Impact of seasonal variation on Escherichia coli concentrations in the riverbed sediments in the Apies River, South Africa

Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking

Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.

Selection of a diagnostic tool for microbial water quality monitoring and management of faecal contamination of water sources in rural communities

The aim of the current study was to evaluate, validate and select microbial water quality monitoring tools to establish their suitability and feasibility for use in rural communities. The monitoring of water quality was performed at three different levels: i) basic level focusing on sanitary inspection and hydrogen sulphide (H2S) test; ii) intermediate level via enumeration of faecal indicator bacteria (faecal coliforms, Escherichia coli, Enterococcus spp. and Clostridium perfringens); and iii) advanced level based on qPCR detecting host-associated genetic markers (BacHum, BacCow, Cytb, Pig-2-Bac, and BacCan) and pathogens (Vibrio cholerae, Escherichia coli O157:H7, and Shiga toxin-producing Escherichia coli). A positive correlation was recorded between sanitary risk and faecal coliforms (r = 0.613 and p < 0.002), E. coli (r = 0.589 and p < 0.003), and Enterococcus spp. (r = 0.625 and p < 0.003). The H2S test showed positive correlations with sanitary risk score (r = 0.623; p < 0.003), faecal coliforms (r = 0.809; p < 0.001), E. coli (r = 0.779; p < 0.001) and Enterococcus spp. (r = 0.799; p < 0.001). Similar correlation patterns were also found with advanced techniques used for detecting host-associated genetic markers, excepted between Clostridium perfringens, and Pig-2-Bac (pig), BacCan (dog), and V. cholerae. The H2S test and sanitary inspections are therefore suitable and cost-effective tools to capacitate rural areas at household level for the monitoring of faecal contamination and management of water sources.

Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli

Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.

Transmission of clones of carbapenem-resistant Escherichia coli between a hospital and an urban wastewater treatment plant

Carbapenem-resistant Enterobacterales (CRE) constitute an urgent threat to worldwide public health. The spread of CRE is facilitated by transmission via the environment. Wastewater treatment plants (WWTPs) are considered to be important sources of antibiotic resistance and hot spots of antibiotic-resistant bacteria (ARB) which can facilitate dissemination of antibiotic resistance genes. In this study, water samples were collected over one year from a WWTP in Jinan, Shandong province, China, from different functional sites in the wastewater treatment process. Carbapenem-resistant Escherichia coli (CREC) were isolated by selective cultivation and whole-genome sequenced to investigate the occurrence and characteristics of CREC in the WWTP. A total of 77 CREC isolates were included in the study and the detection rate of CREC in the WWTP water inlet was found to be 85%. An additional 10 CREC were isolated from a nearby teaching hospital during the sampling period and included for comparison to the environmental isolates. Susceptibility testing showed that all CREC were multidrug-resistant. 6 different carbapenem resistance genes (CRGs) were detected, including blaNDM-5 (n = 75), blaNDM-1 (n = 6), blaNDM-4 (n = 3), blaNDM-6 (n = 1), blaNDM-9 (n = 1), and blaKPC-2 (n = 4). 42 CREC isolates were whole-genome sequenced with Illumina short-read sequencing. 11 of these were also sequenced with Nanopore long-read sequencing. Plasmids carrying CRGs were found to belong to IncX3 (n = 35), IncFII (n = 12), IncFIA (n = 5), IncFIB (n = 2), IncC (n = 1), and IncP6 (n = 1). Clonal dissemination of CREC belonging to ST167, ST448, and ST746 was observed between different parts of the WWTP. Furthermore, isolates from the WWTP, including an isolate belonging to the high-risk ST167 strain, were found to be clonally related to CREC isolated at the hospital. The spread of CRGs is of considerable concern and strategies to prevent environmental dissemination of this contaminant urgently needs to be implemented.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development

Antimicrobial-resistant Escherichia coli in the aquatic environments is considered a strong indicator of sewage or animal waste contamination and antibiotic pollution. Sewer construction and wastewater treatment plant (WWTP) infrastructure may serve as concentrated point sources of contamination of antibiotic-resistant bacteria and antibiotic resistance genes. In this study, we focused on the distribution of antimicrobial-resistant E. coli in two rivers with large drainage areas and different urbanisation levels. E. coli from Kaoping River with drainage mainly from livestock farming had higher resistance to antibiotics (e.g. penicillins, tetracyclines, phenicols, aminoglycosides, and sulpha drugs) and presented more positive detection of antibiotic-resistance genes (e.g. ampC, blaTEM, tetA, and cmlA1) than that from Tamsui River. In Kaoping River with a lower percentage of sewer construction nearby (0-30%) in contrast to a higher percentage of sewer construction (55-92%) in Tamsui River, antimicrobial-resistant E. coli distribution was related to livestock farming waste. In Tamsui River, antimicrobial resistant E. coli isolates were found more frequently in the downstream drainage area of WWTPs with secondary water treatment than that of WWTPs with tertiary water treatment. The Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR showed that the fingerprinting group was significantly related to the sampling site (p < 0.01) and sampling date (p < 0.05). By utilising ERIC-PCR in conjunction with antibiotic susceptibility and antibiotic-resistance gene detection, the relationship among different strains of E. coli could be elucidated. Furthermore, we identified the presence of six extra-intestinal pathogenic E. coli isolates and antibiotic-resistant E. coli isolates near drinking water sources, posing a potential risk to public health through community transmission. In conclusion, this study identified environmental factors related to antibiotic-resistant bacteria and antibiotic-resistance gene contamination in rivers during urban development. The results facilitate the understanding of specific management of different waste streams across different urban areas. Periodic surveillance of the effects of WWTPs and livestock waste containing antibiotic-resistant bacteria and antibiotic-resistance genes on river contamination is necessary.

Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution

Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.

Molecular detection of Fasciola, Schistosoma and Paramphistomum species from freshwater snails occurring in Gauteng and Free State provinces, South Africa

Trematodiases are diseases caused by snail-borne trematode parasites that infect both animals and humans. Fascioliasis, schistosomiasis and paramphistomosis are some of these diseases and they affect millions of livestock, leading to significant economic losses. The aim of the study was to document freshwater snails occurring in selected study sites in the Free State and Gauteng provinces as well as identify and detect larval trematodes that they harbour. Samples were collected from a total of five study sites within two provinces of South Africa. Morphological features were used to identify snail species and were further confirmed genetically by polymerase chain reaction (PCR), sequencing and phylogenetic analysis. The larval trematodes were also detected by PCR, PCR-Restriction Length Fragment Polymorphism (PCR-RLFP), sequencing and phylogenetic analysis. A total of 887 freshwater snails were collected from Free State (n = 343) and Gauteng (n = 544). Five different genera of snails as well as species in the Succineidae family were documented. The snails in descending order of abundance were identified as: Physa (P.) spp. (51%), Succineidae spp. (20%), Galba (G.) truncatula (12%), Pseudosuccinea (Ps.) columella (10%), Planorbella (Pl.) duryi (6%) and Bulinus (B.) truncatus (1%). Approximately 272 DNA pools were created for genetic identification of snails and detection of trematode parasites. Schistosoma species were not detected from any of the snail species. A total prevalence of 46% was obtained for Fasciola hepatica in the identified snail species across all study sites. Overall, the highest prevalence of F. hepatica was obtained in Physa species (24%), whilst the lowest was observed in B. truncatus snails (1%). Forty three percent (43%) of the snail samples were PCR positive for Paramphistomum DNA. This is the first report of P. mexicana in South Africa. Fasciola hepatica was confirmed from all obtained snail species per study site. This is the first reported detection of F. hepatica in Pl. duryi and P. mexicana snails as well as the first confirmation of natural infection from P. acuta in South Africa.

Assessing the impact of COVID-19 restrictions on the microbial quality of an urban water catchment and the associated probability of waterborne infections

The World Health Organization reported that COVID-19 cases reached 611,421,786 globally by September 23, 2022. Six months after the first reported case, the disease had spread rapidly, reaching pandemic status, leading to numerous preventive measures to curb the spread, including a complete shutdown of many activities worldwide. Such restrictions affected services like waste management, resulting in waste accumulation in many communities and increased water pollution. Therefore, the current study investigated if lockdown impacted surface water microbial quality within an urban water catchment in South Africa. Using quantitative microbial risk assessment, the study further assessed changes in the probability of infection (Pi) with gastrointestinal illnesses from exposure to polluted water in the catchment. Escherichia coli data for 2019, 2020 and 2021 - pre-COVID, lockdown, and post-lockdown periods, respectively - were collected from the area's wastewater treatment management authorities. The Pi was determined using a beta-Poisson model. Mean overall E. coli counts ranged from 2.93 ± 0.16 to 5.30 ± 1.07 Log₁₀ MPN/100 mL. There was an overall statistically significant increase in microbial counts from 2019 to 2021. However, this difference was only accounted for between 2019 and 2021 (p = 0.008); the increase was insignificant between 2019 and 2020, and 2020 and 2021. The Pi revealed a similar trend for incidental ingestion of 100 mL and 1 mL of polluted water. No statistically significant difference was observed between the years based on multiple exposures. Although the overall microbial load and Pi estimated within the catchment exceeded the local and international limits recommended for safe use by humans, especially for drinking and recreation, these were not significantly affected by the COVID-19 restrictions. Nevertheless, these could still represent a health hazard to immunocompromised individuals using such water for personal and household hygiene, especially in informal settlements without access to water and sanitation services.

Using machine learning models to predict the effects of seasonal fluxes on Plesiomonas shigelloides population density

Seasonal variations (SVs) affect the population density (PD), fate, and fitness of pathogens in environmental water resources and the public health impacts. Therefore, this study is aimed at applying machine learning intelligence (MLI) to predict the impacts of SVs on P. shigelloides population density (PDP) in the aquatic milieu. Physicochemical events (PEs) and PDP from three rivers acquired via standard microbiological and instrumental techniques across seasons were fitted to MLI algorithms (linear regression (LR), multiple linear regression (MR), random forest (RF), gradient boosted machine (GBM), neural network (NN), K-nearest neighbour (KNN), boosted regression tree (BRT), extreme gradient boosting (XGB) regression, support vector regression (SVR), decision tree regression (DTR), M5 pruned regression (M5P), artificial neural network (ANN) regression (with one 10-node hidden layer (ANN10), two 6- and 4-node hidden layers (ANN64), and two 5- and 5-node hidden layers (ANN55)), and elastic net regression (ENR)) to assess the implications of the SVs of PEs on aquatic PDP. The results showed that SVs significantly influenced PDP and PEs in the water (p < 0.0001), exhibiting a site-specific pattern. While MLI algorithms predicted PDP with differing absolute flux magnitudes for the contributing variables, DTR predicted the highest PDP value of 1.707 log unit, followed by XGB (1.637 log unit), but XGB (mean-squared-error (MSE) = 0.0025; root-mean-squared-error (RMSE) = 0.0501; R² =0.998; medium absolute deviation (MAD) = 0.0275) outperformed other models in terms of regression metrics. Temperature and total suspended solids (TSS) ranked first and second as significant factors in predicting PDP in 53.3% (8/15) and 40% (6/15), respectively, of the models, based on the RMSE loss after permutations. Additionally, season ranked third among the 7 models, and turbidity (TBS) ranked fourth at 26.7% (4/15), as the primary significant factor for predicting PDP in the aquatic milieu. The results of this investigation demonstrated that MLI predictive modelling techniques can promisingly be exploited to complement the repetitive laboratory-based monitoring of PDP and other pathogens, especially in low-resource settings, in response to seasonal fluxes and can provide insights into the potential public health risks of emerging pathogens and TSS pollution (e.g., nanoparticles and micro- and nanoplastics) in the aquatic milieu. The model outputs provide low-cost and effective early warning information to assist watershed managers and fish farmers in making appropriate decisions about water resource protection, aquaculture management, and sustainable public health protection.

Sediment-associated heavy metal contamination and potential ecological risk along an urban river in South Africa

Sediment contamination by heavy metals poses one of the worst environmental risks to aquatic ecosystems worldwide. The study explored sediment-associated heavy metal contamination and potential ecological risk along the Molopo River in Mahikeng, South Africa. Total concentrations of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), nickel (Ni), lead (Pb), and zinc (Zn) were analysed using inductively coupled plasma mass spectrometry. Various indices were applied to assess the level of contamination and ecological risk. Most heavy metal concentrations at selected upstream and downstream sites were below average shale, except Cr, Cu, Hg, Pb, and Zn. The contamination factor (CF) indicates that the level of contamination was low (CF < 1) at most sampling sites, except Cr, Cu, Pb and Zn, which varied from moderate (1 CF < 3) to considerable (3 ≤ CF < 6) contamination. The enrichment factor (EF) shows that Cd, Cr, Cu, and Zn were moderate (2 EF < 5) to significantly enriched (5 EF < 20) at the affected sites. The results suggest anthropogenic enrichment (EF > 2) of Cd, Cr, Cu, and Zn. The threshold effect concentration and probable effect concentration sediment quality guidelines predicted that Cr, Cu, and Ni concentrations were more likely to have harmful effects on bottom-dwelling organisms. Pearson correlation and principal component analysis reveal that Cd, Cr, Cu, Ni, Pb, and Zn had a common anthropogenic source. We attribute the source to industrial and wastewater effluent, vehicle traffic, and runoff from various urban surfaces in the city. The study provides baseline data for heavy metal monitoring in the study area. Future research and monitoring should focus on heavy metals that cause concern because of their concentrations (Cr, Cu, Pb, and Zn) and potential ecological risk (Cr, Cu, and Ni).

Food animals as reservoirs and potential sources of multidrug-resistant diarrheagenic E. coli pathotypes: Focus on intensive pig farming in South Africa

Background

Diarrheagenic E. coli (DEC) strains are a major cause of diarrheal diseases in both developed and developing countries. Healthy asymptomatic animals may be reservoirs of zoonotic DEC, which may enter the food chain via the weak points in hygiene practices.

Aim

We investigated the prevalence of DEC along the pig production continuum from farm-to-fork.

Methods

A total of 417 samples were collected from specific points along the pig production system, that is, farm, transport, abattoir and food. E. coli was isolated and enumerated using Colilert. Ten isolates from each Quanti-tray were selected randomly and phenotypically identified using eosin methylene blue agar selective media. Real-time polymerase chain reaction (PCR) was used to confirm the species and to classify them into the various diarrheagenic pathotypes. Antimicrobial susceptibility was determined against a panel of 20 antibiotics using the Kirby-Bauer disk diffusion method and EUCAST guideline.

Results

The final sample size consisted of 1044 isolates, of which 45.40% (474/1044) were DEC and 73% (762/1044) were multidrug-resistant. Enteroinvasive E. coli (EIEC) was the most predominant DEC at all the sampling sites.

Conclusion

The presence of DEC in food animal production environments and food of animal origin could serve as reservoirs for transmitting these bacteria to humans, especially in occupationally exposed workers and via food. Adherence to good hygienic practices along the pig production continuum is essential for mitigating the risk of transmission and infection, and ensuring food safety.

Biological Indicators for Fecal Pollution Detection and Source Tracking: A Review

Fecal pollution, commonly detected in untreated or less treated sewage, is associated with health risks (e.g., waterborne diseases and antibiotic resistance dissemination), ecological issues (e.g., release of harmful gases in fecal sludge composting, proliferative bacterial/algal growth due to high nutrient loads) and economy losses (e.g., reduced aqua farm harvesting). Therefore, the discharge of untreated domestic sewage to the environment and its agricultural reuse are growing concerns. The goals of fecal pollution detection include fecal waste source tracking and identifying the presence of pathogens, therefore assessing potential health risks. This review summarizes available biological fecal indicators focusing on host specificity, degree of association with fecal pollution, environmental persistence, and quantification methods in fecal pollution assessment. The development of practical tools is a crucial requirement for the implementation of mitigation strategies that may help confine the types of host-specific pathogens and determine the source control point, such as sourcing fecal wastes from point sources and nonpoint sources. Emerging multidisciplinary bacterial enumeration platforms are also discussed, including individual working mechanisms, applications, advantages, and limitations.

Occurrence and distribution of fecal indicators and pathogenic bacteria in seawater and Perna perna mussel in the Gulf of Annaba (Southern Mediterranean)

The identification of fecal contamination in coastal marine ecosystems is one of the main requirements for evaluation of potential risks to human health. The objective of this study was to investigate the occurrence and distribution of fecal indicators and pathogenic bacteria in seawaters and mussels collected monthly during a period of 1 year from four different sites in Northeastern Algeria (sites S1 to S4), through biochemical and molecular analyses. Our research is the first to use molecular analysis to unambiguously identify the potentially pathogenic bacteria present in Algerian Perna perna mussels. The obtained results revealed that the levels of fecal indicator bacteria (FIB) from both P. perna and seawater samples largely exceeded the permissible limits at S2 and S3. This is mainly related to their location close to industrial and coastal activity zones, which contain a mixture of urban, agricultural, and industrial pollutants. Besides, P. perna collected from all sites were severalfold more contaminated by FIB than seawater samples, primarily during the warm season of the study period. Biochemical and molecular analyses showed that isolated bacteria from both seawater and mussels were mainly potentially pathogenic species such as E. coli, Salmonella spp., Staphylococcus spp., Klebsiella spp., Pseudomonas spp., and Proteus spp.

Environmental determinants of E. coli, link with the diarrheal diseases, and indication of vulnerability criteria in tropical West Africa (Kapore, Burkina Faso)

In 2017, diarrheal diseases were responsible for 606 024 deaths in Sub-Saharan Africa. This situation is due to domestic and recreational use of polluted surface waters, deficits in hygiene, access to healthcare and drinking water, and to weak environmental and health monitoring infrastructures. Escherichia coli (E. coli) is an indicator for the enteric pathogens that cause many diarrheal diseases. The links between E. coli, diarrheal diseases and environmental parameters have not received much attention in West Africa, and few studies have assessed health risks by taking into account hazards and socio-health vulnerabilities. This case study, carried out in Burkina Faso (Bagre Reservoir), aims at filling this knowledge gap by analyzing the environmental variables that play a role in the dynamics of E. coli, cases of diarrhea, and by identifying initial vulnerability criteria. A particular focus is given to satellite-derived parameters to assess whether remote sensing can provide a useful tool to assess the health hazard. Samples of surface water were routinely collected to measure E. coli, enterococci and suspended particulate matter (SPM) at a monitoring point (Kapore) during one year. In addition, satellite data were used to estimate precipitation, water level, Normalized Difference Vegetation Index (NDVI) and SPM. Monthly epidemiological data for cases of diarrhea from three health centers were also collected and compared with microbiological and environmental data. Finally, semi-structured interviews were carried out to document the use of water resources, contact with elements of the hydrographic network, health behavior and condition, and water and health policy and prevention, in order to identify the initial vulnerability criteria. A positive correlation between E. coli and enterococci in surface waters was found indicating that E. coli is an acceptable indicator of fecal contamination in this region. E. coli and diarrheal diseases were strongly correlated with monsoonal precipitation, in situ SPM, and Near Infra-Red (NIR) band between March and November. Partial least squares regression showed that E. coli concentration was strongly associated with precipitation, Sentinel-2 reflectance in the NIR and SPM, and that the cases of diarrhea were strongly associated with precipitation, NIR, E. coli, SPM, and to a lesser extent with NDVI. Moreover, E. coli dynamics were reproduced using satellite data alone, particularly from February to mid-December (R2 = 0.60) as were cases of diarrhea throughout the year (R2 = 0.76). This implies that satellite data could provide an important contribution to water quality monitoring. Finally, the vulnerability of the population was found to increase during the rainy season due to reduced accessibility to healthcare and drinking water sources and increased use of water of poor quality. During this period, surface water is used because it is close to habitations, easy to use and free from monetary or political constraints. This vulnerability is aggravated by marginality and particularly affects the Fulani, whose concessions are often close to surface water (river, lake) and far from health centers.

Analysis of Wastewater Reveals the Spread of Diverse Extended-Spectrum β-Lactamase-Producing E. coli Strains in uMgungundlovu District, South Africa

Wastewater treatment plants (WWTPs) are major reservoirs of antibiotic-resistant bacteria (ARB), favouring antibiotic resistance genes (ARGs) interchange among bacteria and they can provide valuable information on ARB circulating in a community. This study characterised extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from the influent and effluent of four WWTPs in uMgungundlovu District, KwaZulu-Natal, South Africa. E. coli was enumerated using the membrane filtration method and confirmed using the API 20E test and real-time polymerase chain reaction. ESBL-producers were phenotypically identified by their susceptibility to the third-generation cephalosporins using the disc diffusion and the double-disc synergy methods against cefotaxime (30 µg) with and without 10 µg clavulanic acid. Genotypic verification was by PCR of the TEM, SHV, and CTX-M genes. The clonality of isolates was assessed by ERIC-PCR. The highest E. coli count ranged between 1.1 × 10⁵ (influent) and 4.3 × 10³ CFU/mL (effluent). Eighty pure isolates were randomly selected, ten from the influent and effluent of each of the four WWTP. ESBLs were phenotypically confirmed in 49% (n = 39) of the isolates, of which 77% (n = 30) were genotypically confirmed. Seventy-three percent of the total isolates were multidrug-resistant (MDR). Only two isolates were susceptible to all antibiotics. Overall, resistance to first and second-generation cephalosporins was higher than to third and fourth generation cephalosporins. Also, 15% of the isolates were resistant to carbapenems. The CTX-M-type ESBL (67%; n = 20) was the most common ESBL antibiotic resistance gene (ARG) followed by TEM (57%; n = 17) and SHV-types (27%; n = 8). Also, a substantial number of isolates simultaneously carried all three ESBL genes. ERIC-PCR revealed a high diversity of isolates. The diversity of the isolates observed in the influent samples suggest the potential circulation of different ESBL-producing strains within the studied district, requiring a more comprehensive epidemiological study to prevent the spread of ESBL-producing bacteria within impoverished communities.

Antibiotic resistance in shellfish and major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea

Shellfish-growing areas in marine environments are affected by pollutants that mainly originate from land, including streams, domestic wastewater, and the effluents of wastewater treatment plants (WWTPs), which may function as reservoirs of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The objective of this study was to identify the occurrence and distribution of antibiotic resistance at five oyster sampling sites and 11 major inland pollution sources in the drainage basin of Kamak Bay, Republic of Korea. Culture-based methods were used to estimate the diversity and abundance of antibiotic-resistant Escherichia coli strains isolated from oysters and major inland pollution sources. The percentages of ARB and multiple antibiotic resistance index values were significantly high in discharge water from small fishing villages without WWTPs. However, the percentages of antibiotic-resistant E. coli isolates from oysters were low, as there was no impact from major inland pollutants. Fourteen ARGs were also quantified from oysters and major inland pollution sources. Although most ARGs except for quinolones were widely distributed in domestic wastewater discharge and effluent from WWTPs, macrolide resistance genes (ermB and msrA) were detected mainly from oysters in Kamak Bay. This study will aid in tracking the sources of antibiotic contamination in shellfish to determine the correlation between shellfish and inland pollution sources.

Spatial and temporal variations of faecal indicator bacteria in Lake Bunyonyi, South-Western Uganda

Background Microbial water quality serves to indicate health risks associated with the consumption of contaminated water. Nevertheless, little is known about the microbiological characteristics of water in Lake Bunyonyi. This study was therefore undertaken to examine the spatial and temporal variations of faecal indicator bacteria (FIB) in relation to physicochemical parameters in Lake Bunyonyi. Result The FIB concentration was consistently measured during sampling months and correlated with each other showing the presumed human faecal pollution in the lake. The highest concentration values for E. coli (64.7 ± 47.3 CFU/100 mL) and enterococci (24.6 ± 32.4 CFU/100 mL were obtained in the station close to the Mugyera trading centre. On a temporal basis, the maximum values were recorded during the rainy season in October 2019 (70.7 ± 56.5 CFU/100 mL for E. coli and 38.44 ± 31.8 CFU/100 mL for enterococci. FIB did not differ significantly among the study stations (p > 0.05) but showed significant temporal variations among the months (p < 0.05) with concentrations being significantly high in wet season than dry season (U = 794, p < 0.0001 for E. coli; U = 993.5, p = 0.008 for enterococci). Spearman’s rank correlation revealed that FIB concentrations were significantly positively correlated with turbidity and DO concentration levels (p < 0.05). Approximately 97.2% of the water samples had E. coli and enterococci concentrations levels below USEPA threshold for recreational waters. Likewise, 98.1 and 90.7% of samples recorded E. coli and enterococci counts exceeding the UNBS, APHA, WHO and EU threshold values for drinking water. Conclusion The FIB counts show that the Lake Bunyonyi water is bacteriologically unsuitable for drinking unless it is treated since the FIB pose health risks to consumers. Besides, the water can be used for recreational purposes.

Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert^®/Quanti-Tray 2000^® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 10⁷ MPN/g) than unamended soil (2.89 × 10⁷ MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant Enterococcus spp. in Intensive Pig Farming in South Africa

Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of Enterococcus spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. Enterococcus spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert^®/Quanti-Tray^® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% E. faecalis, 6.7% E. faecium, 2.5% E. casseliflavus, 0.4% E. gallinarum, and 11.2% other Enterococcus spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. E. faecium displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the tetM, aph(3′)-IIIa, and ermB genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was gelE. Clonality revealed that E. faecalis isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). E. faecium isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including Enterococcus spp. as an indicator in antibiotic resistance surveillance systems in food animals.

From Farm-to-Fork: E. Coli from an Intensive Pig Production System in South Africa Shows High Resistance to Critically Important Antibiotics for Human and Animal Use

Antibiotic resistance profiles of Escherichia coli were investigated in an intensive pig production system in the uMgungundlovu District, South Africa, using the 'farm-to-fork' approach. Four hundred seventeen (417) samples were collected from pig and pig products at different points (farm, transport, and abattoir). E. coli was isolated and enumerated using the Colilert^® 18/Quanti-Tray^® 2000 system. Ten isolates from each Quanti-tray were selected randomly and putatively identified on eosin methylene blue agar. Real-time PCR targeting the uidA gene was used to confirm isolates to the genus level. The Kirby-Bauer disc diffusion method was used to determine the isolates' antibiotic susceptibility profiles against 20 antibiotics. A total of 1044 confirmed E. coli isolates were obtained across the three critical points in the food chain. Resistance was observed to all the antibiotics tested with the highest and lowest rates obtained against tetracycline (88.5%) and meropenem (0.2%), respectively. Resistance was also observed to chloramphenicol (71.4%), ampicillin (71.1%), trimethoprim-sulfamethoxazole (61.3%), amoxicillin-clavulanate (43.8%), cephalexin (34.3%), azithromycin (23.9%), nalidixic acid (22.1%), cefoxitin (21.1%), ceftriaxone (18.9%), ciprofloxacin (17.3%), cefotaxime (16.9%), gentamicin (15.5%), cefepime (13.8%), ceftazidime (9.8%), amikacin (3.4%), piperacillin-tazobactam (1.2%), tigecycline (0.9%), and imipenem (0.3%). Multidrug resistance (MDR) was observed in 71.2% of the resistant isolates with an overall multiple antibiotic resistance (MAR) index of 0.25, indicating exposure to high antibiotic use environments at the farm level. A high percentage of resistance was observed to growth promoters and antibiotics approved for veterinary medicine in South Africa. Of concern was resistance to critically important antibiotics for animal and human use and the watch and reserve categories of antibiotics. This could have adverse animal and human health consequences from a food safety perspective, necessitating efficient antibiotic stewardship and guidelines to streamline antibiotic use in the food-animal production chain.

Evaluation of recreational risks due to exposure of antibiotic-resistance bacteria from environmental water: A proposed framework

This research provides a framework for the human health risk assessment due to exposure of AR (antibiotic resistance) E. coli from recreational water (swimming activity). Literature-based epidemiological studies were used for f-value formulation (i.e., AR E. coli/total number of E. coli isolates) and the theoretical calculation of AR and non-AR E. coli concentrations. Risk was estimated using calculated values by considering four different dose-response (D-R) scenarios with known characteristics due to current lack of availability of D-R for AR bacteria. f-values ranged between 0.14 and 0.59 and the order of calculated theoretical values of maximum AR E. coli are as follows: ampicillin or amoxicillin (38 CFU/dip) > co-trimoxazole (19 CFU/dip) ~ tetracycline (18 CFU/dip) > ceftriaxone or cefotaxime or ceftazidime (10 CFU/dip) ~ ciprofloxacin or ofloxacin (9 CFU/dip). The risk of infection was considerably high for theoretical calculated concentration values regardless of the chosen D-R model (annual risk of infection (95th percentile) = 1, Spearman's rank correlation coefficient = -0.06 to 0.94), under the conditions studied. Further, AR levels of human gastrointestinal-tract were determined using literature-reported data in stool samples and indicated that the resistance level was very high in healthy human (range: 3.7 × 10⁷-8.4 × 10⁷ CFU/g of wet lumen content). The maximum allowable concentration values for AR E. coli and non-ARB (0.0075 CFU/dip and 2.56 CFU/dip) were found to be smaller than the USEPA recreational water quality guidelines (≤126 CFU/100 mL), which can help the USEPA and other regulatory bodies in revisiting the current guidelines. So based on the noted results, we can conclude that the maintenance of inventory of actual measured concentration of ARB in the recreational water sites is needed to prevent unwanted complication related to the treatment of infectious sustained by resistant microbes.

Longitudinal Surveillance of Antibiotic Resistance in Escherichia coli and Enterococcus spp. from a Wastewater Treatment Plant and Its Associated Waters in KwaZulu-Natal, South Africa

We assessed the prevalence, distribution, and antibiotic resistance patterns of Escherichia coli and Enterococcus spp. isolated from raw and treated wastewater of a major wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa and the receiving river water upstream and downstream from the WWTP discharge point. Escherichia coli and enterococci were isolated and counted using the Colilert^®-18 Quanti-Tray^® 2000 and Enterolert^®-18 Quanti-Tray 2000 systems, respectively. A total of 580 quantitative PCR-confirmed E. coli and 579 enterococci were randomly chosen from positive samples and tested for in vitro antibiotic susceptibility using the disk diffusion assay against 20 and 16 antibiotics, respectively. The removal success of the bacterial species through the treatment procedure at the WWTP was expressed as log removal values (LRVs). Most E. coli were susceptible to meropenem (94.8%) and piperacillin-tazobactam (92.9%), with most Enterococcus susceptible to ampicillin (97.8%) and vancomycin (96.7%). In total, 376 (64.8%) E. coli and 468 (80.8%) Enterococcus isolates showed multidrug resistance (MDR). A total of 42.4% (246/580) E. coli and 65.1% (377/579) enterococci isolates had multiple antibiotic resistance indices >0.2. The LRV for E. coli ranged from 2.97 to 3.99, and for enterococci the range was observed from 1.83 to 3.98. A high proportion of MDR E. coli and enterococci were present at all sampled sites, indicating insufficient removal during wastewater treatment. There is a need to appraise the public health risks associated with bacterial contamination of environmental waters arising from such WWTPs to protect the health of users of the receiving water bodies.

Quantitative microbial risk assessment for waterborne pathogens in a wastewater treatment plant and its receiving surface water body

BACKGROUND

Access to safe water for drinking and domestic activities remains a challenge in emerging economies like South Africa, forcing resource-limited communities to use microbiologically polluted river water for personal and household purposes, posing a public health risk. This study quantified bacterial contamination and the potential health hazards that wastewater treatment plant (WWTP) workers and communities may face after exposure to waterborne pathogenic bacteria in a WWTP and its associated surface water, respectively.

RESULTS

Escherichia coli (Colilert®-18/ Quanti-Tray® 2000) and enterococci (Enterolert®/ Quanti-Tray® 2000) were quantified and definitively identified by real-time polymerase chain reaction targeting the uidA and tuf genes, respectively. An approximate beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with pathogenic E. coli. Mean E. coli concentration ranged from 2.60E+ 02/100 mL to 4.84E+ 06/100 mL; enterococci ranged from 2.60E+ 02/100 mL to 3.19E+ 06/100 mL across all sampled sites. Of the 580 E. coli isolates obtained from this study, 89.1% were intestinal, and 7.6% were extraintestinal pathogenic E. coli. The 579 enterococci obtained were 50.4% E. faecalis (50.4%), 31.4% E. faecium, 3.5%, E. casseliflavus and 0.7% E. gallinarum. The community health risk stemming from the use of the water for recreational and domestic purposes revealed a greater health risk (Pi) from the ingestion of 1 mL of river water from upstream (range, 55.1-92.9%) than downstream (range, 26.8-65.3%) sites. The occupational risk of infection with pathogenic E. coli for workers resulting from a once-off unintentional consumption of 1 mL of water was 0% (effluent) and 23.8% (raw influent). Multiple weekly exposures of 1 mL over a year could result in a Pi of 1.2 and 100% for the effluent and influent, respectively.

CONCLUSION

Our findings reveal that there is a potentially high risk of infection for WWTP workers and communities that use river water upstream and downstream of the investigated WWTP.

Impact of informal settlements and wastewater treatment plants on helminth egg contamination of urban rivers and risks associated with exposure

The quality of surface water could be influenced by both anthropogenic and natural factors. This study was designed to determine the impact of informal settlement and wastewater treatment plants on helminth egg contamination of urban rivers and the risks associated with everyday use. We also ascertained the accumulation of these eggs in the river sediments. The study was carried out in two rivers in the eThekwini Municipality of South Africa. Grab samples were taken at different points over a 10-month period. Ascaris spp., hookworm, Toxocara spp., Trichuris spp. and Taenia spp. were the helminth eggs detected in both the water column and sediments, with mean Ascaris spp. eggs of 0-6.3 (± 5.1)/L in the water and 0-6.8 (± 5.2)/kg in sediment samples. The helminth egg concentrations showed seasonal variation, probably due to changes in infection levels of the populations or natural factors, such as rainfall. The informal settlements had a greater impact than treated wastewater. For every 10,000 recreational users of the rivers 19 to 58 may be infected under undisturbed conditions, increasing to 29-88 individuals when the riverbed is disturbed. The risk from agricultural use of the rivers was above the tolerable risk values applicable for wastewater reuse, recommended by the World Health Organization. This calls for a re-evaluation of the policies governing surface water quality assessment, where the inclusion of helminth eggs and sediment monitoring will be critical.

Occurrence and ecological determinants of the contamination of floodplain wetlands with Klebsiella pneumoniae and pathogenic or antibiotic-resistant Escherichia coli

The survival and multiplication of human pathogenic and antibiotic-resistant bacteria in ecosystems is of increasing concern but has been little explored. Wetlands can be contaminated by water fluxes from rivers and may present environmental conditions leading to bacterial survival and multiplication. To test this hypothesis, we sampled 16 wetlands located along three rivers of the Jura Massif, France. The bacterial contamination of the wetland and river waters was measured monthly over a one-year cycle together with the water physico-chemical characteristics. We assessed the abundance of three pathogenic species: Escherichia coli,Klebsiella pneumoniaeand Pseudomonas aeruginosa. The concentrations of E. coli producing extended-spectrum β-lactamase (ESBL E. coli) or belonging to the phylogenetic group B2 (E. coli B2–more pathogenic) were also measured. We found that rivers carried total E. coli, ESBL E. coli, and K. pneumoniae to wetlands. ESBL E. coli poorly survived in wetlands, whereas total E. coli and K. pneumoniae possibly met favourable physico-chemical conditions for survival and multiplication in these habitats. K. pneumoniae peaked in summer in warm and shallow wetlands. Total E. coli and E. coli B2 potentially reached wetlands through sources other than rivers (hillslope groundwater or leaching from contaminated fields).

Surface Water and Groundwater Quality in South Africa and Mozambique—Analysis of the Most Critical Pollutants for Drinking Purposes and Challenges in Water Treatment Selection

According to a recent report by the World Health Organization (WHO), the countries which still have limited access to water for drinking purposes are mainly those in the Sub-Saharan region. In this context, the current study provides an overview of the quality of surface water and groundwater in rural and peri-urban areas of the Republic of South Africa (RSA) and Mozambique (MZ) in terms of concentrations of conventional pollutants, inorganic chemicals, microorganisms, and micropollutants. Their values were compared with the drinking water standards available for the two countries. Regarding surface water, it was found that microorganisms occur at high concentrations; nickel (RSA) and boron (MZ) are other critical parameters. Regarding groundwater, arsenic and lead (RSA) and boron, sodium, and chloride (MZ) are the main critical substances. With regard to micropollutants, their surface water concentrations are much higher than those in European rivers. The highest values were for ibuprofen, acetylsalicylic acid, clozapine, and estriol. Suitable treatment is necessary to produce safe water depending on the main critical pollutants but, at the same time, action should be taken to improve wastewater treatment in rural areas to improve and safeguard surface water bodies and groundwater which are sources for drinking needs.

Modelling the effects of physicochemical variables and anthropogenic activities as ecological drivers of Plesiomonas shigelloides distribution and freshwaters quality

Spatio-temporal distribution of pathogens in freshwater is driven by environmental variables (EVs), natural, and human-induced activities and the spread of infections and disease outbreaks are triggered significantly by these processes. The role of EVs and anthropogenic activities on the distribution of Plesiomonas shigelloides is not well understood; hence this study aimed at modelling the effects of EVs and anthropogenic gradients on the densities of Plesiomonas in freshwaters and freshwater quality. Three freshwaters were sampled from February to December 2017. The EVs and Plesiomonas densities of the freshwaters were determined using standard techniques, while partial least square path modelling and correlation analysis were performed on the data collected. Factors underpinning the quality of the freshwaters were identified through principal component analysis (PCA). Most EVs fell within the bounds of recommended permissible limits except turbidity, TSS, salinity and TDS. Results revealed a significant increase of Plesiomonas densities with an increase in the magnitude of path coefficients and intensities of anthropogenic activities along the freshwaters. The distribution of Plesiomonas correlated with temperature (r = 0.69, p < 0.01), TSS (r = 0.30, p < 0.01), TBS (r = 0.28, p < 0.01), and BOD (r = 0.39, p < 0.01). Similarly, a significant correlation existed between conductivity and TDS (r = 0.97, p < 0.01) and salinity (r = 0.99, p < 0.01). Network analysis of EVs identified three closed networks essential for freshwaters quality and Plesiomonas distribution with nodes of variables under synergistic latent influences. Overall, PCA identified four drivers of the freshwater quality and in part, Plesiomonas density; namely, nutrient loading; thermal and organic pollutions, aesthetic pollution, and pH modulators. Higher component score indicated a greater impact of nutrient loading on the freshwater quality. The study concluded that Plesiomonas distribution is largely shaped by anthropogenic gradients and EVs in rivers, and these may play a major role in its dissemination along freshwater milieus.

Where Did They Come from-Multi-Drug Resistant Pathogenic Escherichia coli in a Cemetery Environment?

Human burial in cemeteries facilitates the decomposition of corpses without posing a public health danger. However, the role of cemeteries as potential environmental reservoirs of drug-resistant pathogens has not been studied. Thus, we investigated cemeteries as potential environmental reservoirs of multi-drug resistant (MDR) pathogenic Escherichia coli. E. coli isolates were obtained from water samples (collected from surface water bodies and boreholes in three cemeteries) after isolation using the Colilert^® 18 system. Pathogenic potentials of the isolates were investigated using real-time polymerase chain reactions targeting seven virulence genes (VGs) pertaining to six E. coli pathotypes. The resistance of isolates to eight antibiotics was tested using the Kirby–Bauer disc diffusion method. The mean E. coli concentrations varied from <1 most probable number (MPN)/100 mL to 2419.6 MPN/100 mL with 48% of 100 isolates being positive for at least one of the VGs tested. Furthermore, 87% of the isolates were resistant to at least one of the antibiotics tested, while 72% of the isolates displayed multi-drug resistance. Half of the MDR isolates harboured a VG. These results suggest that cemeteries are potential reservoirs of MDR pathogenic E. coli, originating from surrounding informal settlements, which could contaminate groundwater if the cemeteries are in areas with shallow aquifers.

Comparative predictive modelling of the occurrence of faecal indicator bacteria in a drinking water source in Norway

Presently, concentrations of fecal indicator bacteria (FIB) in raw water sources are not known before water undergoes treatment, since analysis takes approximately 24h to produce results. Using data on water quality and environmental variables, models can be used to predict real time concentrations of FIB in raw water. This study evaluates the potentials of zero-inflated regression models (ZI), Random Forest regression model (RF) and adaptive neuro-fuzzy inference system (ANFIS) to predict the concentration of FIB in the raw water source of a water treatment plant in Norway. The ZI, RF and ANFIS faecal indicator bacteria predictive models were built using physico-chemical (pH, temperature, electrical conductivity, turbidity, color, and alkalinity) and catchment precipitation data from 2009 to 2015. The study revealed that pH, temperature, turbidity, and electrical conductivity in the raw water were the most significant factors associated with the concentration of FIB in the raw water source. Compared to the other models, the ANFIS model was superior (Mean Square Error=39.49, 0.35, 0.09, 0.23CFU/100ml respectively for coliform bacteria, E. coli, Intestinal enterococci and Clostridium perfringens) in predicting the variations of FIB in the raw water during model testing. However, the model was not capable of predicting low counts of FIB during both training and testing stages of the models. The ZI and RF models were more consistent when applied to testing data, and they predicted FIB concentrations that characterized the observed FIB concentrations. While these models might need further improvement, results of this study indicate that ZI and RF regression models have high prospects as tools for the real-time prediction of FIB in raw water sources for proactive microbial risk management in water treatment plants.

Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use

Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens.

Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa

To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r² values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r² values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.

Riverbed Sediments as Reservoirs of Multiple Vibrio cholerae Virulence-Associated Genes: A Potential Trigger for Cholera Outbreaks in Developing Countries

Africa remains the most cholera stricken continent in the world as many people lacking access to safe drinking water rely mostly on polluted rivers as their main water sources. However, studies in these countries investigating the presence of Vibrio cholerae in aquatic environments have paid little attention to bed sediments. Also, information on the presence of virulence-associated genes (VAGs) in environmental ctx-negative V. cholerae strains in this region is lacking. Thus, we investigated the presence of V. cholerae VAGs in water and riverbed sediment of the Apies River, South Africa. Altogether, 120 samples (60 water and 60 sediment samples) collected from ten sites on the river (January and February 2014) were analysed using PCR. Of the 120 samples, 37 sediment and 31 water samples were positive for at least one of the genes investigated. The haemolysin gene (hlyA) was the most isolated gene. The cholera toxin (ctxAB) and non-O1 heat-stable (stn/sto) genes were not detected. Genes were frequently detected at sites influenced by human activities. Thus, identification of V. cholerae VAGs in sediments suggests the possible presence of V. cholerae and identifies sediments of the Apies River as a reservoir for potentially pathogenic V. cholerae with possible public health implications.

Abundance of Pathogenic Escherichia coli Virulence-Associated Genes in Well and Borehole Water Used for Domestic Purposes in a Peri-Urban Community of South Africa

In the absence of pipe-borne water, many people in Africa, especially in rural communities, depend on alternative water sources such as wells, boreholes and rivers for household and personal hygiene. Poor maintenance and nearby pit latrines, however, lead to microbial pollution of these sources. We evaluated the abundance of Escherichia coli and the prevalence of pathogenic E. coli virulence genes in water from wells, boreholes and a river in a South African peri-urban community. Monthly samples were collected between August 2015 and November 2016. In all, 144 water samples were analysed for E. coli using the Colilert 18 system. Virulence genes (eagg, eaeA, stx1, stx2, flichH7, ST, ipaH, ibeA) were investigated using real-time polymerase chain reaction. Mean E. coli counts ranged between 0 and 443.1 Most Probable Number (MPN)/100 mL of water sample. Overall, 99.3% of samples were positive for at least one virulence gene studied, with flicH7 being the most detected gene (81/140; 57.6%) and the stx2 gene the least detected gene (8/140; 5.7%). Both intestinal and extraintestinal pathogenic E. coli genes were detected. The detection of virulence genes in these water sources suggests the presence of potentially pathogenic E. coli strains and is a public health concern.

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9-35.8 times original values. Using Shields criterion, river-flow of 0.15-0.69 m³/s could cause bed particle entrainment; while ~1.57-7.23 m³/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality.

Developing an antibacterial super-hydrophilic barrier between bacteria and membranes to mitigate the severe impacts of biofouling

Biofouling produces concentrated microbial populations with highly resistive biofilms and is considered to be a serious obstacle for a wide range of membrane technology applications. An antibacterial super-hydrophilic barrier could help to reduce biofouling by preventing direct contact between membranes and bacteria. In this study, an antibacterial super-hydrophilic barrier consisting of a layer of TiO₂ nanoparticles (NPs) was developed on polyvinylidene fluoride (PVDF)-based membrane via a facile technique. The results demonstrated that the presence of TiO₂ NPs eliminated the first step of biofouling, ie bacterial adhesion to the membrane. In addition, after bacterial deposition onto the membrane during ultrafiltration (UF), the TiO₂ NPs significantly retarded bacterial growth and reproduction (the second step of biofouling). During UF, the membrane flux decreased due to bacterial deposition, but 85% of the flux was recovered through physical cleaning using water. This study sheds light on the potential advantages of antibacterial super-hydrophilic membranes for biofouling mitigation.

Quantitative microbial risk assessment (QMRA) shows increased public health risk associated with exposure to river water under conditions of riverbed sediment resuspension

Although higher microbial concentrations have been reported in sediments than in the overlying water column, most quantitative microbial risk assessment (QMRA) studies have not clearly indicated the contribution of sediment-borne pathogens to estimated risks. Thus, the present study aimed at determining the public health risk associated with exposure to pathogenic bacteria in polluted river water under undisturbed conditions and conditions of sediment resuspension in the Apies River, Gauteng, South Africa. Microbial pathogens were isolated and identified using culture and molecular methods. The beta-Poisson dose-response model was used to estimate the probability of infection (Pi) with the various pathogens, following accidental/intentional ingestion of 1mL or 100mL (or 50mL) of untreated river water. Mean wet season Escherichia coli counts ranged between 5.8E+01 and 8.8E+04MPN/100mL (water column) and between 2.40E+03 and 1.28E+05MPN/100mL (sediments). Mean dry season E. coli counts ranged between 5.11E+00 and 3.40E+03MPN/100mL (water column) and between 5.09E+00 and 6.30E+03MPN/100mL (sediments). Overall (water and sediments) Vibrio cholerae was the most detected pathogen (58.8%) followed by Salmonella spp. (23.9%) and Shigella (10.1%). Ingestion of 1mL of river water could lead to 0%-4% and 1%-74% Pi with E. coli during the dry and wet season, respectively. During the dry season, the Pi with V. cholerae, Salmonella spp. and Shigella spp. were 0%-1.39%, 0%-4.11% and 0%-0.16% respectively, depending on volume of water ingested. The risks of infections with all microorganisms increased during the wet season. A 2-log increase in water E. coli count following sediments disturbance led to approximately 10 times higher Pi with E. coli than when sediments were undisturbed. Therefore, the use of the untreated water from the Apies River for drinking, household purposes or recreational activities poses a potential health risk to the users of the river.

Occurrence of diarrhoeagenic Escherichia coli virulence genes in water and bed sediments of a river used by communities in Gauteng, South Africa

In most developing countries, especially in Southern Africa, little is known about the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes in riverbed sediments. The present study sought to investigate the presence of DEC virulence genes in riverbed sediments of the Apies River, a river used by many communities in Gauteng, South Africa. Water and sediment samples were collected from the river between July and August 2013 (dry season) and also between January and February 2014 (wet season) following standard procedures. Isolation of E. coli was done using the Colilert®-18 Quanti-Tray® 2000 system. DNA was extracted from E. coli isolates using the InstaGene™ matrix from Bio-Rad and used as template DNA for real-time PCR. Water pH, temperature, dissolved oxygen, electrical conductivity and turbidity were measured in situ. Over 59 % of 180 samples analysed were positive for at least one of the seven DEC virulence genes investigated. The eaeA gene was the most isolated gene (29.44 %) while the ipaH gene the least isolated (8.33 %). The ipaH gene (p = 0.012) and the ST gene (stIa, p = 0.0001, and stIb, p = 0.019) were positively correlated with temperature. The detection of diarrhoeagenic E. coli virulence genes in the sediments of the Apies River shows that the sediments of this river might not only be a reservoir of faecal indicator bacteria like E. coli but also pathogenic strains of this bacterium. These organisms could represent a public health risk for poor communities relying on this water source for various purposes such as drinking and recreational use. There is therefore an urgent need to monitor these DEC pathotypes especially in areas without adequate water supplies.