highest level of resistance in both methicillin sensitiveS. aureus(MSSA) and MRSA was observed against tetracycline.ConclusionsWe found an inverse association betweenS. aureusandS. pneumoniaecolonization among HIV-infected children. Continued assessment of the impact of pneumococcal conjugate vaccines and anti-retroviral therapy on nasopharyngeal bacterial ecology is warranted.

The aim of this study is to evaluate the diagnostic value of different clinical samples from humans such as blood/serum, stool, and urine as compared to the routinely used nasopharyngeal swab samples for the detection of SARS-CoV2 in COVID-19 patients. We followed COVID-19 patients for three weeks and collected samples on three occasions that is, on the day of admission to the hospital (Day zero), after one week (Day-8), and after the second week (Day-15). The data shows that on the day of the admission of the patients, NPS has a 64% positivity rate, followed by stool, urine, and serum, 38%, 18%, and 17%, respectively. And we observed a nearly similar pattern of positivity rate in the subsequent week’s samples.

Scaling up of diagnostic capacity is needed to mitigate the global pandemic of SARS-CoV2. However, there are challenges including shortage of sample collection swabs and transport medium. Saliva has been recommended as a simple, low-cost, non-invasive option. However, data from different populations and settings are limited. Here, we showed that saliva could be a good alternative sample to diagnose COVID-19 patients. Pair of NPS-saliva samples was collected from 152 symptomatic; confirmed COVID-19 patients, and compared their positivity rate, viral load, and duration of viral shedding. From 152 patients, 80 (52.63%) tested positive and 72 (47.37%) were negative for SARSA-CoV2 in NPS sample. In saliva, 129 (92.14%) were tested positive and 11 (7.86%) were negative on the day of admission to hospital. The overall percent agreement of RT-PCR result of Saliva to NPS was 70% (196/280). A comparison of viral load from 72 NPS-saliva pair samples on day of admission shows saliva contains significantly higher viral load (P