Sewage surveillance of SARS-CoV-2 at student campus residences in the Western Cape, South Africa.

The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic capacity is limited in defined communities, posing a challenge in tracking and tracing new infections. Monitoring student residences, which are considered infection hotspots, with targeted wastewater surveillance is crucial. This study evaluated the efficacy of SARS-CoV-2 targeted wastewater surveillance for outbreak mitigation at Stellenbosch University's student residences in South Africa. Using torpedo-style passive sampling devices, wastewater samples were collected biweekly from manholes at twelve Stellenbosch University Tygerberg (SUT) campus and Stellenbosch University-Main (SUM) campus student residences. The surveillance led to an early warning detection of SARS-CoV-2 presence on campus, followed by an informed management strategy leading to restriction of student activities on campus and a delay in the onset of the third wave that was experienced throughout the country. Moreover, the study highlighted the extent of possible infections at defined locations even when a low number of confirmed coronavirus disease 2019 (COVID-19) cases were reported. The study also tracked the surge of the Delta and Omicron variants in the student residences using the Thermo Fisher TaqMan® RT-qPCR genotyping assay.

Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity.

With increasing emergence of antimicrobial resistant bacteria (ARB) and the risk this poses to public health, there are growing concerns regarding water pollution contributing to the spread of antimicrobial resistance (AMR) through inadequate amenities and the rapid rate of urbanization. In this study, the impact of different anthropogenic factors on the prevalence of AMR in the urban water cycle in Stellenbosch, South Africa (SA) was examined. Carbapenem, colistin, gentamicin and sulfamethoxazole resistant Gram-negative bacteria were recovered by selectively culturing aqueous, biofilm and sediment samples from sites impacted to varying degrees by informal settlements, residential, industrial, and agricultural activities, as well as a municipal wastewater treatment works (WWTW). A metagenomic approach determined community profiles and dominant AMR genes at various sites, while carbapenem resistant colonies were characterized using whole genome sequencing (WGS). Isolates recovered from agricultural sites exhibited relatively high levels of resistance to carbapenems and colistin, whereas sites impacted by domestic run-off had a higher prevalence of resistance to gentamicin and sulfamethoxazole, corresponding to usage data in SA. Similar microbial taxa were identified in raw sewage, sites downstream of informal settlements, and industrial areas that have limited waste removal infrastructure while WWTW were seen to reduce the prevalence of ARB in treated wastewater when operating efficiently. The results indicate the multiple complex drivers underpinning environmental dissemination of AMR and suggest that WWTW assist in removing AMR from the environment, reinforcing the necessity of adequate waste removal infrastructure and antibiotic stewardship measures to mitigate AMR transmission. IMPORTANCE The results from this study are of importance as they fill a gap in the data available on environmental AMR in South Africa to date. This study was done in parallel with co-investigators focusing on the prevalence of various antimicrobials at the same sites selected in our study, verifying that the sites that are influenced by informal settlements and WWTW influent had higher concentrations of antimicrobials and antimicrobial metabolites. The various locations of the sample sites selected, the frequency of the samples collected over a year, and the different types of samples collected at each site all contribute to informing how AMR in the environment might be affected by anthropogenic activity.

Spatial and Temporal Trends of SARS-CoV-2 RNA from Wastewater Treatment Plants over 6 Weeks in Cape Town, South Africa.

Recent scientific trends have revealed that the collection and analysis of data on the occurrence and fate of SARS-CoV-2 in wastewater may serve as an early warning system for COVID-19. In South Africa, the first COVID-19 epicenter emerged in the Western Cape Province. The City of Cape Town, located in the Western Cape Province, has approximately 4 million inhabitants. This study reports on the monitoring of SARS-CoV-2 RNA in the wastewater of the City of Cape Town's wastewater treatment plants (WWTPs) during the peak of the epidemic. During this period, the highest overall median viral RNA signal was observed in week 1 (9200 RNA copies/mL) and declined to 127 copies/mL in week 6. The overall decrease in the amount of detected viral SARS-CoV-2 RNA over the 6-week study period was associated with a declining number of newly identified COVID-19 cases in the city. The SARS-CoV-2 early warning system has now been established to detect future waves of COVID-19.

A two-year study of emerging micro-pollutants and drugs of abuse in two Western Cape wastewater treatment works (South Africa).

This study evaluated the occurrence and fate of fourteen contaminants of emerging concern (CECs) at two South African wastewater treatment works (WWTW). Daily loads of the drug targets were calculated in the aqueous phase of influent- and effluent wastewater to evaluate their fate at the treatment works, along with population-normalised daily loads in raw influent wastewater to identify community-wide substance use patterns in the two study areas. Environmental risk characterisation of the CECs at WWTW effluent discharge was done using conventional risk quotient (RQ) estimations. A significant reduction of most CECs was observed at both WWTW locations, except for some that have been previously recorded to persist through various WWTW processes globally, including the illicit drug methaqualone that was reported here for the first time to evaluate its fate during wastewater treatment, substance use trends, and potential toxicological risk. Moderate-to high-RQs were estimated for several target CECs during the sampling period for both treatment facilities. The results presented here suggest the need for a multi-disciplinary approach to WWTW monitoring of CECs and highlight the need for further refinement of risk assessment approaches to mitigate recalcitrant- or pseudo-persistent CECs in wastewater discharge. Such refinement should include: (1) identifying the potential ecological risk on a wider range of sentinel indicators, (2) interaction of CECs with various biochemical pathways (including sub-lethal toxicity responses), (3) identifying the persistence and toxicological risks of breakdown products and (4) partitioning of CECs in the aqueous environment and/or bioaccumulation in freshwater biota.