Invisible Epidemic: Metagenomic Evidence of Persistent Pathogens in South African Wastewater
1
Community Health Studies, Durban University of Technology, Durban, South Africa
2
Institute of Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
3
Sequencing Core Facility, National Institute for Communicable Diseases, Division of National Health Laboratory Service, Sandringham, South Africa
Popul. Med. 2026;8(Supplement Supplement 1):
ABSTRACT
ABSTRACT:
Wastewater-based epidemiology (WBE) has become a vital tool for monitoring community health by detecting infectious disease signals that clinical data may overlook. In South Africa, where antimicrobial resistance (AMR), tuberculosis (TB), and HIV remain major public health concerns, integrating WBE within a One Health framework can address surveillance gaps linking human, environmental, and animal health. This study aimed to investigate cross-kingdom pathogen persistence in wastewater from major South African cities to inform equitable and sustainable health strategies. Influent and effluent wastewater samples (n = 126) were collected from seven wastewater treatment plants across Durban, Johannesburg, and Cape Town between October and December. Shotgun metagenomic sequencing was used to profile bacterial, eukaryotic, and viral taxa. Data processing was performed using SqueezeMeta and Kraken2 pipelines and normalized using DESeq2 in R v4.4.3. Diversity metrics and multivariate analyses were applied to evaluate microbial composition across cities and treatment stages. Metagenomic profiling revealed high microbial diversity across sites. Escherichia coli, Klebsiella pneumoniae, and Streptococcus suis were dominant bacterial species, while Mycobacterium tuberculosis was consistently detected in both influent and effluent. All WHO-priority and ESKAPE pathogens were identified among the top 50 taxa. Among fungi, Aspergillus fumigatus and Fusarium proliferatum persisted post-treatment, whereas Pneumocystis jirovecii declined markedly. Viral reads, though limited by DNA-centric extraction, included HIV, Betapolyomavirus hominis, and Human mastadenovirus F. This tri-city cross-kingdom assessment reveals persistent pathogenic taxa across wastewater treatment systems, underscoring the limitations of conventional disinfection and the public health risks of pathogen release. Integrating metagenomic WBE into One Health surveillance frameworks could strengthen early detection of infectious diseases and AMR threats in low- and middle-income countries, advancing health equity and sustainable public health preparedness.
Wastewater-based epidemiology (WBE) has become a vital tool for monitoring community health by detecting infectious disease signals that clinical data may overlook. In South Africa, where antimicrobial resistance (AMR), tuberculosis (TB), and HIV remain major public health concerns, integrating WBE within a One Health framework can address surveillance gaps linking human, environmental, and animal health. This study aimed to investigate cross-kingdom pathogen persistence in wastewater from major South African cities to inform equitable and sustainable health strategies. Influent and effluent wastewater samples (n = 126) were collected from seven wastewater treatment plants across Durban, Johannesburg, and Cape Town between October and December. Shotgun metagenomic sequencing was used to profile bacterial, eukaryotic, and viral taxa. Data processing was performed using SqueezeMeta and Kraken2 pipelines and normalized using DESeq2 in R v4.4.3. Diversity metrics and multivariate analyses were applied to evaluate microbial composition across cities and treatment stages. Metagenomic profiling revealed high microbial diversity across sites. Escherichia coli, Klebsiella pneumoniae, and Streptococcus suis were dominant bacterial species, while Mycobacterium tuberculosis was consistently detected in both influent and effluent. All WHO-priority and ESKAPE pathogens were identified among the top 50 taxa. Among fungi, Aspergillus fumigatus and Fusarium proliferatum persisted post-treatment, whereas Pneumocystis jirovecii declined markedly. Viral reads, though limited by DNA-centric extraction, included HIV, Betapolyomavirus hominis, and Human mastadenovirus F. This tri-city cross-kingdom assessment reveals persistent pathogenic taxa across wastewater treatment systems, underscoring the limitations of conventional disinfection and the public health risks of pathogen release. Integrating metagenomic WBE into One Health surveillance frameworks could strengthen early detection of infectious diseases and AMR threats in low- and middle-income countries, advancing health equity and sustainable public health preparedness.
| eISSN: | 2654-1459 |
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