Irrigation water quality and the benefits of implementing good agricultural practices during tomato (Lycopersicum esculentum) production

Metabolic plasticity of Salmonella enterica as adaptation strategy in river water

The survival of Salmonella in subtropical river water depends on genetic and metabolic reorganization for the expression of alternative metabolic pathways in response to starvation, which allows Salmonella to use environmental carbon sources (C-sources). However, knowledge regarding the metabolic plasticity of Salmonella serotypes for C-source utilization when exposed to these conditions remains unclear. The aim of this study was to evaluate the metabolic response and level of environmental C-source consumption by environmental Salmonella (Oranienburg and Saintpaul) and clinical Salmonella (Typhi) serotypes by comparing laboratory growth against exposure to river water conditions. Metabolic characterization was performed using a Biolog® EcoPlate^TM containing 31 C-sources. The results obtained under laboratory growth conditions showed that environmental serotypes used 74.1% of the C-sources, whereas the clinical serotype used 45.1%. In contrast, in river water, all strains used up to 96.7% of the C-sources. Salmonella exposure to river water increases its capacity to use environmental C-sources.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.

Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico

Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.

Phenotypic traits of carbon source utilization in environmental Salmonella strains isolated from river water

Salmonella in the environment have evolved genetically to maintain a stable cell metabolism. Nevertheless, a lack of common nutrients (such as glucose) causes these strains to metabolize alternative carbon sources. In this study, 21 strains of Salmonella Oranienburg isolated from subtropical river water were evaluated to compare their adaptation and preconditioning abilities for the consumption of environmental carbon sources (ECS). The results obtained in this study attributed important biological characteristics to the adaptation of the metabolism of Salmonella strains to diverse ECS; these characteristics include but are not limited to variations in plasticity and natural preconditioning in closely related microorganisms, such as environmental isolates belonging to the serotype Oranienburg.

The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains

Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.

Characterization of biofilm formation by Salmonella enterica at the air-liquid interface in aquatic environments

Survival of bacterial pathogens in different environments is due, in part, to their ability to form biofilms. Four wild-type Salmonella enterica strains, two Oranienburg and two Saintpaul isolated from river water and animal feces, were tested for biofilm formation at the air-liquid interface under stressful conditions (pH and salinity treatments such as pH 3, NaCl 4.5 w/v; pH 7, NaCl 4.5 w/v; pH 10, NaCl 4.5 w/v; pH 3, Nacl 0.5 w/v; pH 7, NaCl 0.5 w/v; and pH 10, NaCl 0.5 w/v); Salmonella Typhimurium DT104 was used as a control strain. Salmonella Oranienburg and Saintpaul from feces were moderately hydrophobic and motile, while S. Saintpaul from water and the control strain S. Typhimurium showed high hydrophobicity, which helped them form more resistant biofilms than S. Oranienburg. Under stressful conditions, all strains experienced difficulties in forming biofilms. Salmonella Saintpaul and Typhimurium expressed the red dry and rough (RDAR) morphotype and were able to form biofilm at air-liquid interface, contrarily to Oranienburg that showed incomplete rough morphology. This study contributes to the knowledge of biofilm formation as a survival strategy for Salmonella in aquatic environments.

Effect of river water exposition on adhesion and invasion abilities of Salmonella Oranienburg and Saintpaul

This study was performed to evaluate in vitro the adherence and invasiveness capacity of Salmonella Oranienburg and Saintpaul (isolated from river water) exposed to laboratory and river water growth conditions and inoculated into epithelial HEp-2 cell. Results showed that Salmonella Oranienburg and Salmonella Saintpaul showed lower ability to adhere and invade epithelial HEp-2 cells under both growth conditions as compared to Salmonella Typhimurium reference strain. S. Oranienburg adhesion capacity was not affected by the growth conditions, while S. Saintpaul exposed to river water significantly (p < 0.05) decreased its adhesion capacity by 75.7 %. On the contrary, S. Oranienburg exposed to river water reduced its invasion efficiency by 80 %, whereas S. Saintpaul showed no differences between growth conditions. In conclusion, this study suggests that the exposure to non-host conditions, such as river water, adversely affects the adhesion and invasiveness of Salmonella serotypes differently, impacting on their ability to re-enter a new host.

Differences in carbon source utilization of Salmonella Oranienburg and Saintpaul isolated from river water

Long-term exposure to river water by non-indigenous micro-organisms such as Salmonella may affect metabolic adaptation to carbon sources. This study was conducted to determine differences in carbon source utilization of Salmonella Oranienburg and Salmonella Saintpaul (isolated from tropical river water) as well as the control strain Salmonella Typhimurium exposed to laboratory, river water, and host cells (Hep-2 cell line) growth conditions. Results showed that Salmonella Oranienburg and Salmonella Saintpaul showed better ability for carbon source utilization under the three growth conditions evaluated; however, S. Oranienburg showed the fastest and highest utilization on different carbon sources, including D-Glucosaminic acid, N-acetyl-D-Glucosamine, Glucose-1-phosphate, and D-Galactonic acid, while Salmonella Saintpaul and S. Typhimurium showed a limited utilization of carbon sources. In conclusion, this study suggests that environmental Salmonella strains show better survival and preconditioning abilities to external environments than the control strain based on their plasticity on diverse carbon sources use.

Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7

BACKGROUND

Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol.

METHODS

In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome.

RESULTS

Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome.

CONCLUSION

These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.

Fecal contamination in irrigation water and microbial quality of vegetable primary production in urban farms of Metro Manila, Philippines

Microbial contamination of fresh produce can present a severe risk to public health. By conducting a rigorous survey of irrigation waters, the impacts of fecal contamination on the quality of produce could be assessed. In this study, surface waters were observed to be contaminated with Escherichia coli, Salmonella spp., and somatic coliphages. Culture methods show that out of 373 irrigation water, soil, and vegetable samples collected for a 1-year period, 232 (62.20%) were found positive for E. coli, 213 (57.26%) for somatic coliphages, and 2 (0.53%) for Salmonella spp. Out of 190 water samples, 167 (87.9%) were found to have E.coli, 174 (91.6%) have somatic coliphages, and 1 (0.5%) with Salmonella spp. In soil samples, 36 of 91 (39.6%) have E. coli, 31 (34.0%) have somatic coliphages, and none with Salmonella spp. Lastly, out of 92 vegetable samples, 29 (31.5%), 8 (8.7%), and 1 (1.1%) were found to have E. coli, somatic coliphages, and Salmonella spp., respectively. Molecular analysis confirmed the presence of bacterial contaminants. Seasonal weather conditions were noted to have an effect on the presence and number of these fecal indicator organisms. The observed data suggest that contaminated irrigation water may greatly affect the quality of fresh produce from these agricultural operations.