A genome-based investigation of the Priestia species isolated from anthrax endemic regions in Kruger National Park.

Priestia is a genus that was renamed from the genus Bacillus based on the conserved signature indels (CSIs) in protein sequences that separate Priestia species from Bacillus, with the latter only including species closely related to B. subtilis and B. cereus. Diagnosis of anthrax, a zoonotic disease, is implicated by tripartite anthrax virulence genes (lef, pagA, and cya) and poly-γ-D-glutamic acid capsular genes cap-ABCDE of Bacillus anthracis. Due to the amplification of anthrax virulence genes in Priestia isolates, the search for homologous anthrax virulence genes within the Priestia genomes (n = 9) isolated from animal blood smears was embarked upon through whole genome sequencing. In silico taxonomic identification of the isolates was conducted using genome taxonomy database (GTDB), average nucleotide identity (ANI), and multi-locus sequence typing (MLST), which identified the genomes as P. aryabhattai (n = 5), P. endophytica (n = 2) and P. megaterium (n = 2). A pan-genome analysis was further conducted on the Priestia genomes, including the screening of virulence, antibiotic resistance genes and mobile genetic elements on the sequenced genomes. The oligoribonuclease NrnB protein sequences showed that Priestia spp. possess a unique CSI that is absent in other Bacillus species. Furthermore, the CSI in P. endophytica is unique from other Priestia spp. Pan-genomic analysis indicates that P. endophytica clusters separately from P. aryabhattai and P. megaterium. In silico BLASTn genome analysis using the SYBR primers, Taqman probes and primers that target the chromosomal marker (Ba-1), protective antigen (pagA), and lethal factor (lef) on B. anthracis, showed partial binding to Priestia regions encoding for hypothetical proteins, pyridoxine biosynthesis, hydrolase, and inhibitory proteins. The antibiotic resistance genes (ARG) profile of Priestia spp. showed that the genomes contained no more than two ARGs. This included genes conferring resistance to rifamycin and fosfomycin on P. endophytica, as well as clindamycin on P. aryabhattai and P. megaterium. Priestia genomes lacked B. anthracis plasmids and consisted of plasmid replicon types with unknown functions. Furthermore, the amplification of Priestia strains may result in false positives when qPCR is used to detect the virulence genes of B. anthracis in soil, blood smears, and/or environmental samples.

Distribution of antibiotic resistance genes and antibiotic residues in drinking water production facilities: Links to bacterial community.

There is a rapid spread of antibiotic resistance in the environment. However, the impact of antibiotic resistance in drinking water is relatively underexplored. Thus, this study aimed to quantify antibiotic resistance genes (ARGs) and antibiotic residues in two drinking water production facilities (NW-E and NW-C) in North West Province, South Africa and link these parameters to bacterial communities. Physicochemical and ARG levels were determined using standard procedures. Residues (antibiotics and fluconazole) and ARGs were quantified using ultra-high performance liquid chromatography (UHPLC) chemical analysis and real-time PCR, respectively. Bacterial community compositions were determined by high-throughput 16S rRNA sequencing. Data were analysed using redundancy analysis and pairwise correlation. Although some physicochemical levels were higher in treated than in raw water, drinking water in NW-E and NW-C was safe for human consumption using the South African Water Quality Guideline (SAWQG). ARGs were detected in raw and treated water. In NW-E, the concentrations of ARGs (sul1, intl1, EBC, FOX, ACC and DHA) were higher in treated water than in raw water. Regarding antimicrobial agents, antibiotic and fluconazole concentrations were higher in raw than in treated water. However, in NW-C, trimethoprim concentrations were higher in raw than in treated water. Redundancy analysis showed that bacterial communities were not significantly correlated (Monte Carlo simulations, p-value >0.05) with environmental factors. However, pairwise correlation showed significant differences (p-value <0.05) for Armatimonas, CL500-29 marine group, Clade III, Dickeya and Zymomonas genera with environmental factors. The presence of ARGs and antibiotic residues in the current study indicated that antibiotic resistance is not only a clinical phenomenon but also in environmental settings, particularly in drinking water niches. Consumption of NW-E and NW-C treated water may facilitate the spread of antibiotic resistance among consumers. Thus, regulating and monitoring ARGs and antibiotic residues in drinking water production facilities should be regarded as paramount.

Genome mining of Escherichia coli WG5D from drinking water source: unraveling antibiotic resistance genes, virulence factors, and pathogenicity.

BACKGROUND: Escherichia coli, a ubiquitous inhabitant of the gut microbiota, has been recognized as an indicator of fecal contamination and a potential reservoir for antibiotic resistance genes. Its prevalence in drinking water sources raises concerns about the potential dissemination of antibiotic resistance within aquatic ecosystems and the subsequent impact on public health. The ability of E. coli to acquire and transfer resistance genes, coupled with the constant exposure to low levels of antibiotics in the environment, underscores the need for comprehensive surveillance and rigorous antimicrobial stewardship strategies to safeguard the quality and safety of drinking water supplies, ultimately mitigating the escalation of antibiotic resistance and its implications for human well-being. METHODS: WG5D strain, isolated from a drinking water distribution source in North-West Province, South Africa, underwent genomic analysis following isolation on nutrient agar, anaerobic cultivation, and DNA extraction. Paired-end Illumina sequencing with a Nextera XT Library Preparation kit was performed. The assembly, annotation, and subsequent genomic analyses, including phylogenetic analysis using TYGS, pairwise comparisons, and determination of genes related to antimicrobial resistance and virulence, were carried out following standard protocols and tools, ensuring comprehensive insights into the strain's genomic features. RESULTS: This study explores the notable characteristics of E. coli strain WG5D. This strain stands out because it possesses multiple antibiotic resistance genes, encompassing tetracycline, cephalosporin, vancomycin, and aminoglycoside resistances. Additionally, virulence-associated genes indicate potential heightened pathogenicity, complemented by the identification of mobile genetic elements that underscore its adaptability. The intriguing possibility of bacteriophage involvement and factors contributing to pathogenicity further enriches our understanding. We identified E. coli WG5D as a potential human pathogen associated with a drinking water source in South Africa. The analysis provided several antibiotic resistance-associated genes/mutations and mobile genetic elements. It further identified WG5D as a potential human pathogen. The occurrence of E. coli WG5D raised the awareness of the potential pathogens and the carrying of antibiotic resistance in drinking water. CONCLUSIONS: The findings of this study have highlighted the advantages of the genomic approach in identifying the bacterial species and antibiotic resistance genes of E. coli and its potential as a human pathogen.

Genetic diversity and whole genome sequence analysis data of multidrug resistant atypical enteropathogenic Escherichia coli O177 strains: An assessment of food safety and public health implications.

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.

Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity.

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.

A Chewable Cure "Kanna": Biological and Pharmaceutical Properties of Sceletium tortuosum.

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.

Relating the prevalence of plasmid-mediated AmpC beta-lactamase genes to aquatic environmental factors.

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.

Complete Genomic Analysis of VRE From a Cattle Feedlot: Focus on 2 Antibiotic Resistance.

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.

Occurrence of Antibiotic-Resistant Bacteria and Genes in Two Drinking Water Treatment and Distribution Systems in the North-West Province of South Africa.

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 ß-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 < 0.05) after treatment for site A, compared to significantly lower ß-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.

Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features.

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, ß-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.

Bioactive Compound Produced by Endophytic Fungi Isolated From Pelargonium sidoides Against Selected Bacteria of Clinical Importance.

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.

Draft Genome Sequences of Potentially Pathogenic Clostridium perfringens Strains from Environmental Surface Water in the North West Province of South Africa.

Surface water systems in South Africa are experiencing a major decline in quality due to various anthropogenic factors. This poses a possible health risk for humans. Here, we present the draft genome sequences of three Clostridium perfringens isolates obtained from a fecally polluted river system in the North West province of South Africa.

Global distribution and current research of AmpC beta-lactamase genes in aquatic environments: A systematic review.

AmpC beta-lactamase genes are some of the most common antibiotic resistance genes and require special attention once they have become mobilised. The detection of these genes is well documented in clinical settings. However, there is insufficient knowledge of both plasmid and genomic AmpC genes in aquatic environments. This systematic review aimed to determine the extent of the knowledge gap in the literature regarding the prevalence of AmpC beta-lactamase genes in aquatic systems. Using selected criteria, a total of 27 databases were searched for applicable peer-reviewed journal articles. No date and language restrictions were applied. Journal articles that highlighted the detection of AmpC beta-lactamase genes in environmental aquatic systems, including wastewater treatment plants, were included. Of the 950 literature sources that were identified, 50 were selected for full text analysis based on predetermined criteria. Studies on AmpC genes detection were traced in 23 countries. These studies focused on surface water (24), wastewater (17), sea water (4) and both surface and wastewater (5). Most studies did not specifically aim to detect AmpC genes, but to detect antibiotic resistance genes in general. Presently no surveillance protocols, standardised detection methods or environmental limits exist for these genes and, due to a paucity of research in this field, it is unlikely that such systems will be implemented in the near future. The implications and dynamics of AmpC genes in aquatic systems remain unclear and require intense research to ensure the sustainability of environmental systems and human health.

Transcriptome and differentially expressed genes of Busseola fusca (Lepidoptera: Noctuidae) larvae challenged with Cry1Ab toxin.

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.

The prevalence and diversity of AmpC ß-lactamase genes in plasmids from aquatic systems.

This study aimed to investigate the presence and diversity of AmpC ß-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC ß-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0.0 to 29.38 copies per picogram of DNA). Some samples in which ampC was not detected, intI1 was present. Amplicons of ampC genes were subjected to restriction digest using HindIII. Samples where the restriction markers were absent were purified by cloning followed by plasmid extraction, PCR amplification, and sequencing of individual AmpC gene fragments. Phylogenetic analysis identified all positive AmpC genes as Class C ß-lactamases, comprising of ampC, CMY- and ACT-families. Detecting AmpC and intl1 genes on plasmids suggests a high risk of horizontal gene transfer and potential dissemination of these and other antibiotic resistance genes surrounding immediate aquatic environments. Consequences of ß-lactamase diversity in aquatic ecosystems are relatively unexplored in South African aquatic ecosystems.

Heavy metal tolerance traits of filamentous fungi isolated from gold and gemstone mining sites

ABSTRACT Increased environmental pollution has necessitated the need for eco-friendly clean-up strategies. Filamentous fungal species from gold and gemstone mine site soils were isolated, identified and assessed for their tolerance to varied heavy metal concentrations of cadmium (Cd), copper (Cu), lead (Pb), arsenic (As) and iron (Fe). The identities of the fungal strains were determined based on the internal transcribed spacer 1 and 2 (ITS 1 and ITS 2) regions. Mycelia growth of the fungal strains were subjected to a range of (0-100 Cd), (0-1000 Cu), (0-400 Pb), (0-500 As) and (0-800 Fe) concentrations (mgkg-1) incorporated into malt extract agar (MEA) in triplicates. Fungal radial growths were recorded every three days over a 13-days' incubation period. Fungal strains were identified as Fomitopsis meliae, Trichoderma ghanense and Rhizopus microsporus. All test fungal exhibited tolerance to Cu, Pb, and Fe at all test concentrations (400-1000 mgkg-1), not differing significantly (p > 0.05) from the controls and with tolerance index >1. T. ghanense and R. microsporus demonstrated exceptional capacity for Cd and As concentrations, while showing no significant (p > 0.05) difference compared to the controls and with a tolerance index >1 at 25 mgkg-1 Cd and 125 mgkg-1 As. Remarkably, these fungal strains showed tolerance to metal concentrations exceeding globally permissible limits for contaminated soils. It is envisaged that this metal tolerance trait exhibited by these fungal strains may indicate their potentials as effective agents for bioremediative clean-up of heavy metal polluted environments.

Tolerance and growth kinetics of bacteria isolated from gold and gemstone mining sites in response to heavy metal concentrations.

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.

Heavy metal tolerance traits of filamentous fungi isolated from gold and gemstone mining sites.

Increased environmental pollution has necessitated the need for eco-friendly clean-up strategies. Filamentous fungal species from gold and gemstone mine site soils were isolated, identified and assessed for their tolerance to varied heavy metal concentrations of cadmium (Cd), copper (Cu), lead (Pb), arsenic (As) and iron (Fe). The identities of the fungal strains were determined based on the internal transcribed spacer 1 and 2 (ITS 1 and ITS 2) regions. Mycelia growth of the fungal strains were subjected to a range of (0-100 Cd), (0-1000 Cu), (0-400 Pb), (0-500 As) and (0-800 Fe) concentrations (mgkg-1) incorporated into malt extract agar (MEA) in triplicates. Fungal radial growths were recorded every three days over a 13-days' incubation period. Fungal strains were identified as Fomitopsis meliae, Trichoderma ghanense and Rhizopus microsporus. All test fungal exhibited tolerance to Cu, Pb, and Fe at all test concentrations (400-1000mgkg-1), not differing significantly (p>0.05) from the controls and with tolerance index >1. T. ghanense and R. microsporus demonstrated exceptional capacity for Cd and As concentrations, while showing no significant (p>0.05) difference compared to the controls and with a tolerance index >1 at 25mgkg-1 Cd and 125mgkg-1 As. Remarkably, these fungal strains showed tolerance to metal concentrations exceeding globally permissible limits for contaminated soils. It is envisaged that this metal tolerance trait exhibited by these fungal strains may indicate their potentials as effective agents for bioremediative clean-up of heavy metal polluted environments.

Antibiotic resistance, efflux pump genes and virulence determinants in Enterococcus spp. from surface water systems.

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 ß-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.

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae).

Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is a stemborer pest that attacks maize (Zea mays) throughout sub-Saharan Africa. Genetically modified maize has been shown to be effective against B. fusca. However, resistance of B. fusca against Bt-maize has developed and spread throughout South Africa. Previous studies suggested that gut microbiota contribute to mortality across a range of Lepidoptera. To fully assess the role of microbiota within the gut, it is essential to understand the microbiota harboured by natural B. fusca populations. This study aimed to identify the gut-associated bacteria by 16S rRNA gene sequencing. A total of 78 bacterial strains were characterised from the midgut of B. fusca larvae that were collected from 30 sites across the maize producing region of South Africa. Molecular phylogenetic analyses revealed bacteria affiliated to Proteobacteria, Actinobacteria, and Firmicutes. Taxonomic distribution placed these isolates into 15 different genera representing 20 species. The majority of bacteria identified belong to the genera Bacillus, Enterococcus, and Klebsiella. The B. fusca gut represents an intriguing and unexplored niche for analysing microbial ecology. The study could provide opportunities for developing new targets for pest management and contribute to understanding the phenomenon of resistance evolution of this species.