scholarly journals Identifying Host Sources of Fecal Pollution: Diversity of Escherichia coli in Confined Dairy and Swine Production Systems

2005 ◽  
Vol 71 (10) ◽  
pp. 5992-5998 ◽  
Author(s):  
Zexun Lu ◽  
David Lapen ◽  
Andrew Scott ◽  
Angela Dang ◽  
Edward Topp
Keyword(s):  
Escherichia Coli ◽  
Dairy Farm ◽  
Sampling Strategy ◽  
Farming Systems ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking ◽  
E Coli ◽  
Repetitive Extragenic Palindromic Pcr ◽  
Repetitive Extragenic Palindromic

ABSTRACT Repetitive extragenic palindromic PCR fingerprinting of Escherichia coli is one microbial source tracking approach for identifying the host source origin of fecal pollution in aquatic systems. The construction of robust known-source libraries is expensive and requires an informed sampling strategy. In many types of farming systems, waste is stored for several months before being released into the environment. In this study we analyzed, by means of repetitive extragenic palindromic PCR using the enterobacterial repetitive intergenic consensus primers and comparative analysis using the Bionumerics software, collections of E. coli obtained from a dairy farm and from a swine farm, both of which stored their waste as a slurry in holding tanks. In all fecal samples, obtained from either barns or holding tanks, the diversity of the E. coli populations was underrepresented by collections of 500 isolates. In both the dairy and the swine farms, the diversity of the E. coli community was greater in the manure holding tank than in the barn, when they were sampled on the same date. In both farms, a comparison of stored manure samples collected several months apart suggested that the community composition changed substantially in terms of the detected number, absolute identity, and relative abundance of genotypes. Comparison of E. coli populations obtained from 10 different locations in either holding tank suggested that spatial variability in the E. coli community should be accounted for when sampling. Overall, the diversity in E. coli populations in manure slurry storage facilities is significant and likely is problematic with respect to library construction for microbial source tracking applications.

Occurrence of antibiotic resistance inEscherichia colifrom surface waters and fecal pollution sources near Hamilton, Ontario

2005 ◽  
Vol 51 (6) ◽  
pp. 501-505 ◽  
Author(s):  
Thomas A Edge ◽  
Stephen Hill
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Surface Waters ◽  
Municipal Wastewater ◽  
Average Rate ◽  
Fecal Pollution ◽  
Pollution Sources ◽  
Source Tracking ◽  
E Coli ◽  
Bird Feces

Antibiotic resistance was examined in 462 Escherichia coli isolates from surface waters and fecal pollution sources around Hamilton, Ontario. Escherichia coli were resistant to the highest concentrations of each of the 14 antibiotics studied, although the prevalence of high resistance was mostly low. Two of 12 E. coli isolates from sewage in a CSO tank had multiple resistance to ampicillin, ciprofloxacin, gentamicin, and tetracycline above their clinical breakpoints. Antibiotic resistance was less prevalent in E. coli from bird feces than from municipal wastewater sources. A discriminant function calculated from antibiotic resistance data provided an average rate of correct classification of 68% for discriminating E. coli from bird and wastewater fecal pollution sources. The preliminary microbial source tracking results suggest that, at times, bird feces might be a more prominent contributor of E. coli to Bayfront Park beach waters than municipal wastewater sources.Key words: antibiotic resistance, Escherichia coli, surface water, fecal pollution.

scholarly journals Evaluation of a human-associated genetic marker for Escherichia coli (H8) for fecal source tracking in Thailand

2020 ◽  
Vol 82 (12) ◽  
pp. 2929-2936
Author(s):  
Pimchanok Nopprapun ◽  
Suwanna Kitpati Boontanon ◽  
Hidenori Harada ◽  
Nawatch Surinkul ◽  
Shigeo Fujii
Keyword(s):  
Escherichia Coli ◽  
Genetic Marker ◽  
Treatment Plant ◽  
Fecal Pollution ◽  
Source Tracking ◽  
Host Group ◽  
E Coli ◽  
Specificity And Sensitivity ◽  
Polymerase Chain ◽  
Animal Feces

Abstract High levels of microbial fecal pollution are a major concern in many countries. A human-associated genetic marker for Escherichia coli (H8) has recently been developed for fecal source tracking. The assessment of the H8 marker performance is crucial before it can be applied as a suitable method for fecal source tracking in each country. The performance (specificity and sensitivity) of the H8 marker was evaluated by using non-target host groups (cattle, buffalo, chicken, duck, and pig feces) and target host groups (influent and effluent from a wastewater treatment plant and septages). SYBR based real-time PCR (polymerase chain reaction) was done on 400 E. coli isolates from non-target and target host groups after E. coli isolation. It was found that the specificity from animal feces samples collected in Thailand was 96%. Moreover, influent, effluent, and septage samples showed the values of the sensitivity at 18, 12, and 36%, respectively. All of the non-target host groups were found to be significantly different with positive proportions from the target host group (septage samples) (p ≤ 0.01). Based on the results, this marker is recommended for use as a human-associated E. coli marker for identifying sources of fecal pollution in Thailand.

scholarly journals Methods To Increase Fidelity of Repetitive Extragenic Palindromic PCR Fingerprint-Based Bacterial Source Tracking Efforts

2005 ◽  
Vol 71 (1) ◽  
pp. 512-518 ◽  
Author(s):  
Wail M. Hassan ◽  
Shiao Y. Wang ◽  
Rudolph D. Ellender
Keyword(s):  
Quality Factor ◽  
Source Tracking ◽  
Blind Test ◽  
E Coli ◽  
Bacterial Source Tracking ◽  
Correct Assignment ◽  
Average Similarity ◽  
Maximum Similarity ◽  
Repetitive Extragenic Palindromic Pcr ◽  
Repetitive Extragenic Palindromic

ABSTRACT The goal of the study was to determine which similarity coefficient and statistical method to use to produce the highest rate of correct assignment (RCA) in repetitive extragenic palindromic PCR-based bacterial source tracking. In addition, the use of standards for deciding whether to accept or reject source assignments was investigated. The use of curve-based coefficients Cosine Coefficient and Pearson's Product Moment Correlation yielded higher RCAs than the use of band-based coefficients Jaccard, Dice, Jeffrey's x, and Ochiai. When enterococcal and Escherichia coli isolates from known sources were used in a blind test, the use of maximum similarity produced consistently higher RCAs than the use of average similarity. We also found that the use of a similarity value threshold and/or a quality factor threshold (the ratio of the average fingerprint similarity within a source to the average similarity of this source's isolates to an unknown) to decide whether to accept source assignments of unknowns increases the reliability of source assignments. Applying a similarity value threshold improved the overall RCA (ORCA) by 15 to 27% when enterococcal fingerprints were used and 8 to 29% when E. coli fingerprints were used. Applying the quality factor threshold resulted in a 22 to 32% improvement in the ORCA, depending on the fingerprinting technique used. This increase in reliability was, however, achieved at the expense of decreased numbers of isolates that were assigned a source.

scholarly journals Genetic diversity and antimicrobial resistance of Escherichia coli as microbial source tracking tools of Karaj River, Iran

2017 ◽  
Vol 17 (5) ◽  
pp. 1468-1478
Author(s):  
Roohollah Kheiri ◽  
Leili Akhtari
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Microbial Source Tracking ◽  
Source Tracking ◽  
Enterobacterial Repetitive Intergenic Consensus ◽  
Genetic Characteristics ◽  
Sample Group ◽  
E Coli ◽  
Cattle Faeces

The aim of this study was to analyze the enterobacterial repetitive intergenic consensus (ERIC)-types, phylo-groups and antimicrobial resistance (AMR) patterns of Escherichia coli and to investigate if these approaches are suitable for microbial source tracking (MST). E. coli strains were isolated from cattle faeces and Karaj River. For genetic diversity, AMR profile, and phylo-grouping, we applied ERIC-PCR, disk diffusion, and multiplex-PCR, respectively. Fifty isolates from each sample group were used in the study. ERIC fingerprinting produced ten different bands, demonstrating 64 unique and 36 repetitive profiles. Six isolates from the river showed the same ERIC pattern of the cattle, of which four expressed the same AMR profile. E. coli isolates from water were represented in A, B1, C, and D phylo-groups. Phylo-groups A, B1, and E were more prevalent in the cattle isolates and B2 was absent in both sources. Three of the water isolates with the same ERIC-type and AMR to cattle isolates showed the same phylo-groups. Genetic characteristics, AMR, and phylo-groups of the isolates from the river are diverse and complex. For accurate MST, complementary approaches should be applied together and a comprehensive library should be provided.

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

2009 ◽  
Vol 55 (3) ◽  
pp. 269-276 ◽  
Author(s):  
Tanya Kon ◽  
Susan C. Weir ◽  
E. Todd Howell ◽  
Hung Lee ◽  
Jack T. Trevors
Keyword(s):  
Escherichia Coli ◽  
Repetitive Element ◽  
Microbial Source Tracking ◽  
Lake Huron ◽  
Source Tracking ◽  
Chain Reaction ◽  
Recreational Waters ◽  
E Coli ◽  
Potential Sources ◽  
Polymerase Chain

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

scholarly journals Comparison of Ribotyping and Repetitive Extragenic Palindromic-PCR for Identification of Fecal Escherichia coli from Humans and Animals

2003 ◽  
Vol 69 (3) ◽  
pp. 1836-1839 ◽  
Author(s):  
C. Andrew Carson ◽  
Brian L. Shear ◽  
Mark R. Ellersieck ◽  
Jennifer D. Schnell
Keyword(s):  
Escherichia Coli ◽  
Fecal Pollution ◽  
Dna Fingerprints ◽  
Animal Hosts ◽  
Repetitive Extragenic Palindromic Pcr ◽  
Repetitive Extragenic Palindromic

ABSTRACT This report compares the performances of two popular genotypic methods used for tracking the sources of fecal pollution in water, ribotyping and repetitive extragenic palindromic-PCR (rep-PCR). The rep-PCR was more accurate, reproducible, and efficient in associating DNA fingerprints of fecal Escherichia coli with human and animal hosts of origin.

scholarly journals Relative Decay of Bacteroidales Microbial Source Tracking Markers and Cultivated Escherichia coli in Freshwater Microcosms

2010 ◽  
Vol 76 (10) ◽  
pp. 3255-3262 ◽  
Author(s):  
Linda K. Dick ◽  
Erin A. Stelzer ◽  
Erin E. Bertke ◽  
Denise L. Fong ◽  
Donald M. Stoeckel
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Microbial Source Tracking ◽  
Decay Rates ◽  
Source Tracking ◽  
Rrna Gene ◽  
Fecal Indicator ◽  
Gene Markers ◽  
E Coli ◽  
Log Reduction

ABSTRACT Fecal indicator bacteria (FIB), commonly used to regulate sanitary water quality, cannot discriminate among sources of contamination. The use of alternative quantitative PCR (qPCR) methods for monitoring fecal contamination or microbial source tracking requires an understanding of relationships with cultivated FIB, as contamination ages under various conditions in the environment. In this study, the decay rates of three Bacteroidales 16S rRNA gene markers (AllBac for general contamination and qHF183 and BacHum for human-associated contamination) were compared with the decay rate of cultivated Escherichia coli in river water microcosms spiked with human wastewater. The following five sets of microcosms were monitored over 11 days: control, artificial sunlight, sediment exposure, reduced temperature, and no autochthonous predation. Decay was characterized by estimation of the time needed to produce a 2-log reduction (t 99). No treatment-associated differences in the decay of the 4 targets were evident except with reduced predation, where E. coli, qHF183, and BacHum markers had lower levels of decay by day 3. However, there were substantial target-associated differences. Decay curves for the AllBac marker indicated a larger persistent population than those of the other targets. Exposure to sunlight, sediment, and reduced predation resulted in more rapid decay of the human-associated markers relative to cultivable E. coli, but there were no differences in t 99 values among the 4 targets under control conditions or at reduced temperatures. Further evaluation of epidemiological relationships will be needed in order to relate the markers directly to health risk. These findings suggest that the tested human-associated markers can complement E. coli as indicators of the human impact on sanitary water quality under the constrained conditions described in this paper.

scholarly journals Automated Targeted Sampling of Waterborne Pathogens and Microbial Source Tracking Markers Using Near-Real Time Monitoring of Microbiological Water Quality

Water ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 2069
Author(s):  
Jean-Baptiste Burnet ◽  
Marc Habash ◽  
Mounia Hachad ◽  
Zeinab Khanafer ◽  
Michèle Prévost ◽  
...  
Keyword(s):  
Water Quality ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Source Tracking ◽  
Waterborne Pathogens ◽  
Short Term ◽  
Sampling Methodology ◽  
E Coli ◽  
Biochemical Indicator ◽  
Microbiological Water Quality

Waterborne pathogens are heterogeneously distributed across various spatiotemporal scales in water resources, and representative sampling is therefore crucial for accurate risk assessment. Since regulatory monitoring of microbiological water quality is usually conducted at fixed time intervals, it can miss short-term fecal contamination episodes and underestimate underlying microbial risks. In the present paper, we developed a new automated sampling methodology based on near real-time measurement of a biochemical indicator of fecal pollution. Online monitoring of β-D-glucuronidase (GLUC) activity was used to trigger an automated sampler during fecal contamination events in a drinking water supply and at an urban beach. Significant increases in protozoan parasites, microbial source tracking markers and E. coli were measured during short-term (<24 h) fecal pollution episodes, emphasizing the intermittent nature of their occurrence in water. Synchronous triggering of the automated sampler with online GLUC activity measurements further revealed a tight association between the biochemical indicator and culturable E. coli. The proposed event sampling methodology is versatile and in addition to the two triggering modes validated here, others can be designed based on specific needs and local settings. In support to regulatory monitoring schemes, it should ultimately help gathering crucial data on waterborne pathogens more efficiently during episodic fecal pollution events.

scholarly journals Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance

2019 ◽  
Vol 12 (7) ◽  
pp. 984-993 ◽  
Author(s):  
Md. Abdus Sobur ◽  
Abdullah Al Momen Sabuj ◽  
Ripon Sarker ◽  
A. M. M. Taufiqur Rahman ◽  
S. M. Lutful Kabir ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
One Health ◽  
Dairy Farm ◽  
Antibiotic Resistance Genes ◽  
Salmonella Spp ◽  
Antibiotic Resistant ◽  
E Coli

Aim: The present study was carried out to determine load of total bacteria, Escherichia coli and Salmonella spp. in dairy farm and its environmental components. In addition, the antibiogram profile of the isolated bacteria having public health impact was also determined along with identification of virulence and resistance genes by polymerase chain reaction (PCR) under a one-health approach. Materials and Methods: A total of 240 samples of six types (cow dung - 15, milk - 10, milkers' hand wash - 10, soil - 10 water - 5, and vegetables - 10) were collected from four dairy farms. For enumeration, the samples were cultured onto plate count agar, eosin methylene blue, and xylose-lysine deoxycholate agar and the isolation and identification of the E. coli and Salmonella spp. were performed based on morphology, cultural, staining, and biochemical properties followed by PCR. The pathogenic strains of E. coli stx1, stx2, and rfbO157 were also identified through PCR. The isolates were subjected to antimicrobial susceptibility test against 12 commonly used antibiotics by disk diffusion method. Detection of antibiotic resistance genes ereA, tetA, tetB, and SHV were performed by PCR. Results: The mean total bacterial count, E. coli and Salmonella spp. count in the samples ranged from 4.54±0.05 to 8.65±0.06, 3.62±0.07 to 7.04±0.48, and 2.52±0.08 to 5.87±0.05 log colony-forming unit/g or ml, respectively. Out of 240 samples, 180 (75%) isolates of E. coli and 136 (56.67%) isolates of Salmonella spp. were recovered through cultural and molecular tests. Among the 180 E. coli isolates, 47 (26.11%) were found positive for the presence of all the three virulent genes, of which stx1 was the most prevalent (13.33%). Only three isolates were identified as enterohemorrhagic E. coli. Antibiotic sensitivity test revealed that both E. coli and Salmonella spp. were found highly resistant to azithromycin, tetracycline, erythromycin, oxytetracycline, and ertapenem and susceptible to gentamycin, ciprofloxacin, and imipenem. Among the four antibiotic resistance genes, the most observable was tetA (80.51-84.74%) in E. coli and Salmonella spp. and SHV genes were the lowest one (22.06-25%). Conclusion: Dairy farm and their environmental components carry antibiotic-resistant pathogenic E. coli and Salmonella spp. that are potential threat for human health which requires a one-health approach to combat the threat.

scholarly journals Heterogeneity of uidA gene in environmental Escherichia coli populations

2005 ◽  
Vol 3 (3) ◽  
pp. 297-304 ◽  
Author(s):  
Clarivel Lasalde ◽  
Roberto Rodriguez ◽  
Gary A. Toranzos ◽  
Henry H. Smith
Keyword(s):  
Escherichia Coli ◽  
Genetic Heterogeneity ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dry Weight ◽  
Source Tracking ◽  
Tropical Rain Forests ◽  
Rain Forests ◽  
E Coli ◽  
Gradient Gel Electrophoresis

Previous studies have shown that Escherichia coli can be isolated from non-polluted rivers and from bromeliad axilae in pristine areas of tropical rain forests. Finding E. coli in pristine environments is unusual because this bacterium is thought to only survive in the gut of warm-blooded animals and thus its presence should indicate recent fecal contamination. The aims of this study were 1) to determine if E. coli is part of the native soil microbiota in tropical rain forests and 2) to determine if genetic heterogeneity exists among E. coli populations. High concentrations of total coliforms (104–105 cells per 10 g of soil dry weight) and low concentrations of thermotolerant coliforms (101–102 cells per 10 g dry soil, the majority of these were found to be E. coli) were detected. PCR using uidA-specific primers was done on DNA purified from E. coli isolates and the resulting amplicons analysed by denaturing-gradient gel electrophoresis (DGGE). Out of several hundred isolates, mixtures of nine different amplicons were consistently observed. The different patterns of DGGE observed indicate that the E. coli populations in these pristine soils are genetically heterogeneous. Fecal and environmental E. coli isolates were also analysed by pulsed-field gel electrophoresis (PFGE) which showed high DNA sequence variation among the E. coli isolates. Because of these differences in the genomes, PFGE did not allow grouping of environmental versus human isolates of E. coli when compared side to side. The apparent genetic polymorphisms, as a result of genetic heterogeneity, observed in isolates from the same pristine site indicate that source tracking may be difficult to carry out using E. coli as the target organism.

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