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.

Evaluation of crAssphages as a potential marker of human viral contamination in environmental water and fresh leafy greens.

CrAssphages are human gut bacteriophages with potential use as an indicator of human fecal contamination in water and other environmental systems. We determined the prevalence and abundance of crAssphages in water, food, and fecal samples and compared these estimates with the prevalence of norovirus. Samples were tested using two crAssphage-specific qPCR assays (CPQ056 and TN201-203) and for norovirus using TaqMan realtime RT-PCR. CrAssphage was detected in 40% of human fecal specimens, 61% of irrigation water samples, 58.5% of stream water samples, and 68.5% of fresh leafy greens samples. Interestingly, across all sample categories, crAssphage concentrations were 2-3 log10 higher than norovirus concentrations. The correlation of detection of crAssphage and norovirus was significant for the irrigation water samples (r = 0.74, p = 7.4e-06). Sequences obtained from crAssphage positive samples from human fecal and stream water samples phylogenetically clustered with genotype I crAssphages, whereas sequences derived from irrigation water samples clustered differently from other genotypes. Our data show that crAssphages were prevalent in norovirus-positive water samples and in fresh leafy green samples, there was a strong correlation between the presence of crAssphage and norovirus. CrAssphage genomic copies were consistently higher than norovirus copies in all sample types. Overall, our findings suggest that crAssphages could be used as reliable indicators to monitor fecal-borne virus contamination within the food safety chain.

Prevalence of Campylobacter spp., Salmonella spp., and Listeria monocytogenes, and Population Levels of Food Safety Indicator Microorganisms in Retail Raw Chicken Meat and Ready-To-Eat Fresh Leafy Greens Salads Sold in Greece.

The presence of microbial pathogens in foods compromises their safety resulting in foodborne illnesses, public health disorders, product recalls, and economic losses. In this work, 60 samples of chilled raw chicken meat and 40 samples of packaged ready-to-eat (RTE) fresh leafy greens salads, sold in Greek retail stores (butchers and supermarkets), were analyzed for the presence of three important foodborne pathogenic bacteria, i.e., Campylobacter spp., Salmonella spp., and Listeria monocytogenes, following the detection protocols of the International Organization for Standardization (ISO). In parallel, the total aerobic plate count (APC), Enterobacteriaceae, total coliforms, Escherichia coli, and staphylococci were also enumerated as hygiene (safety) indicator organisms. When present, representative typical colonies for each pathogen were biochemically verified, following the ISO guidelines. At the same time, all the Campylobacter isolates from chicken (n = 120) were identified to the species level and further phylogenetically discriminated through multiplex and repetitive sequence-based (rep) polymerase chain reaction (PCR) methods, respectively. Concerning raw chicken, Campylobacter spp. were recovered from 54 samples (90.0%) and Salmonella spp. were recovered from 9 samples (15.0%), while L. monocytogenes was present in 35 samples (58.3%). No Campylobacter was recovered from salads, and Salmonella was present in only one sample (2.5%), while three salads were found to be contaminated with L. monocytogenes (7.5%). The 65% of the Campylobacter chicken isolates belonged to C. jejuni, whereas the rest, 35%, belonged to C. coli. Alarmingly, APC was equal to or above 106 CFU/g in 53.3% and 95.0% of chicken and salad samples, respectively, while the populations of some of the other safety indicators were in some cases also high. In sum, this study unravels high occurrence percentages for some pathogenic and food safety indicator microorganisms in raw chicken meat and RTE fresh leafy greens salads sold in Greek retail, highlighting the need for more extensive microbiological control throughout the food production chain (from the farm/field to the market).

Safety and Quality of Romaine Lettuce Accessible to Low Socioeconomic Populations Living in Houston, TX.

ABSTRACT: Previous empirical evidence has demonstrated that low-socioeconomic status (SES) communities have higher rates of gastroenteritis; however, there is a paucity of literature on the safety and quality of food (fresh produce) accessible to these communities. The overarching goal of this study was to investigate the microbial safety and quality of romaine lettuce from low- and high-SES neighborhoods in the Houston, TX, area. Loose-leaf romaine lettuce was purchased from low- and high-SES neighborhood retailers, and aerobic plate count, coliform, Escherichia coli, yeast, and mold assays were conducted. In addition, enrichment was performed on all samples for Listeria monocytogenes, Staphylococcus aureus, Salmonella spp., and E. coli O157:H7, and reverse transcriptase PCR analysis was carried out. The results showed that E. coli, coliform, yeast, and mold were present in significantly higher counts (P < 0.05) in produce obtained from low-SES neighborhoods compared with high-SES neighborhoods. The reverse transcriptase PCR results showed that 38% of samples from high-SES areas were positive for S. aureus versus 87% of samples from low-SES areas. None of the samples from high-SES areas were positive for the other pathogens. The samples from low-SES areas were positive for E. coli O157:H7 (4%), Salmonella spp. (53%), L. monocytogenes (13%), and S. aureus (87%). These results demonstrate a significant disparity in the quality and safety of romaine lettuce accessible to low- versus high-SES populations. Future studies can be designed to identify the specific cause of this challenge by investigating the food supply chain.