Spatiotemporal urban water profiling for the assessment of environmental and public exposure to antimicrobials (antibiotics, antifungals, and antivirals) in the Eerste River Catchment, South Africa

Pollution by antimicrobials and antibiotic resistance genes in East Africa: Occurrence, sources, and potential environmental implications

The escalating burden of antimicrobial pollution in East Africa poses severe threats to public health, environmental integrity, and economic stability. Environmental compartments such as soil and water serve as reservoirs for these pollutants such as antimicrobials and antibiotic resistance genes, creating selective pressure that accelerates the emergence of antimicrobial resistance (AMR). These dynamic fosters the proliferation of multidrug-resistant pathogens, or "superbugs," complicating infection management and amplifying health risks in a region already challenged by inadequate healthcare and sanitation infrastructure. Furthermore, pollution by antimicrobials and antibiotic resistance genes critically disrupts ecological processes, such as nutrient cycling and organic matter degradation, diminishing soil fertility, water quality, and agricultural productivity, thereby threatening food security and overall ecological health. Current surveillance efforts, including the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the East Africa Public Health Laboratory Networking Project (EAPHLNP), have made strides in tracking AMR trends and guiding policy decisions. However, these efforts remain insufficient to address the growing crisis. This study highlights the urgent need for integrated strategies, including stringent antibiotic usage regulations, advanced wastewater treatment technologies, and comprehensive environmental surveillance. Therefore, there is a need to address the intersections of health, agriculture, and environment, to mitigate AMR and its far-reaching consequences to ensure public health safety and sustainability.

Antimicrobials and antimicrobial resistance genes in the shadow of COVID-19 pandemic: A wastewater-based epidemiology perspective

Higher usage of antimicrobial agents in both healthcare facilities and the communities has resulted in an increased spread of resistant bacteria. However, the improved infection prevention and control practices may also contribute to decreasing antimicrobial resistance (AMR). In the present study, wastewater-based epidemiology (WBE) approach was applied to explore the link between COVID-19 and the community usage of antimicrobials, as well as the prevalence of resistance genes. Longitudinal study has been conducted to monitor the levels of 50 antimicrobial agents (AAs), 24 metabolites, 5 antibiotic resistance genes (ARGs) and class 1 integrons (intI 1) in wastewater influents in 4 towns/cities over two years (April 2020 - March 2022) in the South-West of England (a total of 1,180 samples collected with 87,320 individual AA measurements and 8,148 ARG measurements). Results suggested higher loads of AAs and ARGs in 2021-22 than 2020-21, with beta-lactams, quinolones, macrolides and most ARGs showing statistical differences. In particular, the intI 1 gene (a proxy of environmental ARG pollution) showed a significant increase after the ease of the third national lockdown in England. Positive correlations for all quantifiable parent AAs and metabolites were observed, and consumption vs direct disposal of unused AAs has been identified via WBE. This work can help establish baselines for AMR status in communities, providing community-wide surveillance and evidence for informing public health interventions. Overall, studies focused on AMR from the start of the pandemic to the present, especially in the context of environmental settings, are of great importance to further understand the long-term impact of the pandemic on AMR.

Co-selection for antibiotic resistance by environmental contaminants

The environment is increasingly recognised as a hotspot for the selection and dissemination of antibiotic resistant bacteria and antibiotic resistance genes. These can be selected for by antibiotics and non-antibiotic agents (such as metals and biocides), with the evidence to support this well established by observational and experimental studies. However, there is emerging evidence to suggest that plant protection products (such as herbicides), and non-antibiotic drugs (such as chemotherapeutic agents), can also co-select for antibiotic resistance. This review aims to provide an overview of four classes of non-antibiotic agents (metals, biocides, plant protection products, and non-antibiotic drugs) and how they may co-select for antibiotic resistance, with a particular focus on the environment. It also aims to identify key knowledge gaps that should be addressed in future work, to better understand these potential co-selective agents.

Antifungal drugs in the aquatic environment: A review on sources, occurrence, toxicity, health effects, removal strategies and future challenges

Fungal infections pose a significant global health burden, resulting in millions of severe cases and deaths annually. The escalating demand for effective antifungal treatments has led to a rise in the wholesale distribution of antifungal drugs, which consequently has led to their release into the environment, posing a threat to ecosystems and human health. This article aims to provide a comprehensive review of the presence and distribution of antifungal drugs in the environment, evaluate their potential ecological and health risks, and assess current methods for their removal. Reviewed studies from 2010 to 2023 period have revealed the widespread occurrence of 19 various antifungals in natural waters and other matrices at alarmingly high concentrations. Due to the inefficiency of conventional water treatment in removing these compounds, advanced oxidation processes, membrane filtration, and adsorption techniques have been developed as promising decontamination methods.In conclusion, this review emphasizes the urgent need for a comprehensive understanding of the presence, fate, and removal of antifungal drugs in the environment. By addressing the current knowledge gaps and exploring future prospects, this study contributes to the development of strategies for mitigating the environmental impact of antifungal drugs and protecting ecosystems and human health.

Riverine mycobiome dynamics: From South African tributaries to laboratory bioreactors

Riverine fungi have the capacity for both pathogenicity, pertinent for countries with elevated immunosuppressed individuals, and bioremediation potential. The purpose was (i) to screen for the presence of clinically relevant riverine fungi and associations with anthropogenic influence, and (ii) the acclimatisation of environmental communities toward potential bioremediation application. Communities were harvested from polluted rivers in Stellenbosch, South Africa, and mycobiomes characterised by high-throughput amplicon sequencing. The remainder of the biomass was inoculated into continuous bioreactors with filtered river water or sterile minimal medium. Seven weeks later, the mycobiomes were re-sequenced. At least nine clinically relevant species were detected, including agents of mycoses belonging to the genus Candida. The occurrence of genera that harbour opportunisticstrains was significantly higher (P = 0.04) at more polluted sites. Moreover, positive correlations occured between some genera and pollution indices, demonstrating the potential of fungi for addition to water quality indicators. Despite biomass increase, almost all pathogens were undetectable after seven weeks, demonstrating less resilience in conditions mimicking rivers. Thus, when screening riverine biomes for bioremediation potential, ambient reactors select against human pathogens. This indicates a transient introduction of allochthonous opportunistic species into rivers due to insufficient sanitation, and the potential of bioremediation strategies that selects for environmental rather than pathogenic traits.

Direct injection liquid chromatography-tandem mass spectrometry as a sensitive and high-throughput method for the quantitative surveillance of antimicrobials in wastewater

Environmental antimicrobial pollution and antimicrobial resistance pose a threat to environmental and human health. Wastewater analysis has been identified as a promising tool for antimicrobial monitoring and the back-estimation of antimicrobial consumption, but current pretreatment methods are tedious and complicated, limiting their scope for high-throughput analysis. A sensitive direct injection method for the quantification of 109 antimicrobials and their metabolites in wastewater samples was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The method was validated for both wastewater influent and effluent in terms of specificity, calibration range, matrix effect, filtration loss, accuracy, precision, limit of detection (LOD), and limit of quantification (LOQ). Most analytes achieved calibration of R2 > 0.99, and the calibration range was from 0.0002 to 150 μg L-1. Recoveries ranged consistently between ~50 % and ~100 % and losses were attributed to sample filtration. Method LOQs were determined as low as 0.0003 μg L-1, and acceptable accuracy (75 %-125 %) and precision (within 25 %) were achieved for >90 % of the analytes. The method was subsequently further assessed using wastewater of raw influent and treated effluent collected from 6 Australian wastewater treatment plants in 2021. In total, 37 analytes were detected in influent and 22 in effluent. Most of them could be quantified at concentrations ranging from 0.0053 to 160 μg L-1, with benzalkonium chloride-C12, amoxicilloic acid, and cephalexin detected at the highest concentrations. The current study provides a straightforward analytical method for antimicrobial monitoring in wastewater with a fast and simple pretreatment procedure.

Antibiotic residues of drinking-water and its human exposure risk assessment in rural Eastern China

Trace levels of antibiotics were frequently found in drinking-water, leading a growing concern that drinking-water is an important exposure source to antibiotics in humans. In this study, we investigated antibiotics in tap water and well water in two rural residential areas in Eastern China to assess the related human health exposure risks in drinking-water. Twenty-seven antibiotics were analyzed using ultra performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UPLC-MS/MS). The average daily dose (ADD) and the health risk quotient (HRQ) for exposure to antibiotics in humans were evaluated using 10000 times of Monte Carlo simulations. Ten antibiotics were detected in drinking-water samples, with the maximum concentrations of antibiotic mixture of 8.29 ng/L in tap water and 2.95 ng/L in well water, respectively. Macrolides and sulfonamides were the predominant contaminants and showed the seasonality. Azithromycin had the highest detection frequencies (79.71-100%), followed by roxithromycin (25.71-100%) and erythromycin (21.43-86.96%). The estimated ADD and HRQ for human exposure to antibiotic mixture through drinking-water was less than 0.01 μg/kg/day and 0.01, respectively, which varied over sites, water types, seasons and sex. Ingestion route was more important than dermal contact route (10-6 to 10-4 μg/kg/day magnitude vs. 10-11 to 10-8 μg/kg/day magnitude). Macrolides also contributed mainly to health exposure risks to antibiotics through drinking-water, whose HRQ accounted for 46% to 67% of the total HRQs. Although the individual antibiotic and their combined effects contributed to acceptable health risks for human, the long-term exposure patterns to low-dose antibiotics in drinking-water should not be ignored.

Quantifying community-wide antibiotic usage via urban water fingerprinting: Focus on contrasting resource settings in South Africa

There has been a significant increase in antimicrobial agents (AAs) usage, globally - however the relative consumption is unevenly distributed between nations. Inappropriate use of antibiotics can harbour inherent antimicrobial resistance (AMR); therefore, it is important to understand and monitor community-wide prescribing and consumption behaviours throughout different communities around the world. Wastewater-Based Epidemiology (WBE) is a novel tool enabling low cost and large scale studies focussed on AA usage patterns. The back-calculation of community antimicrobial intake was performed from quantities measured in municipal wastewater and informal settlement discharge in the city of Stellenbosch, utilising WBE. Seventeen antimicrobials, and their human metabolites, were evaluated, in concordance with prescription records corresponding to the catchment region. The proportional excretion, biological/chemical stability, and method recovery of each analyte were all crucial factors in the efficacy of the calculation. Mass per day measurements were normalised to the catchment area via population estimates. Municipal wastewater treatment plant population estimates were used to normalise the wastewater samples and prescription data (mg/day/1000 inhabitants). Population estimates for the informal settlements were less accurate due to a lack of reliable sources that were relevant to the sampling time period. Both mass loads and normalised loads suggested higher than average usage throughout the settlements, relative to municipal wastewater. This was seen most prominently in emtricitabine and lamivudine; but also, sulfamethoxazole, trimethoprim, sulfadiazine, clindamycin, ciprofloxacin, ofloxacin, and doxycycline. Urban water fingerprinting (UWF) data triangulation with prescription datasets showed good correlations for several antimicrobial agents (AAs) (e.g., clindamycin, clarithromycin, ofloxacin, and doxycycline). It also revealed discrepancies in usage for some compounds (e.g., tetracycline and sulfapyridine). This might be linked with a lack of pharma compliance in prescription datasets; erroneous association of prescription boundaries with the sewerage catchment; and/or uncertainties within the sewerage catchment (e.g., population estimations). The UWF tool provided a comprehensive overview of multiclass AAs usage, both prescription and over-the counter. For example, tetracycline was not reported in available prescription statistics, but was detected at an average of 18.4 mg/day/1000inh; and no antiviral prescriptions were obtained, but emtricitabine and lamivudine were quantified at 2415.4 and 144.4 mg/day/1000inh, respectively. A lack of clarity regarding prescriptions and a lack of inclusion of several critical (often over-the-counter) medications in public health databases makes WBE a useful and comprehensive epidemiology tool for tracking pharma usage within a catchment.

Occurrence of contaminants of emerging concern in the Eerste River, South Africa: Towards the optimisation of an urban water profiling approach for public- and ecological health risk characterisation

The study evaluated the presence and fate of various contaminants of emerging concern (CECs) from a South African wastewater treatment works (WWTW) and surface waters located around an urban setting. A total of 45 CECs were quantified from nine sampling locations over an 11-month period. Daily loads (g/day) of the target analytes in the WWTW showed persistence of some CECs, along with population-normalised daily loads (mg/day/1000inh) of pharmaceuticals and drugs of abuse (DOA) that were estimated for the first time in the study area. Multiple chemical markers were recorded in river water located upstream of the WWTW discharge throughout the study period, suggesting a high degree of diffuse pollution from urban communities in the study area that are not connected to sewage networks or where sanitation services are limited. The potential of using defined surface water locations to perform community-wide substance use profiling for non-sewered communities was also explored. Environmental risk characterisation for the WWTW effluent and surface waters throughout the study period provided multiple risk quotients (RQ) for the target list of CECs spanning over various sentinel trophic levels. High risk profiles (RQ > 1.0) with a frequency of exceedance (FoE) larger than 75 % were recorded for several CECs in both WWTW effluent and surface water locations that suggest potential long-term ecological health risk impacts of pollution hotspot areas in the river catchment situated around the urban area. We present challenges in surface water quality within the study area that is relatable, or may even present more challenging, in other low- or middle-income country (LMICs) settings. The study also highlighted some challenges and limitations associated with the much-needed application of wastewater-based epidemiology (WBE) intervention in non-sewered communities that can inform on public health and communal substance use profiles of the entire urban setting.

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.

Assessment of community-wide antimicrobials usage in Eastern China using wastewater-based epidemiology

Wastewater-based epidemiology (WBE) has potential to identify the epidemiological links between people, animals, and the environment, as part of antimicrobial resistance (AMR) surveillance. In this study, we investigated six wastewater treatment plants (WWTPs) serving six communities located in two regions in Eastern China: Site A in Zhejiang and site B in Jiangsu province to assess the public use of antimicrobial agents (AA). Fifty antimicrobials and 24 of their metabolites were quantified using ultraperformance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UPLC-MS/MS). Spatiotemporal trends were established for measured concentrations, daily loads, and population-normalised daily loads. Daily AA mass loads varied between 1.6 g/day and 324.6 g/day reflecting the WWTP scales, with macrolides and β-lactams showing the highest overall environmental burden at 223.7 g/day and 173.7 g/day, respectively. Emissions of antibiotic residues from manufacturing have been observed, with the peak daily load 12-fold higher than the overall load from a community serving a population of over 600,000. Community exposure levels of 225.2 ± 156.2 mg/day/1000 inhabitant and 351.9 ± 133.5 mg/day/1000 inhabitant were recorded in site A and B, respectively. Paired parent-metabolites analysis identified a large proportion (64-78%) of un-metabolised metronidazole and clindamycin at site B, indicating improper disposal of unused drugs either in the community or in livestock production. Consumption levels, calculated via WBE, suggested relatively low antimicrobial usage in Eastern China compared to other areas in China. This first application of WBE in Eastern China to assess the community-wide exposure to AAs has potential to inform regional antimicrobial stewardship.