Respiratory pathogens detected in specimens collected for COVID-19 surveillance in Zambia

In Zambia, knowledge on the landscape of respiratory pathogens that circulated during the coronavirus disease 2019 (COVID-19) pandemic is limited.

This study investigated respiratory pathogens that circulated in Zambia during the COVID-19 pandemic.

Nasopharyngeal specimens collected between July 2020 and July 2021 for COVID-19 testing in hospitals, ports of entry, persons seeking certificates for international travel and in communities were used.

Proportional age-stratified sampling was used to select 128 specimens. The samples were screened for 33 other respiratory pathogens using the Fast Track Diagnostics multiplex molecular assay.

Overall, 71.1% (n = 91/128) tested positive for at least one respiratory pathogen. Bacterial respiratory pathogens were more predominant (70.3%, n = 90/128) than viral (51.6%, n = 66/128). Staphylococcus aureus was the most prevalent, detected in 22.7% (n = 29/128). The prevalence of influenza was 13.3% (n = 17/128). Rhinovirus had a prevalence of 3.1% (n = 4/128), while it was 10.1% (n = 13/128) for adenovirus. Children, adolescents and the elderly accounted for most influenza-positive specimens, 76.5% (n = 13/17), while 100% (n = 3/3) of specimens positive for Moraxella catarrhalis were from children. All specimens testing positive for Haemophilus influenzae, 100% (n = 5/5) were from children and adolescents. Co-infections were detected in 57.1% (n = 52/91) of specimens testing positive for at least one pathogen.

Bacterial respiratory pathogens appeared to predominate circulation during the COVID-19 pandemic period.

Bacterial respiratory pathogens should not be neglected when implementing public health mitigation measures.