Characterization of bacterial pathogens in rural and urban irrigation water

A bottom-up view of antimicrobial resistance transmission in developing countries

Antimicrobial resistance (AMR) is tracked most closely in clinical settings and high-income countries. However, resistant organisms thrive globally and are transmitted to and from healthy humans, animals and the environment, particularly in many low- and middle-income settings. The overall public health and clinical significance of these transmission opportunities remain to be completely clarified. There is thus considerable global interest in promoting a One Health view of AMR to enable a more realistic understanding of its ecology. In reality, AMR surveillance outside hospitals remains insufficient and it has been very challenging to convincingly document transmission at the interfaces between clinical specimens and other niches. In this Review, we describe AMR and its transmission in low- and middle-income-country settings, emphasizing high-risk transmission points such as urban settings and food-animal handling. In urban and food production settings, top-down and infrastructure-dependent interventions against AMR that require strong regulatory oversight are less likely to curtail transmission when used alone and should be combined with bottom-up AMR-containment approaches. We observe that the power of genomics to expose transmission channels and hotspots is largely unharnessed, and that existing and upcoming technological innovations need to be exploited towards containing AMR in low- and middle-income settings.

Prevalence of Escherichia coli strains in horticultural farms from Argentina: antibiotic resistance, biofilm formation, and phylogenetic affiliation

Escherichia coli is the bacteria most commonly used as an indicator of fecal contamination in agricultural environments. Moreover, E. coli is categorized as a priority pathogen due to its widespread antibiotic resistance. This study aimed to characterize E. coli strains isolated from 10 horticultural farms. Isolates were obtained from samples of vegetable crops (n = 62), the surrounding soil (n = 62), poultry litter (n = 8), and groundwater (n = 6). Phyllo-grouping assignment was performed on the total of E. coli isolates. Antibiograms and quantification of the minimal inhibitory concentration (MIC) were performed with antibiotics commonly used in humans. Biofilm formation capacity was studied by quantifying cells attached to culture tubes. Overall, 21 E. coli isolates were obtained. Three phylogenetic groups (A, B1, and C) and two Escherichia clade IV and IV-V were identified in the collection by polymerase chain reaction. Sixty-seven percent of the E. coli isolates were resistant to amoxicillin-clavulanic acid and/or ampicillin. Amoxicillin MIC values ranged from 11.9 to >190.5 µg/mL and ampicillin MIC values ranged from 3 to >190.5 µg/mL. All the E. coli isolates, resistant and non-resistant, had biofilm forming capacity. The presence of phenotypic resistance on fresh produce and environmental matrices could present significant opportunities for contamination that result in health risks for consumers. To the authors' best knowledge, this is the first environmental assessment of resistant E. coli occurrence in horticultural farms in South America.

Detection of extended-spectrum beta-lactamase cefotaxime resistance and virulence genes in Escherichia coli by duplex quantitative real-time PCR and melt curve analysis

Emerging virulent and antibiotic-resistant pathogens present a global public health risk. Routine monitoring of prevalence within the clinical, environmental and food production setting is vital. Quantitative real-time PCR (qPCR) coupled with melting curve analysis can rapidly and accurately characterize pathogens. We evaluated commercial qPCR mixes based on SYBR Green l and EvaGreen for developing an assay for simultaneously detecting antibiotic resistance (extended-spectrum beta-lactamase, ESBL and bla_CTX-M ) and virulence (stx1, stx2 and eae) genes in Escherichia coli (n = 12) isolated from irrigation water and irrigated vegetables. SYBR Green and EvaGreen detected two amplicons (stx1 and bla_CTX-M ) and (stx2 and eae) in a single reaction. A higher mean melting temperature (T_m ) separation between targeted amplicons and smoother melting curves were observed with the EvaGreen suggesting better performance when targeting multiple amplicons. Through simple stepwise optimization of DNA, cycling, primers, reaction volume and melting curve scanning rate, we adopted a conventional PCR assay for detection of large amplicons (375-1580 bp) for qPCR. This may facilitate development of cost-effective tailor-made assays for rapid and accurate monitoring of emerging foodborne and environmental pathogens in resource constrained regions.

A High Resolution DNA Melting Curve Analysis for the Rapid and Efficient Molecular Diagnostics of Extended Spectrum β-Lactamase Determinants from Foodborne Escherichia coli

The accurate identification of Extended-Spectrum β-Lactamase (ESBL) genes in Gram-negative bacteria is necessary for surveillance and epidemiological studies of transmission through foods. We report a novel rapid, cheap, and accurate closed tube molecular diagnostic tool based on two multiplex HRM protocols for analysis of the predominant ESBL families encountered in foods. The first multiplex PCR assay targeted blaCTX-M including phylogenetic groups 1 (CTX-M-1-15, including CTX-M-1, CTX-M-3 and CTX-M-15), 2 (CTX-M-2), and 9 (CTX-M-9-14, including CTX-M-9 and CTX-M-14). The second assay involved blaTEM /bla CTX-M /blaSHV, including TEM variants (TEM-1 and TEM-2), SHV-1-56 (SHV-1, SHV-2 and SHV-56), and CTX-M-8-41 (CTX-M-8, CTX-M-25, CTX-M-26 and CTX-M-39 to CTX-M-41). The individual melting curves were differentiated by a temperature shift according to the type of ESBL gene. The specificity and sensitivity of the first assay were 100% and 98%, respectively. For the second assay, the specificity and sensitivity were 87% and 89%, respectively. The detection of ESBL variants or mutations in existing genes was also demonstrated by the subtyping of a variant of the CTXM-1-15. The HRM is a potential tool for the rapid detection of present β-lactamase genes and their characterization in a highly sensitive, closed-tube, inexpensive method that is applicable in high throughput studies.

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella. This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment.

Enteroaggregative Escherichia coli is the predominant diarrheagenic E. coli pathotype among irrigation water and food sources in South Africa

Diarrheagenic E. coli (DEC) has been implicated in foodborne outbreaks worldwide and have been associated with childhood stunting in the absence of diarrhoea. Infection is extraordinarily common, but the routes of transmission have not been determined. Therefore, determining the most prevalent pathotypes in food and environmental sources may help provide better guidance to various stakeholders in ensuring food safety and public health and advancing understanding of the epidemiology of enteric disease. We characterized 205 E. coli strains previously isolated from producer distributor bulk milk (PDBM)(118), irrigation water (48), irrigated lettuce (29) and street vendor coleslaw (10) in South Africa. Enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC) and diffusely adherent E. coli (DAEC) were sought. We used PCR and partial gene sequencing for all 205 strains while 46 out of 205 that showed poor resolution were subsequently characterized using cell adherence (HeLa cells). PCR and partial gene sequencing of aatA and/or aaiC genes confirmed EAEC (2%, 5 out of 205) as the only pathotype. Phylogenetic analysis of sequenced EAEC strains with E. coli strains in GenBank showing ≥80% nucleotide sequence similarity based on possession of aaiC and aatA generated distinct clusters of strains separated predominantly based on their source of isolation (food source or human stool) suggesting a potential role of virulence genes in source tracking. EAEC 24%, 11 out of 46 strains (PDBM = 15%, irrigation water = 7%, irrigated lettuce = 2%) was similarly the predominant pathotype followed by strains showing invasiveness to HeLa cells, 4%, 2 out of 46 (PDBM = 2%, irrigated lettuce = 2%), among stains characterized using cell adherence. Therefore, EAEC may be the leading cause of DEC associated food and water-borne enteric infection in South Africa. Additionally, solely using molecular based methods targeting virulence gene determinants may underestimate prevalence, especially among heterogeneous pathogens such as EAEC.

Quantitative Risk Assessment of Hemolytic Uremic Syndrome Associated with Consumption of Bulk Milk Sold Directly from Producer to Consumer in South Africa

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin-producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. Hazard characterization was based on an exponential dose-response model to calculate the probability of illness from STEC infection in individuals 5 years and younger and individuals older than 5 years. The estimated mean STEC level was 0.12 CFU/mL (95% confidence interval [CI]: 0 to 1.2; σ = 0.34) for raw PDBM and 0.08 CFU/mL (95% CI: 0 to 1; σ = 0.27) for pasteurized PDBM. A higher risk of HUS cases per year was recorded in raw than in pasteurized PDBM and also in individuals younger than 5 years of age. For every 100,000 servings consumed, the expected median numbers of HUS cases per year from raw PDBM were 52 for 5 years and younger and 3.2 for older than 5 years. The median numbers of cases per year for pasteurized PDBM were 47 for 5 years and younger and 2.9 for older than 5 years. Sensitivity analysis revealed that serving volume and time taken to sell PDBM at producer-distributor outlets were the factors with the greatest impact on probability of illness. The models developed in this study are an example of risk assessments for milk produced and marketed from similar scenarios across the globe.

Quantitative assessment of human exposure to extended spectrum and AmpC β-lactamases bearing E. coli in lettuce attributable to irrigation water and subsequent horizontal gene transfer

The contribution of the fresh produce production environment to human exposure with bacteria bearing extended spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) has not been reported. High prevalence of ESBLs/AmpC bearing E. coli as well as a high gene transfer efficiency of lettuce and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used for the quantitative exposure assessment and models were constructed in Ms. Excel spreadsheet with farm to consumption chain accounted for by primary production, processing, retail and consumer storage. Probability distributions were utilised to take into account the variability of the exposure estimates. Exposure resulting from ESBL/AmpC positive E. coli and gene transfer was taken into account. Monte Carlo simulation was carried out using @Risk software followed by sensitivity and scenario analysis to assess most effective single or combinations of mitigation strategies for the ESBL/AmpC positive E. coli events from farm to fork. Three percent of South African lettuce consumers are exposed to lettuce contaminated with about 106.4±106.7 (95% CI: 105.1-107) cfu of ESBL/AmpC positive E. coli per serving. The contribution of originally positive isolates and conjugative genetic transfer was 106±106.7 (95% CI: 105-107) and 105.2±105.6 (95% CI: 103.9-105.8) cfu per serving respectively. Proportion of ESBL/AmpC positive E. coli (Spearman's correlation coefficient (ρ)=0.85), conjugative gene transfer (ρ=0.05-0.14), washing in chlorine water (ρ=0.18), further rinsing (ρ=0.15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation water microbial quality variation (87.4% reduction), storage period (49.9-87.4% reduction) and growth rate reduction by 75% (90% reduction). Reduction in growth rate together with storage time (92.1-99.4%) and reduction in storage time combined with E. coli concentration in irrigation water (95-96% reduction) were most effective combinations of mitigation measures. The high variation in exposure reflected the high irrigation water quality variation. The exposure levels may impose higher consumer risk than acceptable for irrigation water risk. E. coli contamination and growth related measures, as well as measures to reduce contamination with antimicrobial resistant E. coli from lettuce production environment are recommended. This exposure model could form a basis for the development of similar models assessing the impact of contaminated irrigation water and gene transfer in other microbial hazards, antimicrobial resistance types and fresh produce types.

Genetic Diversity and Antibiotic Resistance of Escherichia coli Isolates from Different Leafy Green Production Systems

Foodborne disease outbreaks linked to contaminated irrigation water and fresh produce are a public health concern. The presence of Escherichia coli isolates from irrigation water and leafy green vegetables in different food production systems (large commercial farms, small-scale farms, and homestead gardens) was investigated. The prevalence of antibiotic resistance and virulence in these isolates was further assessed, and links between water source and irrigated crops were identified using antimicrobial and genotypic analyses. Presumptive E. coli isolates were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy, and identities were confirmed by PCR using the uidA gene. Antimicrobial susceptibility was evaluated with the Kirby Bauer disk diffusion test; the presence of virulence genes was determined with enterobacterial repetitive intergenic consensus PCR assays. Of the 130 E. coli isolates from water (n =60) and leafy green vegetables (n =70), 19 (14.6%) were resistant to one antibiotic (tetracycline) and 92 (70.7%) were resistant to various antibiotics (including ampicillin, cefoxitin, and nalidixic acid). All E. coli isolates were susceptible to ceftriaxone and gentamicin. The virulence gene stx₂ was detected in E. coli isolates from irrigation water (8 [13.3%] of 60 isolates) and cabbages (3 [7.5%] of 40), but the virulence genes eae and stx₁ were not detected in any tested isolates from irrigation water and fresh produce samples. The prevalence of multidrug-resistant E. coli was lower in isolates from GLOBALG.A.P.-certified farms than in isolates from noncertified commercial and small-scale farms and homestead gardens. A link between the E. coli isolates from irrigation water sources and leafy green vegetables was established with phenotypic (antimicrobial) and genotypic (DNA fingerprinting) analyses. However, a link between virulence genes and the prevalence of antimicrobial resistance could not be established.

Pathogenic and commensal Escherichia coli from irrigation water show potential in transmission of extended spectrum and AmpC β-lactamases determinants to isolates from lettuce

There are few studies on the presence of extended-spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) in bacteria that contaminate vegetables. The role of the production environment in ESBL/AmpC gene transmission is poorly understood. The occurrence of ESBL/AmpC in Escherichia coli (n = 46) from lettuce and irrigation water and the role of irrigation water in the transmission of resistant E. coli were studied. The presence of ESBL/AmpC, genetic similarity and phylogeny were typed using genotypic and phenotypic techniques. The frequency of β-lactamase gene transfer was studied in vitro. ESBLs/AmpC were detected in 35 isolates (76%). Fourteen isolates (30%) produced both ESBLs/AmpC. Prevalence was highest in E. coli from lettuce (90%). Twenty-two isolates (48%) were multi-resistant with between two and five ESBL/AmpC genes. The major ESBL determinant was the CTX-M type (34 isolates). DHA (33% of isolates) were the dominant AmpC β lactamases. There was a high conjugation efficiency among the isolates, ranging from 3.5 × 10(-2) to 1 × 10(-2)  ± 1.4 × 10(-1) transconjugants per recipient. Water isolates showed a significantly higher conjugation frequency than those from lettuce. A high degree of genetic relatedness between E. coli from irrigation water and lettuce indicated possible common ancestry and pathway of transmission.