Multiplex PCR-DNA probe assay for the detection of pathogenic Escherichia coli

Evaluation of bottled drinking water and occurrence of multidrug-resistance and biofilm producing bacteria in Nepal

Health consequences arising from unsafe drinking water and water insecurity lead to increased reliance on usage of bottled water. Biofilm-producing antibiotic-resistant bacteria in bottled water may pose a risk to public health. This study aims to assess the quality of bottled drinking water with a focus on biofilm-producing and drug-resistant coliform. We analyzed 60 bottled water samples of 30 different brands purchased from Kathmandu for physicochemical and microbial analysis. The parameters pH, iron, total coliform count, Escherichia coli count, and fecal coliform count exceeded National Drinking Water Quality Standards, 2022 in 30.00%, 16.67%, 66.67%, 23.33%, and 16.67% of samples, respectively. Water quality index measurement showed 36.67% and 6.67% of bottled water samples were categorized as grade A and grade B indicating excellent and good water quality, respectively. However, 56.67% of bottled water samples fall under grade E meaning unsuitable for drinking. Among 14 coliform isolates, 85.71% and 14.29% were identified as E. coli and Klebsiella spp, respectively. The antibiotic susceptibility testing revealed that 28.57% of the isolates were multidrug-resistant and Gentamicin resistant isolates comprised 71.43%. However, none of the isolates were carbapenem (meropenem) resistant. In this study, 42.87% of the isolates were found biofilm producers with 14.29% each of strong, moderate, and weak biofilm producers. The genetic potential of biofilm-producing capacity of the isolates was assessed by Polymerase Chain Reaction amplification of bcsA and csgD genes. Our results showed that 66.67% and 50.00% of the isolates harbored bcsA and csgD genes, respectively. This study highlights potential public health hazards associated with the consumption of bottled water containing biofilm-producing and drug-resistant bacteria in Nepal.

Antibacterial activity of combined aditoprim and sulfamethoxazole against Escherichia coli from swine and a dose regimen based on pharmacokinetic-pharmacodynamic modeling

The mortality of livestock caused by pathogenic Escherichia coli (E. coli) still accounts for a large proportion of deaths in large-scale production and reproduction, which causes devastating economic losses to the pig breeding industry. The aims of this study were to investigate the antibacterial activity of combined aditoprim (ADP) and sulfamethoxazole (SMZ) against clinical isolates of E. coli from pigs and to develop a pharmacokinetic-pharmacodynamic (PK-PD) model to formulate the optimal dose of ADP/SMZ for the treatment of pig colibacillosis. Blood and ileum fluid samples were collected at different times after single intramuscular injection of ADP/SMZ (5/25 mg/kg b.w.) to healthy pigs and E. coli-infected pigs. Concentrations of ADP and SMZ in plasma and ileum fluid were analyzed by HPLC. The peak concentration (C_max ) and the area under the concentration-time curve (AUC_0-24h ) in ileum fluid of healthy pigs were 1.76 ± 0.27 µg/ml and 18.92 ± 2.87 µg·h/ml for ADP and 19.15 ± 2.63 µg/ml and 125.70 ± 11.86 µg·h/ml for SMZ, respectively. C_max and AUC_0-24h in ileum fluid of infected pigs were 1.88 ± 0.13 µg/ml and 15.12 ± 0.75 µg·h/ml for ADP and 19.71 ± 3.68 µg/ml and 133.92 ± 17.14 µg·h/ml for SMZ, respectively. The minimum inhibitory concentrations (MICs) of combined ADP and SMZ (ADP/SMZ) against 185 strains of E. coli from pigs were determined. The MIC₅₀ and MIC₉₀ of ADP/SMZ were 0.5/2.5 and 4/20 µg/ml, respectively. The MIC of the selected pathogenic E. coli SHC28 was 0.5/2.5 µg/ml in Mueller-Hinton broth and 0.25/1.25 µg/ml in ileum fluid, respectively. In vitro, the mutant prevention concentration, the post-antibiotic effect, growth, and time-killing curves in vitro and ex vivo of ADP/SMZ against the isolate SHC28 were assayed for PD studies. The results showed that ADP/SMZ exhibited strong concentration-dependent antimicrobial activity against E. coli. After integrating the in vivo pharmacokinetic parameters of infected pigs and ex vivo PD data using the sigmoid E_max (Hill) equation, the AUC_24h /MIC values in ileum fluid for bacteriostatic, bactericidal, and bacterial eradication were 18.84, 65.39, and 110.68 h, respectively. In conclusion, a dosage of 3.45/17.25 mg/kg ADP/SMZ by intramuscular injection daily for 3 consecutive days may be sufficient to treat swine colibacillosis due to E. coli with a MIC of 0.5/2.5 µg/ml.

Identification of enteropathogenic Escherichia coli in children with acute diarrheic syndrome from Sucre State, Venezuela

INTRODUCTION

Diarrheagenic Escherichia coli is an important causative agent of acute diarrheic syndrome. 

OBJECTIVE

To identify clonal groups of enteropathogenic E. coli (EPEC), in 485 children with acute diarrhea aged 0 to 10 years attending health care centers in Arismendi, Benítez and Sucre municipalities, Sucre state, Venezuela, from March to December, 2011. 

MATERIALS AND METHODS

After obtaining the informed consent, stool samples were collected. Escherichia coli was identified using standard coproculture methods and serology with polyvalent and monovalent antisera. DNA was isolated, and eae (intimin) and bfpA (bundlin) genes were amplified through two multiplex polymerase chain reactions (PCR). 

RESULTS

The presence of bacterial infection was determined in 39.6% of coprocultures. The prevalence of E. coli was 54.7%; 82.9% of these isolates were positive by serology for the evaluated serogroups and serotypes, which were mostly identified in children between 0 and 2 years (37.9%); 48.6% of E. coli strains amplified the eae gene; of these, 58.8% were classified as typical EPEC (eae+ y bfp+). EPEC II was the most common serogroup (38.7%), with predominance of typical EPEC (60%). In positive strains for eae gene, the β intimin allele was the most frequently identified (74.5%). Only four strains with O157:H7 serotype were identified, which showed no PCR amplification of the eae and bfpA genes. 

CONCLUSION

This study showed the importance of molecular tests to identify diarrheagenic E. coli strains causing clinical conditions of varying severity.

Co-detection of virulent Escherichia coli genes in surface water sources

McNemar’s test and the Pearson Chi-square were used to assess the co-detection and observed frequency, respectively, for potentially virulent E. coli genes in river water. Conventional multiplex Polymerase Chain Reaction (PCR) assays confirmed the presence of the aggR gene (69%), ipaH gene (23%) and the stx gene (15%) carried by Enteroaggregative E. coli (EAEC), Enteroinvasive E. coli (EIEC) and Enterohermorrhagic E. coli (EHEC), respectively, in river water samples collected from the Berg River (Paarl, South Africa). Only the aggR gene was present in 23% of samples collected from the Plankenburg River system (Stellenbosch, South Africa). In a comparative study, real-time multiplex PCR assays confirmed the presence of aggR (EAEC) in 69%, stx (EHEC) in 15%, ipaH (EIEC) in 31% and eae (EPEC) in 8% of the river water samples collected from the Berg River. In the Plankenburg River, aggR (EAEC) was detected in 46% of the samples, while eae (EPEC) was present in 15% of the water samples analyzed using real-time multiplex PCR in the Plankenburg River. Pearson Chi-square showed that there was no statistical difference (p > 0.05) between the conventional and real-time multiplex PCRs for the detection of virulent E. coli genes in water samples. However, the McNemar’s test showed some variation in the co-detection of virulent E. coli genes, for example, there was no statistical difference in the misclassification of the discordant results for stx versus ipaH, which implies that the ipaH gene was frequently detected with the stx gene. This study thus highlights the presence of virulent E. coli genes in river water and while early detection is crucial, quantitative microbial risk analysis has to be performed to identify and estimate the risk to human health.

Distribution of indigenous bacterial pathogens and potential pathogens associated with roof-harvested rainwater

The harvesting of rainwater is gaining acceptance among many governmental authorities in countries such as Australia, Germany, and South Africa, among others. However, conflicting reports on the microbial quality of harvested rainwater have been published. To monitor the presence of potential pathogenic bacteria during high-rainfall periods, rainwater from 29 rainwater tanks was sampled on four occasions (during June and August 2012) in a sustainable housing project in Kleinmond, South Africa. This resulted in the collection of 116 harvested rainwater samples in total throughout the sampling period. The identities of the dominant, indigenous, presumptive pathogenic isolates obtained from the rainwater samples throughout the sampling period were confirmed through universal 16S rRNA PCR, and the results revealed that Pseudomonas (19% of samples) was the dominant genus isolated, followed by Aeromonas (16%), Klebsiella (11%), and Enterobacter (9%). PCR assays employing genus-specific primers also confirmed the presence of Aeromonas spp. (16%), Klebsiella spp. (47%), Legionella spp. (73%), Pseudomonas spp. (13%), Salmonella spp. (6%), Shigella spp. (27%), and Yersinia spp. (28%) in the harvested rainwater samples. In addition, on one sampling occasion, Giardia spp. were detected in 25% of the eight tank water samples analyzed. This study highlights the diverse array of pathogenic bacteria that persist in harvested rainwater during high-rainfall periods. The consumption of untreated harvested rainwater could thus pose a potential significant health threat to consumers, especially children and immunocompromised individuals, and it is recommended that harvested rainwater be treated for safe usage as an alternative water source.

Prevalence of virulence genes associated with pathogenic Escherichia coli strains isolated from domestically harvested rainwater during low- and high-rainfall periods

The possible health risks associated with the consumption of harvested rainwater remains one of the major obstacles hampering its large-scale implementation in water limited countries such as South Africa. Rainwater tank samples collected on eight occasions during the low- and high-rainfall periods (March to August 2012) in Kleinmond, South Africa, were monitored for the presence of virulence genes associated with Escherichia coli. The identity of presumptive E. coli isolates in rainwater samples collected from 10 domestic rainwater harvesting (DRWH) tanks throughout the sampling period was confirmed through universal 16S rRNA PCR with subsequent sequencing and phylogenetic analysis. Species-specific primers were also used to routinely screen for the virulent genes, aggR, stx, eae, and ipaH found in enteroaggregative E. coli (EAEC), enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), and enteroinvasive E. coli, respectively, in the rainwater samples. Of the 92 E. coli strains isolated from the rainwater using culture based techniques, 6% were presumptively positively identified as E. coli O157:H7 using 16S rRNA. Furthermore, virulent pathogenic E. coli genes were detected in 3% (EPEC and EHEC) and 16% (EAEC) of the 80 rainwater samples collected during the sampling period from the 10 DRWH tanks. This study thus contributes valuable information to the limited data available regarding the ongoing prevalence of virulent pathotypes of E. coli in harvested rainwater during a longitudinal study in a high-population-density, periurban setting.

Role of rpoS in Escherichia coli O157:H7 strain H32 biofilm development and survival

The protein RpoS is responsible for mediating cell survival during the stationary phase by conferring cell resistance to various stressors and has been linked to biofilm formation. In this study, the role of the rpoS gene in Escherichia coli O157:H7 biofilm formation and survival in water was investigated. Confocal scanning laser microscopy of biofilms established on coverslips revealed a nutrient-dependent role of rpoS in biofilm formation, where the biofilm biomass volume of the rpoS mutant was 2.4- to 7.5-fold the size of its rpoS(+) wild-type counterpart in minimal growth medium. The enhanced biofilm formation of the rpoS mutant did not, however, translate to increased survival in sterile double-distilled water (ddH(2)O), filter-sterilized lake water, or unfiltered lake water. The rpoS mutant had an overall reduction of 3.10 and 5.30 log(10) in sterile ddH(2)O and filter-sterilized lake water, respectively, while only minor reductions of 0.53 and 0.61 log(10) in viable counts were observed for the wild-type form in the two media over a 13-day period, respectively. However, the survival rates of the detached biofilm-derived rpoS(+) and rpoS mutant cells were comparable. Under the competitive stress conditions of unfiltered lake water, the advantage conferred by the presence of rpoS was lost, and both the wild-type and knockout forms displayed similar declines in viable counts. These results suggest that rpoS does have an influence on both biofilm formation and survival of E. coli O157:H7 and that the advantage conferred by rpoS is contingent on the environmental conditions.

Class 1 integrons, selected virulence genes, and antibiotic resistance in Escherichia coli isolates from the Minjiang River, Fujian Province, China

Widespread fecal pollution of surface waters in developing countries is a threat to public health and may represent a significant pathway for the global dissemination of antibiotic resistance. The Minjiang River drainage basin in Fujian Province is one of China's most intensive livestock and poultry production areas and is home to several million people. In the study reported here, Escherichia coli isolates (n = 2,788) were sampled (2007 and 2008) from seven surface water locations in the basin and evaluated by PCR for carriage of selected genes encoding virulence factors, primarily for swine disease. A subset of isolates (n = 500) were evaluated by PCR for the distribution and characteristics of class 1 integrons, and a subset of these (n = 200) were evaluated phenotypically for resistance to a range of antibiotics. A total of 666 (24%) E. coli isolates carried at least one of the virulence genes elt, fedA, astA, fasA, estA, stx(2e), paa, and sepA. Forty-one percent of the isolates harbored class 1 integrons, and these isolates had a significantly higher probability of resistance to tobramycin, cefoperazone, cefazolin, ciprofloxacin, norfloxacin, azitromycin, and rifampin than isolates with no class 1 integron detected. Frequencies of resistance to selected antibiotics were as high as or higher than those in fecal, wastewater, and clinical isolates in published surveys undertaken in China, North America, and Europe. Overall, E. coli in the Minjiang River drainage basin carry attributes with public health significance at very high frequency, and these data provide a powerful rationale for investment in source water protection strategies in this important agricultural and urban setting in China.

Detection of enterotoxigenic K99 (F5) and F41 from fecal sample of calves by molecular and serological methods

Enterotoxigenic Escherichia coli (ETEC) is one of the major causes of neonatal calf diarrhea. Almost all ETEC bacteria are known to adhere to receptors on the small intestinal epithelium via their fimbriae, (F5 (K99) and F41).This study was undertaken to investigate the phenotypic and genotypic screening of virulence genes in E. coli K99 and F41. During January 2008 to December 2009, 298 diarrheic neonatal calves at 1-30 days old were studied by multiplex PCR, isolation, and serological grouping. Of the 298 diarrheic samples, 268 E. coli were isolated, of which 16 samples (5.3%) were positive for having the F5 (K99) fimbrial gene by PCR while all of the E. coli isolates also carried F41 fimbrial genes. Twenty-five percent of the isolates were proven not to be toxigenic as they did not possess the STa enterotoxin gene.

Molecular screening and risk factors of enterotoxigenic Escherichia coli and Salmonella spp. in diarrheic neonatal calves in Egypt

The aim of the present study was to carry out molecular epidemiological investigation on enterotoxigenic Escherichia coli (ETEC) K99 and Salmonella spp. in diarrheic neonatal calves. Fecal samples were obtained from 220 diarrheic calves at 9 farms related to four governorates in central and northern Egypt. E. coli and Salmonella spp. isolates were examined for E. coli K99 and Salmonella spp. using PCR. ETEC K99 was recovered from 20 (10.36 %) out of 193 isolates, whereas Salmonella spp. was recovered from nine calves (4.09%). Multivariable logistic regression was used to evaluate the risk factors associated with both infections. ETEC K99 was significantly affected by age (P<0.01; OR: 1.812; CI 95%: 0.566-1.769), colostrum feeding practice (P<0.01; OR: 5.525; CI 95%: 2.025-15.076), rotavirus infection (P<0.001; OR: 2.220; CI 95%: 0.273-1.251), vaccination of pregnant dams with combined vaccine against rotavirus, coronavirus and E. coli (K99) (P<0.001; OR: 4.753; CI 95%: 2.124-10.641), and vitamin E and selenium administration to the pregnant dam (P<0.01; OR: 3.933; CI 95%: 0.703-1.248). Infection with Salmonella spp. was found to be significantly affected by the animal age (P<0.05; OR: 0.376; CI 95%: 0.511-1.369), Hygiene (P<0.05; OR: 0.628; CI 95%: 1.729-5.612), and region (P<0. 01; OR: 0.970; CI 95%: 0.841-1.624). The results of the present study indicate the importance of PCR as rapid, effective and reliable tool for screening of ETEC and Salmonella spp. when confronted with cases of undifferentiated calf diarrhea. Moreover, identification of the risk factors associated with the spreading of bacteria causing diarrhea may be helpful for construction of suitable methods for prevention and control.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.

Detection of Escherichia coli, Salmonella spp., Shigella spp., Yersinia enterocolitica, Vibrio cholerae, and Campylobacter spp. enteropathogens by 3-reaction multiplex polymerase chain reaction

The magnitude of bacterial diarrhea in developing countries is largely unknown because affordable detection methods are not available. We have developed a polymerase chain reaction (PCR)-based assay for use in areas with limited resources to screen for diarrheogenic strains from clinical isolates. To simplify the assay and minimize reagents, our method implemented the use of plasmids rather than bacteria as template controls and the use of bacterial suspensions or crude DNA preparations rather than purified genomic DNA as template DNA. The assay consisted of 3 PCR reactions using 3 groups of 5 to 6 primer pairs to identify the 11 most common bacterial diarrheogenic pathogens. The 3-reaction multiplex PCR amplifies DNA targets specific for each 1 of the 6 Escherichia coli diarrheogenic strains and the 5 non-E. coli diarrheogenic strains, including Salmonella spp., Shigella spp., Campylobacter spp., Yersinia enterocolitica, and Vibrio cholerae. The assay may provide an important epidemiologic tool to investigate the role of diarrheogenic bacterial pathogens in areas of the world with limited resources.

Detection of diarrheagenic Escherichia coli by use of melting-curve analysis and real-time multiplex PCR

Diarrheagenic Escherichia coli strains are important causes of diarrhea in children from the developing world and are now being recognized as emerging enteropathogens in the developed world. Current methods of detection are too expensive and labor-intensive for routine detection of these organisms to be practical. We developed a real-time fluorescence-based multiplex PCR for the detection of all six of the currently recognized classes of diarrheagenic E. coli. The primers were designed to specifically amplify eight different virulence genes in the same reaction: aggR for enteroaggregative E. coli, stIa/stIb and lt for enterotoxigenic E. coli, eaeA for enteropathogenic E. coli and Shiga toxin-producing E. coli (STEC), stx(1) and stx(2) for STEC, ipaH for enteroinvasive E. coli, and daaD for diffusely adherent E. coli (DAEC). Eighty-nine of ninety diarrheagenic E. coli and 36/36 nonpathogenic E. coli strains were correctly identified using this approach (specificity, 1.00; sensitivity, 0.99). The single false negative was a DAEC strain. The total time between preparation of DNA from E. coli colonies on agar plates and completion of PCR and melting-curve analysis was less than 90 min. The cost of materials was low. Melting-point analysis of real-time multiplex PCR is a rapid, sensitive, specific, and inexpensive method for detection of diarrheagenic E. coli.

Development of a monoclonal antibody-based co-agglutination test to detect enterotoxigenic Escherichia coli isolated from diarrheic neonatal calves

Escherichia coli (E. coli) strains were collected from young diarrheic calves in farms and field. Strains that expressed the K99 (F5) antigen were identified by agglutination tests using reference antibodies to K99 antigen and electron microscopy. The K99 antigen from a selected field strain (SAR-14) was heat-extracted and fractionated on a Sepharose CL-4B column. Further purification was carried out by sodium deoxycholate treatment and/or ion-exchange chromatography. Monoclonal antibodies to purified K99 antigen were produced by the hybridoma technique, and a specific clone, NEK99-5.6.12, was selected for propagation in tissue culture. The antibodies, thus obtained, were affinity-purified, characterized and coated onto Giemsa-stained Cowan-I strain of Staphylococcus aureus (S. aureus). The antibody-coated S. aureus were used in a co-agglutination test to detect K99+ E. coli isolated from feces of diarrheic calves. The specificity of the test was validated against reference monoclonal antibodies used in co-agglutination tests, as well as in ELISA. Specificity of the monoclonal antibodies was also tested against various Gram negative bacteria. The developed antibodies specifically detected purified K99 antigen in immunoblots, as well as K99+ E. coli in ELISA and co-agglutination tests. The co-agglutination test was specific and convenient for large-scale screening of K99+ E. coli isolates.

Octaplex PCR and fluorescence-based capillary electrophoresis for identification of human diarrheagenic Escherichia coli and Shigella spp

A multiplex PCR assay, amplifying seven specific virulence genes and one internal control gene in a single reaction, was developed to identify the five main pathotypes of diarrheagenic Escherichia coli and Shigella spp. The virulence genes selected for each category were Stx1, Stx2, and eaeA for enterohemorrhagic E. coli (EHEC), eaeA for enteropathogenic E. coli (EPEC), STIb and LTI for enterotoxigenic E. coli (ETEC), ipaH for enteroinvasive E. coli (EIEC) and Shigella spp., and aggR for enteroaggregative E. coli (EAEC). Each forward primer was labelled with a fluorochrome and the PCR products were separated by multicolour capillary electrophoresis on an ABI PRISM310 Genetic Analyzer (Applied Biosystems). If present, several gene variants of each virulence gene were identified. The internal control gene rrs, encoding 16S rRNA, was amplified in all 110 clinical strains analyzed. Virulence genes were demonstrated in 103 (94%) of these strains. In the majority of the cases (98/103, 95%), classification obtained by the novel multiplex PCR assay was in agreement with that previously determined by phenotypic assays combined with other molecular genetic approaches. Numerous multiplex PCR assays have been published, but only a few of them detect all five E. coli pathotypes within a single reaction, and none of them has used multicolour capillary electrophoresis to separate the PCR products. The octaplex PCR assay followed by capillary electrophoresis presented in the present paper provides a simple, reliable, and rapid procedure that in a single reaction identifies the five main pathotypes of E. coli, and Shigella spp. This assay will replace the previous molecular genetic methods used in our laboratory and work as an important supplement to the more time-consuming phenotypic assays.

Rapid identification and differentiation of clinical isolates of enteropathogenic Escherichia coli (EPEC), atypical EPEC, and Shiga toxin-producing Escherichia coli by a one-step multiplex PCR method

Enteropathogenic Escherichia coli (EPEC), atypical enteropathogenic E. coli, and Shiga toxin-producing E. coli differ in their virulence factor profiles, clinical manifestations, and prognosis, and they require different therapeutic measures. We developed and evaluated a robust multiplex PCR to identify these pathogroups based on sequences complementary to escV, bfpB, stx1, and stx2.

Evaluation of denaturing gradient gel electrophoresis to differentiate Escherichia coli populations in secondary environments

The development of methodology to differentiate mixed populations of Escherichia coli in the secondary habitat might improve monitoring of fecal pollution indicators and facilitate the development of strategies to mitigate bacterial pollution. The objective of this study was to determine the ability of denaturing gradient gel electrophoresis (DGGE) to differentiate mixed assemblages of E. coli in the natural environment. After confirming the identity of 184 environmental bacterial isolates as E. coli, each was subjected to polymerase chain reaction (PCR) of the beta-glucuronidase gene (uidA) followed by DGGE fingerprinting. The ability of DGGE to discriminate individual isolates at the strain level was determined by comparing fingerprints to those resulting from a standard, library-dependent fingerprinting method, BOX-PCR. Computerized analysis of fingerprints indicated that DGGE and BOX-PCR identified 15 and 21 unique phylotypes respectively. Rank-abundance plots comparing the numerical distribution of unique E. coli phylotypes detected by both methods revealed no difference in resolution at the population level. In water and sediment samples from two beaches, DGGE effectively distinguished indigenous E. coli populations with an average rate of correct classification (site-based) of 83%. Denaturing gradient gel electrophoresis of uidA genes isolated and PCR-amplified from environmental samples appears to be an effective tool to differentiate unique E. coli populations and should be useful to characterize E. coli dynamics in the secondary environment.