Prevalence and characterization of Escherichia coli isolated from the Upper Oconee Watershed in Northeast Georgia

Sohyun Cho; Lari M. Hiott; John B. Barrett; Elizabeth A. McMillan; Sandra L. House; Shaheen B. Humayoun; Eric S. Adams; Charlene R. Jackson; Jonathan G. Frye

doi:10.1371/journal.pone.0197005

Abstract

Surface waters are important sources of water for drinking, industrial, agricultural, and recreational uses; hence, contamination of water by fecal, pathogenic, or antimicrobial resistant (AR) bacteria is a major environmental and public health concern. However, very little data is available on prevalence of these bacteria in surface water throughout a watershed. This study aimed to characterize Escherichia coli present in the Upper Oconee Watershed, a mixed-use watershed in Athens, GA, USA for potential pathogenicity and AR. E. coli were enumerated by colony counts, cultured by enrichment and direct plating, and characterized by phylo-groups, diarrheagenic pathotypes, and antimicrobial susceptibility. From the analysis, 99.3% (455/458) of the total samples were positive for E. coli resulting in 496 isolates. E. coli counts were as high as 1.2×10⁴ CFU/100 ml, which is above the United States Environmental Protection Agency (U.S. EPA) threshold for recreational water (235 CFU/100 ml based on a one-time measurement). Phylo-groups B2 (31.7%; 157/496) and B1 (30.8%; 153/496) were the most prevalent among the isolates. Enteropathogenic E. coli (EPEC) (19/496) and Shiga toxin-producing E. coli (STEC) (1/496) were the only diarrheagenic pathotypes detected. AR was observed in 6.9% (34/496) of the isolates, 15 of which were multidrug resistant (MDR; resistance to two or more classes of antimicrobials). Tetracycline resistance was most often detected (76.5%; 26/34), followed by ampicillin (32.4%; 11/34), streptomycin (23.5%; 8/34), sulfisoxazole (23.5%; 8/34), and nalidixic acid (14.7%; 5/34). Results from this study showed that E. coli is prevalent in high levels in the Upper Oconee Watershed, suggesting possible widespread fecal contamination. The presence of pathogenic, AR E. coli in the watershed indicates that environmental water can serve as a reservoir of resistant bacteria that may be transferred to humans through drinking and recreational activities.

Citation: Cho S, Hiott LM, Barrett JB, McMillan EA, House SL, Humayoun SB, et al. (2018) Prevalence and characterization of Escherichia coli isolated from the Upper Oconee Watershed in Northeast Georgia. PLoS ONE 13(5): e0197005. https://doi.org/10.1371/journal.pone.0197005

Editor: A. Mark Ibekwe, USDA-ARS Salinity Laboratory, UNITED STATES

Received: February 14, 2018; Accepted: April 24, 2018; Published: May 8, 2018

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: Funded by United States Department of Agriculture, Agricultural Research Service Intramural funding Project Number: 6040-32000-009-00 https://iapreview.ars.usda.gov/research/projects/projects.htm?ACCN_NO=430182. Centers for Disease Control and Prevention. Broad Agency Announcement to address antibiotic resistance, Agricultural Research Service Sub-Project Number: 6040-32000-009-08R https://www.cdc.gov/drugresistance/solutions-initiative/innovations-to-slow-AR.html.

Competing interests: The authors have declared that no competing interests exist.

Introduction

Escherichia coli, which normally resides in the intestinal flora of warm-blooded animals, including humans, is ubiquitous in the environment and has been used as an indicator of fecal contamination to assess the safety and quality of water [1]. Although most E. coli strains are harmless, certain strains are pathogenic and cause diseases such as watery diarrhea, bloody diarrhea, urinary tract infection, meningitis, and sepsis, which can lead to death [2, 3]. The normally zoonotic bacterial pathogen has been responsible for waterborne outbreaks in humans through contaminated drinking and recreational water not only in developing countries, but also in industrialized countries [4–9]. Environmental water sources are prone to bacterial pollution from both humans and animals. Possible human sources include discharge of wastewater, sewage leaks, and failing septic tanks, as well as municipal, residential, medical, and industrial waste facilities. Animal sources include runoffs from animal farms, land application of animal manure, pet wastes from parks, and wildlife such as raccoons and deer. Since surface waters are often used for recreational and drinking purposes, the presence of pathogenic E. coli in waterways may increase the likelihood of human infections after exposure to these water sources.

The Upper Oconee Watershed, located in the Southern Piedmont of Georgia, USA, is a historically agricultural region that has experienced rapid urban development. While two-thirds of the watershed still remains undeveloped with rural residential, forest and agricultural lands, the remaining land areas have transitioned to urban and suburban residential areas [10]. The Upper Oconee Watershed is not only impacted by dense residential development, industrialization, and sporadic sewer spills, but also includes land areas heavily devoted to agriculture, including poultry, dairy cattle, and beef cattle production [11, 12]. Since the watershed provides water for municipal and recreational purposes, monitoring the water quality is a public health concern. The Upper Oconee Watershed Network (UOWN) is a nonprofit organization dedicated to protecting streams and rivers within the Upper Oconee Watershed [13]. Since January 2000, the UOWN has been monitoring the surface water and its reporting indicates recurrent fecal contamination of the surface water within the watershed as evidenced by high fecal coliform and E. coli levels [11, 14–16].

The goal of this study was to investigate seasonal and spatial prevalence and characteristics of E. coli present in the Upper Oconee Watershed in and around Athens, Georgia. Since previous reports only included data on fecal indicator levels within the surface water of the Upper Oconee Watershed [11, 14–16], the present study attempted to further examine surface water quality for recreational and drinking purposes by investigating each E. coli isolate for its potential to cause disease and its antimicrobial resistance (AR). Environmental water samples were collected each season for two years and fecal contamination was determined by enumerating E. coli colony counts. E. coli was isolated from each water sample and characterized for phylo-group, pathotype, and AR phenotype. Susceptibility testing with 14 antimicrobials that are largely used for treating human and animal infections was used to determine AR phenotypes, because AR E. coli could be a public health concern as they can potentially restrict treatment options in the event of an infection. This study provides unique data on E. coli prevalence and characteristics in a mixed-use watershed that is representative of what residents of rural, urban, and suburban areas may be exposed to through the recreational, agricultural, and municipal use of surface water. Although there have been several studies on E. coli in surface water, most of these studies focused on a single waterway rather than a watershed, and the few studies of watersheds were usually limited in sampling events, sites, or time period. This study is unique in that it provides data on an entire watershed sampled over two years and numerous sampling sites.

Materials and methods

Sampling area

The rivers and streams sampled in this study were located in the Upper Oconee Watershed (USGS Cataloging unit 03070101). As previously described [17], the study area is approximately 600 km² and located within the lower Appalachian Piedmont of Northeastern Georgia, USA. Sampling sites were located along the North Oconee River (NORO), Middle Oconee River (MIDO), and their tributaries. A part of the study area is developed and densely populated consisting of urban residential areas that depend primarily on community sewers for effluent wastewater [17]. Other parts of the area mainly consist of forested, agricultural, and rural or suburban residential areas with poultry, dairy, and beef farming, largely depending on private septic systems for effluents [17]. Sampling sites were selected by the UOWN to represent a range of land uses (Fig 1). Maps and site descriptions for the sampling sites are available from the UOWN website [13] and in Fig 1. The exact locations of the sites with the GPS coordinates are in S1 Table. No specific permissions were required to collect water samples from these public access sites and no wildlife, endangered, or protected species were involved in this study.

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Fig 1. Map of water sampling sites in the Upper Oconee Watershed.

The map of the Upper Oconee Watershed in Georgia with the enlarged map of the study area. Sampling sites where AR E. coli were isolated are in red, where EPEC were isolated are in blue, where STEC was isolated is in green, and where both AR E. coli and EPEC were isolated are in purple (sites labeled). Other sites, where all E. coli isolates were pan-susceptible and non-pathogenic, are in yellow.

https://doi.org/10.1371/journal.pone.0197005.g001

Water collection and enumeration of E. coli in water samples

One-liter water samples were collected once each season for two years from 2015 Winter to 2016 Fall at different locations in the Upper Oconee Watershed with the assistance of the UOWN volunteers. The number of water samples collected each time varied from 30 to 100, depending on available manpower and access to the sampling sites. Samples were stored at 4°C until processing the next day.

E. coli counts were enumerated in duplicates using Petrifilm^™ E. coli/Coliform count plates (3M^™, St. Paul, MN, USA) according to manufacturer’s directions. E. coli enumeration was carried out before the filtration of water samples by inoculating two Petrifilm^™ plates with 1 ml of water each per sample. Plates were incubated at 37°C, and colonies were enumerated after 18–20 h of incubation. E. coli counts were averaged from the duplicate plates and expressed as CFU/100 ml.

Isolation and identification of E. coli

Filtration of water samples was performed as previously described [17]. Briefly, 0.5 g of cellulose filter powder (Aqua Dew^™, Lahore, Pakistan) was added to water samples, and the water samples were filtered onto 47-mm glass fiber filters of 0.3 μm pore size (Pall Corporation, Ann Arbor, MI, USA), which had been preloaded with another 0.5 g of cellulose filter powder suspended in 15 ml of sterile water. The filter, along with the filter powder, was incubated in 25 ml of 1X buffered peptone water (BD Difco^™, Franklin Lakes, NJ, USA) for non-selective pre-enrichment of samples. All overnight samples were incubated at 37°C for 18–20 h.

For E. coli isolation, 0.1 ml of each peptone broth enrichment was streaked on a CHROMagar ECC agar plate (CHROMagar Microbiology, Paris, France). One year of samples were also plated onto CHROMagar O157 agar plates (CHROMagar Microbiology). However, this medium yielded no O157 isolates and its use was discontinued (data not shown). In addition to CHROMagar ECC agar plates, m-TEC agar plates (HiCrome^™, Mumbai, India), which are normally used in the EPA method, were also used for isolation of E. coli during the 2015 Winter and Summer seasons. However, the m-TEC agar did not give consistent results and often failed to yield E. coli isolates, therefore that method was also discontinued. After a 37°C overnight incubation, one colony having the typical appearance of E. coli was selected from each positive plate. Presumptive positive E. coli isolates were then confirmed using the VITEK^®2 System and the VITEK 2 GN colorimetric identification cards (BioMérieux, Durham, NC, USA) according to manufacturer’s directions. All bacterial isolates were stored in LB (Luria-Bertani) broth (BD Difco^™), containing 30% glycerol at -80°C.

Phylogenetic analysis and identification of diarrheagenic pathotypes of E. coli

For genotypic profiling of E. coli, phylo-group and diarrheagenic pathotype identifications were performed. E. coli were grouped into eight phylo-groups, A, B1, B2, C, D, E, F, and cryptic clade I, using the quadruplex phylo-typing PCR method as previously described [18]. E. coli ATCC 25922 and ATCC BAA-196 were used as control strains. The diarrheagenic pathotypes were determined using PCR methods for detection of the following genes: pCVD, ipaH, est, elt, stx1, stx2, eaeA, and hlyA. Using previously described methods, E. coli isolates were characterized as enteroaggregative E. coli (EAEC) (pCVD+) [19], enteroinvasive E. coli (EIEC) (ipaH+) [20], enterotoxigenic E. coli (ETEC) (est+, elt+) [20], enterohemorrhagic E. coli (EHEC) (stx1+ and/or stx2+, eaeA+, hlyA+) [19], enteropathogenic E. coli (EPEC) (eaeA+, stx1-, stx2-, hlyA-) [21], and Shiga toxin-producing E. coli (STEC) (stx1+ and/or stx2+, eaeA-, hlyA-) [21]. The following E. coli strains were included as positive control strains: ATCC 29552 (EAEC), ATCC 35401 (ETEC), ATCC 43893 (EIEC), and ATCC 43895 (EPEC, EHEC, and STEC). The STEC isolate was tested for serogroups O111 and O157 using a method previously described [21]. PCR was performed as described in the given references using whole-cell templates that were prepared by suspending a single bacterial colony in 200 μl of sterile deionized water. Amplified PCR products were then analyzed by electrophoresis on 2% agarose gel and visualized by staining with ethidium bromide.

Antimicrobial susceptibility testing

Minimum inhibitory concentrations (MIC) of all E. coli isolates were determined by broth-microdilution using the Sensititre^™ semi-automated antimicrobial susceptibility system (TREK Diagnostic Systems Inc., Cleveland, OH, USA) and the Sensititre^™ custom National Antimicrobial Resistance Monitoring System (NARMS) plate CMV3AGNF according to manufacturer’s directions. MICs of the isolates for the 14 antimicrobials were determined, and each isolate was classified as resistant, intermediate, or susceptible to the antimicrobials tested using the breakpoints set by Clinical and Laboratory Standards Institute (CLSI) [22]. For azithromycin, without CLSI approved breakpoints, the epidemiological cutoff value for wild-type Salmonella (MIC > 16 μg/ml) was used [23, 24]. The 14 antimicrobials and the breakpoints (μg/ml) for determining resistances were as follows: amoxicillin/clavulanic acid (≥ 32/16), ampicillin (≥ 32), azithromycin (> 16), cefoxitin (≥ 32), ceftiofur (≥ 8), ceftriaxone (≥ 4), chloramphenicol (≥ 32), ciprofloxacin (≥ 1), gentamicin (≥ 16), nalidixic acid (≥ 32), streptomycin (≥ 64), sulfisoxazole (≥ 512), tetracycline (≥ 16), and trimethoprim/sulfamethoxazole (≥ 4/76). For the analysis, isolates identified as intermediate were considered susceptible to the drug. E. coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Enterococcus faecalis ATCC 29212, and Staphylococcus aureus ATCC 29213 were used as control strains for MIC determination.

Results

Prevalence of E. coli

A total of 458 water samples were collected from eight seasonal sampling events. The sampling site locations are shown on the map in Fig 1 and listed in S1 Table with each site’s GPS coordinates. The number of sampling sites positive for E. coli and the number of isolates recovered from the sites are shown in Table 1. E. coli was recovered from 99.3% (455/458) of the total sampling sites, with the recovery rate for each sampling ranging from 96.7% to 100.0%, and a total of 496 E. coli were isolated. Although only one colony was selected from each positive plate, higher number of isolates than the number of sites is due to the use of mTEC agar in addition to CHROMagar ECC agar. Multiple media were used for the isolation of E. coli in order to test the efficacy of each media.

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Table 1. E. coli isolates recovered from sampling sites.

https://doi.org/10.1371/journal.pone.0197005.t001

E. coli colony count results for each season is shown in Fig 2 in log₁₀ CFU/100 ml. Approximately 39% (177/458) of the total samples exceeded the United States Environmental Protection Agency (U.S. EPA) threshold for recreational activities, which is 235 CFU/100 ml based on a one-time measurement [1]. The average of the E. coli counts per season was above the threshold during six out of the eight sampling seasons, while the median E. coli counts exceeded the threshold only in Spring and Summer seasons of 2016. The E. coli counts were as low as undetectable (detection limit of 50 CFU/100 ml) and as high as 1.2×10⁴ CFU/100 ml. The number of sampling sites that exceeded 235 CFU/100 ml for each sampling event is shown in Table 2.

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Fig 2. Seasonal distribution of E. coli in the Upper Oconee Watershed in colony forming units [CFU] per 100 ml.

X-axis represents each sampling season with the numbers in parenthesis indicating the total number of water samples. Y-axis represents the E. coli counts in log₁₀ CFU/100 ml. The threshold represents the EPA threshold for water quality for recreational purposes.

https://doi.org/10.1371/journal.pone.0197005.g002

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Table 2. Sites with E. coli counts exceeding the U.S. EPA threshold for each sampling event^{^a}.

https://doi.org/10.1371/journal.pone.0197005.t002

Identification and characterization of E. coli

Phylo-groups and diarrheagenic pathotypes of E. coli isolates recovered from surface water are shown in Tables 3 and 4. Using the quadruplex phylo-typing method, six phylo-groups (A, B1, B2, C, E, and F) were identified while three isolates could not be assigned a phylo-group (unknown; U). The most prevalent groups were B2 (31.7%; 157/496) and B1 (30.8%; 153/496). Fewer isolates were identified as groups E (23.2%; 115/496), A (6.7%; 33/496), F (4.6%; 23/496), and C (2.4%; 12/496).

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Table 3. Phylo-groups and diarrheagenic pathotypes of E. coli isolated from surface water.

https://doi.org/10.1371/journal.pone.0197005.t003

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Table 4. Antimicrobial resistant and pathogenic E. coli isolated from surface water, phylo-group, and sample site location from Fig 1.

https://doi.org/10.1371/journal.pone.0197005.t004

Out of a total of 496 E. coli isolates, 19 EPEC and 1 STEC, positive for stx2, were detected (Table 4). The STEC isolate did not belong to serogroup O157 or O111. The majority of EPEC (15/19) isolates belonged to phylo-group B2 while the STEC belonged to phylo-group B1. No EAEC, EIEC, EHEC, or ETEC were detected. Locations where EPEC and the STEC were isolated are indicated on Fig 1.

Most of the E. coli isolates were susceptible to the 14 drugs tested with only 6.9% (34/496) of the isolates exhibiting resistance to any of the drugs. These 34 AR E. coli were isolated from 24 sampling sites; eight of the sites had two AR E. coli isolated from them, and one site had three AR E. coli isolated from it. For this study, we considered resistance to two or more classes of antimicrobials as multidrug resistance (MDR). We chose this cut off to indicate resistance to multiple classes of antimicrobials rather than resistance to multiple antimicrobials, which if in the same class could be conferred by a single gene or genetic mutation. Therefore, using this definition helps to indicate that an isolate which is resistant to multiple classes of antimicrobials may have multiple mechanisms of AR. MDR was observed in 15 of the isolates. Eleven different MDR patterns were detected, including one isolate resistant to seven antimicrobials (Table 4). Resistance to all of the 14 drugs tested was observed in the E. coli isolates from this study. Resistance to tetracycline was the most prevalent (76.5%; 26/34), followed by resistance to ampicillin (32.4%; 11/34), streptomycin (23.5%; 8/34), sulfisoxazole (23.5%; 8/34), and nalidixic acid (14.7%; 5/34). Locations from which AR E. coli were isolated are shown on Fig 1. Interestingly, none of the EPEC or STEC isolates was resistant to any of the antimicrobials tested.

Discussion

Prevalence of E. coli in the watershed

The results of this study indicated that E. coli was highly prevalent in the Upper Oconee Watershed as E. coli was isolated from almost every water site sampled each season. Due to the ubiquity of E. coli, no seasonal variations in presence was detectable; however, colony counts did vary. E. coli colony counts were determined using the 3M^™ Petrifilm^™ method, which is often used for volunteer-based water quality monitoring for its effectiveness, cost efficiency, and simplicity of use and storage [25–27]. Consistent with the previous reports on the water quality of the Upper Oconee Watershed [11, 14–16], high E. coli counts were detected in the present study, which is evidence for widespread fecal contamination within the watershed. The E. coli counts of the water samples often exceeded the EPA threshold for recreational activities such as swimming and water skiing, which is 235 CFU/100 ml based on a one-time measurement [1]. The E. coli counts exceeded the threshold more often in the spring and summer seasons than in the fall and winter seasons, likely due to warmer water temperatures supporting growth of this enteric bacterium. In general, rural streams had acceptable E. coli counts while urban and suburban streams had higher levels of E. coli counts, which may be attributed to surface runoff from built infrastructure, leaking sewer lines, and failing septic systems. E. coli counts exceeding 10³ CFU/100 ml were frequently observed which warrant special attention as it may indicate direct sewage contamination [25].

Pathogenic potential of E. coli in the watershed

Phylo-grouping PCR results showed that a third of all the E. coli isolates belonged to phylo-group B2, which is known to be associated with virulence and accounts for the majority of extra-intestinal infections [28]. The second most prevalent group was B1, to which commensal E. coli typically belong [28]. None of the isolates belonged to phylo-group D, which was contrary to previous reports that have shown a sizeable percentage of the group D isolates in environmental water samples [29–31]. The percentages of E. coli isolates that belonged to phylo-group D were 25.0% in the Mid-Atlantic region of the U.S. [29], 10.8% in the Yeongsan River basin of South Korea [30], and as high as 80.0% in the St. Clair River and Detroit River [31]. However, as opposed to the previous studies that used a triplex PCR developed by Clermont et al. in 2000 [32], the current study used a quadruplex PCR which was developed by Clermont et al. in 2012 as an improvement of the previous PCR method [18]. With the refined knowledge of E. coli phylogenetic group structure using multi-locus sequence type (MLST) data, new phylo-groups C, E, F, and Escherichia clade I were recognized and included in the phylo-typing PCR method, demonstrating the significant percentage of incorrect phylo-group assignment of E. coli strains using the previous triplex PCR [18, 33]. Unfortunately, few studies in the literature have yet to use the quadruplex PCR method to characterize E. coli isolates from surface water. Therefore, it is unclear if it is the use of the different methods that has resulted in the difference in the percentages of the phylo-groups or if the phylo-groups follow a region- or site- specific pattern.

EPEC was rarely isolated in water samples in this study, with a total of 19 EPEC isolates detected. Humans are the main reservoir of EPEC, which causes watery diarrhea primarily in children under two years old [2]. Although this strain of E. coli persists in developing countries as a cause of diseases [2], EPEC is no longer a public threat in developed countries and only 30 cases of EPEC infections were confirmed in the U.S. from 2014 to 2016 [2, 34–36]. A majority of EPEC belonged to phylo-group B2, which was consistent with previous studies that have reported that B2 strains tend to harbor more virulence determinants than the strains that belong to other phylo-groups [37–39]. Only one STEC was detected in any water sample during any season in the present study. Because this stx2-positive isolate does not have any other virulence factor, such as eaeA, and cattle are known to be a vast reservoir of STEC [3], it is very probable that this STEC isolate originated from an animal source. E. coli O157, responsible for most human infections among the STECs in developed countries [3, 21], has often been detected from surface water [40, 41]. E. coli O157 outbreaks involving surface water contaminated with human and animal feces have been previously documented as well [5, 7, 9]. However, the present study did not detect any E. coli O157 isolates. While EAEC, EHEC, EIEC, and ETEC have been previously identified in surface water [42], none were detected in the Upper Oconee Watershed similar to findings for the St. Clair and Detroit rivers [31]. Locations from which the EPEC and STEC isolates were collected are indicated in Fig 1. Overall, not many diarrheagenic strains of E. coli have been identified from the Upper Oconee Watershed; nevertheless, the isolation of EPEC and STEC from the surface water does suggest potential exposure of environmental water to fecal contamination of human and/or animal origin.

Antimicrobial resistant E. coli in the watershed

Only a small portion of water samples harbored E. coli resistant to any of the 14 drugs tested. However, it is important to note that our isolation method did not use antimicrobials to select for resistant strains; therefore, the level of 6.9% resistant E. coli likely represented a true level of resistant E. coli in the watershed, which is not trivial considering the high level of some of the sample colony counts. Resistance was observed most often to tetracycline, followed by ampicillin, streptomycin, sulfisoxazole, and nalidixic acid. The high resistance rate to tetracycline has been previously reported in other studies [43–45], indicating that the resistance to tetracycline is prevalent in environmental water. This observation was expected as tetracycline is one of the most widely used antimicrobials for treatment of human and animal infections as well as the historic use for agricultural purposes as growth promoters [46, 47]. The frequency of resistance to the antimicrobials listed above corresponded with findings from other regions, while the prevalence of AR in E. coli from the Upper Oconee Watershed was less than expected based on levels seen in other environmental water sources [38, 43–45]. High levels of AR to a variety of antimicrobials have been reported for E. coli isolates from aquatic environment, as high as 82% in other regions of the country [38, 43–45], and as high as 100% in other parts of the world [48–50]. The difference in the level of AR with the E. coli isolates from this study may be partially due to the antimicrobial drugs chosen for testing. Variances in the therapeutic drugs used and the levels of fecal contamination may also have contributed to the difference.

AR E. coli were mostly recovered from residential areas. The exact locations of the sites with the GPS coordinates are in S1 Table and locations where AR positive samples were collected are indicated in Fig 1. The city of Athens, which encompasses Clarke County and some parts of Oconee and Jackson Counties, is served by a sewer system with surprisingly high cases of sewage problems [51]. These include the case of an unknown amount of improperly treated wastewater being discharged into a creek over an unknown period of time [52], increasing the likelihood of isolating AR E. coli of human source within the residential land areas. A few other sites from where AR E. coli were recovered were located near agricultural operations i.e. MIDO 103, MIDO 305, MIDO 505, and MIDO 507. There were cattle pastures, a poultry farm, and a small horse farm near the sampling sites which could have been potential sources of AR E. coli isolated.

McNutt Creek flows through suburban residential and commercial areas of Athens. Several sampling sites were located along the creek and its tributaries, and the quality of water has been shown to be a concern due to high E. coli counts and the presence of AR and pathogenic E. coli. Four out of 19 EPEC isolates and six out of 34 AR E. coli isolates were collected from McNutt Creek alone. McNutt Creek is on the EPA Total Maximum Daily Load (TMDL) 303(d) list of Impaired Waters in terms of fecal coliform due to nonpoint sources and urban runoff [53]. Continuous monitoring of the creek to track the sources of contamination is required to gather data for the improvement of the creek’s water quality.

Although there are several papers on E. coli from surface waters of different locations around the world, relatively little has been studied about E. coli prevalence, pathotypes, and antimicrobial susceptibility in surface waters of a mixed-use watershed in the U.S. One of the most similar studies was reported by Ibekwe et al. who collected samples from 20 sites quarterly over a twelve-month period from the middle Santa Anna River in Southern California, USA [45]. However, the watershed drained by that river is dominated by a large area of cattle farms and discharges from three wastewater treatment plants. In addition, that study also sampled sediments thus representing the environment in and around the river, whereas our study focused on bacteria within the moving water column indicative of what residents would be exposed to by recreational, agricultural, and municipal use of surface water. Our study area was diverse and represented land use from the undeveloped forest, agricultural and rural residential lands (about 62% of the land in the watershed) to densely developed industrial and suburban- residential lands (about 38%). Water samples were collected quarterly for two years from 100 different sampling sites that encompassed the entire watershed, incorporating not only relatively pristine streams but also streams with a history of human impacts, such as runoff from agricultural activities as well as contaminated effluents from wastewater treatment plants, discharges from failing septic systems, and sewer line leaks. As approximately half of the U.S. population lives in suburban areas [54], this mixed-use watershed may be a good representation of the conditions many U.S. residents are exposed to by surface water used for recreational, agricultural, and municipal purposes.

This study has shown the seasonal and spatial prevalence and characteristics of E. coli in surface water of the Upper Oconee Watershed, Athens, GA, including the presence of pathogenic and AR E. coli. E. coli resistant to therapeutic drugs were not highly prevalent in the environment and these commensal bacteria may not appear to be a risk to public health. However, E. coli is known to harbor AR genes on plasmids, transposons, and integrons, and these mobile genetic elements can be transferred between organisms of the same species or different genera through horizontal gene transfer [55, 56]. Therefore, further studies are required to assess risks associated with E. coli harboring AR genes and the potential of transferring these genes to other bacteria, including commensal E. coli and other bacterial pathogens which could have a detrimental impact on public health.

Supporting information

S1 Table. Master file of the E. coli isolated from the Upper Oconee Watershed.

^a amoxicillin/clavulanic acid (Amo), ampicillin (Amp), azithromycin (Azi), cefoxitin (Fox), ceftiofur (Tio), ceftriaxone (Axo), chloramphenicol (Chl), ciprofloxacin (Cip), gentamicin (Gen), nalidixic acid (Nal), streptomycin (Str), sulfisoxazole (Sul), tetracycline (Tet), trimethoprim/sulfamethoxazole (Tri). ^bEPEC: enteropathogenic E. coli and STEC: Shiga toxin-producing E. coli.

https://doi.org/10.1371/journal.pone.0197005.s001

(PDF)

Acknowledgments

The authors gratefully acknowledge Elizabeth A. Ottesen and Erin K. Lipp for helpful discussions. We thank Jacob M. Mcdonald for the map of the UOWN sampling sites. We also thank the Ottesen laboratory personnel, Bruno Giri, Phillip Bumpers, the UOWN science and monitoring committee, and the UOWN volunteers for their assistance in collecting the water samples. The mention of trade names or commercial products in this manuscript is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.

References

1. U.S. Environmental Protection Agency (EPA). Ambient water quality criteria for bacteria- 1986. Washington, D.C.: U.S. EPA, Office of Water Regulations and Standards Division; 1986. EPA-A440/5-84-002.
2. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998; 11(1): 142–201. Erratum in: Clin Microbiol Rev. 1998; 11(2): 403. pmid:9457432
- View Article
- PubMed/NCBI
- Google Scholar
3. Gyles CL. Shiga toxin-producing Escherichia coli: an overview. J Anim Sci. 2007; 85 (13 Suppl): E45–E62. pmid:17085726.
- View Article
- PubMed/NCBI
- Google Scholar
4. Rosenberg ML, Koplan JP, Wachsmuth IK, Wells JG, Gangarosa EJ, Guerrant RL, et al. Epidemic diarrhea at Crater Lake from enterotoxigenic Escherichia coli. A large waterborne outbreak. Ann Intern Med. 1977; 86(6): 714–718. pmid:326116.
- View Article
- PubMed/NCBI
- Google Scholar
5. Keene WE, McAnulty JM, Hoesly FC, Williams LP, Hedberg K, Oxman GL, et al. A swimming-associated outbreak of hemorrhagic colitis caused by Escherichia coli O157:H7 and Shigella sonnei. New Engl J Med. 1994; 331(9): 579–584. pmid:8047082.
- View Article
- PubMed/NCBI
- Google Scholar
6. McCarthy TA, Barrett NL, Hadle JL, Salsbury B, Howard RT, Dingman DW, et al. Hemolytic-uremic syndrome and Escherichia coli O121 at a lake in Connecticut, 1999. Pediatr. 2001; 108(4): E59. pmid:11581467.
- View Article
- PubMed/NCBI
- Google Scholar
7. Waterborne outbreak of gastroenteritis associated with a contaminated municipal water supply, Walkerton, Ontario, May-June 2000. Can Commun Dis Rep. 2000; 26(20): 170–173. pmid:11211701.
- View Article
- PubMed/NCBI
- Google Scholar
8. Isaacson M, Canter PH, Effler P, Arntzen L, Bomans P, Heenan R. Haemorrhagic colitis epidemic in Africa. Lancet. 1993; 341(8850): 961. pmid:8096294.
- View Article
- PubMed/NCBI
- Google Scholar
9. Probert WS, Miller GM, Ledin KE. Contaminated stream water as source for Escherichia coli O157 illness in children. Emerg Infect Dis. 2017; 23(7): 1216–1218. pmid:28628436
- View Article
- PubMed/NCBI
- Google Scholar
10. Metropolitan North Georgia Water Planning District. Water resource management plan. Appendix A: River basin profiles. Atlanta (GA): Metropolitan North Georgia Water Planning District; 2016. EN0507151024SPB.
11. Fisher DS, Steiner JL, Endale DM, Stuedemann JA, Schomberg HH, Franzluebbers AJ, et al. The relationship of land use practices to surface water quality in the Upper Oconee Watershed of Georgia. Forest Ecol Manag. 2000; 128 (1–2): 39–48.
- View Article
- Google Scholar
12. National Agricultural Statistics Service (NASS) [Internet]. Explore statistics; c2017 [cited 2017 December 11]. United States Department of Agriculture (USDA), NASS. https://www.nass.usda.gov/Quick_Stats/.
13. uown.org [Internet]. Athens (GA): Upper Oconee Watershed Network [cited 2017 December 11]. http://www.uown.org/.
14. Little E, Eggert S, Wenner D, Rasmussen T, Conners D, Fisher D. Results from six years of community-based volunteer water quality monitoring by the Upper Oconee Watershed Network. Proceedings of the 2007 Georgia Water Resources Conference; 2007 Mar 27–29; Athens, GA.
15. Conners DE, Eggert S, Keyes J, Merrill M. Community-based water quality monitoring by the Upper Oconee Watershed Network. Proceedings of the 2001 Georgia Water Resources Conference; 2001 Mar 26–27; Athens, GA.
16. Fisher DS, Dillard AL, Usery LE, Steiner JL, Neely CL. Water quality in the headwaters of the Upper Oconee Watershed. Proceedings of the 2001 Georgia Water Resources Conference; 2001 Mar 26–27; Athens, GA.
17. Meinersmann RJ, Berrang ME, Jackson CR, Fedorka-Cray PJ, Ladely S, Little E, et al. Salmonella, Campylobacter and Enterococcus spp.: their antimicrobial resistance profiles and their spatial relationships in a synoptic study of the Upper Oconee River basin. Microb Ecol. 2008; 55(3): 444–452. pmid:17687594.
- View Article
- PubMed/NCBI
- Google Scholar
18. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep. 2013; 5(1): 58–65. pmid:23757131.
- View Article
- PubMed/NCBI
- Google Scholar
19. Nguyen TV, Van PL, Huy CL, Gia KN, Weintraub A. Detection and characterization of diarrheagenic Escherichia coli from young children in Hanoi, Vietnam. J Clin Microbiol. 2005; 43(2): 755–760. pmid:15695676
- View Article
- PubMed/NCBI
- Google Scholar
20. Toma C, Lu Y, Higa N, Nakasone N, Chinen I, Baschkier A, et al. Multiplex PCR assay for identification of human diarrheagenic Escherichia coli. J Clin Microbiol. 2003; 41(6): 2669–2671. pmid:12791900
- View Article
- PubMed/NCBI
- Google Scholar
21. Paton AW, Paton JC. Detection and characterization of shiga toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2, eaeA, enterohemorrhagic E. coli hlyA, rfbO111, and rfbO157. J Clin Microbiol. 1998; 36(2): 598–602. pmid:9466788
- View Article
- PubMed/NCBI
- Google Scholar
22. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing; 26th ed. CLSI Supplement M100S. Wayne (PA): CLSI; 2016.
23. European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoint tables for interpretation of MICs and zone diameters; Version 4.0., 2014. EUCAST; 2014.
24. Sjölund-Karlsson M, Joyce K, Blickenstaff K, Ball T, Haro J, Medalla FM, et al. Antimicrobial susceptibility to azithromycin among Salmonella enterica isolates from the United States. Antimicrob Agents Chemother 2011; 55(9): 3985–3989. pmid:21690279
- View Article
- PubMed/NCBI
- Google Scholar
25. Georgia Adopt-A-Stream. Bacterial monitoring. Atlanta (GA): Georgia Adopt-A-Stream, Environmental Protection Division, Department of Natural Resources; 2014.
26. Schraft H, Watterworth LA. Enumeration of heterotrophs, fecal coliforms and Escherichia coli in water: comparison of 3M^™ Petrifilm^™ plates with standard plating procedures. J Microbiol Methods. 2005; 60(3): 335–342. pmid:15649535.
- View Article
- PubMed/NCBI
- Google Scholar
27. Vail JH, Morgan R, Merino CR, Gonzales F, Miller R, Ram JL. Enumeration of waterborne Escherichia coli with petrifilm plates: comparison to standard methods. J Environ Qual. 2003; 32(1): 368–373. pmid:12549577.
- View Article
- PubMed/NCBI
- Google Scholar
28. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, et al. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 1999; 67(2): 546–553. pmid:9916057
- View Article
- PubMed/NCBI
- Google Scholar
29. Higgins J, Hohn C, Hornor S, Frana M, Denver M, Joerger R. 2007. Genotyping of Escherichia coli from environmental and animal samples. J Microbiol Methods. 2007; 70(2): 227–235. pmid:17521755.
- View Article
- PubMed/NCBI
- Google Scholar
30. Jang J, Di DY, Lee A, Unno T, Sadowsky MJ, Hur HG. Seasonal and genotypic changes in Escherichia coli phylogenetic groups in the Yeongsan River Basin of South Korea. PLoS ONE. 2014; 9(7): e100585. pmid:24999864
- View Article
- PubMed/NCBI
- Google Scholar
31. Hamelin K, Bruant G, El-Shaarawi A, Hill S, Edge TA, Fairbrother J, et al. Occurrence of virulence and antimicrobial resistance genes in Escherichia coli isolates from different aquatic ecosystems within the St. Clair River and Detroit River areas. Appl Environ Microbiol. 2007; 73(2):477–484. pmid:17085696
- View Article
- PubMed/NCBI
- Google Scholar
32. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol. 2000; 66(10): 4555–4558. pmid:11010916
- View Article
- PubMed/NCBI
- Google Scholar
33. Gordon DM, Clermont O, Tolley H, Denamur E. Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ Microbiol. 2008; 10(10): 2484–2496. pmid:18518895.
- View Article
- PubMed/NCBI
- Google Scholar
34. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2011, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2014.
35. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2013, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2015.
36. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2014, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2016.
37. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, et al. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol. 2007; 24(11): 2373–2384. pmid:17709333
- View Article
- PubMed/NCBI
- Google Scholar
38. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, et al. The Link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 1999; 67(2): 546–553. pmid:9916057
- View Article
- PubMed/NCBI
- Google Scholar
39. Boyd EF, Hartl DL. Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J Bacteriol. 1998; 180(5): 1159–1165. pmid:9495754.
- View Article
- PubMed/NCBI
- Google Scholar
40. Gu G, Luo Z, Cevallos-Cevallos JM, Adams P, Vellidis G, Wright A, et al. Factors affecting the occurrence of Escherichia coli O157 contamination in irrigation ponds on produce farms in the Suwannee River Watershed. Can J Microbiol. 2013; 59(3): 175–182. pmid:23540335.
- View Article
- PubMed/NCBI
- Google Scholar
41. Maal-Bared R, Bartlett KH, Bowie WR, Hall ER. Phenotypic antibiotic resistance of Escherichia coli and E. coli O157 isolated from water, sediment and biofilms in an agricultural watershed in British Columbia. Sci Total Environ. 2013; 443: 315–323. pmid:23202379.
- View Article
- PubMed/NCBI
- Google Scholar
42. Sidhu JS, Ahmed W, Hodgers L, Toze S. Occurrence of virulence genes associated with diarrheagenic pathotypes in Escherichia coli isolates from surface water. Appl Environ Microbiol. 2013; 79(1): 328–335. pmid:23124225
- View Article
- PubMed/NCBI
- Google Scholar
43. Parveen S, Murphree RL, Edmiston L, Kaspar CW, Portier KM, Tamplin ML Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Appl Environ Microbiol. 1997; 63(7): 2607–2612. pmid:9212410
- View Article
- PubMed/NCBI
- Google Scholar
44. Li X, Watanabe N, Xiao C, Harter T, McCowan B, Liu Y, et al. Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California. Environ Monit Assess. 2014; 186(2): 1253–1260. pmid:24097011.
- View Article
- PubMed/NCBI
- Google Scholar
45. Ibekwe AM, Murinda SE, Graves AK. Genetic diversity and antimicrobial resistance of Escherichia coli from human and animal sources uncovers multiple resistances from human sources. PLoS ONE. 2011; 6(6): e20819. pmid:21687635
- View Article
- PubMed/NCBI
- Google Scholar
46. Chopra I, Roberts M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev. 2001; 65(2): 232–260. pmid:11381101
- View Article
- PubMed/NCBI
- Google Scholar
47. Daghrir R, Drogui P. 2013. Tetracycline antibiotics in the environment: a review. Environ Chem Lett. 2013; 11(3): 209–227.
- View Article
- Google Scholar
48. Olaniran AO, Naicker K, Pillay B. Antibiotic resistance profiles of Escherichia coli isolates from river sources in Durban, South Africa. World J Microbiol Biotechnol. 2009; 25(10):1743–1749.
- View Article
- Google Scholar
49. Zhang X, Li Y, Liu B, Wang J, Feng C, Gao M, et al. Prevalence of veterinary antibiotics and antibiotic-resistant Escherichia coli in the surface water of a livestock production region in Northern China. PLoS One. 2014; 9(11): e111026. pmid:25372873
- View Article
- PubMed/NCBI
- Google Scholar
50. Titilawo Y, Obi L, Okoh A. Antimicrobial resistance determinants of Escherichia coli isolates recovered from some rivers in Osun State, South-Western Nigeria: implications for public health. Sci Total Environ. 2015; 523: 82–94. pmid:25862994.
- View Article
- PubMed/NCBI
- Google Scholar
51. Erin G [Internet]. Athens’ outdated sewage infrastructure may endanger local waterways. Grady Newsource; 2016 May 10 [cited 2017 December 11]. http://gradynewsource.uga.edu/blog/2016/05/10/athens-outdated-sewage-infrastructure-may-endanger-local-waterways/.
52. Lee B [Internet]. Oconee County reporting a sewer spill into Barber Creek due to Mars Hill widening project. Oconee County Observations; 2015 August 26 [cited 2017 December 11]. http://www.oconeecountyobservations.org/2015/08/oconee-county-reporting-sewer-spill.html.
53. Environmental Protection Division (EPD). Draft 2016 Integrated 305(b)/303(d) List—Streams. Atlanta (GA): Gerogia Department of Natural Resources, EPD; 2016.
54. Hobbs F, Stoops N. Demographic trends in the 20th century, Census 2000 special reports, series CENSR-4. Washington (DC): U.S. Census Bureau; 2002.
55. Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev. 2009; 73(4): 750–774. Erratum in: Microbiol Mol Biol Rev. 2010; 74(3): 477–78. pmid:19946140
- View Article
- PubMed/NCBI
- Google Scholar
56. Davison J. Review: Genetic Exchange between bacteria in the environment. Plasmid. 1999; 42(2):73–91. pmid:10489325.
- View Article
- PubMed/NCBI
- Google Scholar

[ref1] 1. U.S. Environmental Protection Agency (EPA). Ambient water quality criteria for bacteria- 1986. Washington, D.C.: U.S. EPA, Office of Water Regulations and Standards Division; 1986. EPA-A440/5-84-002.

[ref2] 2. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998; 11(1): 142–201. Erratum in: Clin Microbiol Rev. 1998; 11(2): 403. pmid:9457432
View Article
PubMed/NCBI
Google Scholar

[3] View Article

[4] PubMed/NCBI

[5] Google Scholar

[ref3] 3. Gyles CL. Shiga toxin-producing Escherichia coli: an overview. J Anim Sci. 2007; 85 (13 Suppl): E45–E62. pmid:17085726.
View Article
PubMed/NCBI
Google Scholar

[7] View Article

[8] PubMed/NCBI

[9] Google Scholar

[ref4] 4. Rosenberg ML, Koplan JP, Wachsmuth IK, Wells JG, Gangarosa EJ, Guerrant RL, et al. Epidemic diarrhea at Crater Lake from enterotoxigenic Escherichia coli. A large waterborne outbreak. Ann Intern Med. 1977; 86(6): 714–718. pmid:326116.
View Article
PubMed/NCBI
Google Scholar

[11] View Article

[12] PubMed/NCBI

[13] Google Scholar

[ref5] 5. Keene WE, McAnulty JM, Hoesly FC, Williams LP, Hedberg K, Oxman GL, et al. A swimming-associated outbreak of hemorrhagic colitis caused by Escherichia coli O157:H7 and Shigella sonnei. New Engl J Med. 1994; 331(9): 579–584. pmid:8047082.
View Article
PubMed/NCBI
Google Scholar

[15] View Article

[16] PubMed/NCBI

[17] Google Scholar

[ref6] 6. McCarthy TA, Barrett NL, Hadle JL, Salsbury B, Howard RT, Dingman DW, et al. Hemolytic-uremic syndrome and Escherichia coli O121 at a lake in Connecticut, 1999. Pediatr. 2001; 108(4): E59. pmid:11581467.
View Article
PubMed/NCBI
Google Scholar

[19] View Article

[20] PubMed/NCBI

[21] Google Scholar

[ref7] 7. Waterborne outbreak of gastroenteritis associated with a contaminated municipal water supply, Walkerton, Ontario, May-June 2000. Can Commun Dis Rep. 2000; 26(20): 170–173. pmid:11211701.
View Article
PubMed/NCBI
Google Scholar

[23] View Article

[24] PubMed/NCBI

[25] Google Scholar

[ref8] 8. Isaacson M, Canter PH, Effler P, Arntzen L, Bomans P, Heenan R. Haemorrhagic colitis epidemic in Africa. Lancet. 1993; 341(8850): 961. pmid:8096294.
View Article
PubMed/NCBI
Google Scholar

[27] View Article

[28] PubMed/NCBI

[29] Google Scholar

[ref9] 9. Probert WS, Miller GM, Ledin KE. Contaminated stream water as source for Escherichia coli O157 illness in children. Emerg Infect Dis. 2017; 23(7): 1216–1218. pmid:28628436
View Article
PubMed/NCBI
Google Scholar

[31] View Article

[32] PubMed/NCBI

[33] Google Scholar

[ref10] 10. Metropolitan North Georgia Water Planning District. Water resource management plan. Appendix A: River basin profiles. Atlanta (GA): Metropolitan North Georgia Water Planning District; 2016. EN0507151024SPB.

[ref11] 11. Fisher DS, Steiner JL, Endale DM, Stuedemann JA, Schomberg HH, Franzluebbers AJ, et al. The relationship of land use practices to surface water quality in the Upper Oconee Watershed of Georgia. Forest Ecol Manag. 2000; 128 (1–2): 39–48.
View Article
Google Scholar

[36] View Article

[37] Google Scholar

[ref12] 12. National Agricultural Statistics Service (NASS) [Internet]. Explore statistics; c2017 [cited 2017 December 11]. United States Department of Agriculture (USDA), NASS. https://www.nass.usda.gov/Quick_Stats/.

[ref13] 13. uown.org [Internet]. Athens (GA): Upper Oconee Watershed Network [cited 2017 December 11]. http://www.uown.org/.

[ref14] 14. Little E, Eggert S, Wenner D, Rasmussen T, Conners D, Fisher D. Results from six years of community-based volunteer water quality monitoring by the Upper Oconee Watershed Network. Proceedings of the 2007 Georgia Water Resources Conference; 2007 Mar 27–29; Athens, GA.

[ref15] 15. Conners DE, Eggert S, Keyes J, Merrill M. Community-based water quality monitoring by the Upper Oconee Watershed Network. Proceedings of the 2001 Georgia Water Resources Conference; 2001 Mar 26–27; Athens, GA.

[ref16] 16. Fisher DS, Dillard AL, Usery LE, Steiner JL, Neely CL. Water quality in the headwaters of the Upper Oconee Watershed. Proceedings of the 2001 Georgia Water Resources Conference; 2001 Mar 26–27; Athens, GA.

[ref17] 17. Meinersmann RJ, Berrang ME, Jackson CR, Fedorka-Cray PJ, Ladely S, Little E, et al. Salmonella, Campylobacter and Enterococcus spp.: their antimicrobial resistance profiles and their spatial relationships in a synoptic study of the Upper Oconee River basin. Microb Ecol. 2008; 55(3): 444–452. pmid:17687594.
View Article
PubMed/NCBI
Google Scholar

[44] View Article

[45] PubMed/NCBI

[46] Google Scholar

[ref18] 18. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep. 2013; 5(1): 58–65. pmid:23757131.
View Article
PubMed/NCBI
Google Scholar

[48] View Article

[49] PubMed/NCBI

[50] Google Scholar

[ref19] 19. Nguyen TV, Van PL, Huy CL, Gia KN, Weintraub A. Detection and characterization of diarrheagenic Escherichia coli from young children in Hanoi, Vietnam. J Clin Microbiol. 2005; 43(2): 755–760. pmid:15695676
View Article
PubMed/NCBI
Google Scholar

[52] View Article

[53] PubMed/NCBI

[54] Google Scholar

[ref20] 20. Toma C, Lu Y, Higa N, Nakasone N, Chinen I, Baschkier A, et al. Multiplex PCR assay for identification of human diarrheagenic Escherichia coli. J Clin Microbiol. 2003; 41(6): 2669–2671. pmid:12791900
View Article
PubMed/NCBI
Google Scholar

[56] View Article

[57] PubMed/NCBI

[58] Google Scholar

[ref21] 21. Paton AW, Paton JC. Detection and characterization of shiga toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2, eaeA, enterohemorrhagic E. coli hlyA, rfbO111, and rfbO157. J Clin Microbiol. 1998; 36(2): 598–602. pmid:9466788
View Article
PubMed/NCBI
Google Scholar

[60] View Article

[61] PubMed/NCBI

[62] Google Scholar

[ref22] 22. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing; 26th ed. CLSI Supplement M100S. Wayne (PA): CLSI; 2016.

[ref23] 23. European Committee on Antimicrobial Susceptibility Testing (EUCAST). Breakpoint tables for interpretation of MICs and zone diameters; Version 4.0., 2014. EUCAST; 2014.

[ref24] 24. Sjölund-Karlsson M, Joyce K, Blickenstaff K, Ball T, Haro J, Medalla FM, et al. Antimicrobial susceptibility to azithromycin among Salmonella enterica isolates from the United States. Antimicrob Agents Chemother 2011; 55(9): 3985–3989. pmid:21690279
View Article
PubMed/NCBI
Google Scholar

[66] View Article

[67] PubMed/NCBI

[68] Google Scholar

[ref25] 25. Georgia Adopt-A-Stream. Bacterial monitoring. Atlanta (GA): Georgia Adopt-A-Stream, Environmental Protection Division, Department of Natural Resources; 2014.

[ref26] 26. Schraft H, Watterworth LA. Enumeration of heterotrophs, fecal coliforms and Escherichia coli in water: comparison of 3M^™ Petrifilm^™ plates with standard plating procedures. J Microbiol Methods. 2005; 60(3): 335–342. pmid:15649535.
View Article
PubMed/NCBI
Google Scholar

[71] View Article

[72] PubMed/NCBI

[73] Google Scholar

[ref27] 27. Vail JH, Morgan R, Merino CR, Gonzales F, Miller R, Ram JL. Enumeration of waterborne Escherichia coli with petrifilm plates: comparison to standard methods. J Environ Qual. 2003; 32(1): 368–373. pmid:12549577.
View Article
PubMed/NCBI
Google Scholar

[75] View Article

[76] PubMed/NCBI

[77] Google Scholar

[ref28] 28. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, et al. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 1999; 67(2): 546–553. pmid:9916057
View Article
PubMed/NCBI
Google Scholar

[79] View Article

[80] PubMed/NCBI

[81] Google Scholar

[ref29] 29. Higgins J, Hohn C, Hornor S, Frana M, Denver M, Joerger R. 2007. Genotyping of Escherichia coli from environmental and animal samples. J Microbiol Methods. 2007; 70(2): 227–235. pmid:17521755.
View Article
PubMed/NCBI
Google Scholar

[83] View Article

[84] PubMed/NCBI

[85] Google Scholar

[ref30] 30. Jang J, Di DY, Lee A, Unno T, Sadowsky MJ, Hur HG. Seasonal and genotypic changes in Escherichia coli phylogenetic groups in the Yeongsan River Basin of South Korea. PLoS ONE. 2014; 9(7): e100585. pmid:24999864
View Article
PubMed/NCBI
Google Scholar

[87] View Article

[88] PubMed/NCBI

[89] Google Scholar

[ref31] 31. Hamelin K, Bruant G, El-Shaarawi A, Hill S, Edge TA, Fairbrother J, et al. Occurrence of virulence and antimicrobial resistance genes in Escherichia coli isolates from different aquatic ecosystems within the St. Clair River and Detroit River areas. Appl Environ Microbiol. 2007; 73(2):477–484. pmid:17085696
View Article
PubMed/NCBI
Google Scholar

[91] View Article

[92] PubMed/NCBI

[93] Google Scholar

[ref32] 32. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol. 2000; 66(10): 4555–4558. pmid:11010916
View Article
PubMed/NCBI
Google Scholar

[95] View Article

[96] PubMed/NCBI

[97] Google Scholar

[ref33] 33. Gordon DM, Clermont O, Tolley H, Denamur E. Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ Microbiol. 2008; 10(10): 2484–2496. pmid:18518895.
View Article
PubMed/NCBI
Google Scholar

[99] View Article

[100] PubMed/NCBI

[101] Google Scholar

[ref34] 34. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2011, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2014.

[ref35] 35. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2013, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2015.

[ref36] 36. Centers for Disease Control and Prevention (CDC). Surveillance for Foodborne Disease Outbreaks, United States, 2014, Annual Report. Atlanta (GA): US Department of Health and Human Services, CDC; 2016.

[ref37] 37. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, et al. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol. 2007; 24(11): 2373–2384. pmid:17709333
View Article
PubMed/NCBI
Google Scholar

[106] View Article

[107] PubMed/NCBI

[108] Google Scholar

[ref38] 38. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, et al. The Link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 1999; 67(2): 546–553. pmid:9916057
View Article
PubMed/NCBI
Google Scholar

[110] View Article

[111] PubMed/NCBI

[112] Google Scholar

[ref39] 39. Boyd EF, Hartl DL. Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J Bacteriol. 1998; 180(5): 1159–1165. pmid:9495754.
View Article
PubMed/NCBI
Google Scholar

[114] View Article

[115] PubMed/NCBI

[116] Google Scholar

[ref40] 40. Gu G, Luo Z, Cevallos-Cevallos JM, Adams P, Vellidis G, Wright A, et al. Factors affecting the occurrence of Escherichia coli O157 contamination in irrigation ponds on produce farms in the Suwannee River Watershed. Can J Microbiol. 2013; 59(3): 175–182. pmid:23540335.
View Article
PubMed/NCBI
Google Scholar

[118] View Article

[119] PubMed/NCBI

[120] Google Scholar

[ref41] 41. Maal-Bared R, Bartlett KH, Bowie WR, Hall ER. Phenotypic antibiotic resistance of Escherichia coli and E. coli O157 isolated from water, sediment and biofilms in an agricultural watershed in British Columbia. Sci Total Environ. 2013; 443: 315–323. pmid:23202379.
View Article
PubMed/NCBI
Google Scholar

[122] View Article

[123] PubMed/NCBI

[124] Google Scholar

[ref42] 42. Sidhu JS, Ahmed W, Hodgers L, Toze S. Occurrence of virulence genes associated with diarrheagenic pathotypes in Escherichia coli isolates from surface water. Appl Environ Microbiol. 2013; 79(1): 328–335. pmid:23124225
View Article
PubMed/NCBI
Google Scholar

[126] View Article

[127] PubMed/NCBI

[128] Google Scholar

[ref43] 43. Parveen S, Murphree RL, Edmiston L, Kaspar CW, Portier KM, Tamplin ML Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Appl Environ Microbiol. 1997; 63(7): 2607–2612. pmid:9212410
View Article
PubMed/NCBI
Google Scholar

[130] View Article

[131] PubMed/NCBI

[132] Google Scholar

[ref44] 44. Li X, Watanabe N, Xiao C, Harter T, McCowan B, Liu Y, et al. Antibiotic-resistant E. coli in surface water and groundwater in dairy operations in Northern California. Environ Monit Assess. 2014; 186(2): 1253–1260. pmid:24097011.
View Article
PubMed/NCBI
Google Scholar

[134] View Article

[135] PubMed/NCBI

[136] Google Scholar

[ref45] 45. Ibekwe AM, Murinda SE, Graves AK. Genetic diversity and antimicrobial resistance of Escherichia coli from human and animal sources uncovers multiple resistances from human sources. PLoS ONE. 2011; 6(6): e20819. pmid:21687635
View Article
PubMed/NCBI
Google Scholar

[138] View Article

[139] PubMed/NCBI

[140] Google Scholar

[ref46] 46. Chopra I, Roberts M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol Mol Biol Rev. 2001; 65(2): 232–260. pmid:11381101
View Article
PubMed/NCBI
Google Scholar

[142] View Article

[143] PubMed/NCBI

[144] Google Scholar

[ref47] 47. Daghrir R, Drogui P. 2013. Tetracycline antibiotics in the environment: a review. Environ Chem Lett. 2013; 11(3): 209–227.
View Article
Google Scholar

[146] View Article

[147] Google Scholar

[ref48] 48. Olaniran AO, Naicker K, Pillay B. Antibiotic resistance profiles of Escherichia coli isolates from river sources in Durban, South Africa. World J Microbiol Biotechnol. 2009; 25(10):1743–1749.
View Article
Google Scholar

[149] View Article

[150] Google Scholar

[ref49] 49. Zhang X, Li Y, Liu B, Wang J, Feng C, Gao M, et al. Prevalence of veterinary antibiotics and antibiotic-resistant Escherichia coli in the surface water of a livestock production region in Northern China. PLoS One. 2014; 9(11): e111026. pmid:25372873
View Article
PubMed/NCBI
Google Scholar

[152] View Article

[153] PubMed/NCBI

[154] Google Scholar

[ref50] 50. Titilawo Y, Obi L, Okoh A. Antimicrobial resistance determinants of Escherichia coli isolates recovered from some rivers in Osun State, South-Western Nigeria: implications for public health. Sci Total Environ. 2015; 523: 82–94. pmid:25862994.
View Article
PubMed/NCBI
Google Scholar

[156] View Article

[157] PubMed/NCBI

[158] Google Scholar

[ref51] 51. Erin G [Internet]. Athens’ outdated sewage infrastructure may endanger local waterways. Grady Newsource; 2016 May 10 [cited 2017 December 11]. http://gradynewsource.uga.edu/blog/2016/05/10/athens-outdated-sewage-infrastructure-may-endanger-local-waterways/.

[ref52] 52. Lee B [Internet]. Oconee County reporting a sewer spill into Barber Creek due to Mars Hill widening project. Oconee County Observations; 2015 August 26 [cited 2017 December 11]. http://www.oconeecountyobservations.org/2015/08/oconee-county-reporting-sewer-spill.html.

[ref53] 53. Environmental Protection Division (EPD). Draft 2016 Integrated 305(b)/303(d) List—Streams. Atlanta (GA): Gerogia Department of Natural Resources, EPD; 2016.

[ref54] 54. Hobbs F, Stoops N. Demographic trends in the 20th century, Census 2000 special reports, series CENSR-4. Washington (DC): U.S. Census Bureau; 2002.

[ref55] 55. Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev. 2009; 73(4): 750–774. Erratum in: Microbiol Mol Biol Rev. 2010; 74(3): 477–78. pmid:19946140
View Article
PubMed/NCBI
Google Scholar

[164] View Article

[165] PubMed/NCBI

[166] Google Scholar

[ref56] 56. Davison J. Review: Genetic Exchange between bacteria in the environment. Plasmid. 1999; 42(2):73–91. pmid:10489325.
View Article
PubMed/NCBI
Google Scholar

[168] View Article

[169] PubMed/NCBI

[170] Google Scholar

Figures

Abstract

Introduction

Materials and methods

Sampling area

Water collection and enumeration of E. coli in water samples

Isolation and identification of E. coli

Phylogenetic analysis and identification of diarrheagenic pathotypes of E. coli

Antimicrobial susceptibility testing

Results

Prevalence of E. coli

Identification and characterization of E. coli

Discussion

Prevalence of E. coli in the watershed

Pathogenic potential of E. coli in the watershed

Antimicrobial resistant E. coli in the watershed

Supporting information

S1 Table. Master file of the E. coli isolated from the Upper Oconee Watershed.

Acknowledgments

References