Wildlife identified as major source of Escherichia coli in agriculturally dominated watersheds by BOX A1R-derived genetic fingerprints

Risk assessment of three sheep stocking modes via identification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes

In order to protect the prairie ecological environment, intensive farming has become a prevalent method of sheep stocking. However, the link between captivity stocking mode and ecological risk of sheep feces is still poorly understood. In this study, metagenomics was used to identify the environmental risk of sheep feces among three stocking modes. Our results showed that captivity mode (C) elevated antibiotic resistance in feces, with the abundance of antibiotic resistance genes (ARGs) (5.381 copies/cell) higher than that of half-pen stocking (Fh) (1.093 copies/cell) and grazing mode (Fr) (0.315 copies/cell) (Duncan's test, P < 0.05). Virulence factor genes (VFGs) analysis showed offensive virulence factors had the highest abundance in captivity feces (C: 3.826 copies/cell, Fh: 0.342 copies/cell, Fr: 0.163 copies/cell) (Duncan's test, P < 0.05). 15 metagenome-assembled genomes (MAGs) were identified as potential pathogenic antibiotic resistant bacteria (PARB) and revealed that Escherichia, Klebsiella may be the main host of ARGs and VFGs in sheep feces. Furthermore, the minimal inhibition concentrations (MIC) of tetracycline of E. coli in the captivity feces was 8.6 times and 4.7 times than that of grazing and half-pen stocking samples, respectively. The Non-metric multidimensional scaling (NMDS) revealed that high stocking density leads to feces causing increased harm to the environment. Although feces from sheep raised in captivity and half-pen stocking modes are easier to collect, they are more harmful to the environment and aerobic composting should be done before their application to farmland. This work provides a guideline for better control of the environmental risk of sheep feces from different stocking modes.

Management-intensive grazing impacts on total Escherichia coli, E. coli O157:H7, and antibiotic resistance genes in a riparian stream

The impacts of management-intensive grazing (MIG) of cattle on concentrations of total Escherichia coli, total suspended solids (TSS), and nitrate-nitrite nitrogen (NO₃ + NO₂-N), and occurrence of E. coli O157:H7 and selected antibiotic resistance genes (ARGs) in stream water and/or sediments were evaluated. Cattle were grazed for two-week periods in May in each of three years. Overall, grazing increased total E. coli in downstream water by 0.89 log₁₀ MPN/100 mL (p < 0.0001), and downstream total E. coli concentrations were higher than upstream over all sampling intervals. Downstream TSS levels also increased (p ≤ 0.0294) during grazing. In contrast, there was a main effect of treatment for downstream NO₃ + NO₂-N to be lower than upstream (3.59 versus 3.70 mg/L; p = 0.0323). Overwintering mallard ducks increased total E. coli and TSS concentrations in January and February (p < 0.05). For precipitation events during the 24 h before sampling, each increase of 1.00 cm of rainfall increased total E. coli by 0.49 log₁₀ MPN/100 mL (p = 0.0005). In contrast, there was no association of previous 24 h precipitation volume on TSS (p = 0.1540), and there was a negative linear effect on NO₃ + NO₂-N (p = 0.0002). E. coli O157:H7 prevalence was low, but the pathogen was detected downstream up to 2½ months after grazing. Examination of ARGs sul1, ermB, bla_ctx-m-32, and intI1 identified the need for additional research to understand the impact of grazing on the ecology of these resistance determinants in pasture-based cattle production. While E. coli remained higher in downstream water compared to upstream, MIG may reduce the magnitude of the downstream E. coli concentrations. Likewise, the MIG strategy may prevent large increases in TSS and NO₃ + NO₂-N concentrations during heavy rain events. Results indicate that MIG can limit the negative effects of cattle grazing on stream water quality.

Microbial water quality at contrasting recreational areas in a mixed-use watershed in eastern Canada

Recreational water use is an important source of human enteric illness. Enhanced (episodic) surveillance of natural recreational waters as a supplement to beach monitoring can enrich our understanding of human health risks. From 2011 to 2013, water sampling was undertaken at recreational sites on a watershed in eastern Canada. This study compared the prevalence and associations of human enteric pathogens and fecal indicator organisms. Beach water samples had lower pathogen presence than those along the main river, due to different pollution sources and the hydrological disposition. Pathogen profiles identified from the beach sites suggested a more narrow range of sources, including birds, indicating that wild bird management could help reduce public health risks at these sites. The presence and concentration of indicator organisms did not differ significantly between beaches and the river. However, higher concentrations of generic Escherichia coli were observed when Salmonella and Cryptosporidium were present at beach sites, when Salmonella was present at the river recreational site, and when verotoxigenic E. coli were present among all sites sampled. In this watershed, generic E. coli concentrations were good indicators of potential contamination, pathogen load, and elevated human health risk, supporting their use for routine monitoring where enhanced pathogen testing is not possible.

Longitudinal Surveillance and Risk Assessment of Resistance in Escherichia coli to Enrofloxacin from A Large-Scale Chicken Farm in Hebei, China

The purpose of this study was to investigate the changes of resistance phenotype and plasmid-mediated quinolone resistance genes (PMQRs) in Escherichia coli (E. coli) during enrofloxacin (ENR) administration in different breeding cycles. In 2020, 983 strains of E. coli were isolated from different samples in different cycles at the broiler farm with the largest single batch of slaughter capacity in Hebei Province, China. All samples were from chicken, environmental, and human sources. The sensitivity of the isolates to various antibiotics was determined by broth microdilution method. The findings of this study include: (1) the total isolation rate of E. coli in the four cycles was 63.83% (983/1540); (2) the average resistance rate of E. coli from 1-day-old chickens to enrofloxacin was as high as 75% in each cycle, and with the use of enrofloxacin, the resistance rate of E. coli from chickens gradually increased to 100%; (3) 107 strains of E. coli randomly selected from different cycles and sources demonstrated the multi-drug resistance phenotypes. The highest resistance rate was doxycycline (100%), and the lowest was erythromycin (54.21%); (4) the detection rate of PMQRs of E. coli from chickens in different cycles were always higher than that from environmental and human. In particular, the PMQRs pollution rate of chicken seedlings in each cycle were generally higher than that of other sources; (5) We used SPSS software to analyze the Kendall rank correlation of the experimental data. The resistance of E. coli isolated from this farm to ciprofloxacin (CIP) may increase along with the increase of resistance to enrofloxacin (Kendall's tau-b = 0.190, p = 0.021). All these data highlight the serious problem of bacterial resistance in this farm. Therefore, it is urgent to provide guidance for the prevention and control of colibacillosis and drug resistance in this farm.

Microbial source tracking of fecal contamination in Laguna Lake, Philippines using the library-dependent method, rep-PCR

Laguna Lake is an economically important resource in the Philippines, with reports of declining water quality due to fecal pollution. Currently, monitoring methods rely on counting fecal indicator bacteria, which does not supply information on potential sources of contamination. In this study, we predicted sources of Escherichia coli in lake stations and tributaries by establishing a fecal source library composed of rep-PCR DNA fingerprints of human, cattle, swine, poultry, and sewage samples (n = 1,408). We also evaluated three statistical methods for predicting fecal contamination sources in surface waters. Random forest (RF) outperformed k-nearest neighbors and discriminant analysis of principal components in terms of average rates of correct classification in two- (84.85%), three- (82.45%), and five-way (74.77%) categorical splits. Overall, RF exhibited the most balanced prediction, which is crucial for disproportionate libraries. Source tracking of environmental isolates (n = 332) revealed the dominance of sewage (47.59%) followed by human sources (29.22%), poultry (12.65%), swine (7.23%), and cattle (3.31%) using RF. This study demonstrates the promising utility of a library-dependent method in augmenting current monitoring systems for source attribution of fecal contamination in Laguna Lake. This is also the first known report of microbial source tracking using rep-PCR conducted in surface waters of the Laguna Lake watershed.

Impacts of a large invasive mammal on water quality in riparian ecosystems

Wild pigs (Sus scrofa) are a highly invasive species in many regions of the world and can act as ecosystem engineers in areas where they are established. In riparian ecosystems, wild pigs may affect water quality parameters and introduce fecal bacteria, although previous studies have reported conflicting results. We propose four conditions that we believe are needed for an accurate assessment of wild pig impacts on water quality and address each one in our study. Water samples were collected between May 2018 and June 2019 in riparian watersheds on a privately owned property in Alabama that was densely populated by wild pigs (treatment) and in watersheds at a nearby national forest without an established population. Samples were analyzed for concentrations of water quality parameters, such as anions and cations, dissolved oxygen, total suspended solids, N, dissolved organic C, and Escherichia coli and other fecal coliforms. An additional 38 samples were analyzed using quantitative polymerase chain reaction for swine fecal bacteroidetes. At treatment watersheds, specific conductivity and concentrations of organic N and C, SO₄ ^2- , and Ca²⁺ were between 2 and 11 times that of reference watersheds. Escherichia coli values at treatment watersheds were 40 times reference watershed values. DNA from swine fecal bacteroidetes was detected in 70% of treatment samples and 0% of reference samples. Wild pigs are a threat to water quality in riparian areas, and our results indicate that it may be important to control populations upstream of major drinking water sources and recreational areas.

Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal

High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coliE. coli survives in extrahost environments (e.g., soil) and could be dispersed across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli strains is of importance in assessing the contamination risk of agricultural products. Here, using multilocus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York State, USA, and compared the distribution of E. coli and the influence that environmental selection and dispersal have on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution appears to be shaped by relatively strong environmental selection, likely from soil phosphorus, and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land use types was relatively homogeneous; this distribution appeared to be a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal.IMPORTANCE Understanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli Agricultural areas in such watersheds may have a higher risk of produce contamination due to fewer environmental constraints and higher potential of dispersal of enteric bacteria between locations. Thus, there is a perceived trade-off between priorities of environmental conservation and public health in on-farm food safety, with limited ecological data supporting or refuting the role of wildlife in dispersing pathogens under normal operating conditions. By combining field sampling and spatial modeling, we explored ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can benefit agricultural, environmental, and public health scientists who aim to reduce the risk of food contamination by enteric bacteria while minimizing negative impacts on wildlife habitats.

Selecting rep-PCR markers to source track fecal contamination in Laguna Lake, Philippines

Fecal contamination is one of the factors causing deterioration of Laguna Lake. Although total coliform levels are constantly monitored, no protocol is in place to identify their origin. This can be addressed using the library-dependent microbial source tracking (MST) method, repetitive element sequence-based polymerase chain reaction (rep-PCR) fingerprinting. Serving as a prerequisite in developing the host-origin library, we assessed the discriminatory power of three fingerprinting primers, namely BOX-A1R, (GTG)₅, and REP1R-1/2-1. Fingerprint profiles were obtained from 290 thermotolerant Escherichia coli isolated from sewage waters and fecal samples of cows, chickens, and pigs from regions surrounding the lake. Band patterns were converted into binary profiles and were classified using the discriminant analysis of principal components. Results show that: (1) REP1R-1/2-1 has a low genotyping success rate and information content; (2) increasing the library size led to more precise estimates of library accuracy; and (3) combining fingerprint profiles from BOX-A1R and (GTG)₅ revealed the best discrimination (average rate of correct classification (ARCC) = 0.82 ± 0.06) in a two-way categorical split; while (4) no significant difference was found between the combined profiles (0.74 ± 0.15) and using solely BOX-A1R (0.76 ± 0.09) in a four-way split. Testing the library by identifying known isolates from a separate dataset has shown that a two-way classification performed better (ARCC = 0.66) than a four-way split (ARCC = 0.29). The library can be developed further by adding more representative isolates per host source. Nevertheless, our results have shown that combining profiles from BOX-A1R and (GTG)₅ is recommended in developing the MST library for Laguna Lake.

Temporal and spatial variability of instream indicator bacteria (Escherichia coli) and implications for water quality monitoring

Many water quality monitoring programs quantify Escherichia coli, an indicator of fecal contamination and potential sewage pollution. However, interpretation of E. coli data can be complex due to abiotic factors that influence its growth and mortality. The goal of this study was to quantify the variability of E. coli in a river and assess the impact of that variability on water quality monitoring study design and sewage pollution source identification. Over 1900 samples were collected and analyzed from 2007 to 2017 in the Norwalk River in Connecticut. Sixty-six percent of the samples collected during weekly to monthly monitoring had E. coli concentrations below 200 CFU/100 mL, indicating that elevated bacteria concentrations were captured infrequently. Patterns observed during daily sampling indicated that the randomization of sampling days within a week may support the identification of pollution sources driven by human behavioral patterns. Spatial autocorrelation in bacteria concentrations was not observed between sites, indicating that the sample locations were not spaced sufficiently close together to be redundant for monitoring. On finer spatial scales however, detection of a known pollution source was found to be challenging at even short distances downstream, with less than 25% of the original source concentration detected at 10 m downstream and less than 10% by 1000 m downstream, suggesting that a high density of study sites may be needed to detect potential sources. These findings can be used to better understand the natural variability of this important indicator organism in freshwater systems, and inform more efficient and effective monitoring.

Effectiveness of BOX-PCR in Differentiating Genetic Relatedness among Salmonella enterica Serotype 4,[5],12:i:- Isolates from Hospitalized Patients and Minced Pork Samples in Northern Thailand

Salmonella enterica Serotype 4,[5],12:i:-, a monophasic variant of S. Typhimurium, with high virulence and multidrug resistance is distributed globally causing pathogenicity to both humans and domesticated animals. BOX-A1R-based repetitive extragenic palindromic-PCR (BOX)-PCR proved to be superior to three other repetitive element-based PCR typing methods, namely, enterobacterial repetitive intergenic consensus (ERIC)-, poly-trinucleotide (GTG)₅-, and repetitive extragenic palindromic (REP)-PCR (carried out under a single optimized amplification condition), in differentiating genetic relatedness among S. 4,[5],12:i:- isolates from feces of hospitalized patients (n=12) and isolates from minced pork samples of S. 4,[5],12:i:- (n=6), S. Typhimurium (n=6), and Salmonella Serogroup B (n=4) collected from different regions of northern Thailand. Construction of phylogenetic trees from amplicon size patterns allowed allocation of Salmonella isolates into clusters of similar genetic relatedness, with BOX-PCR generating more unique clusters for each serotype than the other three typing methods. BOX-, (GTG)₅-, and REP-PCR indicated significant genetic relatedness between S. 4,[5],12:i:- isolates 1 and 9 from hospitalized patients and S. 4,[5],12:i:- isolate en 29 from minced pork, suggesting a possible route of transmission. Thus, BOX-PCR provides a suitable molecular typing method for discriminating genetic relatedness among Salmonella spp. of the same and different serotypes and should be suitable for application in typing and tracking route of transmission in Salmonella outbreaks.

Genetic diversity of Escherichia coli isolates from surface water and groundwater in a rural environment

The genetic characteristics among Escherichia coli strains can be grouped by origin of isolation. Then, it is possible to use the genotypes as a tool to determine the source of water contamination. The aim of this study was to define water aptitude for human consumption in a rural basin and to assess the diversity of E. coli water populations. Thus, it was possible to identify the main sources of fecal contamination and to explore linkages with the hydrogeological environment and land uses. The bacteriological analysis showed that more than 50% of samples were unfit for human consumption. DNA fingerprinting analysis by BOX-PCR indicated low genotypic diversity of E. coli isolates taken from surface water and groundwater. The results suggested the presence of a dominant source of fecal contamination. The relationship between low genotypic diversity and land use would prove that water contamination comes from livestock. The genetic diversity of E. coli isolated from surface water was less than that identified in groundwater because of the different hydraulic features of both environments. Furthermore, each one of the two big strain groups identified in this basin is located in different sub-basins, showing that hydrological dynamics exerts selective pressure on bacteria DNA.

Balancing ecosystem function, services and disservices resulting from expanding goose populations

As goose populations increase in abundance, their influence on ecological processes is increasing. We review the evidence for key ecological functions of wild goose populations in Eurasia and North America, including aquatic invertebrate and plant propagule transport, nutrient deposition in terrestrial and aquatic ecosystems, the influence of goose populations on vegetation biomass, carbon storage and methane emission, species diversity and disease transmission. To estimate the implications of their growing abundance for humans, we explore how these functions contribute to the provision of ecosystem services and disservices. We assess the weight, extent and trends among such impacts, as well as the balance of their value to society. We examine key unresolved issues to enable a more balanced assessment of the economic costs or benefits of migratory geese along their flyways, including the spatial and temporal variation in services and their contrasting value to different user groups. Many ecological functions of geese are concluded to provide neither services nor disservices and, ecosystem disservices currently appear to outweigh services, although this varies between regions. We consider an improved quantification of ecosystem services and disservices, and how these vary along population flyways with respect to variation in valuing certain cultural services, and under different management scenarios aimed at reducing their disservices, essential for a more balanced management of goose populations.

Detection of hepatitis E virus and other livestock-related pathogens in Iowa streams

Manure application is a source of pathogens to the environment. Through overland runoff and tile drainage, zoonotic pathogens can contaminate surface water and streambed sediment and could affect both wildlife and human health. This study examined the environmental occurrence of gene markers for livestock-related bacterial, protozoan, and viral pathogens and antibiotic resistance in surface waters within the South Fork Iowa River basin before and after periods of swine manure application on agricultural land. Increased concentrations of indicator bacteria after manure application exceeding Iowa's state bacteria water quality standards suggest that swine manure contributes to diminished water quality and may pose a risk to human health. Additionally, the occurrence of HEV and numerous bacterial pathogen genes for Escherichia coli, Enterococcus spp., Salmonella sp., and Staphylococcus aureus in both manure samples and in corresponding surface water following periods of manure application suggests a potential role for swine in the spreading of zoonotic pathogens to the surrounding environment. During this study, several zoonotic pathogens were detected including Shiga-toxin producing E. coli, Campylobacter jejuni, pathogenic enterococci, and S. aureus; all of which can pose mild to serious health risks to swine, humans, and other wildlife. This research provides the foundational understanding required for future assessment of the risk to environmental health from livestock-related zoonotic pathogen exposures in this region. This information could also be important for maintaining swine herd biosecurity and protecting the health of wildlife near swine facilities.

Investigation on the temporal variation and source tracking of faecal bacteria in a forest dominated watershed (Comox Lake), British Columbia, Canada

AIMS

The aims of this study were to investigate the temporal variation in Escherichia coli density and its sources at the drinking water intake of Comox Lake for a period of 3 years (2011-2013).

METHODS AND RESULTS

Density of E. coli was assessed by standard membrane filtration method. Source tracking of E. coli were done by using BOX-A1R-based rep-PCR DNA fingerprinting method. Over the years, the mean E. coli density ranged from nondetectable to 9·8 CFU 100 ml(-1) . The density of E. coli in each of the years did not show any significant difference (P > 0·05); however, a comparatively higher density was observed during the fall. Wildlife was (64·28%, 153/238) identified as the major contributing source of E. coli, followed by human (18·06%, 43/238) and unknown sources (17·64%, 42/238). Although the sources were varied by year and season, over all, the predominant contributing sources were black bear, human, unknown, elk, horse and gull.

CONCLUSIONS

The findings of this investigation identified the multiple animal sources contributing faecal bacteria into the drinking water intake of Comox Lake and their varying temporal occurrence.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study can reliably inform the authorities about the most vulnerable period (season) of faecal bacterial loading and their potential sources in the lake for improving risk assessment and pollution mitigation.

Diverse and abundant multi-drug resistant E. coli in Matang mangrove estuaries, Malaysia

E.coli, an important vector distributing antimicrobial resistance in the environment, was found to be multi-drug resistant, abundant, and genetically diverse in the Matang mangrove estuaries, Malaysia. One-third (34%) of the estuarine E. coli was multi-drug resistant. The highest antibiotic resistance prevalence was observed for aminoglycosides (83%) and beta-lactams (37%). Phylogenetic groups A and B1, being the most predominant E. coli, demonstrated the highest antibiotic resistant level and prevalence of integrons (integron I, 21%; integron II, 3%). Detection of phylogenetic group B23 downstream of fishing villages indicates human fecal contamination as a source of E. coli pollution. Enteroaggregative E. coli (1%) were also detected immediately downstream of the fishing village. The results indicated multi-drug resistance among E. coli circulating in Matang estuaries, which could be reflective of anthropogenic activities and aggravated by bacterial and antibiotic discharges from village lack of a sewerage system, aquaculture farms and upstream animal husbandry.

Transport of through a Thick Vadose Zone

Livestock manure applications on fields can be a source of contamination in water resources, including groundwater. Although fecal indicators like have often been detected in tile drainage systems, few studies have monitored groundwater at depth after manure treatments, especially at sites with a deep, heterogeneous vadose zone. Our hypothesis was that microbial transport through a thick vadose zone would be limited or nonexistent due to attenuation processes, subsurface thickness, and heterogeneity. This study tested this hypothesis by monitoring concentrations beneath a 12-m-thick vadose zone of coarse, heterogeneous glacial sediments after surface application of liquid swine manure. was detected on all 23 sample dates over the 5-mo period (4 Apr. 2012-13 Aug. 2012), with particularly elevated concentrations 1 wk after application and lasting for 5 wk. Variable low-level concentrations before and after the elevated period suggest remobilization and delayed transport of microorganisms to the water table without additional loadings within the flow field. These findings suggest preferential flow pathways allowing deep infiltration of manure bacteria as well as a continued source of bacteria, with variable retention and travel times, over several months. Preferential flow pathways at this site include soil macropores, depression focused infiltration, and pathways related to subsurface heterogeneity and/or fracture flow through finer-grained diamict beds. Further research is needed to confirm the relative contribution of sources, constrain travel times, and define specific transport pathways.

Detection of multi-drug resistant Escherichia coli in the urban waterways of Milwaukee, WI

Urban waterways represent a natural reservoir of antibiotic resistance which may provide a source of transferable genetic elements to human commensal bacteria and pathogens. The objective of this study was to evaluate antibiotic resistance of Escherichia coli isolated from the urban waterways of Milwaukee, WI compared to those from Milwaukee sewage and a clinical setting in Milwaukee. Antibiotics covering 10 different families were utilized to determine the phenotypic antibiotic resistance for all 259 E. coli isolates. All obtained isolates were determined to be multi-drug resistant. The E. coli isolates were also screened for the presence of the genetic determinants of resistance including ermB (macrolide resistance), tet(M) (tetracycline resistance), and β-lactamases (bla OXA, bla SHV, and bla PSE). E. coli from urban waterways showed a greater incidence of antibiotic resistance to 8 of 17 antibiotics tested compared to human derived sources. These E. coli isolates also demonstrated a greater incidence of resistance to higher numbers of antibiotics compared to the human derived isolates. The urban waterways demonstrated a greater abundance of isolates with co-occurrence of antibiotic resistance than human derived sources. When screened for five different antibiotic resistance genes conferring macrolide, tetracycline, and β-lactam resistance, clinical E. coli isolates were more likely to harbor ermB and bla OXA than isolates from urban waterway. These results indicate that Milwaukee's urban waterways may select or allow for a greater incidence of multiple antibiotic resistance organisms and likely harbor a different antibiotic resistance gene pool than clinical sources. The implications of this study are significant to understanding the presence of resistance in urban freshwater environments by supporting the idea that sediment from urban waterways serves as a reservoir of antibiotic resistance.

Reach specificity in sediment E. coli population turnover and interaction with waterborne populations

Sediment-borne Escherichia coli can elevate waterborne concentrations through sediment resuspension or hyporheic exchange. This study sought to correlate hydrological, sediment transport, and water quality variables with: (i) the temporal stability of sediment E. coli populations [concentrations, strain richness and similarity (Raup-Crick index)]; and (ii) the contribution of sediment E. coli to the water column as defined through a library-dependent microbial source tracking approach that matched waterborne E. coli isolates to sediment E. coli populations. Three monitoring locations differing in their hydrological characteristics and adjacent upland fecal sources (dairy operation, low-density residential, and tile-drained cultivated field) were investigated. Sediment E. coli population turnover was influenced by sediment transport at upstream, high-energy reaches, but not at the downstream low-energy reach. Sediment contributions to the water column averaged 13% and 18%, and fecal sources averaged 17% and 21% at the upstream sites adjacent to dairy operations and low-density residential areas, respectively. Waterborne E. coli at the downstream site had low matches to E. coli from reach sediments (1%), higher matches to the upstream sediments (27% and 12%), and an average of 14% matches to the tile drained field. The percentage of waterborne E. coli matching sediment-borne E. coli at each stream reach varied in correlations to hydrological and sediment transport variables, suggesting reach-specific differences in the role of sediment resuspension and hyporheic exchange on E. coli transport.

Occurrence of diarrheagenic virulence genes and genetic diversity in Escherichia coli isolates from fecal material of various avian hosts in British Columbia, Canada

Contamination of surface water by fecal microorganisms originating from human and nonhuman sources is a public health concern. In the present study, Escherichia coli isolates (n = 412) from the feces of various avian host sources were screened for various virulence genes: stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae (enteropathogenic E. coli [EPEC]), est-h, est-p, and elt (encoding heat-stable toxin [ST] variants STh and STp and heat-labile toxin [LT], respectively) (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). None of the isolates were found to be positive for stx1, while 23% (n = 93) were positive for only stx2, representing STEC, and 15% (n = 63) were positive for only eae, representing EPEC. In addition, five strains obtained from pheasant were positive for both stx2 and eae and were confirmed as non-O157 by using an E. coli O157 rfb (rfbO157) TaqMan assay. Isolates positive for the virulence genes associated with ETEC and EIEC were not detected in any of the hosts. The repetitive element palindromic PCR (rep-PCR) fingerprint analysis identified 143 unique fingerprints, with an overall Shannon diversity index of 2.36. Multivariate analysis of variance (MANOVA) showed that the majority of the STEC and EPEC isolates were genotypically distinct from nonpathogenic E. coli and clustered independently. MANOVA analysis also revealed spatial variation among the E. coli isolates, since the majority of the isolates clustered according to the sampling locations. Although the presence of virulence genes alone cannot be used to determine the pathogenicity of strains, results from this study show that potentially pathogenic STEC and EPEC strains can be found in some of the avian hosts studied and may contaminate surface water and potentially impact human health.

Evaluation of Repetitive Extragenic Palindromic-PCR for Discrimination of FecalEscherichia colifrom Humans, and Different Domestic- and Wild-Animals

The objective of this study was to investigate the potential of repetitive extragenic palindromic anchored polymerase chain reaction (rep-PCR) in differentiating fecal Escherichia coli isolates of human, domestic- and wild-animal origin that might be used as a molecular tool to identify the possible source(s) of fecal pollution of source water. A total of 625 fecal E. coli isolates of human, 3 domestic- (cow, dog and horse) and 7 wild-animal (black bear, coyote, elk, marmot, mule deer, raccoon and wolf) species were characterized by rep-PCR DNA fingerprinting technique coupled with BOX A1R primer and discriminant analysis. Discriminant analysis of rep-PCR DNA fingerprints of fecal E. coli isolates from 11 host sources revealed an average rate of correct classification of 79.89%, and 84.6%, 83.8%, 83.3%, 82.5%, 81.6%, 80.8%, 79.8%, 79.3%, 77.4%, 73.2% and 63.6% of elk, human, marmot, mule deer, cow, coyote, raccoon, horse, dog, wolf and black bear fecal E. coli isolates were assigned to the correct host source. These results suggest that rep-PCR DNA fingerprinting procedures can be used as a source tracking tool for detection of human- as well as animal-derived fecal contamination of water.

Escherichia coli contamination of lettuce grown in soils amended with animal slurry

A pilot study was conducted to assess the transfer of Escherichia coli from animal slurry fertilizer to lettuce, with E. coli serving as an indicator of fecal contamination and as an indicator for potential bacterial enteric pathogens. Animal slurry was applied as fertilizer to three Danish agricultural fields prior to the planting of lettuce seedlings. At harvest, leaves (25 g) of 10 lettuce heads were pooled into one sample unit (n = 147). Soil samples (100 g) were collected from one field before slurry application and four times during the growth period (n = 75). E. coli was enumerated in slurry, soil, and lettuce on 3M Petrifilm Select E. coli Count Plates containing 16 mg/liter streptomycin, 16 mg/liter ampicillin, or no antimicrobial agent. Selected E. coli isolates (n = 83) originating from the slurry, soil, and lettuce were genotyped by pulsed-field gel electrophoresis (PFGE) to determine the similarity of isolates. The slurry applied to the fields contained 3.0 to 4.5 log CFU/g E. coli. E. coli was found in 36 to 54% of the lettuce samples, streptomycin-resistant E. coli was found in 10.0 to 18.0% of the lettuce samples, and ampicillin-resistant E. coli in 0 to 2.0% of the lettuce samples (the detection limit was 1 log CFU/g). The concentration of E. coli exceeded 2 log CFU/g in 19.0% of the lettuce samples. No E. coli was detected in the soil before the slurry was applied, but after, E. coli was present until the last sampling day (harvest), when 10 of 15 soil samples contained E. coli. A relatively higher frequency of E. coli in lettuce compared with the soil samples at harvest suggests environmental sources of fecal contamination, e.g., wildlife. The higher frequency was supported by the finding of 21 different PFGE types among the E. coli isolates, with only a few common PFGE types between slurry, soil, and lettuce. The frequent finding of fecal-contaminated lettuce indicates that human pathogens such as Salmonella and Campylobacter can be present and represent food safety hazards.

Using Campylobacter spp. and Escherichia coli data and Bayesian microbial risk assessment to examine public health risks in agricultural watersheds under tile drainage management

Human campylobacteriosis is the leading bacterial gastrointestinal illness in Canada; environmental transmission has been implicated in addition to transmission via consumption of contaminated food. Information about Campylobacter spp. occurrence at the watershed scale will enhance our understanding of the associated public health risks and the efficacy of source water protection strategies. The overriding purpose of this study is to provide a quantitative framework to assess and compare the relative public health significance of watershed microbial water quality associated with agricultural BMPs. A microbial monitoring program was expanded from fecal indicator analyses and Campylobacter spp. presence/absence tests to the development of a novel, 11-tube most probable number (MPN) method that targeted Campylobacter jejuni, Campylobacter coli, and Campylobacter lari. These three types of data were used to make inferences about theoretical risks in a watershed in which controlled tile drainage is widely practiced, an adjacent watershed with conventional (uncontrolled) tile drainage, and reference sites elsewhere in the same river basin. E. coli concentrations (MPN and plate count) in the controlled tile drainage watershed were statistically higher (2008-11), relative to the uncontrolled tile drainage watershed, but yearly variation was high as well. Escherichia coli loading for years 2008-11 combined were statistically higher in the controlled watershed, relative to the uncontrolled tile drainage watershed, but Campylobacter spp. loads for 2010-11 were generally higher for the uncontrolled tile drainage watershed (but not statistically significant). Using MPN data and a Bayesian modelling approach, higher mean Campylobacter spp. concentrations were found in the controlled tile drainage watershed relative to the uncontrolled tile drainage watershed (2010, 2011). A second-order quantitative microbial risk assessment (QMRA) was used, in a relative way, to identify differences in mean Campylobacter spp. infection risks among monitoring sites for a hypothetical exposure scenario. Greater relative mean risks were obtained for sites in the controlled tile drainage watershed than in the uncontrolled tile drainage watershed in each year of monitoring with pair-wise posterior probabilities exceeding 0.699, and the lowest relative mean risks were found at a downstream drinking water intake reference site. The second-order modelling approach was used to partition sources of uncertainty, which revealed that an adequate representation of the temporal variation in Campylobacter spp. concentrations for risk assessment was achieved with as few as 10 MPN data per site. This study demonstrates for the first time how QMRA can be implemented to evaluate, in a relative sense, the public health implications of controlled tile drainage on watershed-scale water quality.

Identification of source of faecal pollution of Tirumanimuttar River, Tamilnadu, India using microbial source tracking

Efficient management of deteriorating water bodies can be achieved by determining the sources of faecal pollution. Resourceful techniques for discrimination of the sources of Escherichia coli in surface water have recently been developed, including the use of river water to facilitate faecal indicator surveillance, identification of sources of faecal contamination and employing relevant management practices to maintain water quality. This study was conducted to employ microbial source tracking (MST) techniques for the determination of the sources of faecal pollution based on a water quality investigation of the physico-chemical characteristics and coliform count point of the Tirumanimuttar River. To accomplish this, an MST library-based antibiotic resistance analysis, serotyping and the genomic tool rep-PCR techniques were applied, and the obtained results were analysed statistically. Among 135 and 70 E. coli isolates present in the library and water samples collected from the river and nearby well water sources, respectively, most showed intrinsic, high or moderate resistance to antibiotics. Isolates from human and pig faecal sources were 92% homologous with the samples from the river, whereas isolates from sewage and dairy cattle showed 89% and 80% homology, respectively. These findings indicated that the Tirumanimuttar River is subjected to stress from anthropogenic activities and runoff contaminated with agricultural and human faecal contamination. The sources of faecal pollution identified in this study may facilitate the monitoring and management of the Tirumanimuttar River.

Repetitive element (REP)-polymerase chain reaction (PCR) analysis of Escherichia coli isolates from recreational waters of southeastern Lake Huron

Repetitive element-polymerase chain reaction (REP-PCR) DNA fingerprinting and library-based microbial source tracking (MST) methods were utilized to investigate the potential sources of Escherichia coli pollution in recreational waters of southeastern Lake Huron. In addition to traditional sources such as humans, agriculture, and wildlife, environmentally persistent E. coli isolates were included in the identification library as a separate library unit consisting of the E. coli strains isolated from interstitial water on the beach itself. Our results demonstrated that the dominant source of E. coli pollution of the lake was agriculture, followed by environmentally adapted E. coli strains, wildlife, and then humans. A similar ratio of contributing sources was observed in all samples collected from various locations including the river discharging to the beach in both 2005 and 2006. The high similarity between the compositions of E. coli communities collected simultaneously in the river and in the lake suggests that tributaries were the major overall sources of E. coli to the lake. Our findings also suggest that environmentally adapted strains (EAS) of E. coli should be included as one of the potential sources in future microbial source tracking efforts.

Domestic wastewater influent profiling using mitochondrial real-time PCR for source tracking animal contamination

Real-time PCR amplifying mammalian and avian mitochondrial DNA (mtDNA) was developed to characterize domestic and light industrial wastewater influent from two municipal wastewater treatment facilities (WWTF) over a 24-week period. Influent samples were assayed with species-specific primers and dual-labeled probes for human, bovine, swine, dog, cat, Canada goose and white-tailed deer to detect and quantify eukaryotic mtDNA contributors to local municipal wastewaters. Human (mean=9.6 x 10(4) copies/ml) and dog (mean=5.3 x 10(2) copies/ml) mtDNA were detected in all 24 samples (12 samples/site). Bovine and swine mtDNA were detected sporadically and at lower levels than human mtDNA, means=3.0 x 10(4) and 9.5 x 10(2) copies/ml, respectively. Domestic cat, Canada goose and white-tailed deer were detected only once in 24 samples. Mitochondrial DNA concentrations were compared to other bacterial, chemical and spectrophotometric parameters. Human mtDNA was positively correlated with ammonia concentration (P=0.01) and initial OD(600) reading (P=0.02) at one WWTF. Bovine mtDNA was positively correlated with biological oxygen demand (BOD) (P=0.02), final DNA concentration (P=0.03), initial and final humic acid concentrations (P=0.01, P=0.01), and final OD(600) (P=0.03) at one WWTF and total suspended solids (TSS) (P=0.04, P=0.09) at both facilities. Fecal coliforms were not positively or negatively correlated with mtDNA concentrations of any species assayed. For source tracking purposes, a combination of human (10(5) copies/ml) and dog mtDNA signal (10(2) copies/ml) could be indicative of municipal domestic wastewater contamination of environmental waters.

Research priorities for coordinating management of food safety and water quality

Efforts to exclude disease organisms from farms growing irrigated lettuce and leafy vegetables on California's central coast are conflicting with traditionally accepted strategies to protect surface water quality. To begin resolving this dilemma, over 100 officials, researchers, and industry representatives gathered in April 2007 to set research priorities that could lead to effective co-management of both food safety and water quality. Following the meeting, research priorities were refined and ordered by way of a Delphi process completed by 35 meeting participants. Although water quality and food safety experts conceptualized the issues differently, there were no deep disagreements with respect to research needs. Top priority was given to investigating the fate of pathogens potentially present on farms. Intermediate priorities included characterizing the influence of specific farm management practices on food safety and improving our understanding of vector processes. A scientific subdiscipline focusing on competing risks is needed to characterize and resolve conflicts between human and environmental health.

Transmission identification of Escherichia coli aerosol in chicken houses to their environments using ERIC-PCR

In order to study E. coli aerosol spreading from chicken houses to their surrounding air, air samples, including indoor and outdoor air (upwind 10 and 50 m as well as downwind 10, 50, 100, 200 and 400 m away) of 5 chicken houses were collected using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli concentrations (CFU/m(3) air) collected from different sampling sites were calculated. E. coli strains from chicken feces samples were also isolated. Furthermore, the enterobacterial repetitive intergenic consensus (ERIC)-PCR method was applied to amplify the isolated E. coli strain DNA samples. Through the genetic similarity analyses of the E. coli obtained from different sampling sites, the spreading of bioaerosol from animal houses to the ambient air was characterized. The results showed that the isolated E. coli concentrations in indoor air (9-63 CFU/m(3)) in 5 chicken houses were higher than those in upwind and downwind air, but there were no significant differences between the indoor and downwind sites 10 m away from all the 5 houses (P>0.05). The phylogenetic tree indicated that a part of the E. coli (34.1%) isolated from indoor air had 100% similarity with those isolated from feces, and that most of E. coli isolated (54.5%) from downwind at 10, 50, 100 or even 200 m had 100% similarity with those isolated from indoor air or feces too. But those isolated from upwind air had a lower similarity (73%-92%) with corresponding strains isolated from indoor air or feces. Our results suggested that some strains isolated from downwind air and indoor air originated in the chicken feces, but most of isolates obtained from upwind air samples did not come from the chicken feces or indoor air. Effective hygienic measures should be taken in animal farms to prevent or minimize downwind spreading of microorganism aerosol.

Phenotyping and genotyping of antibiotic-resistant Escherichia coli isolated from a natural river basin

Scientists have become increasingly concerned about the occurrence of antibacterial resistance in the environment. In this study, Escherichia coli resistant to one or more antibiotics among nine antibiotics was screened from Wenyu River Basin in Beijing, China, with mean frequency of 48.7 +/- 8.7% of 388 isolates in summer and 47 +/- 6% of 236 isolates in winter. The mean multiantibiotic resistance (MAR) index in summer was 0.11 +/- 0.03, slightly lower than that (0.14 +/- 0.04) in winter. Most frequent resistance appeared for sulfonamides, tetracycline, and ampicillin. The distribution of 20 tetracycline, three sulfonamide, and three beta-lactam resistance genes was assessed in the resistant isolates. While 97% of the ampicillin (AMP) resistant mechanism could be explained by the resistance gene TEM, 90% of the tetracycline (TC) and 96% of the sulfonamide (SXT) resistances could be explained by tet(A), tet(B), tet(M), and their combinations and sul(I), sul(II), sul(III), and their combinations, respectively. tet(M), a tetracycline-resistant gene originally detected in Gram-positive bacteria, and its combinations with tet(A) or tet(B) were first detected in E. coli isolated from a natural river basin, suggesting that tet(M) in E. coli might have been transferred from other bacterial species through horizontal gene transfer, which was supported by the fact that no tet(M) was detected in the isolates of human and chicken sources, except for only one isolate from swine. The source of sulfonamide-resistant E. coli in the river was supposed to be mainly from humans, based on a comparison of the sulfonamide resistance genotypes in animals and humans.

Meeting water requirements of cattle on the Canadian prairies

This paper examines some of the issues producers have in meeting the drinking water requirements of livestock on the Canadian prairies where they are dependent on varied ground and surface water sources. In supplying water for their cattle, producers often have problems that can affect their present and future operations. Water quality is one such problem as it can affect both the health and performance of livestock. The impact of the water quality in earthen reservoirs, the presence of sulphates in both surface and ground water, and toxins from cyanobacteria all have the potential to reduce herd productivity in the Canadian prairies. Another concern is the impact that grazing cattle can have on riparian vegetation, stream morphology, fish habitat and pollution of waterways. Damage is often caused by uncontrolled and season long grazing of cattle along water courses; options for controlling the damage are discussed. Finally, competition for a diminishing supply of water in the semi-arid Canadian prairies will become a major problem in the future. To remain viable and competitive, the livestock industry will have to develop and adopt strategies to address these issues.