Evidence of Exposure to Multiple Zoonotic Pathogens in Humans in Lusaka, Zambia: Insights from Metagenomic Next-Generation Sequencing

Zoonotic diseases present a growing public health challenge, particularly in sub-Saharan Africa (SSA) due to close interactions between humans and animals and poor diagnostic capacity. This pilot study investigated human exposure to zoonotic pathogens in Zambia, among 47 COVID-19 suspected patients from whom nasopharyngeal samples were collected between November 2020 and February 2021 at two major COVID-19 referral centers in Lusaka. Using metagenomic next-generation sequencing (mNGS), the study identified a diverse range of pathogens, including bacterial, fungal, viral, and parasitic species. The prevalence zoonotic pathogens was 57.4%. Noteworthy zoonoses included Bacillus anthracis, Sporothrix schenckii, Listeria monocytogenes, Yersinia pestis, Streptococcus suis, Vibrio parahaemolyticus, Brucella melitensis, Rickettsia prowazekii, Shewanella algae, Rickettsia japonica, Coxiella burnetii, Leptospira borgpetersenii, Erysipelothrix rhusiopathiae, Brucella abortus, Bartonella quintana, Banna virus, Vibrio alginolyticus, Bartonella clarridgeiae, Rickettsia canadensis, Leishmania braziliensis, Trypanosoma brucei, Pasteurella multocida, and Arcobacter butzleri. Despite moderate diversity in the microbial community, no significant demographic or health-related factors, including age, gender, or comorbidities such as HIV, were found to be statistically associated with zoonotic pathogen infection. The findings provide valuable data on the presence of zoonotic pathogens in humans in Zambia and highlight the need for more comprehensive research into zoonotic diseases in both clinical and non-clinical settings.