Pyrosequencing targeting the V1-V3 hypervariable of the 16S rDNA was used to investigate the bacterial diversity in river and roof-harvested rainwater (RHRW) used for potable purposes by rural households in Luthengele village in the Eastern Cape Province of South Africa. The phylum Proteobacteria dominated the data set (80.5% of all reads), while 4.2% of the reads could not be classified to any of the known phyla at a probability of 0.8 or higher (unclassified bacteria). At class level, the classes; Betaproteobacteria (50.4% of all reads), Alphaproteobacteria (16.2%), Verrucomicrobiae (6.6%), Planctomycetacia (5.7%) and Sphingobacteria (3%) dominated the data set in all the samples. Although the class Verrucomicrobiae constituted 6.6% of all sequences, 88.6% of the sequences were from the river sample where the class represented 43.7% of the observed sequences in the sample. The bacteria community structure clearly showed significant similarities between RHRW and differences with the river water control sample, suggesting different levels of contamination and environmental factors affecting the various water sources. Moreover, signatures of potential pathogens including Legionella, Acinetobacter, Pseudomonas, Clostridia, Chromobacterium, Yersinia and Serratia were detected, and the proportions of Legionella were relatively higher suggesting a potential health risk to households using RHRW. This work provides guidance for prioritizing subsequent culturable and quantitative analysis, to ensure that potentially significant pathogens are not left out of risk estimations.

Human bocavirus (HBoV) is known to be associated with a variety of clinical manifestation including acute gastroenteritis (AGE). Despite their global prevalence, no data is available on the epidemiology of HBoV associated with AGE in South Africa (SA). Between April 2009 and April 2015, 3765 stool specimens were collected from children less than 5 years of age hospitalized with diarrhea. Specimens were screened for selected enteric viruses by enzyme immunoassay and quantitative polymerase chain reaction, bacteria by culture and parasites by staining and microscopy. HBoV was detected in 5.63% (212 of 3765) of cases, the majority of which were children ≤2 years (92%, 195 of 212), and were common in the summer and autumn months (60%; 128 of 212). Further investigations of coinfections showed that bacteria (adjusted odds ratio [aOR] = 2.20; 95% confidence interval [CI], 1.41‐3.45; P = .001) and sapovirus (aOR = 2.05; 95% CI, 1.08‐3.86; P = .027) were significantly associated with HBoV in multivariate analysis. HBoV genotyping was successful in 191 of the 212 samples with HBoV‐1 being the most prevalent genotype observed (79.6%; 152 of 191) followed by HBoV‐3 (13.6%; 26 of 191), HBoV‐2 (5.2%; 10 of 191), and HBoV‐4 (1.6%; 3 of 191). The high prevalence of HBoV‐1, a virus known to be associated with respiratory infections, and the association between HBoV‐positive specimens and already established AGE agents, suggests that HBoV may play a limited role in the observed AGE cases in SA.

The information on fungal diversity and succession in table grapes during preharvest growth stages is critical in the development of a more targeted control strategy, to improve postharvest quality of table grapes.

Cladobotryum species and strain diversity of isolates collected from cobweb symptomatic Agaricus bisporus or infected casing soil were investigated due to increased incidences of the disease in the South African mushroom industry. Samples were collected from mushroom farms located in Gauteng, the Western Cape and KwaZulu Natal Provinces of South Africa.Moreover, cobweb disease isolates from the USA and Ireland were included in the study as reference cultures. Isolates were characterised using culture and conidia morphology and were identified as Cladobotryum mycophilum. The isolates were characterised by rapid colony growth between 48 and 72 h on malt extract agar and potato dextrose agar, all but two isolates (GP-15 and KZN-2) produced the pink colour of aurofurasin. All isolates could infect A. bisporus fruiting bodies with varying degrees of aggressiveness. Isolates were sequenced for their ITS, and BLAST analysis showed highest similarity (99-100%) to several ITS sequences of Hypomyces odoratus/C. mycophilum for 35 of the isolates except for one from Ireland that was identified as H. rosellus/C. dendroides. Phylogenetic analysis of the isolates showed South African cobweb disease of mushrooms to be caused by a wide diversity of strains some of which may have originated from elsewhere in the world.

In most countries, fresh produce sold at local markets is usually not analyzed for agricultural chemical residues as export products are, which raises concerns about the perceived safety levels of local food supplies in contrast with exported products. The aim of this study was to determine pesticide residue levels in fruits and vegetables sold at two of the biggest fresh produce markets in Africa. A total of 199 fruit and vegetable samples were collected between 2012 and 2014 and analyzed for 74 pesticides commonly used in the horticultural sector. Of the samples analyzed, 91% were compliant with set maximum residue levels (MRLs). The remaining samples either contained unregistered chemicals (8%) or exceeded set MRL values (1%). Products containing more than one pesticide residue constituted 4.02% of all samples tested. Imazalil and iprodione were found to be the most frequently detected pesticides (12 samples each). Boscalid, endosulfan, profenofos, and procymidone were associated with the most noncompliance, including exceeding MRL values or being unregistered for the specific crop. The establishment of a national pesticide monitoring program is essential for the country and would ensure that pesticides are used in accordance with good agricultural practices.

Six years of pesticide residue data from fresh produce destined for the export market were analyzed for the period 2009 to 2014. A total of 37,838 fruit (99.27%) and vegetable (0.73%) data sets analyzed for the presence of 73 pesticides were compared. Pesticides were detected on 56.46% of samples, of which 0.78% had multiple residues. Noncompliances detected were because of the use of unregistered pesticides (0.73%), values that exceeded established maximum residue levels (MRLs) (0.32%), or the combination of values that exceeded MRLs and the use of unregistered pesticide residues (0.003%). The most commonly detected pesticides that exceeded established MRLs were imazalil (37.71%), prochloraz (28.69%), and iprodione (5.74%). The unregistered pesticide most often found on grapes and avocados was also imazalil (62.23%) and, on nectarines and avocados, diphenylamine (11.15%). Exceedances of MRL values were mostly associated with oranges (43.44%), avocados (27.87%), grapefruits (7.38%), and lemons (6.56%). Residual pesticide monitoring on fruits and vegetables is a key tool to ensure conformity with regulatory requirements and compliance with good agricultural practices and the trade requirements set by the importing country.

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 show the potential of agricultural fruit production environments to act as reservoirs of clinically important Salmonella serovars.

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 E. coli. A total of 239 Escherichia coli were isolated from thirty fresh pigeon faecal samples (130 isolates), 11 RHRW tanks from three sites in Pretoria (78) and two in Johannesburg (31). 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 were antibiotic resistant than those from RHRW. 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.