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Wang J, Kaur S, Kayabasi A, Ranjbaran M, Rath I, Benschikovski I, Raut B, Ra K, Rafiq N, Verma MS. A portable, easy-to-use paper-based biosensor for rapid in-field detection of fecal contamination on fresh produce farms. Biosens Bioelectron 2024; 259:116374. [PMID: 38754195 DOI: 10.1016/j.bios.2024.116374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Laboratory-based nucleic acid amplification tests (NAATs) are highly sensitive and specific, but they require the transportation of samples to centralized testing facilities and have long turnaround times. During the Coronavirus Disease 2019 (COVID-19) pandemic, substantial advancement has been achieved with the development of paper-based point-of-care (POC) NAATs, offering features such as low cost, being easy to use, and providing rapid sample-to-answer times. Although most of the POC NAATs innovations are towards clinical settings, we have developed a portable, paper-based loop-mediated isothermal amplification (LAMP) testing platform for on-farm applications, capable of detecting Bacteroidales as a fecal contamination biomarker. Our integrated platform includes a drop generator, a heating and imaging unit, and paper-based biosensors, providing sensitive results (limit of detection 3 copies of Bacteroidales per cm2) within an hour of sample collection. We evaluated this integrated platform on a commercial lettuce farm with a concordance of 100% when compared to lab-based tests. Our integrated paper-based LAMP testing platform holds great promise as a reliable and convenient tool for on-site NAATs. We expect that this innovation will encourage the fresh produce industry to adopt NAATs as a complementary tool for decision-making in growing and harvesting. We also hope that our work can stimulate further research in the development of on-farm diagnostic tools for other agricultural applications, leading to improved food safety and technology innovation.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Ashley Kayabasi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Ishaan Rath
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Ilan Benschikovski
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Bibek Raut
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Kyungyeon Ra
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Nafisa Rafiq
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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Wang J, Ranjbaran M, Verma MS. Bacteroidales as a fecal contamination indicator in fresh produce industry: A baseline measurement. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119641. [PMID: 38064988 DOI: 10.1016/j.jenvman.2023.119641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
Foodborne outbreaks caused by fecal contamination of fresh produce represent a serious concern to public health and the economy. As the consumption of fresh produce increases, public health officials and organizations have pushed for improvements in food safety procedures and environmental assessments to reduce the risk of contamination. Visual inspections and the establishment of "buffer zones" between animal feeding operations and producing fields are the current best practices for environmental assessments. However, a generalized distance guideline and visual inspections may not be enough to account for all environmental risk variables. Here, we report a baseline measurement surveying the background Bacteroidales concentration, as a quantitative fecal contamination indicator, in California's Salinas Valley. We collected a total of 1632 samples from two romaine lettuce commercial fields at the time of harvesting through two seasons in a year. The quantification of Bacteroidales concentration was performed using qPCR, revealing a notably low concentration (0-2.00 copies/cm2) in the commercial fields. To further enhance the applicability of our findings, we developed a user-friendly method for real-world fecal contamination risk assessment that seamlessly integrates with industry practices. Through the generation of heatmaps that visually illustrate varying risk levels across fields, this approach can identify site-specific risks and offer fresh produce stakeholders a more comprehensive understanding of their land. We anticipate this work can encourage the use of Bacteroidales in the fresh produce industry to monitor fecal contamination and prevent future foodborne outbreaks.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohit S Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, 47907, USA; Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA.
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Wang J, Ranjbaran M, Ault A, Verma MS. A loop-mediated isothermal amplification assay to detect Bacteroidales and assess risk of fecal contamination. Food Microbiol 2022; 110:104173. [DOI: 10.1016/j.fm.2022.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/04/2022]
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Fan L, Zhang X, Zeng R, Wang S, Jin C, He Y, Shuai J. Verification of Bacteroidales 16S rRNA markers as a complementary tool for detecting swine fecal pollution in the Yangtze Delta. J Environ Sci (China) 2020; 90:59-66. [PMID: 32081341 DOI: 10.1016/j.jes.2019.11.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/02/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
To correctly assess and properly manage the public health risks associated with exposure to contaminated water, it is necessary to identify the source of fecal pollution in a watershed. In this study, we evaluated the efficacy of our two previously developed real time-quantitative PCR (qPCR) assays for the detection of swine-associated Bacteroidales genetic markers (gene 1-38, gene 3-53) in the Yangtze Delta watershed of southeastern China. The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy (92.5%, 91.7% conditional probability, respectively) in detecting Bacteroidales spp. in water samples. According to binary logistic regression (BLR), these two swine-associated markers were well correlated (P < 0.05) with fecal indicators (Escherichia coli and Enterococci spp.) and zoonotic pathogens (E. coli O157: H7, Salmonella spp. and Campylobacter spp.) in water samples. In contrast, concentrations of conventional fecal indicator bacteria (FIB) were not correlated with zoonotic pathogens, suggesting that they are noneffective at detecting fecal pollution events. Collectively, the results obtained in this study demonstrated that a swine-targeted qPCR assay based on two Bacteroidales genes markers (gene 1-38, gene 3-53) could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.
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Affiliation(s)
- Lihua Fan
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China
| | - Xiaofeng Zhang
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Ruoxue Zeng
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Suhua Wang
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Chenchen Jin
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Yongqiang He
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Jiangbing Shuai
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China.
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Haack SK, Duris JW, Kolpin DW, Focazio MJ, Meyer MT, Johnson HE, Oster RJ, Foreman WT. Contamination with bacterial zoonotic pathogen genes in U.S. streams influenced by varying types of animal agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 563-564:340-350. [PMID: 27139306 DOI: 10.1016/j.scitotenv.2016.04.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Animal waste, stream water, and streambed sediment from 19 small (<32km(2)) watersheds in 12U.S. states having either no major animal agriculture (control, n=4), or predominantly beef (n=4), dairy (n=3), swine (n=5), or poultry (n=3) were tested for: 1) cholesterol, coprostanol, estrone, and fecal indicator bacteria (FIB) concentrations, and 2) shiga-toxin producing and enterotoxigenic Escherichia coli, Salmonella, Campylobacter, and pathogenic and vancomycin-resistant enterococci by polymerase chain reaction (PCR) on enrichments, and/or direct quantitative PCR. Pathogen genes were most frequently detected in dairy wastes, followed by beef, swine and poultry wastes in that order; there was only one detection of an animal-source-specific pathogen gene (stx1) in any water or sediment sample in any control watershed. Post-rainfall pathogen gene numbers in stream water were significantly correlated with FIB, cholesterol and coprostanol concentrations, and were most highly correlated in dairy watershed samples collected from 3 different states. Although collected across multiple states and ecoregions, animal-waste gene profiles were distinctive via discriminant analysis. Stream water gene profiles could also be discriminated by the watershed animal type. Although pathogen genes were not abundant in stream water or streambed samples, PCR on enrichments indicated that many genes were from viable organisms, including several (shiga-toxin producing or enterotoxigenic E. coli, Salmonella, vancomycin-resistant enterococci) that could potentially affect either human or animal health. Pathogen gene numbers and types in stream water samples were influenced most by animal type, by local factors such as whether animals had stream access, and by the amount of local rainfall, and not by studied watershed soil or physical characteristics. Our results indicated that stream water in small agricultural U.S. watersheds was susceptible to pathogen gene inputs under typical agricultural practices and environmental conditions. Pathogen gene profiles may offer the potential to address both source of, and risks associated with, fecal pollution.
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Affiliation(s)
- Sheridan K Haack
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States.
| | - Joseph W Duris
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - Dana W Kolpin
- U.S. Geological Survey, 400 South Clinton Street, Iowa City, IA 52240, United States
| | - Michael J Focazio
- U.S. Geological Survey, 12201 Sunrise Valley Drive, Reston, VA 20192, United States
| | - Michael T Meyer
- U.S. Geological Survey, 4821 Quail Crest Place, Lawrence, KS 66049, United States
| | - Heather E Johnson
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - Ryan J Oster
- U.S. Geological Survey, 6520 Mercantile Way, Suite 5, Lansing, MI 48911, United States
| | - William T Foreman
- U.S. Geological Survey, P.O. Box 25585, Denver, CO 80225, United States
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Comparison of the Prevalences and Diversities of Listeria Species and Listeria monocytogenes in an Urban and a Rural Agricultural Watershed. Appl Environ Microbiol 2015; 81:3812-22. [PMID: 25819965 DOI: 10.1128/aem.00416-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/23/2015] [Indexed: 11/20/2022] Open
Abstract
Foods and related processing environments are commonly contaminated with the pathogenic Listeria monocytogenes. To investigate potential environmental reservoirs of Listeria spp. and L. monocytogenes, surface water and point source pollution samples from an urban and a rural municipal water supply watershed in Nova Scotia, Canada, were examined over 18 months. Presumptive Listeria spp. were cultured from 72 and 35% of rural and urban water samples, respectively, with 24% of the positive samples containing two or three different Listeria spp. The L. innocua (56%) and L. welshimeri (43%) groups were predominant in the rural and urban watersheds, respectively. Analysis by the TaqMan assay showed a significantly (P < 0.05) higher prevalence of L. monocytogenes of 62% versus 17% by the culture-based method. Both methods revealed higher prevalences in the rural watershed and during the fall and winter seasons. Elevated Escherichia coli (≥ 100 CFU/100 ml) levels were not associated with the pathogen regardless of the detection method. Isolation of Listeria spp. were associated with 70 times higher odds of isolating L. monocytogenes (odds ratio = 70; P < 0.001). Serogroup IIa was predominant (67.7%) among the 285 L. monocytogenes isolates, followed by IVb (16.1%), IIb (15.8%), and IIc (0.4%). L. monocytogenes was detected in cow feces and raw sewage but not in septic tank samples. Pulsotyping of representative water (n = 54) and local human (n = 19) isolates suggested genetic similarities among some environmental and human L. monocytogenes isolates. In conclusion, temperate surface waters contain a diverse Listeria species population and could be a potential reservoir for L. monocytogenes, especially in rural agricultural watersheds.
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Riedel TE, Thulsiraj V, Zimmer-Faust AG, Dagit R, Krug J, Hanley KT, Adamek K, Ebentier DL, Torres R, Cobian U, Peterson S, Jay JA. Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources. WATER RESEARCH 2015; 71:227-43. [PMID: 25618519 DOI: 10.1016/j.watres.2014.12.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 12/09/2014] [Accepted: 12/22/2014] [Indexed: 05/08/2023]
Abstract
Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination.
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Affiliation(s)
- Timothy E Riedel
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA.
| | - Vanessa Thulsiraj
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Amity G Zimmer-Faust
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA; Institute of the Environment and Sustainability, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Rosi Dagit
- Resource Conservation District of the Santa Monica Mountains, PO Box 638, Agoura Hills, CA 91301, USA
| | - Jenna Krug
- Resource Conservation District of the Santa Monica Mountains, PO Box 638, Agoura Hills, CA 91301, USA
| | - Kaitlyn T Hanley
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Krista Adamek
- Resource Conservation District of the Santa Monica Mountains, PO Box 638, Agoura Hills, CA 91301, USA
| | - Darcy L Ebentier
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Robert Torres
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Uriel Cobian
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
| | - Sophie Peterson
- UCLA High School Summer Research Program, The Henry Samueli School of Engineering & Applied Science, Office of Academic & Student Affairs, Room 6426, Boelter Hall, Los Angeles, CA 90095, USA
| | - Jennifer A Jay
- Department of Civil and Environmental Engineering, University of California Los, Angeles, Los Angeles, CA 90095, USA
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Bae S, Wuertz S. Decay of host-associated Bacteroidales cells and DNA in continuous-flow freshwater and seawater microcosms of identical experimental design and temperature as measured by PMA-qPCR and qPCR. WATER RESEARCH 2015; 70:205-213. [PMID: 25540834 DOI: 10.1016/j.watres.2014.10.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
It is difficult to compare decay kinetics for genetic markers in an environmental context when they have been determined at different ambient temperatures. Therefore, we investigated the persistence of the host-associated genetic markers BacHum, BacCow and BacCan as well as the general Bacteroidales marker BacUni in both intact Bacteroidales cells and as total intracellular and extracellular marker DNA in controlled batch experiments at two temperatures using PMA-qPCR. Fecal Bacteroidales cells and DNA persisted longer at the lower temperature. Using the modified Arrhenius function to calculate decay constants for the same temperature, we then compared the decay of host-associated Bacteroidales cells and their DNA at 14 °C in field-based flow-through microcosms containing human, cow, and dog feces suspended in freshwater or seawater and previously operated with an identical experimental design. The time for a 2-log reduction (T₉₉) was used to characterize host-associated Bacteroidales decay. Host-associated genetic markers as determined by qPCR had similar T₉₉ values in freshwater and seawater at 14 °C when compared under both sunlight and dark conditions. In contrast, intact Bacteroidales cells measured by PMA-qPCR had shorter T₉₉ values in seawater than in freshwater. The decay constants of Bacteroidales cells were a function of physical (temperature) and chemical (salinity) parameters, suggesting that environmental parameters are key input variables for Bacteroidales survival in a predictive water quality model. Molecular markers targeting total Bacteroidales DNA were less susceptible to the variance of temperature, salinity and sunlight, implying that measurement of markers in both intact cells and DNA could enhance the predictive power of identifying fecal pollution across all aquatic environments. Monitoring Bacteroidales by qPCR alone rather than by PMA-qPCR does not always identify the contribution of recent fecal contamination because a signal may be detected that does not reflect a recent fecal event.
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Affiliation(s)
- Sungwoo Bae
- Department of Civil and Environmental Engineering, 2001 Ghausi Hall, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Stefan Wuertz
- Department of Civil and Environmental Engineering, 2001 Ghausi Hall, University of California, One Shields Avenue, Davis, CA 95616, USA; Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore.
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Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired agricultural watersheds under controlled and conventional tile drainage management. Appl Environ Microbiol 2014; 80:3708-20. [PMID: 24727274 DOI: 10.1128/aem.00254-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization.
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Coherence among different microbial source tracking markers in a small agricultural stream with or without livestock exclusion practices. Appl Environ Microbiol 2013; 79:6207-19. [PMID: 23913430 DOI: 10.1128/aem.01626-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over 1,400 water samples were collected biweekly over 6 years from an intermittent stream protected and unprotected from pasturing cattle. The samples were monitored for host-specific Bacteroidales markers, Cryptosporidium species/genotypes, viruses and coliphages associated with humans or animals, and bacterial zoonotic pathogens. Ruminant Bacteroidales markers did not increase within the restricted cattle access reach of the stream, whereas the ruminant Bacteroidales marker increased significantly in the unrestricted cattle access reach. Human Bacteroidales markers significantly increased downstream of homes where septic issues were documented. Wildlife Bacteroidales markers were detected downstream of the cattle exclusion practice where stream and riparian habitat was protected, but detections decreased after the unrestricted pasture, where the stream and riparian zone was unprotected from livestock. Detection of a large number of human viruses was shown to increase downstream of homes, and similar trends were observed for the human Bacteroidales marker. There was considerable interplay among biomarkers with stream flow, season, and the cattle exclusion practices. There were no to very weak associations with Bacteroidales markers and bacterial, viral, and parasitic pathogens. Overall, discrete sample-by-sample coherence among the different microbial source tracking markers that expressed a similar microbial source was minimal, but spatial trends were physically meaningful in terms of land use (e.g., beneficial management practice) effects on sources of fecal pollution.
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