Spatiotemporal variations in the occurrence of Campylobacter species in the Bloukrans and Swartkops rivers, Eastern Cape, South Africa

An increase in the incidence of Campylobacter species in rivers raises concerns on the safety of river water for humans who get exposed to river water. This study examines the spatiotemporal dynamics of Campylobacter species in the Bloukrans and Swartkops rivers, analysing patterns of its occurrence in relation to meteorological conditions, physicochemical parameters, seasons, and sampling sites. Physico-chemical parameters and meteorological conditions were measured during water sampling from various sites along the rivers over a year, while Polymerase Chain Reaction (PCR) was utilised to detect Campylobacter genus-specific genes and selected antibiotic-resistant genes. Campylobacter was detected in 66.67% (Bloukrans River) and 58.33% (Swartkops River). In the Bloukrans River, multi-drug resistance genes cmeA (20%), cmeB (65%), cmeC (10%), were detected while and tetO was detected at 70%. In the Swartkops River, the corresponding prevalence were 28%, 66.67%, 28.56%, and 76%. The study indicates that sampling season did not significantly impact Campylobacter prevalence. However, variation in Campylobacter occurrence exists among different sites along the rivers, reflecting the influence of site proximity to potential contamination sources. The study suggests that Campylobacter infection may be endemic in South Africa, with rivers serving as potential sources of exposure to humans, thereby contributing to the epidemiology of campylobacteriosis.

Assessment of risk of exposure to Campylobacter species and their antibiotic-resistant genes from selected rivers in the Eastern Cape, South Africa

Contaminated rivers play a critical role in the transmission of Campylobacter and antibiotic-resistant genes (ARGs) in many parts of the world. South Africa is a water-scarce country which relies on its freshwater systems such as rivers for recreation, irrigation, and domestic activities. This study assesses the potential human exposure to Campylobacter and its ARGs from rivers through the ingestion route in two South African rivers. The concentration of viable Campylobacter and ARGs in selected rivers was determined using quantitative PCR. The concentrations were then used to estimate the number of gene copies a person could ingest after swimming in the contaminated water for 1 h (intake burden). The human intake burden of Campylobacter 16 S rRNA copies per 1-h swimming event ranged from 7.1 × 105-3.7 × 106 copies/h for the Bloukrans River, and 9.9 × 101-2.3 × 105 copies/h for the Swartkops River. The intake burden of Campylobacter ARGs ranged from 1.64 × 104-5.8 × 105 copies/h for cmeB; 1.0 × 103-5.7 × 104 copies/h for tetO for the Bloukrans River, and 3.6 × 102-1.551 × 105 copies/h (cmeB) and 9.98 × 102-5.7 × 104 copies/h (tetO) for the Swartkops River. Ingestion of water from contaminated rivers during recreation, cultural, or religious activities may lead to human exposure to ARGs, posing a health risk. In many communities in the world, rivers play an important role in the social and cultural lives of people, and so it is important to monitor the quality of river water. Studies such as these will help prevent the spread of antibiotic-resistant genes and waterborne diseases caused by pathogens such as Campylobacter.

Microplastics as vectors of chemical contaminants and biological agents in freshwater ecosystems: Current knowledge status and future perspectives

Microplastics (MPs) are becoming ubiquitous, and their environmental fate is becoming an issue of concern. Our review aims to synthesize current knowledge status and provide future perspectives regarding the vector effect of MPs for chemical contaminants and biological agents. The evidence in the literature indicates that MPs are a vector for persistent organic pollutants (POPs), metals and pharmaceuticals. Concentrations of chemical contaminant in orders of six-fold higher on MPs surfaces than in the surrounding environmental waters have been reported. Chemical pollutants such as perfluoroalkyl substances (PAFSs), hexachlorocyclohexane (HCHs) and polycyclic aromatic hydrocarbons (PAHs), exhibiting polarities in the range of 3.3-9 are the commonest chemicals reported on MP surfaces. Regarding metals on MPs including chromium (Cr), lead (Pb), cobalt (Co), the presence of C-O and N-H in MPs promote a relatively high adsorption of these metals onto MP surfaces. Regarding pharmaceuticals, not much has been done, but a few studies indicate that commonly used drugs such as ibuprofen, ibuprofen, diclofenac, and naproxen have been associated with MPs. There is sufficient evidence supporting the claim that MPs can act as vectors for viruses, bacterial and antibiotic-resistant bacteria and genes, and MPs act to accelerate horizontal and vertical gene transfer. An area that deserves urgent attention is whether MPs can act as vectors for invertebrates and vertebrates, mainly non-native, invasive freshwater species. Despite the ecological significance of invasive biology, little research has been done in this regard. Overall, our review summarises the state of the current knowledge, identifies critical research gaps and provides perspectives for future research.

A review of antibiotic resistance among Campylobacter species in human, animal, and water sources in South Africa: a One Health Approach

Campylobacter species are among the aetiological agents responsible for 400-500 million human diarrhoea cases per annum. The risk of dissemination of antibiotic-resistant Campylobacter species between humans, animals, and the environment is anticipated, given its transmissibility through these sources. The objective of this paper is to present a situation analysis that reports the current patterns and determinants of Campylobacter antibiotic resistance in South Africa. This review applies the One Health (OH) Approach to systematically review and collate the current antibiotic resistance status among Campylobacter spp. in South Africa. The highest level of resistance of Campylobacter in humans is to azithromycin (69.7%), whereas the lowest level of resistance of Campylobacter is to gatifloxacin (8.3%). In animals, high resistance to common antibiotics erythromycin (95.06%), clindamycin (95.68%), doxycycline (87.65%), erythromycin (90%), tetracycline (84.3%), streptomycin (88%), and ampicillin (73%) while 100% resistance of Campylobacter from water samples to tetracycline, imipenem, is recorded. Furthermore, resistance to clarithromycin (95%), azithromycin (92%), clindamycin (84.2%), doxycycline (80%), and ciprofloxacin (77.8%) is reported among Campylobacter spp. from water samples. The genetic similarity results suggest the movement of antibiotic-resistant Campylobacter spp. between humans and the environment. More research on antibiotic resistance among Campylobacter from other sources, outside clinical isolates, is recommended.

Functional groups of Afrotropical EPT (Ephemeroptera, Plecoptera and Trichoptera) as bioindicators of semi-urban pollution in the Tsitsa River Catchment, Eastern Cape, South Africa

We examined the distribution patterns of Ephemeroptera, Plecoptera, and Trichoptera functional feeding groups (EPT FFGs) in five streams that drain semi-urban landscapes in the Tsitsa River catchment, Eastern Cape Province of South Africa. We undertook macroinvertebrate and physicochemical analysis over four seasons between 2016 and 2017 at eight sites in three land-use categories (Sites 1, 2 and 3), representing an increasing gradient of semi-urban pollution. Five EPT FFGs (shredders, grazers/scrapers, predators, collector-gatherers and collector-filterers) were fuzzy coded and analyzed using RLQ-R (environmental characteristics of samples), L (taxa distribution across samples) and Q (species traits) and fourth-corner analyses. Physicochemical variables, including phosphate-phosphorus, total inorganic nitrogen and temperature, were the most influential variables that significantly influenced the distribution patterns of EPT FFGs in the Tsitsa River. RLQ and the fourth-corner model revealed varying responses of FFGs to semi-urban pollution. Of the five FFGs, collectors were the most abundant EPT FFGs in the study area, exhibiting disparate responses to disturbances, with collector-gatherers associated with impacted sites and significantly associated with phosphate-phosphorus. On the other hand, collector-filterers decreased with increasing semi-urban disturbance and exhibited a significant negative association with phosphate-phosphorus, total inorganic nitrogen and temperature. Overall, this study provides further insights into the environmental factors that influence the distribution patterns of FFGs in Afrotropical streams and the potential use of FFGs as indicators of anthropogenic pollution in tropical streams and rivers.

Overview of African water resources contamination by contaminants of emerging concern

This review look at several classes of contaminants of emerging concern (CECs) in conventional and non-conventional water resources across the African continent's five regions. According to the review, pharmaceuticals, endocrine-disrupting chemicals, personal care products, pesticides, per- and polyfluoroalkyl compounds, and microplastics were found in conventional and non-conventional water resources. Most conventional water resources, such as rivers, streams, lakes, wells, and boreholes, are used as drinking water sources. Non-conventional water sources, such as treated wastewater (effluents), are used for domestic and agricultural purposes. However, CECs remain part of the treated wastewater, which is being discharged to surface water or used for agriculture. Thus, wastewater (effluent) is the main contributor to the pollution of other water resources. For African countries, the prevalence of rising emerging pollutants in water poses a severe environmental threat. There are different adverse effects of CECs, including the development of antibiotic-resistant bacteria, ecotoxicological effects, and several endocrine disorders. Therefore, this needs the urgent attention of the African Union, policymakers, Non-Governmental Organizations, and researchers to come together and tackle the problem.

A global agenda for advancing freshwater biodiversity research

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

The evaluation of biological indices to assess the condition of hillslope seep wetlands in the Tsitsa River Catchment, South Africa

The increase in the degradation of wetlands globally has highlighted the need to assess their ecological condition. Hillslope seep wetlands are among the least studied wetland types, yet they the most vulnerable because of their small size and steep slopes. Human pressure and the vulnerable nature of these wetlands requires wetland assessment tools to assess their condition. This study sought to evaluate the performance of the Floristic Quality Assessment Index for all species (FQAIall), the FQAI for dominant species (FQAIdom), and the Floristic Assessment Quotient for Wetlands (FAQWet) in response to the Anthropogenic Activity Index (AAI) and WET-Health in eleven hillslope seep wetlands and used these indices to assess the degree and intensity of disturbance. Vegetation samples were collected in summer 2016 and winter 2017. All assessment indices, FQAIall, FQAIdom, FAQWet and WET-Health, showed that hillslope seep wetlands were impacted by human activities. FQAIall showed the strongest response to AAI in winter, while FAQWet showed the strongest response to WET-Health. To the best of our knowledge, researchers in South Africa have used only WET-Health to assess wetland condition, and this is the first study to assess the condition of hillslope seep wetlands using a combination of indices (FQAIall, FQAIdom, FAQWet, and WET-Health). Overall, the findings of this study suggest that FQAIall and FAQWet are potentially better tools for assessing the biological condition of hillslope seep wetlands in South Africa.

Are Ephemeroptera, Plecoptera and Trichoptera traits reliable indicators of semi-urban pollution in the Tsitsa River, Eastern Cape Province of South Africa?

The taxonomy-based response pattern of macroinvertebrates to pollution gradient is well established, with tolerant taxa increasing in impacted conditions, while sensitive taxa increase with decreasing deterioration, typical of rural pollution. This study identified rural indicator and sensitive traits of Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa by examining their trait distribution pattern in relation to rural pollution. Physicochemical parameters and EPT were sampled seasonally from August 2016 to April 2017. Eight sites were selected and categorised into three site groups. Site group 1 served as the least impacted site group and Site group 2 as the moderately influenced, whereas Site group 3 was the most impacted. Seven traits were selected and categorised into 27 trait modalities. The response of EPT traits to physicochemical parameters was analysed using the simultaneous analysis of the information contained in three tables: R (environmental characteristics of samples), L (taxa distribution across samples) and Q (species traits) (RLQ) and confirmed with fourth-corner analysis. Three trait attributes, large (10-20 mm), swimming, shredding, streamlined body shape and large body size (≥ 10-20), were considered tolerant signature traits of semi-urban pollution. These trait attributes were associated with the influenced Site group 3 and indicated a significant positive affinity with at least one physicochemical indicator of increasing semi-urban pollution (NH₄-N, NO₃-N, NO₂-N, PO₄-P, EC, turbidity, temperature and pH). Conversely, small body size (< 10 mm), operculate gills, spherical body shape and a preference for sediments were correlated with the least influenced Site group 1 and were considered sensitive traits of semi-urban disturbance. Overall, this study provided critical insights into EPT responses to disturbance, revealing that semi-urban activities influenced EPT traits differently in the Tsitsa River.

Analyzing the contributions of transdisciplinary research to the global sustainability agenda in African cities

It is almost 6 years since the UN's Sustainable Development Goals (SDGs) were adopted, and countries have less than 10 years to achieve the set targets. Unlike most of the world, sub-Saharan African countries have reported only minimal progress, one that the COVID-19 pandemic has unfortunately disrupted. Transdisciplinary research (TDR) has been conceptualized as important for achieving sustainability goals such as the SDGs. In this paper we (i) analyze the contributions of the five TDR projects toward the achievements of the SDGs at the city level in Africa, and (ii) explore the interactions between the assessed SDGs across the five projects. The projects' contributions towards the achievements of the SDGs were examined in three thematic areas: (i) contexts, (ii) processes and (iii) products. The five projects were funded under the Leading Integrated Research for Agenda 2030 in Africa (LIRA) programme. The projects were being implemented in nine cities across five African countries Accra (Ghana), Kumasi (Ghana), Korhogo (Ivory Coast), Abuja Metro (Nigeria), Mbour (Senegal), Cape Town (South Africa), Nelson Mandela Bay Metro (South Africa), Grahamstown (South Africa) and Kampala (Uganda) and data were collected on each of the five projects in these cities. The contextual contributions include co-analysis and reflection on policy and institutional silos and social innovations amenable to contextual complexity. A shift in how actors perceived and conceptualized sustainability challenges and the role of the projects as transformative social agents constituted the two main process contributions. Tool development, virtual models and maps, and handbook are the product contributions by the projects. Our analysis of the SDG interactions indicated the need for cross-sectoral collaborations to ensures resource use efficiency, knowledge and experience sharing, and seamless flow of information and data to accelerate the SDG implementation.

Ephemeroptera, Plecoptera and Trichoptera (EPT) functional feeding group responses to fine grain sediment stress in a river in the Eastern Cape, South Africa

Sedimentation arising from agricultural run-offs, riparian habitat fragmentation and channel bank erosion has long been known to impair the structure and ecological functioning of stream and river ecosystems. This study examined the effects of fine sediment grain sizes on the functional feeding group structure of Ephemeroptera, Plecoptera and Trichoptera (EPT) in the Tsitsa River catchment in the Eastern Cape Province of South Africa. Fine sediments and EPT were sampled between August 2016 and April 2017 from eight selected sampling sites. The eight sites were classified into four groups in terms of fine sediments and turbidity to represent a gradient of sediment stress, with site groups 4 and 3 being less influenced and groups 2 and 1 as the highly influenced groups. EPT genera/species were assigned to five functional feeding groups (FFGs) and their responses to sediment stress assessed. The results of the study showed that of the five FFGs, four (i.e. collector-filterer, collector-gatherer, scraper/grazer and shredder) were significantly different between the four groups, separating the impacted groups from the less impacted groups. Redundancy analysis (RDA) showed that FFGs such as scraper/grazer, collector-gatherer and shredder were tolerant to fine sediment, especially during the dry season. Collector-filterers and predators were the most sensitive FFGs observed in the studied river systems. The RDA results showed that the coarser grain size fractions (very coarse and coarse silt, very fine sand and turbidity) displayed more severe negative effects on EPT FFGs when compared with the finer grain size fractions such as very fine and fine silt. The results obtained in this study provided more insights into the response patterns and functional dynamics of EPTs in the Tsitsa River systems, a knowledge that can contribute to trait-based biomonitoring in South Africa.

Using a trait-based approach for assessing the vulnerability and resilience of hillslope seep wetland vegetation cover to disturbances in the Tsitsa River catchment, Eastern Cape, South Africa

Hill slope seep wetlands are ecologically and economically important ecosystems as they supply a variety of ecosystem services to society. In South Africa, livestock grazing is recognized as one of the most important disturbance factors changing the structure and function of hill slope seep wetlands. This study sought to investigate the potential effect of livestock grazing on the resilience and vulnerability of hillslope seep wetland vegetation cover using a trait-based approach (TBA). Changes in vegetation cover were used as a surrogate for indicating grazing intensity. The degree of human disturbances was assessed using the Anthropogenic Activity Index. A TBA was developed using seven plant traits, resolved into 27 trait attributes. Based on the developed approach, plant species were grouped into vulnerable and resilient groups in relation to grazing pressure. It was then predicted that species belonging to the vulnerable group would be less dominant at the highly disturbed sites, as well as in the winter season when grazing pressure is at its peak. The approach developed enabled accurate predictions of the responses of hillslope plant species to grazing pressure seasonally, but spatially, only for the summer season. The predicted responses during the winter season across sites did not match the observed results, which could be attributed to the difficulty in species identification and accurate estimation of vegetation cover during winter. Overall, the approach developed here provides a general framework for applying the TBA and can thus be tested and applied elsewhere.

Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes

Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.

Evaluating the responses of taxa in the orders Ephemeroptera, Plecoptera and Trichoptera (EPT) to sediment stress in the Tsitsa River and its tributaries, Eastern Cape, South Africa

Excessive delivery of fine sediment has been implicated as the main water quality stressor in the Tsitsa River catchment. This study evaluates the responses of the taxa Ephemeroptera, Plecoptera and Trichoptera (EPT) to suspended sediment and grain size distribution in eight selected study sites in the Tsitsa River catchment. The sampling of macroinvertebrates took place seasonally from August 2016 to April 2017 and EPT identified to either genus or species level. To avoid site redundancy, the sites were clustered into four groups, with groups 1 and 2 being more impacted when compared to groups 3 and 4. The results of the sediment grain size analysis revealed that sediment grain size distribution ranged from 0.121 to 5.61 μm; percent clay and percent silt were the most dominant sediment fractions across all groups. Among the EPT metrics examined, Shannon index, Simpson's index, evenness, Ephemeroptera abundance, EPT abundance and Trichoptera abundance were sensitive, differentiating between sediment groups 3 and 4 (less impacted groups) from 1 and 2 (highly impacted groups). Site groups 3 and 4 supported more EPT species, in terms of the number of individuals and diversity. Species such as Caenis sp., Pseudocloeon glaucum, Oligoneuropsis lawrencei and Baetis sp. were considered sediment-tolerant, displaying strong positive association with influenced groups. Taxa such as Hydropsyche sp., Pseudocloeon sp., Cheumatopsyche sp. and Afronurus sp. were considered sediment-sensitive. Overall, the present study revealed that genera/species within the order EPT were differentially sensitive to fine sediment stress and grain sizes, proving to be useful bioindicators.

Development of macroinvertebrate multimetric index for ecological evaluation of a river in North Central Nigeria

A macroinvertebrate-based multimetric index was developed for River Chanchaga, North Central Nigeria. Macroinvertebrates and physicochemical variables were sampled seasonally between March 2017 and February 2018 from four stations: station 1 (least impacted control station) and three downstream stations 2, 3 and 4. A total of 29 macroinvertebrate metrics in four categories, richness, abundance, composition and diversity, were evaluated for their potential to discriminate between the stations, seasonal stability and redundancy. Of the 29 metrics, only 13 fulfilled all criteria and were then integrated into the final Chanchaga multimeric index (MMIchanchaga). Application of the newly developed multimetric index revealed that water quality at stations 2 and 3 was fair and that of station 4 was poor. Water quality deteriorated slightly during the rainy season compared with the dry season. In terms of the individual component metrics, EPT richness, EPT (%) and Shannon diversity were highly sensitive to water quality impairment. The Bray-Curtis similarity measure revealed that stations 2 and 3 were more similar compared with the similarity between other stations. Overall, the newly developed multimetric index proved useful and represents the first important step in such index development in Nigeria.