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The Wonderfonteinspruit, South Africa, is highly impacted by a century of gold mining activities. The aim of this study was to investigate the physico-chemical properties of the Wonderfonteinspruit and the receiving Mooi River system, the levels of antimicrobial (metals and antibiotics) resistance characteristics and heterotrophic bacteria levels in these water systems. Various physico-chemical parameters were determined. R2A agar and R2A agar supplemented with antimicrobials were used to enumerate heterotrophic bacteria. Morphologically distinct antimicrobial-resistant isolates were purified and screened for antibiotic susceptibility by a disc diffusion method. Selected isolates were identified, and minimum inhibitory concentration ranges determined. Among the antimicrobial resistant isolates, 87% were resistant to at least one antibiotic. Of these, almost 50% were resistant to more than 3 antibiotic classes. A large proportion was resistant to all 7 antibiotics tested. Phyla detected were Proteobacteria, Firmicutes and Bacteriodetes. High MIC levels for metals and antibiotics were detected among all the genera. Results demonstrate potential impacts of physico-chemical properties on levels of antimicrobial-resistant bacteria. Metal-resistant bacteria were also resistant to multiple antibiotics, suggesting that metal pollution from mining may be responsible for co-selection and maintenance of antibiotic-resistant bacteria in this aquatic system.

Draft genomes of multidrug-resistant Shiga toxin-producing Escherichia coli (STEC) strains IPK9(1) and IKS1(2), which were isolated from ready-to-eat foods (kokoro and shawarma) sold in Lagos, Nigeria, are reported. The genomes possessed genetic determinants for virulence and the antibiotic resistance gene for macrolide-associated resistance mdf(A) . Ready-to-eat foods increase public health threats in Nigeria.

Here, we report high-quality annotated draft genomes of eight coagulase-negative staphylococci (CoNS) isolates obtained from South Africa and Nigeria. We explored the prevalence of antibiotic resistance and virulence genes, their association with mobile genetic elements. The pan-genomic analysis highlighted the environmentally driven heterogeneity of the isolates. Isolates from Nigeria had at least one gene for cadmium resistance/tolerance, these genes were not detected in isolates from South Africa. In contrast, isolates from South Africa had a tetM gene, which was not detected among the isolates from Nigeria. The observed genomic heterogeneity correlates with anthropogenic activities in the area where the isolates were collected. Moreover, the isolates used in this study possess an open pan-genome, which could easily explain the environmentally driven heterogeneity.

There has been a rising interest in the levels, diversity and potential impacts of yeasts in aquatic environments. Some of the species isolated from such niches are known pathogens or have pathogenic and antifungal resistance features. This deems it necessary to understand the characteristics and potential health implications of such environmental yeasts species. Studies on these subjects are limited. Most studies on aquatic yeasts have linked them to water pollution. However, the current gold standards to determine microbial pollution of water use bacteria as the main indicator organisms. Including yeasts in water quality standards may provide a different dimension on the quality of water when determining its fit-for-use properties. Pathogenic yeasts cause superficial infections or life-threatening infections, especially in immunocompromised people. Some of the yeast species isolated in recent studies were resistant to commonly used antifungal agents of clinical and veterinary relevance. With the high prevalence rate of HIV in sub-Saharan Africa, particularly in South Africa, antifungal resistance is a public concern as it poses serious medical and economic challenges. Most available studies are concerned with clinical environments only. There is, thus, a need to review the literature that also focuses on aquatic environments.This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.

Microplastics pollution in marine environments is concerning. Microplastics persist and accumulate in various sections of the ocean where they present opportunity for micropollutant accumulation and microbial colonisation. Even though biofilm formation on plastics was first reported in the 1970's, it is only in recent years were plastic associated biofilms have gained research attention. Plastic surfaces pose a problem as they are a niche ready for colonisation by diverse biofilm assemblages, composed of specific bacterial communities and putative pathogens prone to acquiring ARGs and resistance in the biofilm. However, the nature of antibiotic resistance on aquatic plastic debris is not yet fully understood and remains a concern. Given the inevitable increase of plastic production and waste generation, microplastics released into the environment may prove to be problematic. This review explores microplastic waste in the ocean and possible concerns that may arise from the presence of microplastics in conjunction with favourable conditions for the development and dispersal of antibiotic resistance in the ocean and food web.

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

Multi-drug resistance traits of Staphylococcus species especially methicillin-resistant Staphylococcus aureus (MRSA) in the clinical settings are well established. Of environmental concern is hospital effluents discharging into wastewaters. This article investigated the prevalence and detection of antibiotic resistance genes in Staphylococcus species from clinical and environmental sources in Ile-Ife, Nigeria. Standard culture-based and molecular protocols were used. Seventy-six (27 clinical, 14 hospital effluent and 35 environmental) Staphylococcus isolates were recovered: 56.58% were coagulase-negative and 43.42% coagulase-positive (S. aureus). For the clinical isolates, 10, 6, 4, 4 and 1 were isolated from urine, skin, wounds, blood and pus, respectively. Isolates were resistant to methicillin and amoxycillin (91.7%), cloxacillin (88.0%), ciprofloxacin (84.0%), ofloxacin (83.3%), azithromycin (78.0%), ceftazidime (76.0%), gentamycin (75.0%), cefuroxime (75.0%) and erythromycin (72.0%). Nearly, all isolates (90.8%) had multiple antibiotic resistance (MAR) index >0.2. Overall MAR indices for Staphylococcus species isolated from the clinical, hospital effluent and environmental wastewaters were relatively similar (0.482; 0.500; 0.435). mecA, nuc and luk-pvl genes were detected in S. aureus, while mecA was detected in S. arlettae, S. sciuri, S. cohnii, S. epidermidis and S. saprophyticus. This study informs on the potential contamination of environmental waters downstream from hospitals and possible impacts that this could have on human and animal health.

Exposure to antibiotics, biocides, chemical preservatives, and heavy metals in different settings such as wastewater treatment plants (WWTPs) may apply selective pressure resulting in the enrichment of multiple resistant, co- and cross-resistant strains of bacteria. The purpose of this study was to identify and characterize potentially pathogenic triclosan (TCS) - and/or, chloroxylenol (PCMX) tolerant bacteria from sewage and river water in the North-West, Potchefstroom, South Africa. Several potential pathogens were identified, with Aeromonas isolates being most abundant. Clonal relationships between Aeromonas isolates found at various sampling points were elucidated using ERIC-PCR. Selected isolates were characterized for their minimum inhibitory concentrations against the biocides, as well as antibiotic resistance profiles, followed by an evaluation of synergistic and antagonistic interactions between various antimicrobials. Isolates were also screened for the presence of extracellular enzymes associated with virulence. High-performance liquid chromatography revealed the presence of both biocides in the wastewater, but fingerprinting methods did not reveal whether the WWTP is the source from which these organisms enter the environment. Isolates exhibited various levels of resistance to antimicrobials as well as several occurrences of synergy and antagonisms between the biocides and select antibiotics. Several isolates had a very high potential for virulence but further study is required to identify the specific virulence and resistance genes associated with the isolates in question.

Endophytic fungi have the ability to live inside the host plant tissues without causing neither symptoms of diseases/or harm. Opportunistic infections are accountable for majority of the outbreaks, thereby putting a burden on the health system. To investigate and characterize the bioactive compounds for the control of bacteria of clinical importance, extracts from endophytic fungi were isolated from indigenous South African medicinal plants. Extracts from endophytic fungi were isolated from 133 fungal strains and screened against Gram positive and negative bacteria namely Bacillus cereus, Escherichia coli, Enterococcus faecium, and E. gallinarum using disk diffusion. Furthermore, gas chromatography–mass spectrometry was performed to identify the bioactive compounds. Sixteen out of one hundred and thirty-three (12%) fungi extracts exhibited antibacterial properties against some of the selected bacteria. E. coli was found to be the most susceptible in contrast to E. faecium and E. gallinarum which were the most resistant. The isolate MHE 68, identified as Alternaria sp. displayed the greater spectrum of antibacterial activities by controlling selected clinical bacteria strains including resistant E. faecium and E. gallinarum. The chemical analysis of the extract from MHE 68 indicated that linoleic acid (9,12-octadecadienoic acid (Z,Z)) and cyclodecasiloxane could be accountable for the antibacterial activity. This is the first study conducted on the secondary metabolites produced by endophytic fungal strains isolated from the Pelargonium sidoides DC. possessing antibacterial properties.

Sceletium tortuosum (L.) N.E.Br. (Mesembryanthemaceae), commonly known as kanna or kougoed, is an effective indigenous medicinal plant in South Africa, specifically to the native San and Khoikhoi tribes. Today, the plant has gained strong global attraction and reputation due to its capabilities to promote a sense of well-being by relieving stress with calming effects. Historically, the plant was used by native San hunter-gatherers and Khoi people to quench their thirst, fight fatigue and for healing, social, and spiritual purposes. Various studies have revealed that extracts of the plant have numerous biological properties and isolated alkaloids of Sceletium tortuosum are currently being used as dietary supplements for medicinal purposes and food. Furthermore, current research has focused on the commercialization of the plant because of its treatment in clinical anxiety and depression, psychological and psychiatric disorders, improving mood, promoting relaxation and happiness. In addition, several studies have focused on the isolation and characterization of various beneficial bioactive compounds including alkaloids from the Sceletium tortuosum plant. Sceletium was reviewed more than a decade ago and new evidence has been published since 2008, substantiating an update on this South African botanical asset. Thus, this review provides an extensive overview of the biological and pharmaceutical properties of Sceletium tortuosum as well as the bioactive compounds with an emphasis on antimicrobial, anti-inflammatory, anti-oxidant, antidepressant, anxiolytic, and other significant biological effects. There is a need to critically evaluate the bioactivities and responsible bioactive compounds, which might assist in reinforcing and confirming the significant role of kanna in the promotion of healthy well-being in these stressful times.

Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.

Rivers in the North West Province (NWP) of South Africa are polluted by various anthropogenic activities that are associated with agricultural, domestic, industrial, and mining activities. Pollutants and effluent resulting from these activities impact the physico-chemical and biological characteristics of river water. More particularly, domestic and agricultural pollution has been associated with the occurrence of pathogenic yeast species in water. The aim of this study was to determine physico-chemical parameters, yeast levels, and the antifungal susceptibility of pathogenic yeasts in river water. Physico-chemical parameters and yeast levels were determined using standard procedures. Yeasts were identified by biochemical tests and 26S rRNA gene sequencing. Disc diffusion antifungal susceptibility tests were conducted on identified potential pathogenic yeasts. Physico-chemical parameters were within target water quality ranges (TWQR) for livestock farming but were mostly out of range for irrigation. Yeast levels (incubation at 37°C) ranged from 363 to 1 778 CFU/L. There were significant differences (p < 0.05) in the physico-chemical parameters and yeast levels between some seasons and among the river systems under study. A positive association was observed between temperature, COD and yeast levels in all the river systems. Ascomycetes, which were the most prevalent isolates, were identified as Candida spp. (35%), Pichia spp. (13%), Cyberlinera spp. (12%), Meyerozyma spp. (11%), Clavispora spp. (10%), Saccharomyces spp. (6%), Kluyveromyces spp. (5%), Yamadazyma spp. (4%), Trichosporon spp. (3%), and Wickerhamomyces spp. (1%). Antifungal resistance of the potential pathogenic yeasts was as follows: flucytosine and miconazole (100%) > fluconazole (78.5%) > econazole, and miconazole and ketoconazole (49.6%) > nystatin (15.2%). The river water systems explored in the study are used for agricultural, domestic and recreational purposes. Direct contact with the water, especially by immune-compromised people, may pose a health threat and should be further investigated.

Practices in intensive animal farming such as the extensive use of antimicrobials have significant impacts on the genetic make-up of bacterial communities, especially on that of human/animal commensals. In this report, whole genome sequencing of two vancomycin-resistant enterococci (VRE) isolates from a cattle feedlot in the North West Province, South Africa, was used to highlight the threats that extensive antimicrobial usage in intensive animal rearing represents for environmental microbiomes and the food chain. The genomic DNA of the studied strains was extracted using a DNA extraction kit. Whole-genome sequencing was performed through next-generation sequencing. The genomes of Enterococcus durans strain NWUTAL1 and Enterococcus gallinarum strain S52016 consisted of 3,279,618 and 2,374,946 bp, respectively with G + C contents of 40.76 and 43.13%, respectively. Antibiotic resistance genes (ARG), plasmids and virulence factors (involved in biofilm formation, colonization and copper/silver efflux system), were detected in the genomes of both strains. The presence of these genetic determinants in the studied strains is a cause for concern as they may disseminate and find their way into the food chain via horizontal gene transfer amongst bacteria of the different ecological niches. Issues of this nature cannot be undermined and are relevant as far as food safety is concerned.

With the increasing spread of antimicrobial resistance, there is growing attention to the contribution made by drinking water systems. The potential health impact of two drinking water treatment and distribution systems (A and B) in the North-West Province of South Africa was determined by investigating the water quality and occurrence of antimicrobial-resistant heterotrophic bacteria and genes in the raw and treated water over four seasons. Most of the physicochemical parameters except for electrical conductivity were within permissible limits. Coliform bacteria reduced from raw to potable water except for counts higher than the threshold recorded in Summer and Winter. A total of 203 heterotrophic bacterial isolates were recovered on chromogenic R2A medium and subjected to susceptibility testing to twelve antibiotics. Most of the isolates were resistant to &beta, lactam antibiotics and Trimethoprim, whereas they were susceptible to Ciprofloxacin, Erythromycin, and Neomycin. The proportions of Cephalothin and Kanamycin-resistant isolates were significantly higher (p &lt, 0.05) after treatment for site A, compared to significantly lower &beta, lactam, Oxytetracycline, and Trimethoprim-resistant isolates for B. Over 50% of isolates were of high risk, indicating their origin from high antibiotic-use sources. Seventy-one (35%) isolates were multidrug-resistant, out of which the majority (53.5%, n = 38) possessed the strA gene, followed by strB 21 (29.6%), dfrB 13 (18.3%), aadA 11 (15.5%), blaCTX-M 5 (7.0%), and tetA 3 (4.2%). The 16S rRNA gene sequences of the isolates revealed strains belonging to eight bacterial families, some of which are clinically important.

Highlights • Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass. • Serratia marcescens 39_H1 is a plant growth promoting organism. • Genome analysis showed diverse potential biotechnological application of organism. • This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production., Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.

Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

Anthropogenic activities in catchments used for drinking water production largely contaminates source waters, and this may impact the quality of the final drinking water product. These contaminants may also affect taxonomic and functional profiles of the bacterial communities in the drinking water. Here, we report an integrated insight into the microbiome and water quality of four water treatment plants (NWC, NWE, WCA and NWG) that supply portable water to communities in South Africa. A new scoring system based on combined significant changes of physicochemical parameters and microbial abundance from raw to treated water was used to evaluate the effectiveness of the treatment plants at water purification. Physicochemical parameters which include total soluble solids, turbidity, pH, nitrites and phosphorus among others, were measured in source, treated, and distributed water. There were general statistically significant (P ≤ 0.05) differences between raw and treated water, demonstrating the effectiveness of the purification process. Illumina sequencing of the 16S rRNA gene was used for taxonomic profiling of the microbial communities and this data was used to infer functional attributes of the communities. Structure and composition of the bacterial communities differed significantly (P < 0.05) among the treatment plants, only NWE and NWG showed no significant differences (P > 0.05), this correlated with the predicted functional profile of the microbial communities obtained from Phylogenetic Investigation of Communities by Reconstruction of Observed States (PICRUSt), as well as the likely pollutants of source water. Bacteroidetes, Chlorobi and Fibrobacteres significantly differed (P < 0.05) between raw and distributed water. PICRUSt inferred a number of pathways involved in the degradation of xenobiotics such as Dichlorodiphenyltrichloroethane, atrazine and polycyclic aromatic hydrocarbons. More worryingly, was the presence of pathways involved in beta-lactam resistance, potential pathogenic Escherichia coli infection, Vibrio cholerae infection, and Shigellosis. Also present in drinking and treated water were OTUs associated with a number of opportunistic pathogens.

Endophytic fungi have the ability to co-exist with their host plants without causing any harm and are beneficial to both the plant and the fungi. The current study determined the antimicrobial properties and identify the chemical compounds of secondary metabolites produced by endophytic fungi isolated from Sceletium tortuosum L. A total of 60 endophytic fungi produced secondary metabolites that were detected after fermentation and extraction. Antibacterial properties of the secondary metabolites were determined using the disc diffusion assay against pathogenic environmental Gram-positive and Gram-negative bacteria as well as control stains. The chemical compounds were characterized by GC-MS. Overall, 15% of fungal extracts displayed narrow spectrum of activity against the bacteria strains. Despite this, none of the fungal extracts inhibited growth of Enterococcus faecalis (ATCC S1299) and Enterococcus gallinarum (ATCC 700425) while Bacillus cereus (ATCC 10876) was the most susceptible against the fungal extracts. Fusarium oxysporum (GG 008) with accession no. KJ774041.1 displayed significant antibacterial activity that was linked to high levels of 5-hydroxymethylfurfural (HMF) and octadecanoic acid as revealed by GC-MS. This study revealed the presence of bioactive secondary metabolites with antibacterial activities from fungi isolated from Sceletium tortuosum L.

Atypical enteropathogenic E. coli (aEPEC) strains are emerging pathogens responsible for fatal diarrhoea in humans worldwide. The purpose of this study was to investigate genetic diversity, virulence and antimicrobial resistance profiles of aEPEC O177 strains isolated from faeces of cattle reared in intensive and extensive production systems in South Africa. A total of 96 multidrug resistant (MDR) aEPEC O177 isolates were typed using enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphism DNA (RAPD) typing. The resistome, virulome and mobilome of two aEPEC O177 isolates were investigated using WGS analysis. The ERIC typing was efficient and reproducible with a discriminatory index of 0.95. RAPD typing had poor reproducibility with satisfactory discriminatory power of 0.859. The dendrograms constructed based on ERIC and RAPD banding patterns produced 9 and 8 clusters, respectively, which indicate genetic variation among E. coli O177 isolates. WGS analysis revealed that CF-154-A and CF-335-B) isolates belonged to the O177 serotype with H7 and H21, respectively. Both isolates harboured several virulome genes such as intimin (eaeA), haemolysin (hlyA and hlyE), translocated iron receptor (tir), Type III secretion system (eprH, gspL and prgH), bssR and bssS. However, genes encoding shiga toxins were not found in either isolate. Antibiotic resistance genes such as ampC, tet, ermB, sul2, strB AcrD, aph(6)-Ic, aph(6)-Ib, aph(3″)-I, ant (3″)-1a AcrA and acrE were found in the E. coli O177 strains. Furthermore, genome annotation results indicated that both isolates carried plasmids, insertion sequences, prophages and cluster of regularly interspaced short palindromic repeats (CRISPR) type I. Based on in silico multi locus typing (MLST) analysis, the two isolates were assigned to different sequence types (CF-154-A, ST-1308 and CF-335-B, ST-58). Whole genome multi locus typing tree showed that our isolates clustered with E. coli O177:H21 (reference), suggesting the close genomic relatedness among the strains. Overall, these findings showed that cattle carry genetically diverse E. coli O177 strains, which harbour a repertoire of virulome, resistome and mobilome genes. This highlights a need for multidrug resistant E. coli O177 strain surveillance in cattle.

The symbioses between arbuscular mycorrhizal (AM) fungi and plant roots is essential for nutrient uptake and growth of most vascular plants. Soil condition and management influence the density and viability of arbuscular mycorrhizal fungal (AMF) spores. In this study, AMF spore density and viability in soil stockpiles obtained from three opencast coal mines were assessed. Soil samples were randomly collected from stockpiles and an unmined site at depths of ≤20 cm (topsoil) and >20 cm (subsoil) for enumeration of AMF spores and a mycorrhizal trap culture experiment using maize (Zea mays). Roots of trap-plants were assessed for mycorrhization by classical staining as well as detection of nuclear rRNA gene of the Glomeromycota phylum. Number of AMF spores was highest in topsoil from the unmined site and was significantly (p < 0.05) influenced by site × sampling depth interaction. DNA-based detection revealed that AMF colonisation was mostly associated with topsoil than with subsoil. Five operational taxonomic units (OTUs)/ species related to Paraglomus were identified; however, some of the OTUs were phylogenetically distant from defined Paraglomus species on the basis of sequences in the GenBank database. Overall, results suggest that AMF spore density in stockpiles do not differ from an unmined site, but viability may be influenced by soil depth.

High-throughput sequence analysis of microbial communities in food matrices provides unprecedented insights into species richness and potential safety of foods. Here, the bacterial community of soy-daddawa, a fermented indigenous food condiment, was investigated for the first time using high-throughput DNA metabarcoding (16S rRNA gene). Analyses of 1 246 692 high-quality 16S rRNA gene sequences obtained from seven soy-daddawa samples/producers yielded 1520 operational taxonomic units (OTUs). Beta-diversity analysis of soy-daddawa bacterial communities suggested differences between samples, and in some cases, clustering according to geographical proximity of producers. Sixty-five OTUs (taxonomically assigned to 13 phylotypes) comprised the core (100% threshold) bacterial community of soy-daddawa and included Bacillus amyloliquefaciens, B. lichenformis, B. mojavensis, B. pumilus, B. subtilis, B. subtilis subsp. spizizenii, B. tequilensis, Exiguobacterium sp., Staphylococcus epidermidis and S. pseudintermedius. However, genera with known pathogenic species such as Atopostipes, Enterococcus, Granulicatella, Nosocomicoccus, Proteus, Pseudomonas and Vagoccoccus constituted at least 1% (relative abundance) in at least one sample. Insights gained from this study are useful for the development of a starter culture technology for the controlled fermentation of soy-daddawa. Also, the presence of potentially pathogenic species corroborates established global consensus on the microbiological risks associated with spontaneously fermented indigenous foods.

Throughout history, mankind has used plants as their primary source of sustainability, in agricultural commodities, clothing, fragrances, fertilizers, flavours, and providing shelter. There is a strong symbiotic relationship between the plant and its endophytes. Endophytes are harboured within the living plant tissues without causing neither diseases nor symptoms. They produce bioactive compounds that protect the host plants against attack of insects, pathogens and herbivores. The bioactive compounds might be utilized for pharmaceutical, agricultural, or biotechnological applications.This paper reported on the various endophytic fungi strains that were isolated from isolated from a medicinal plant, Sceletium tortuosum. Fifty Sceletium tortuosum plants were collected from three different provinces in South Africa and leaves and roots used to isolate culturable endophytes. Morphological characteristics and a genus specific PCR designed to amplify fungal internal transcribe spacer (ITS) region (ITS1 and ITS4) and elongation factor (EF 1 and 2) was used for identification. A total of 60 fungal isolates belonging to 16 genera were identified and classified. Isolates were identified to species level based on similarities with known sequences in GenBank and a large proportion of the fungi were Fusarium species (37%) followed Aspergillus (25%) and Penicillium (7%) species. Phylogenetic analysis was performed using nuclear ribosomal DNA sequences and three potentially new isolates (DR 019 Fusarium penzigii, DR 010 Phomopsis columnaris, DR 007 Fusarium oxysporum f. sp. lycopersici) were identified in the phylogenic tree that was constructed. Our results offers basic data on the symbiotic/or mutualistic relationship between the medicinal plant Sceletium tortuosum and its endophytic fungi, as well as novel species.

To investigate the biodiversity of endophytic fungi isolated from indigenous Pelargonium sidoides plants using morphological and molecular techniques and also screen isolates for antibacterial activities. In the present study, a total of 50 Pelargonium sidoides plants were collected and the roots were analysed for the presence of endophytic fungi. The fungi were initially sorted according to morphological characteristics. Fungal identities were further confirmed through amplification of sequences encoding Translation Elongation Factor-1α (TEF-1α) gene for Fusarium species and Internal Transcribed Spacer (ITS) regions for all other fungi. Fungi were screened for antibacterial activity by adopting the standard Kirby-Bauer agar disc diffusion method using a pathogenic Escherichia coli strain (Code from the collection) previously isolated from cattle. A total of 133 fungi belonging to 32 genera were successfully isolated and identified in the study based morphological analyses. Fungi belonging to the genus Penicillium were dominant (23%) among the isolates when compared with Fusarium species (12%) as well as Alternaria and Aspergillus that were detected at 11% respectively. Antibacterial agent producing data revealed that Aspergillus sp. (KM458796.1), Penicillium expansum (LC015096.1) and Aspergillus niger (KP172477.1) produced the strongest bactericidal activity against the E. coli strain with growth inhibition zone diameter data of 11 mm, 5 mm and 4 mm respectively. To the best of our knowledge, this is the first study in which the diversity of fungi from Pelargonium sidoides has been assessed and the findings revealed that fungal diversity is directly related to their potential to produce bioactive compounds.

Response and growth kinetics of microbes in contaminated medium are useful indices for the screening and selection of tolerant species for eco-friendly bio-augmentative remediation of polluted environments. In this study, the heavy metal (HM) tolerance, bioaccumulation and growth kinetics of seven bacterial strains isolated from mining sites to 10 HMs (Cd, Hg, Ni, Al, Cr, Pb, Cu, Fe, Mn and Zn) at varied concentrations (25-600 mgL-1) were investigated. The isolates were phylogenetically (16S rRNA gene) related to Lysinibacillus macroides, Achromobacter spanius, Bacillus kochii, B. cereus, Klebsiella pneumoniae, Pseudomonas mosselii and P. nitroreducens. Metal tolerance, effects on lag phase duration and growth rates were assessed using the 96-well micro-titre method. Furthermore, metal bioaccumulation and quantities within cells were determined by transmission electron microscopy and electron dispersive x-ray analyses. Tolerance to Ni, Pb, Fe and Mn occurred at highest concentrations tested. Growth rates increased with increasing Fe concentrations, but reduced significantly (p < .05) with increasing Zn, Cu, Hg, Cd and Al. Significantly higher (p < .05) growth rates (compared to controls) was found with some isolates in Hg (25 mgL-1), Ni (100 mgL-1), Cr (150 mgL-1), Mn (600 mgL-1), Pb (100 mgL-1), Fe (600 mgL-1) and Al (50 mgL-1). Lag phase urations were isolate- and heavy metal-specific, in direct proportion to concentrations. A. spanius accumulated the most Mn and Zn, while B. cereus accumulated the most Cu. Metals accumulated intra-cellularly without cell morphology distortions. The isolates' multi-metal tolerance, intra-cellular metal bioaccumulation and growth kinetics suggest potentials for application in the synergetic biodegradation and bioremediation of polluted environments, especially HM-rich sites.

Artificial neural networks (ANNs) could be used in effective drinking water quality management. This review provides an overview about the history of ANNs and their applications and shortcomings in the drinking water sector. From the papers reviewed, it was found that ANNs might be useful modelling tools due to their successful application in areas such as pipes/infrastructure, membrane filtration, coagulation dosage, disinfection residuals, water quality, etc. The most popular ANNs applied were feed-forward networks, especially Multi-layer Perceptrons (MLPs). It was also noted that over the past decade (2006–2016), ANNs have been increasingly applied in the drinking water sector. This, however, is not the case for South Africa where the application of ANNs in distribution systems is little to non-existent. Future research should be directed towards the application of ANNs in South African distribution systems and to develop these models into decision-making tools that water purification facilities could implement.

Efflux pumps coded for by CDR1, CDR2, FLU1 and MDR1 genes could be responsible for the observed resistant phenotypes in azole-resistant Candida albicans from environmental water. This was demonstrated for clinical isolates. The aim of this study was to determine the presence and genetic similarity between efflux pump genes from clinical and environmental C. albicans isolates. Yeasts were isolated and identified using 26S rRNA gene sequencing. Disk diffusion tests were conducted. PCR was used to detect the presence of efflux genes. The fragments were sequenced and subjected to BLAST and subsequent phylogenetic analysis. Thirty seven C. albicans were identified from five selected rivers; Mooi River (19 isolates), Harts River (9 isolates), Marico River (5 isolates), Crocodile River (3 isolates) and Schoonspruit River (1 isolate). All the isolates were completely resistant to azoles. Efflux pump genes were detected in most (≥60%) of the isolates. Phylogenetic analysis showed high sequence similarity between sequences from environmental isolates and clinical isolates. Resistance to the azoles and the detection of efflux pump genes renders these antifungal agents ineffective. This is a major problem, particularly for the immune-compromised sector of the community of the North West Province and warrants further investigation.

Seasonal variations and proximity to polluted sites, among other factors, play a vital role in soil composition. The impact of spatio-seasonal changes on bacterial and heavy metal content on and ar...

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type.

Antimicrobial resistance is an imminent threat to the effective prevention and treatment of bacterial infections and alternative antimicrobial strategies are desperately needed. Antimicrobial peptides (AMPs) may be promising alternatives to current antibiotics or act as adjuvants to enhance antibiotic potency. Additionally, the use of biodegradable lipid nanoparticles can enhance the antibacterial activity of antibiotics and antimicrobial peptides. In this study, the interaction of the AMPs, nisin Z and melittin, with conventional antibiotics was investigated on Staphylococcus aureus, Staphylococcus epidermidis and Escherichia coli. The effectiveness of nanostructured lipid carriers (NLCs) for the entrapment of nisin Z was also evaluated. Findings revealed that nisin Z exhibited additive interactions with numerous conventional antibiotics. Notable synergism was observed for novobiocin-nisin Z combinations. The addition of the non-antibiotic adjuvant EDTA significantly improved the antimicrobial activity of free nisin Z towards E.coli. NLCs containing nisin Z were effective against Gram-positive species at physiological pH, with an increase in effectiveness in the presence of EDTA. Results indicate that nisin Z may be advantageous as an adjuvant in antimicrobial chemotherapy, while contributing in the battle against antibiotic resistance. NLCs have the potential to enhance the antibacterial activity of nisin Z towards Gram-positive bacterial species associated with skin infections.

Soil microbial communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and role in soil ecosystem processes. Presently, information on structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa is sparse. Here, bacterial communities in three post-coal mining reclamation soils were investigated using community-level physiological profiling (CLPP), enzyme activities, and next-generation sequencing of 16S rRNA gene. Inferences were drawn in reference to adjacent unmined soils. CLPP-based species diversity and proportionality did not differ significantly (P > 0.05) whereas activities of β-glucosidase, urease and phosphatases were significantly (P P P > 0.05), suggesting redundancy in bacterial community functions between reclamation and unmined soils. Silt content, bulk density, pH, electrical conductivity, Na and Ca significantly influenced soil bacterial communities. Overall, results indicate that bacterial community structure reflects underlying differences between soil ecosystems, and suggest the restoration of bacterial diversity and functions over chronological age in reclamation soils.

AAfter a cluster of human pneumonia cases in Wuhan City (China) on 7 January 2020, a novel coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), was identified as the causative agent of the disease COVID‐19 (World Health Organization 2020). It quickly became a global pandemic and continues to rapidly spread across the world, having infected almost 4 million confirmed cases and caused more than 265 000 deaths at time of publication, far surpassing the total cases of SARS and Middle East respiratory syndrome (MERS)

Pseudomonas aeruginosa has been implicated in a wide range of post-operation wound and lung infections. A wide range of acquired resistance and virulence markers indicate surviving strategy of P. aeruginosa. Complete-genome analysis has been identified as efficient approach towards understanding the pathogenicity of this organism. This study was designed to sequence the entire genome of P. aeruginosa UY1PSABAL and UY1PSABAL2; determine drug-resistance profiles and virulence factors of the isolates; assess factors that contribute toward stability of the genomes; and thereafter determine evolutionary relationships between the strains and other isolates from similar sources. The genomes of the MDR P. aeruginosa UY1PSABAL and UY1PSABAL2 were sequenced on the Illumina Miseq platform. The raw sequenced reads were assessed for quality using FastQC v.0.11.5 and filtered for low quality reads and adapter regions using Trimmomatic v.0.36. The de novo genome assembly was made with SPAdes v.3.13 and annotated using Prokka v.2.1.1 annotation pipeline; Rapid Annotation using Subsytems Technology (RAST) server v.2.0; and PATRIC annotation tool v.3.6.2. Antimicrobial resistance genes and virulence determinants were searched through the functional annotation data generated from Prokka, RAST and PATRIC annotation pipelines; In addition to ResFinder and Comprehensive Antibiotic Resistance Database (CARD) which were employed to determine resistance genes. The PHAge Search Tool Enhanced Release (PHASTER) web server was used for the rapid identification and annotation of prophage sequences within bacterial genome. Predictive secondary metabolites were identified with AntiSMASH v.5.0. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and cas genes regions were also investigated with the CRISPRone and CRISPRFinder server. The genome sizes of 7.0 and 6.4 Mb were determined for UY1PSABAL and UY1PSABAL2 strains with G+C contents of 66.1% and 66.48% respectively. β-lactamines resistance genes blaPAO, aminoglycoside phosphorylating enzymes genes aph(3’)-IIb, fosfomycine resistance gene fosA, vancomycin vanW and tetracycline tetA were among identified resistance genes harboured in both isolates. UY1PSABAL bore additional aph(6)-Id, aph(3'')-Ib, ciprofloxacin-modifying enzyme crpP and ribosomal methylation enzyme rmtB. Both isolates were found harbouring virulence markers such as flagella and type IV pili; and also present various type III secretion systems such as exoA, exoS, exoU, exoT. Secondary metabolites such as pyochelin and pyoverdine with iron uptake activity were found within the genomes as well as quorum-sensing systems, and various fragments for prophages and insertion sequences. Only the UY1PSABAL2 contains CRISPR-Cas system. The phylogeny revealed a very close evolutionary relationship between UY1PSABAL and the similar strain isolated from Malaysia; the same trend was observed between UY1PSABAL2 and the strain from Chinese origin. Complete analyses of the entire genomes provide a wide range of information towards understanding pathogenicity of the pathogens in question.

Busseola fusca (Fuller) (Lepidoptera: Noctuidae), a major insect pest of maize in sub-Saharan Africa, has developed high levels of non-recessive resistance to Cry1Ab toxin expressed in genetically modified Bt maize. Multiple resistance mechanisms to various Cry toxins have been identified in Lepidoptera, but no study has yet been done to determine the mechanism of Cry1Ab resistance in B. fusca. Therefore, the larval transcriptome of B. fusca was sequenced, de novo assembled and characterized. Differential expression analysis was performed to compare gene expression profiles of Cry toxin challenged and unchallenged neonate larvae to assess the molecular basis of the defence mechanism employed by this insect. Several genes associated with Cry toxin resistance in other lepidopteran pests were detected in B. fusca. Results suggest that differential expression of metabolic and immune-related genes might explain Cry1Ab toxin defence in this pest (supplemental file). Transcript expression profiles of neonates demonstrated that 33.59% and 60.31% of the 131 differentially expressed genes were upregulated and downregulated in the toxin-challenged neonate larvae, respectively. Transcripts were grouped into two subclusters according to the similarity of their expression patterns. Transcripts in subcluster 1 were moderately upregulated in the toxin-challenged neonate larvae, and, conversely, downregulated in the unchallenged neonate larvae. The solute carrier organic anion transporter, which is involved in insecticide detoxification, was upregulated in the toxin-challenged neonate larvae. Conversely, most of the transcripts in subcluster 2 were moderately downregulated in the toxin-challenged neonate larvae, and upregulated for neonates feeding on non-challenged maize. Four unidentified transcripts were extremely down-regulated in the toxin-challenged neonate larvae, and upregulated in the unchallenged neonate larvae. Further studies are recommended to establish if there is a direct correlation between these differentially expressed genes and the observed resistance. Elucidation of such defence mechanisms is crucial for developing insect resistance management strategies to ensure sustainable use of genetically modified maize in Africa. Nevertheless, this is the first study on gene expression profiles of B. fusca strains challenged with Cry toxin. The transcriptome characterized in this study provides a significant resource base for future studies on B. fusca and contributes to understanding some of the gene regulation and signalling networks involved in the defence of B. fusca against Cry1Ab toxin.

South African surface waters are subject to various forms of pollution. Recent findings in aquatic systems suggest an association exists between yeast diversity, chemical pollutants and land coverage, which are important water quality determinants. Yeast abundance and diversity, as well as antifungal agents in two river systems in South Africa, were investigated and related to the existing land coverage. Yeast abundance and diversity were determined from environmental DNA by quantitative polymerase chain reaction and next-generation sequencing, respectively, of the 26S ribosomal ribonucleic acid (rRNA) gene. Antifungal agents were qualitatively and/or quantitatively detected by ultra-high-pressure liquid chromatography-mass spectrometry. Analyses of 2 031 714 high-quality 26S rRNA sequences yielded 5554 amplicon sequence variants (ASVs)/species. ASV richness and Shannon-Wiener index of diversity reflected the southward flow of the river with higher values observed downstream compared to the upstream. Fluconazole concentrations were quantifiable in only two samples; 178 and 271 ng L−1. Taxonomically, at least 20 yeast species were detected, including the dominant Candida tropicalis, Cryptococcus spp. as well as the lesser dominant Bensingtonia bomiensis, Fereydounia khargensis, Hericium erinaceus, Kondoa changbaiensi, Pseudozyma spp. and Sphacelotheca pamparum. The two dominant species are known opportunistic pathogens which had antifungal resistant traits in previous studies from the same rivers and therefore is a public health threat. The present study provides further evidence that yeasts should be included as part of water quality parameters, especially in developing countries where much of the population are economically disadvantaged, and also immunocompromised due to age and disease.

It is important that environmental parameters that may affect the prevalence of AmpC beta-lactamase genes are investigated to devise frameworks for their surveillance, management and prevention. The aim of this study was thus to determine which environmental parameters are associated with the prevalence of clinically relevant AmpC beta-lactamase genes in aquatic systems. River water was sampled from seven sites in the Crocodile West River, South Africa. Physical-chemical parameters, metal levels and beta-lactam levels were measured. Environmental DNA was extracted from the water samples and six AmpC beta-lactamase gene groups (ACC, ACT/MIR, BIL/LAT/CMY, DHA, FOX, MOX/CMY) were quantified using quantitative PCR. Additionally, 16S rRNA gene metabarcoding analyses were performed on eDNA for each site and metabolic pathways were predicted using PICRUST2. Network analysis was performed to establish co-occurrences of AmpC genes with environmental factors. Quantification results indicated that AmpC gene copy numbers were significantly high (Kruskal Wallis H Test, p 0.05) at Sites 1-3 of the Crocodile West River. In contrast, no significant changes regarding environmental factors were observed across the seven sites. Results of network analysis indicated that the AmpC gene groups had limited associations with all the environmental parameters, except for some key bacterial families, specifically Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. A significant positive correlation between population density and AmpC genes suggested that in more densely populated areas more faecal pollution will be prevalent which is associated with high AmpC gene levels. Areas such as these are also likely to be linked with more antibiotic use which supports the notion that pre-selection of AmpC genes occurs before entering the aquatic environment. Moreover, it was demonstrated that prevalent selectors of AmpC genes do not ensure that continuous selection occurs in an aquatic environment. This information could be vital in future detection and management of AmpC genes in aquatic systems.

Yeasts from water sources have been associated with diseases ranging from superficial mucosal infections to life threatening diseases. The aim of this study was to determine the water quality as well as diversity and antifungal susceptibility of yeasts from two rivers. Yeast levels and physico-chemical parameter data were analyzed by principal component analysis to determine correlations between physico-chemical data and yeast levels. Yeast morphotypes were identified by biochemical tests and 26S rRNA gene sequencing. Disk diffusion antifungal susceptibility tests were conducted. Physico-chemical parameters of the water were within target water quality range (TWQR) for livestock farming. For irrigational use, total dissolved solids and nitrates were not within the TWQR. Yeast levels ranged between 27 ± 10 and 2,573 ± 306 cfu/L. Only non-pigmented, ascomycetous yeasts were isolated. Saccharomyces cerevisiae and Candida glabrata were most frequently isolated. Several other opportunistic pathogens were also isolated. A large number of isolates were resistant to azoles, especially fluconazole, but also to other antifungal classes. Candida species were resistant to almost all the antifungal classes. These water sources are used for recreation and religious as well as for watering livestock and irrigation. Of particular concern is the direct contact of individuals with opportunistic yeast, especially the immune-compromised. Resistance of these yeast species to antifungal agents is a further health concern.

The aim of this study was to evaluate the spatial and temporal variation of microbiological parameters of the Lower Vaal River, with emphasis on the Staphylococci population. River water concentrations of Staphylococci, heterotrophic, total coliforms, fecal coliforms and Streptococci groups of sanitary indicator bacteria were monitored. Results indicated significant contamination from agricultural land use inputs and municipal waste applications. Significant temporal and spatial variation was observed in response to the varying river discharge. Higher microbial concentrations were detected during high river discharge whereas during low river discharge both low and high microbial concentrations were detected. The varying responses associated with river discharge helped to identify the importance of different sources of contamination in the catchment and the mechanisms transferring them. The overall impact of contamination on the water quality of the Vaal River could have potentially serious public health risks but also provide valuable data for integrated water resource management.

Increased heavy metal pollution generated through anthropogenic activities into the environment has necessitated the need for eco-friendly remediation strategies such as mycoremediation. With a view to prospecting for fungi with heavy metal remediation potentials, the tolerance of five Aspergillus species isolated from soils of three active gold and gemstone mining sites in southwestern Nigeria to varied heavy metal concentrations was investigated. Isolated Aspergillus strains were identified based on the internal transcribed spacer 1 and 2 (ITS 1 and ITS 2) regions. Growth of Aspergillus strains were challenged with a range of varied concentrations of heavy metals: cadmium (Cd) (0–100), copper (Cu) (0–1000), lead (Pb) (0–400), arsenic (As) (0–500), and iron (Fe) (0–800) concentrations (ppm) incorporated into Malt Extract Agar (MEA) in triplicates. Mycelial radial growths were recorded at intervals of 3 days during a 13-day incubation period. Aspergillus strains were identified as A. tubingensis, ...

The African maize stem borer, Busseola fusca, feeds on a limited number of host plant species (Calatayud et al. 2014), which include crops such as maize, pearl millet and sorghum. This pest occurs throughout sub-Saharan Africa where it causes economic damage to maize and sorghum crops (Kfir et al. 2002). In an attempt to combat lepidopteran stem borers, genetically modified Bt maize that express insecticidal Cry toxins were developed to kill larvae that feed on these plants (George et al. 2011). Bt maize was introduced into South Africa during 1998 and within the first decade after release, field-evolved resistance of B. fusca to Bt maize was reported (Van Rensburg 2007). Since this first report, resistant populations have been reported from several parts of the maize-production region of South Africa (Kruger et al. 2011; Van den Berg et al. 2013). Explanations provided for this rapid resistance development were confined to agronomical reasons (VanRensburg 2007; Kruger et al. 2009, 2011),non-compliance to refuge requirements (Kruger etal. 2009) and non-recessive inheritance of resistance (Campagne et al. 2013). Notmuchis however understood about the molecular genetics of B.fusca. Previously, Sezonlin et al. (2006b) noted that limited population genetic and phylogeography data are available for B. fusca.

The aim of this study was to report on antibiotic susceptibility patterns as well as highlight the presence of efflux pump genes and virulence genetic determinants in Enterococcus spp. isolated from South African surface water systems. One hundred and twenty-four Enterococcus isolates consisting of seven species were identified. Antimicrobial susceptibility testing revealed a high percentage of isolates was resistant to β-lactams and vancomycin. Many were also resistant to other antibiotic groups. These isolates were screened by PCR, for the presence of four efflux pump genes (mefA, tetK, tetL and msrC). Efflux genes mefA and tetK were not detected in any of the Enterococcus spp. However, tetL and msrC were detected in 17 % of the Enterococcus spp. The presence of virulence factors in the Enterococcus spp. harbouring efflux pump genes was determined. Virulence determinants were detected in 86 % of the Enterococcus spp. harbouring efflux pump genes. Four (asa1, cylA, gel and hyl) of the five virulence factors were detected. The findings of this study have demonstrated that Enterococcus from South African surface water systems are resistant to multiple antibiotics, some of which are frequently used for therapy. Furthermore, these isolates harbour efflux pump genes coding for resistance to antibiotics and virulence factors which enhance their pathogenic potential.

Bacterial community dynamics during soy-daddawa fermentation was investigated using culture-dependent and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) molecular methods. The total titratable acidity (TTA), pH, and bacterial counts (BCs) were monitored daily during a 72-h fermentation period. Bacteria were characterized based on 16S rRNA gene sequencing. TTA ranged from 0.08 to 0.26 mg lactic acid/g, whereas pH ranged from 7.01 to 8.19. BCs increased from 3.9 to 10.61 log CFU/g. Fifty-eight isolates were obtained by culture method and clustered into seven operational taxonomic units (OTUs) at 97% sequence similarity, whereas four OTUs were obtained from the PCR-DGGE method. Taxonomic identification revealed that bacteria belonged to the genera Bacillus, Enterobacter, Enterococcus, and Staphylococcus with B. subtilis being present throughout fermentation. Medically significant isolates, including B. anthracis, Enterococcus casseliflavus, and Enterobacter hormaechei were detected. These results emphasize the need for starter culture utilization and offer a platform for starter culture screening and selection.

Anthropogenic disturbances of soil environments predispose loss of soil ecosystem functions, including its habitat support function. In this study, the potential ecosystem support and habitat functions of soils from stockpiles and post-mining reclamation areas (ranging from 3 to 25 years) in two coal mining sites were assessed using Eisenia andrei bioassays. Endpoints such as avoidance response, mortality, relative growth rate and fecundity were determined. By taking into cognisance the ages of the reclamation areas, inference was drawn on the potential restoration of ecosystem support functions over the years since reclamation. Mortality and fecundity of earthworms did not suggest limited support functions of control and test soils. Net avoidance response (AR) indicated significant differences (P < 0.05) among treatments with only the net AR in a 3-year old reclaimed soil >80%. Earthworms generally preferred (P < 0.05) undisturbed (“reference”) soils to OECD and test soils. Furthermore, trends in AR suggested a negative effect (P < 0.05) of anthropogenic disturbance and a general improvement of soil habitat function in older reclaimed areas. Of all endpoints, the avoidance test was the most sensitive, which generally reflected the differences in soil physicochemical properties among test soils. Although high intra-site variations in soil properties suggest lack of strict adherence to best reclamation practices, coal mining soil environments are not ecologically derelict with regards to supporting biocoenosis