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

Systematic review and meta-analyses of the role of drinking water sources in the environmental dissemination of antibiotic-resistant Escherichia coli in Africa

Escherichia coli are pathogenic and antibiotic-resistant organisms that can spread to humans through water. However, there is sparse synthesised information on the dissemination of antibiotic-resistant E. coli through drinking water in Africa. This review provides an overview of the environmental spread of antimicrobial-resistant E. coli through drinking water in Africa. We performed a systematic review based on PRISMA guidelines, and 40 eligible studies from 12 countries were identified until June 2023. Four electronic databases (PubMed, Elsevier, AJOL, and DOAJ) were searched. Studies that employed phenotypic tests (n = 24/40) in identifying the bacterium outstripped those that utilised genome-based methods (n = 13). Of the 40 studies, nine and five, respectively, assessed the bacterium for antimicrobial resistance (AMR) phenotype and genotype. Multiple antibiotic resistance indices of 0.04-0.1 revealed a low level of antibiotic resistance. The detection of multidrug-resistant E. coli carrying resistance genes in certain water sources suggests that AMR-surveillance expansion should include drinking water.

Diarrhoea among Children Aged 5 Years and Microbial Drinking Water Quality Compliance: Trends Analysis Study in South Africa (2008-2018)

In developing countries such as South Africa, diarrhoeal diseases are reported to be linked to inadequate drinking water quality, sanitation, and hygiene behaviours. The consumption of microbiologically contaminated drinking water has been reported to cause diarrhoea, mortality, and morbidity in children under the age of five years. This study evaluated the microbiological pathogens detected in municipal drinking water and diarrhoea trends for children under 5 years of age in South Africa between 2008 and 2018. A trends analysis study was conducted using secondary data on diarrhoea for children under the age of five years and microbial drinking water quality compliance. A negative correlation was found between the occurrence of microbial pathogens in water, morbidity, and mortality rates of children under the age of 5 years in South Africa. As compliance status improved, the mortality rate among children under 5 years old decreased by 31% over the study period. A conclusion can thus be drawn that the microbiological pathogens detected in drinking water at levels complying with SANS 241:2015 Edition 2 standards and diarrhoea incidences were not the primary cause of the mortality of children under 5 years old in South Africa between 2008 and 2018.

Antibiotic-Resistant Escherichia coli Strains Isolated from Captive Giant Pandas: A Reservoir of Antibiotic Resistance Genes and Virulence-Associated Genes

Recent studies showed that Escherichia coli (E. coli) strains isolated from captive giant pandas have serious resistance to antibiotics and carry various antibiotic resistance genes (ARGs). ARGs or virulence-associated genes (VAGs) carried by antibiotic-resistant E. coli are considered as a potential health threat to giant pandas, humans, other animals and the environment. In this study, we screened ARGs and VAGs in 84 antibiotic-resistant E. coli strains isolated from clinically healthy captive giant pandas, identified the association between ARGs and VAGs and analyzed the phylogenetic clustering of E. coli isolates. Our results showed that the most prevalent ARG in E. coli strains isolated from giant pandas is bla_TEM (100.00%, 84/84), while the most prevalent VAG is fimC (91.67%, 77/84). There was a significant positive association among 30 pairs of ARGs, of which the strongest was observed for sul1/tetC (OR, 133.33). A significant positive association was demonstrated among 14 pairs of VAGs, and the strongest was observed for fyuA/iroN (OR, 294.40). A positive association was also observed among 45 pairs of ARGs and VAGs, of which the strongest was sul1/eaeA (OR, 23.06). The association of ARGs and mobile gene elements (MGEs) was further analyzed, and the strongest was found for flor and intI1 (OR, 79.86). The result of phylogenetic clustering showed that the most prevalent group was group B2 (67.86%, 57/84), followed by group A (16.67%, 14/84), group D (9.52%, 8/84) and group B1 (5.95%, 5/84). This study implied that antibiotic-resistant E. coli isolated from captive giant pandas is a reservoir of ARGs and VAGs, and significant associations exist among ARGs, VAGs and MGEs. Monitoring ARGs, VAGs and MGEs carried by E. coli from giant pandas is beneficial for controlling the development of antimicrobial resistance.

Barriers and facilitators to Water, Sanitation and Hygiene (WaSH) practices in Southern Africa: A scoping review

A healthy and a dignified life experience requires adequate water, sanitation, and hygiene (WaSH) coverage. However, inadequate WaSH resources remain a significant public health challenge in many communities in Southern Africa. A systematic search of peer-reviewed journal articles from 2010 –May 2022 was undertaken on Medline, PubMed, EbscoHost and Google Scholar from 2010 to May 2022 was searched using combinations of predefined search terms with Boolean operators. Eighteen peer-reviewed articles from Southern Africa satisfied the inclusion criteria for this review. The general themes that emerged for both barriers and facilitators included geographical inequalities, climate change, investment in WaSH resources, low levels of knowledge on water borne-diseases and ineffective local community engagement. Key facilitators to improved WaSH practices included improved WaSH infrastructure, effective local community engagement, increased latrine ownership by individual households and the development of social capital. Water and sanitation are critical to ensuring a healthy lifestyle. However, many people and communities in Southern Africa still lack access to safe water and improved sanitation facilities. Rural areas are the most affected by barriers to improved WaSH facilities due to lack of WaSH infrastructure compared to urban settings. Our review has shown that, the current WaSH conditions in Southern Africa do not equate to the improved WaSH standards described in SDG 6 on ensuring access to water and sanitation for all. Key barriers to improved WaSH practices identified include rurality, climate change, low investments in WaSH infrastructure, inadequate knowledge on water-borne illnesses and lack of community engagement.

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.

An assessment of groundwater quality in Zimbabwe's urban areas: case of Mkoba 19 suburb, Gweru

Groundwater quality assessment in urban areas is one of significant endeavours to ensure safety of urban residents who use groundwater especially in areas with erratic tap water supply. The study assessed groundwater quality and vulnerability of residents to water contamination-related diseases in Mkoba 19 suburb in Gweru, Zimbabwe. The research employed a mixed methods research design using both quantitative and qualitative research methods. Laboratory tests, questionnaires, interviews, focus group discussions and observations were used to solicit data. Statistical package for social scientist (SPSS) version 20.0 and Microsoft excel package were adopted for data analysis in this study. The study revealed that Mkoba 19 suburb has more wells than boreholes. Boreholes were evenly distributed over the residential area than wells which were clustered to the southern and northern edges of the suburb. All boreholes in Mkoba 19 were drilled to the depth of 40 m, but wells were dug to varying depths. The study confirmed that borehole water in Mkoba 19 was acidic and thus unsafe for human consumption. Water from wells in Mkoba 19 was confirmed positive of Escherichia coli which shows contamination from sewage and waste dump leachates. The findings of this research indicated that both borehole and well water sources in Mkoba suburb had permissible levels of dissolved oxygen and turbidity. Chi-square tests conducted confirmed that there was an association between water source depth and level of E. coli contamination in water whereas there is no association between water source depth and water pH level. The research confirmed that residents of Mkoba 19 were highly vulnerable to water borne illnesses as they were using contaminated water for domestic purposes without treating it. Basing on similar studies conducted in the past 3 years, it was shown that groundwater quality in Mkoba 19 mimics that of other countries of the developing world, especially in sub-Saharan Africa, which shows that vulnerability to ground water contamination in urban areas is an issue that requires critical attention and almost similar solution. The research recommends that Gweru City Council should upgrade its water supply system especially the pumping system to improve water supply in Mkoba suburb. To minimize water-borne disease outbreaks in the future, urban residents who rely on secondary or tertiary sources of water for domestic purposes should treat water using chlorine, water guards and other water cleansing measures on a regular basis.

Contamination of domestic groundwater systems by verotoxigenic escherichia coli (VTEC), 2003-2019: A global scoping review

Verocytotoxin-producing E. coli (VTEC) are important agents of diarrhoeal disease in humans globally. As a noted waterborne disease, emphasis has been given to the study VTEC in surface waters, readily susceptible to microbial contamination. Conversely, the status of VTEC in potable groundwater sources, generally regarded as a "safe" drinking-water supply remains largely understudied. As such, this investigation presents the first scoping review seeking to determine the global prevalence of VTEC in groundwater supply sources intended for human consumption. Twenty-three peer-reviewed studies were identified and included for data extraction. Groundwater sample and supply detection rates (estimated 0.6 and 1.3%, respectively) indicate VTEC is infrequently present in domestic groundwater sources. However, where generic (fecal indicator) E. coli are present, the VTEC to E. coli ratio was found to be 9.9%, representing a latent health concern for groundwater consumers. Geographically, extracted data indicates higher VTEC detection rates in urban (5.4%) and peri‑urban (4.9%) environments than in rural areas (0.9%); however, this finding is confounded by the predominance of research studies in lower income regions. Climate trends indicate local environments classified as 'temperate' (14/554; 2.5%) and 'cold' (8/392; 2%) accounted for a majority of supply sources with VTEC present, with similar detection rates encountered among supplies sampled during periods typically characterized by 'high' precipitation (15/649; 2.3%). Proposed prevalence figures may find application in preventive risk-based catchment and groundwater quality management including development of Quantitative Microbial Risk Assessments (QMRA). Notwithstanding, to an extent, a large geographical disparity in available investigations, lack of standardized reporting, and bias in source selection, restrict the transferability of research findings. Overall, the mechanisms responsible for VTEC transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between hydrogeological and public health research. Key recommendations and guidelines are provided for prospective studies directed at increasingly integrative and multi-disciplinary research.

Seasonality of drinking water sources and the impact of drinking water source on enteric infections among children in Limpopo, South Africa

Enteric infections and water-related illnesses are more frequent during times of relative water abundance, especially in regions that experience bimodal rainfall patterns. However, it is unclear how seasonal changes in water availability and drinking water source types affect enteric infections in young children. This study investigated seasonal shifts in primary drinking water source type and the effect of water source type on enteric pathogen prevalence in stool samples from 404 children below age 5 in rural communities in Limpopo Province, South Africa. From wet to dry season, 4.6% (n = 16) of households switched from a source with a higher risk of contamination to a source with lower risk, with the majority switching to municipal water during the dry season. In contrast, 2.6% (n = 9) of households switched from a source with a lower risk of contamination to a source with higher risk. 74.5% (n = 301) of the total households experienced interruptions in their water supply, regardless of source type. There were no significant differences in enteric pathogen prevalence between drinking water sources. Intermittent municipal water distribution and household water use and storage practices may have a larger impact on enteric infections than water source type. The limited differences in enteric pathogen prevalence in children by water source could also be due to other exposure pathways in addition to drinking water, for example through direct contact and food-borne transmission.

Mixed Aetiology of Diarrhoea in Infants Attending Clinics in the North-West Province of South Africa: Potential for Sub-Optimal Treatment

Routine diagnostic methods for the aetiologic agents of diarrhoea in most developing countries are usually not sensitive enough, leading to under-diagnosis. Thus, this study investigated possible mixed diarrhoeal aetiology by using cultures and real-time polymerase chain reactions (PCR) in children younger than four years old in the Northwest Province, South Africa. In total, 505 stool samples were collected from symptomatic and asymptomatic children who were attending three clinics and the Brits hospital in Madibeng District, between September 2016 and December 2017. Rotavirus, norovirus, Campylobacter, Arcobacter, and diarrhoeagenic Escherichia coli (DEC) were targeted. Campylobacter spp. (24.6%), Arcobacter (15.8%) and DEC (19.6%) were detected using PCR; only Campylobacter spp. (29.7%) and DEC (26.9%) were detected through the culture. Campylobacter jejuni (36%), Campylobacter coli (28%), Campylobacter upsalensis (12%), and Arcobacter butzleri (15.8%) were the only spp. of Campylobacter and Arcobacter identified. The eaeA gene (31.4%) of enteropathogenic E. coli/enterohaemorrhagic E. coli (EPEC/EHEC) was the most prevalent DEC virulence gene (VG) identified. Rotavirus and norovirus were detected at 23.4% and 20%, respectively. Mixed viral aetiology (7.3%) and the co-infection of A. butzleri and Campylobacter (49%) were recorded. A mixed bacterial-viral aetiology was observed in 0.6% of the specimens. Sensitive diagnostic procedures like PCR should be considered to provide the best treatment to children experiencing diarrhoea.

Characterization and Phylogenetic Analysis of Campylobacter Species Isolated from Paediatric Stool and Water Samples in the Northwest Province, South Africa

Antibiotic-resistant Campylobacter could adversely affect treatment outcomes, especially in children. We investigated the antibiotic susceptibility profiles, virulence potentials and genetic relatedness of Campylobacter spp. from paediatric and water samples in the North West Province, South Africa. Overall, 237 human and 20 water isolates were identified using culture and real-time polymerase chain reaction (PCR). The antibiotic susceptibility profiles were determined using the disk diffusion method. Gradient strips were used to determine the minimum inhibitory concentration of each antibiotic. Antibiotic resistance (gryA, tetO and 23S rRNA 2075G and 2074C) and virulence (cadF and ciaB) genes were also investigated using PCR. A phylogenetic tree to ascertain the clonality between water and clinical isolates was constructed using MEGA 7. Overall, 95% (water) and 64.7% (human) of the isolates were resistant to at least one antibiotic tested. The highest resistance was against clarithromycin (95%) for water and ampicillin (60.7%) for human isolates. The 23S rRNA 2075G/2074C mutation was the most expressed resistance gene. Phylogenetic reconstruction revealed eight intermixed clades within water and human Campylobacter isolates. This study suggests the possible circulation of potentially pathogenic antibiotic-resistant Campylobacter in the Northwest Province, South Africa with drinking water being a possible vector for disease transmission in this area.

The determination of E. coli levels and pathotypes in water sources around Isparta province Turkey

In this study, a total of 57 water samples were collected over different months around the Isparta region. The levels of total and fecal coliform in these water samples were determined. According to an analysis of the results, although the pollution level of these water sources are not high in terms of their total coliform counts, they cannot be used as drinking water. In the water samples taken from Andık Creek, Darı Creek  Dam, and Eğirdir Lake, fecal counts were found to be similar to each other, it is possible to use these waters after refinement. However fecal coliform levels are high in water samples taken from Bezirgan Creek, and these waters cannot be used as drinking water. After the total and fecal coliform counts were determined, the most probable colonies that can be identified to be E. coli were chosen and confirmation tests were performed. In total, 397 colonies were isolated from water samples, and 55 of those were confirmed as E. coli strains. Also, 151 strains were determined to be part of the coliform group. E. coli strains were studied with a real-time PCR to determine some virulence genes. Analysis of the results showed that 29.2% of E. coli strains contained enteropathogenic/enterohemorrhagic E. coli virulence genes, and 14.5% of the isolated E. coli strains contained verotoxigenic E. coli virulence factors. Enteroinvasive E. coli virulence genes were contained in 1.8% of the E. coli strains, and it was found that 54.5% of the isolated E. coli strains contained none of the gene regions investigated.

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.

Diarrhoeal Disease in Relation to Possible Household Risk Factors in South African Villages

Diarrhoeal disease is a significant contributor to child morbidity and mortality, particularly in the developing world. Poor sanitation, a lack of personal hygiene and inadequate water supplies are known risk factors for diarrhoeal disease. Since risk factors may vary by population or setting, we evaluated the prevalence of diarrhoeal disease at the household level using a questionnaire to better understand household-level risk factors for diarrhoea in selected rural areas in South Africa. In a sub-sample of dwellings, we measured the microbial quality of drinking water. One in five households had at least one case of diarrhoea during the previous summer. The most widespread source of drinking water was a stand-pipe (inside yard) (45%) followed by an indoor tap inside the dwelling (29%). Storage of water was common (97%) with around half of households storing water in plastic containers with an opening large enough to fit a hand through. After adjusting for confounders, the occurrence of diarrhoea was statistically significantly associated with sourcing water from an indoor tap (Adjusted Odds Ratio (AOR): 2.73, 95% CI: 2.73, 1.14–6.56) and storing cooked/perishable food in non-refrigerated conditions (AOR: 2.17, 95% CI: 2.17, 1.44–3.26). The highest total coliform counts were found in water samples from kitchen containers followed by stand-pipes. Escherichia coli were most often detected in samples from stand-pipes and kitchen containers. One in four households were at risk of exposure to contaminated drinking water, increasing the susceptibility of the study participants to episodes of diarrhoea. It is imperative that water quality meets guideline values and routine monitoring of quality of drinking water is done to minimise diarrhoea risk in relevant rural communities. The security of water supply in rural areas should be addressed as a matter of public health urgency to avoid the need for water storage.

Antibiotic-Resistant Pathogenic Escherichia Coli Isolated from Rooftop Rainwater-Harvesting Tanks in the Eastern Cape, South Africa

Although many developing countries use harvested rainwater (HRW) for drinking and other household purposes, its quality is seldom monitored. Continuous assessment of the microbial quality of HRW would ensure the safety of users of such water. The current study investigated the prevalence of pathogenic Escherichia coli strains and their antimicrobial resistance patterns in HRW tanks in the Eastern Cape, South Africa. Rainwater samples were collected weekly between June and September 2016 from 11 tanks in various areas of the province. Enumeration of E. coli was performed using the Colilert^®18/Quanti-Tray^® 2000 method. E. coli isolates were obtained and screened for their virulence potentials using polymerase chain reaction (PCR), and subsequently tested for antibiotic resistance using the disc-diffusion method against 11 antibiotics. The pathotype most detected was the neonatal meningitis E. coli (NMEC) (ibeA 28%) while pathotype enteroaggregative E. coli (EAEC) was not detected. The highest resistance of the E. coli isolates was observed against Cephalothin (76%). All tested pathotypes were susceptible to Gentamicin, and 52% demonstrated multiple-antibiotic resistance (MAR). The results of the current study are of public health concern since the use of untreated harvested rainwater for potable purposes may pose a risk of transmission of pathogenic and antimicrobial-resistant E. coli.