A scoping study on the prevalence of Escherichia coli and Enterococcus species in harvested rainwater stored in tanks

Rainwater harvesting (RWH) is a relatively inexpensive technology that has the potential to provide safe water in communities where conventional technologies are difficult to implement. In this study, the microbiological quality of rainwater harvested from rooftops and ground-surface runoff was evaluated based on the concentrations of Escherichia coli, total coliforms and enterococci. Samples were collected from 15 roof-harvested rainwater (RHRW) tanks, 4 ground-surface runoff rainwater harvesting (GRWH) tanks, 3 rivers and 1 spring water source in the Eastern Cape Province of South Africa, and 14 RHRW tanks in Gauteng Province. In the Eastern Cape Province E. coli and enterococci were detected in 7 and 4 of the 15 RHRW tanks, respectively. Enterococci were detected only from one river whereas E. coli was detected in all three rivers; in spring water neither enterococci nor E. coli were detected. Samples from GRWH tanks were positive for E. coli and enterococci in 2 and 3 of the 4 tanks, respectively. In Gauteng Province, E. coli, coliforms and enterococci were detected from 6, 6 and 9 of the 14 rainwater tanks, respectively. On average, E. coli and enterococci were detected in 44.8% of the RHRW tanks, although enterococci concentrations were several times higher than those for E. coli. We further evaluated the significance of urban pigeons as the likely sources of contamination by isolating 156 enterococci from 30 pigeon faecal samples and 208 enterococci from RHRW samples collected from Gauteng Province. Matrix-assisted laser desorption ionisation identification of the various enterococci revealed 4 species – E. faecalis (20.5%), E. mundtii (20.51%), E. faecium (23.1%) and E. casseliflavus (17.3%) – to be dominant in faecal samples, whereas E. casseliflavus (34.6%) and E. mundtii (33.2%) were dominant in RHRW.Keywords: rainwater harvesting, contamination, indicator bacteria, health risk

Antibiotic resistance in Escherichia coli isolates from roof-harvested rainwater tanks and urban pigeon faeces as the likely source of contamination

The objective of this study was to investigate the risks associated with the use of roof-harvested rainwater (RHRW) and the implication of pigeons as the most likely source of contamination by testing for antibiotic resistance profiles of Escherichia coli. A total of 239 E. coli were isolated from thirty fresh pigeon faecal samples (130 isolates), 11 RHRWtanks from three sites in Pretoria (78) and two in Johannesburg (31). E. coli isolates were tested against a panel of 12 antibiotics which included ampicillin, amoxicillin, amikacin, cefoxitin, ceftriaxone, chloramphenicol, ciprofloxacin, cotrimoxazole, enrofloxacin, gentamicin, nalidixic acid and tetracycline. In all samples, resistance to ampicillin (22.7.9 %), gentamicin (23.6 %), amikacin (24 %), tetracycline (17.4) and amoxicillin (16.9 %) were the most frequently encountered form of resistance. However, a relatively higher proportion of isolates from pigeon faeces (67.3 %) were antibiotic resistant than those from RHRW (53.3 %). The highest number of phenotypes was observed for single antibiotics, and no single antibiotic resistance was observed for chloramphenicol, ceftriaxone, gentamicin, cefoxitin, cotrimoxazole, although they were detected in multiple antibiotic resistance (MAR) phenotypes. The highest multiple antibiotic resistance (MAR) phenotypes were observed for a combination of four antibiotics, on isolates from JHB (18.8 %), pigeon faeces (15.2 %) and Pretoria (5.1 %). The most abundant resistance phenotype to four antibiotics, Ak-Gm-Cip-T was dominated by isolates from pigeon faeces (6.8 %) with Pretoria and Johannesburg isolates having low proportions of 1.3 and 3.1 %, respectively. Future studies should target isolates from various environmental settings in which rainwater harvesting is practiced and the characterisation of the antibiotic resistance determinant genes among the isolates.WRC Project No K5/2175, Water Research Commission, 2012http://link.springer.com/journal/106612016-07-31hb201

Relative proportions of E. coli and Enterococcus spp. may be a good indicator of potential health risks associated with the use of roof harvested rainwater stored in tanks

A total of 285 water samples were collected from 71 roof harvested rainwater tanks from four villages in different provinces over a two-year (2013–2014) period during the early (October to December) and late (January to March) rainy season. Water quality was evaluated based on Escherichia coli, faecal coliforms and Enterococcus spp. prevalence using the IDEXX Quanti-Tray quantification system. Real-Time PCR was used to analyse a subset of 168 samples for the presence of Shigella spp., Salmonella spp. and E. coli virulence genes (stx1, stx2 and eaeA). Escherichia coli were detected in 44.1% of the samples, Enterococcus spp. in 57.9% and faecal coliforms in 95.7%. The most prevalent E. coli concentrations in harvested rainwater were observed in 29.1% of samples and 22.5% for Enterococcus spp. and, were within 1–10 cfu/100 ml and 10–100 cfu/100 ml, respectively, whereas those for faecal coliforms (36.6%) were within 100–1000 cfu/100 ml. On average 16.8% of the samples had neither E. coli nor Enterococcus spp. detected, while 33.9% had only Enterococcus spp. and 23.7% had only E. coli. E. coli and Enterococcus spp. were detected together in 25.5% of the samples. Evaluation of samples for potential pathogenic bacteria showed all tested samples to be negative for the Shigella spp. ipaH gene, while five tested positive for Salmonella ipaB gene. None of the samples tested positive for the stx1 and stx2 genes, and only two tested positive for the eaeA gene. These findings are potentially useful in the development of a simplified risk assessment strategy based on the concentrations of indicator bacteria.This study was undertaken as part of a Water Research Commission (WRC) unsolicited project: “Evaluation of the risks associated with the use of rainwater harvested from roofs, for domestic use and, homestead food gardens; and groundwater for domestic use and livestock watering” (WRC Project No K5/2175, Water Research Commission, 2013).http://link.springer.com/journal/106612019-03-01hj2018Plant Production and Soil Scienc

Prevalence and serovar diversity of Salmonella spp. in primary horticultural fruit production environments

Increases in foodborne disease outbreaks associated with fresh produce have necessitated the need to identify potential sources of microbial contamination in produce and agricultural environments. The present study evaluated Salmonella prevalence and serovar diversity in fruit (225), water (140) and surface (126) samples, from three commercial farms and associated packhouses, located in different farming regions in South Africa. Fruit and water samples were collected from both orchards and packhouses, while surface samples were collected from conveyer belts and hands of packhouse employees. Salmonella was detected in 26 of the 491 (5.3%) samples. Environmental samples (water and surfaces) recorded a slightly higher proportion (3.1%; 15/491) of positive samples compared to fruit samples (2.2%; 11/491). Salmonella was not detected on employee hands and river water samples. A total of 263 Salmonella isolates were obtained from the 26 positive samples by standard culture methods, preliminarily identified through matrix-assisted laser desorption ionisationtime of flight mass spectroscopy (MALDI-TOF MS) and API 20E, and confirmed by invA gene. Of the 39 representative isolates serotyped the serovars Muenchen (33.3%), Typhimurium (30.8%), Heidelberg (20.5%), Bsilla (7.7%), Salmonella subspecies IIb: 17: r: z (5.1%) and one untypable strain were identified. Most samples had multiple serovars with orchard water form one site recording the highest serovar diversity (4 serovars). Our findings show the potential of agricultural fruit production environments to act as reservoirs of clinically important Salmonella serovars.National Research Foundation Research Infrastructure Support Programmes (NRF-RISP).http://www.elsevier.com/locate/foodcont2017-11-30hb2016Plant Scienc

A scoping study on the prevalence of Escherichia coli and Enterococcus species in harvested rainwater stored in tanks

Rainwater harvesting (RWH) is a relatively inexpensive technology that has the potential to provide safe water in communities where conventional technologies are difficult to implement. In this study, the microbiological quality of rainwater harvested from rooftops and ground-surface runoff was evaluated based on the concentrations of Escherichia coli, total coliforms and enterococci. Samples were collected from 15 roof-harvested rainwater (RHRW) tanks, 4 ground-surface runoff rainwater harvesting (GRWH) tanks, 3 rivers and 1 spring water source in the Eastern Cape Province of South Africa, and 14 RHRW tanks in Gauteng Province. In the Eastern Cape Province E. coli and enterococci were detected in 7 and 4 of the 15 RHRW tanks, respectively. Enterococci were detected only from one river whereas E. coli was detected in all three rivers; in spring water neither enterococci nor E. coli were detected. Samples from GRWH tanks were positive for E. coli and enterococci in 2 and 3 of the 4 tanks, respectively. In Gauteng Province, E. coli, coliforms and enterococci were detected from 6, 6 and 9 of the 14 rainwater tanks, respectively. On average, E. coli and enterococci were detected in 44.8% of the RHRW tanks, although enterococci concentrations were several times higher than those for E. coli. We further evaluated the significance of urban pigeons as the likely sources of contamination by isolating 156 enterococci from 30 pigeon faecal samples and 208 enterococci from RHRW samples collected from Gauteng Province. Matrix-assisted laser desorption ionisation identification of the various enterococci revealed 4 species – E. faecalis (20.5%), E. mundtii (20.51%), E. faecium (23.1%) and E. casseliflavus (17.3%) – to be dominant in faecal samples, whereas E. casseliflavus (34.6%) and E. mundtii (33.2%) were dominant in RHRW.This study was undertaken as part of a Water Research Commission (WRC) unsolicited project: ‘Evaluation of the risks associated with the use of rainwater harvested from roofs, for domestic use and, homestead food gardens; and groundwater for domestic use and livestock watering’ (WRC Project No K5/2175, Water Research Commission, 2012).http://www.wrc.org.zahttp://www.ajol.info/index.php/wsaam2016Microbiology and Plant Patholog

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing

AIMS : To investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small-scale farms as well as homestead gardens using pyrosequencing. METHODS AND RESULTS : Next generation sequencing analysis of the V1–V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (64·5%), class Gammaproteobacteria (56·6%) and genus Aeromonas (14·4%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (16·3%) from the one commercial farm harboured more sequences than cabbage from the small-scale farm (1·3%) or homestead gardens (1·9%). Escherichia sequences were detected in both irrigation water (4·6%) and on cabbage (1·3%) samples from the small-scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (1·9%) from the small-scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens. CONCLUSION : Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop. SIGNIFICANCE AND IMPACT OF THE STUDY : Microbial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.This study was part of a solicited research project (K5/1875/4: Evaluation of the risks associated with the use of rainwater harvested from rooftops, for domestic use and homestead food gardens; and groundwater for domestic use and livestock watering) .The Water Research Commission, the Department of Agriculture, Forestry, and Fisheries, Republic of South Africa and the DST-NRF Centre of Excellence in Food Security, South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-26722018-10-30hj2017Plant Production and Soil Scienc

Antimicrobial resistance profiles of Salmonella spp. from agricultural environments in fruit production systems

Foodborne disease outbreaks involving fresh produce have increased in recent years. The risk of infection from contaminated food is worsened by the increased prevalence of antibiotic-resistant strains. This study evaluated the prevalence of antibiotic resistance in Salmonella isolates (n?=?263) from agricultural production systems through to the final packed product. Salmonella isolates were preliminarily identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI-TOF MS) and API 20E and identities confirmed by invA gene polymerase chain reaction. Antimicrobial susceptibility was performed with 15 antimicrobial agents using the Kirby Bauer disk diffusion test. Of the 263 Salmonella isolates assessed, 59.3% were resistant to one or more antimicrobials. The most frequently detected resistance was against chloramphenicol and kanamycin (46.7%), trimethoprim sulfamethoxazole (28%), and streptomycin (14%), and the less frequently detected resistance was toward ampicillin (1.14%), amikacin (0.76%), and amoxicillin clavulanic acid (0.38%). Multiple antimicrobial resistance (MAR) (resistance to ?3 antibiotics) was found in 48.7% (76/156) isolates. The most common MAR phenotype was to chloramphenicol and trimethoprim/sulfamethoxazole kanamycin (43.6%). Resistance to chloramphenicol, kanamycin, or trimethoprim/sulfamethoxazole was only observed in MAR phenotypes. All isolates were susceptible to ceftiofur, cefoxitin, ceftriaxone, ciprofloxacin, nalidixic acid, gentamicin, and tetracycline. This study confirms the importance of fresh produce production environments as potential reservoirs and fresh produce as carriers of antibiotic-resistant Salmonella spp. with significant clinical importance. Further studies to evaluate the actual level of health risk from these pathogens should include characterization of the antibiotic resistance determinant genes among the isolates.The National Research Foundation (NRF)http://www.liebertpub.com/fpd2017-09-30Plant Scienc

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes

AIMS : To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. METHODS AND RESULTS : Viable bacteria, yeast and fungi counts, and the pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extent of degreening effects varied between the citrus varieties. Pyrosequencing analysis showed a total of 4409 bacteria and 5792 fungi nonchimeric unique sequences with an average of 1102 bacteria and 1448 fungi reads per sample. Dominant phyla on the citrus carpoplane were Proteobacteria (53·5%), Actinobacteria (19·9%), Bacteroidetes (5·6%) and Deinococcus–Thermus (5·4%) for bacteria and Ascomycota (80·5%) and Basidiomycota (9·8%) for fungi. Beginning with freshly harvested fruit fungal diversity declined significantly after drenching, but had little effect on bacteria and populations recovered during degreening treatments, including those for Penicillium sp. CONCLUSION : Packhouse processing greatly influences microbial communities on the citrus carpoplane. SIGNIFICANCE AND IMPACT OF THE STUDY : A broad orange biome was described with pyrosequencing and gave insight into the likely survival and persistence of pathogens, especially as they may affect the quality and safety of the packed product. A close examination of the microbiota of fruit and the impact of intervention strategies on the ecological balance may provide a more durable approach to reduce losses and spoilage.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-26722018-04-30hj2018Plant Production and Soil Scienc

Mango endophyte and epiphyte microbiome composition during fruit development and post-harvest stages

The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.Supplementary Materials: Figure S1: Taxonomic abundance of pathogenic fungal species at the preharvest (A) and postharvest stages (B) on the fructoplane, stem-end pulp and fruit stems of cv. Tommy Atkins mangoes. FP, fructoplane; SEP, stem-end pulp; S, fruit stem.https://www.mdpi.com/journal/horticulturaeam2022Plant Production and Soil Scienc

Bacterial community dynamics and functional profiling of soils from conventional and organic cropping systems

Soil microbiomes play an integral role in agricultural production systems. Understanding of the complex microbial community structure and responses to conventional compared to organic cropping systems is crucial for sustainable production and ecosystems health. This study investigated soil microbial community structure responses based on a four year long field experiment. Bacterial communities characterizing conventional and organic cropping systems were evaluated using Illumina MiSeq high-throughput sequencing targeting the V4-V5 variable region of the 16S rRNA gene. Soil bacterial community structure showed a cropping system dependant distribution, with nitrogen cycling taxa (Bacillus, Niastella, Kribbella, and Beijerinckia) dominant in conventional cropping systems, while carbon cycling taxa (Dokdonella, Caulobacter, Mathylibium, Pedobacter, Cellulomonas and Chthoniobacter and Sorangium) were abundant in organic cropping systems. Functional prediction of the bacterial biomes showed conventional cropping systems to harbour a community adapted to carbon-limited environments, with organic cropping systems dominated by those involved in the degradation of complex organic compounds. These findings suggest the existence of niche specific communities and functional specialization between cropping systems with potential use in soil management through selective promotion of organisms beneficial to soil health.This work forms part of the research of the Centre of Excellence (“CoE”) in Food Security sponsored by the Department of Science and Innovation, Republic of South Africa (“DSI”) and administered by the National Research Foundation (“NRF”).http://www.elsevier.com/locate/apsoilhj2022Plant Production and Soil Scienc