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Huang X, Toro M, Reyes-Jara A, Moreno-Switt AI, Adell AD, Oliveira CJB, Bonelli RR, Gutiérrez S, Álvarez FP, Rocha ADDL, Kraychete GB, Chen Z, Grim C, Brown E, Bell R, Meng J. Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations. WATER RESEARCH 2024; 264:122208. [PMID: 39116611 DOI: 10.1016/j.watres.2024.122208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.
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Affiliation(s)
- Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA; Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile (PUC), Santiago, Chile
| | - Aiko D Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Santiago, Chile
| | - Celso J B Oliveira
- Laboratório de Avaliação de Produtos de Origem Animal, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Raquel R Bonelli
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Sebastián Gutiérrez
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Francisca P Álvarez
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile (PUC), Santiago, Chile
| | - Alan Douglas de Lima Rocha
- Laboratório de Avaliação de Produtos de Origem Animal, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Gabriela B Kraychete
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA.
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2
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Acheamfour CL, Parveen S, Gutierrez A, Handy ET, Behal S, Kim D, Kim S, East C, Xiong R, Haymaker JR, Micallef SA, Rosenberg Goldstein RE, Kniel KE, Sapkota AR, Hashem F, Sharma M. Detection of Salmonella enterica and Listeria monocytogenes in alternative irrigation water by culture and qPCR-based methods in the Mid-Atlantic U.S. Microbiol Spectr 2024; 12:e0353623. [PMID: 38376152 PMCID: PMC10986563 DOI: 10.1128/spectrum.03536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Alternative irrigation waters (rivers, ponds, and reclaimed water) can harbor bacterial foodborne pathogens like Salmonella enterica and Listeria monocytogenes, potentially contaminating fruit and vegetable commodities. Detecting foodborne pathogens using qPCR-based methods may accelerate testing methods and procedures compared to culture-based methods. This study compared detection of S. enterica and L. monocytogenes by qPCR (real-time PCR) and culture methods in irrigation waters to determine the influence of water type (river, pond, and reclaimed water), season (winter, spring, summer, and fall), or volume (0.1, 1, and 10 L) on sensitivity, accuracy, specificity, and positive (PPV), and negative (NPV) predictive values of these methods. Water samples were collected by filtration through modified Moore swabs (MMS) over a 2-year period at 11 sites in the Mid-Atlantic U.S. on a bi-weekly or monthly schedule. For qPCR, bacterial DNA from culture-enriched samples (n = 1,990) was analyzed by multiplex qPCR specific for S. enterica and L. monocytogenes. For culture detection, enriched samples were selectively enriched, isolated, and PCR confirmed. PPVs for qPCR detection of S. enterica and L. monocytogenes were 68% and 67%, respectively. The NPV were 87% (S. enterica) and 85% (L. monocytogenes). Higher levels of qPCR/culture agreement were observed in spring and summer compared to fall and winter for S. enterica; for L. monocytogenes, lower levels of agreement were observed in winter compared to spring, summer, and fall. Reclaimed and pond water supported higher levels of qPCR/culture agreement compared to river water for both S. enterica and L. monocytogenes, indicating that water type may influence the agreement of these results. IMPORTANCE Detecting foodborne pathogens in irrigation water can inform interventions and management strategies to reduce risk of contamination and illness associated with fresh and fresh-cut fruits and vegetables. The use of non-culture methods like qPCR has the potential to accelerate the testing process. Results indicated that pond and reclaimed water showed higher levels of agreement between culture and qPCR methods than river water, perhaps due to specific physiochemical characteristics of the water. These findings also show that season and sample volume affect the agreement of qPCR and culture results. Overall, qPCR methods could be more confidently utilized to determine the absence of Salmonella enterica and Listeria monocytogenes in irrigation water samples examined in this study.
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Affiliation(s)
- Chanelle L. Acheamfour
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
- Department of Biological Sciences, Delaware State University, Dover, Delaware, USA
| | - Salina Parveen
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Alan Gutierrez
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Eric T. Handy
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Sara Behal
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Donghyun Kim
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Seongyun Kim
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
- Department of Environmental System Engineering, Chonnam National University, Yeosu, Republic of Korea
| | - Cheryl East
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Ray Xiong
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Joseph R. Haymaker
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Shirley A. Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Rachel E. Rosenberg Goldstein
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Kalmia E. Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Fawzy Hashem
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Manan Sharma
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
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Weller DL, Murphy CM, Love TMT, Danyluk MD, Strawn LK. Methodological differences between studies confound one-size-fits-all approaches to managing surface waterways for food and water safety. Appl Environ Microbiol 2024; 90:e0183523. [PMID: 38214516 PMCID: PMC10880618 DOI: 10.1128/aem.01835-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/14/2023] [Indexed: 01/13/2024] Open
Abstract
Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.
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Affiliation(s)
- Daniel L. Weller
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Claire M. Murphy
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
| | - Tanzy M. T. Love
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Michelle D. Danyluk
- Department of Food Science and Human Nutrition, Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, USA
| | - Laura K. Strawn
- Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA
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4
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Murphy CM, Weller DL, Strawn LK. Scale and detection method impacted Salmonella prevalence and diversity in ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167812. [PMID: 37852489 DOI: 10.1016/j.scitotenv.2023.167812] [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: 07/27/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Site-specific approaches for managing food safety hazards in agricultural water require an understanding of foodborne pathogen ecology. This study identified factors associated with Salmonella contamination in Virginia ponds. Grab samples (250 mL, N = 600) were collected from 30 sites across nine ponds. Culture- and culture-independent (CIDT)-based methods were used to detect Salmonella in each sample. Salmonella isolated by culture-based methods were serotyped by Kauffman-White classification. Environmental data were collected for each sample. McNemar's χ2 was used to determine if Salmonella detection differed by testing method. Separate mixed effect models were used to identify environmental factors associated with culture and CIDT-based Salmonella detection. Separate models were built for each pond, and for all ponds combined. Salmonella detection differed significantly (p < 0.001) between CIDT (31 %; 183/600)- and culture (13 %; 77/600)-based methods. Culture-based methods yielded 11 different serovars. All cultured Salmonella samples were confirmed by CIDT; 42.1 % of CIDT Salmonella-positive samples could be cultured. Associations between environmental factors and Salmonella detection also varied substantially by pond and detection method. In the all-pond model, associations were observed for five factors (total coliforms, Escherichia coli, air temperature, UV, rain) for both culture- and CIDT-based Salmonella detection. Rain prior to sampling (24 h) increased odds of Salmonella detection for culture (OR = 5.09) and CIDT (OR = 3.62) in the all-pond model. When all the pond data were used, models masked associations at the individual pond level, as there were noticeable differences between ponds and the odds of isolating Salmonella by environmental factors. Ponds were within a 187-ha area in this study, emphasizing water management needs to be individualized (i.e., assess hazards/risks by pond). Results also highlight detection methods and scale strongly affect observed water quality and should be considered when developing monitoring programs to develop guidance for growers.
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Affiliation(s)
- Claire M Murphy
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA
| | - Daniel L Weller
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Boulevard, Rochester, NY 14642, USA
| | - Laura K Strawn
- Department of Food Science and Technology, Virginia Tech, 1230 Washington Street SW, Blacksburg, VA 24061, USA.
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5
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Kraft AL, Wells JE, Frye JG, Ibekwe AM, Durso LM, Hiott L, East C, McConn BR, Franklin AM, Boczek LA, Garland JL, Kabera C, McDermott PF, Ottesen AR, Zheng J, Cook KL, Sharma M. A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167189. [PMID: 37748604 DOI: 10.1016/j.scitotenv.2023.167189] [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: 06/16/2023] [Revised: 09/05/2023] [Accepted: 09/16/2023] [Indexed: 09/27/2023]
Abstract
Developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the National Antimicrobial Resistance Monitoring System (NARMS). There are no specified methods for recovery of S. enterica in surface waters in the U.S. A multi-laboratory evaluation of four methods - bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B2 (SM), and dead-end ultrafiltration (DEUF) - was undertaken to recover S. enterica from surface water. In Phase 1, one-liter volumes of water were collected from the same site on five different dates. Water was shipped and analyzed at four different laboratory locations (A, B, C, and D) for recovery of 1) inoculated fluorescent S. Typhimurium strain (ca. 30 CFU/L) and 2) Salmonella present in the water sampled. At each location, BW, VMMS, or SM recovery was performed on five separate 1 L water samples. Twenty 1 L water samples were subjected to each recovery method, and overall, sixty 1 L samples were assayed for Salmonella. Inoculated, fluorescent Salmonella Typhimurium and environmental Salmonella spp. were recovered from 65 % (39/60) and 45 % (27/60) of water samples, respectively. BW, VMMS, and SM recovered fluorescent S. Typhimurium from 60 %, 60 %, and 75 % of inoculated samples, respectively. Analysis by Chi-squared test determined laboratory location had a significant (p < 0.05) effect on fluorescent S. Typhimurium recovery compared to method or date of water collection. In Phase 2, recovery of inoculated fluorescent S. Typhimurium from 1 L samples by SM and DEUF was compared at laboratory locations B and D. SM and DEUF recovered fluorescent S. Typhimurium from 100 % (20/20) and 95 % (19/20) of inoculated water samples, respectively; laboratory location (p > 0.05) did not affect Salmonella recovery. Uniform laboratory methodology and training should be prioritized in conducting Salmonella recovery from surface water in laboratories.
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Affiliation(s)
- Autumn L Kraft
- Oak Ridge Institute for Science and Education, U.S. Department of Agriculture, Agricultural Research Service (USDA ARS), Beltsville, MD, United States of America
| | - Jim E Wells
- USDA ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States of America
| | - Jonathan G Frye
- USDA ARS, U.S. National Poultry Research Center, Bacterial Epidemiology & Antimicrobial Resistance Research, Athens, GA, United States of America
| | - Abasiofiok M Ibekwe
- USDA ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States of America
| | - Lisa M Durso
- USDA ARS, Agroecoystem Management Research, Lincoln, NE, United States of America
| | - Lari Hiott
- USDA ARS, U.S. National Poultry Research Center, Bacterial Epidemiology & Antimicrobial Resistance Research, Athens, GA, United States of America
| | - Cheryl East
- USDA ARS, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States of America
| | - Betty R McConn
- Oak Ridge Institute for Science and Education, U.S. Department of Agriculture, Agricultural Research Service (USDA ARS), Beltsville, MD, United States of America
| | - Alison M Franklin
- U.S. Environmental Protection Agency (U.S. EPA), Center for Environmental Measurement and Modeling, Cincinnati, OH, United States of America
| | - Laura A Boczek
- U.S. EPA, National Risk Management Research Laboratory, Cincinnati, OH, United States of America
| | - Jay L Garland
- U.S. EPA, Center for Environmental Solutions and Emergency Response, Cincinnati, OH, United States of America
| | - Claudine Kabera
- Food and Drug Administration (FDA), Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), Laurel, MD, United States of America
| | - Patrick F McDermott
- Food and Drug Administration (FDA), Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), Laurel, MD, United States of America
| | - Andrea R Ottesen
- Food and Drug Administration (FDA), Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), Laurel, MD, United States of America
| | - Jie Zheng
- FDA, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, MD, United States of America
| | - Kimberly L Cook
- USDA ARS, Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States of America
| | - Manan Sharma
- USDA ARS, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States of America.
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Yalin D, Craddock HA, Assouline S, Ben Mordechay E, Ben-Gal A, Bernstein N, Chaudhry RM, Chefetz B, Fatta-Kassinos D, Gawlik BM, Hamilton KA, Khalifa L, Kisekka I, Klapp I, Korach-Rechtman H, Kurtzman D, Levy GJ, Maffettone R, Malato S, Manaia CM, Manoli K, Moshe OF, Rimelman A, Rizzo L, Sedlak DL, Shnit-Orland M, Shtull-Trauring E, Tarchitzky J, Welch-White V, Williams C, McLain J, Cytryn E. Mitigating risks and maximizing sustainability of treated wastewater reuse for irrigation. WATER RESEARCH X 2023; 21:100203. [PMID: 38098886 PMCID: PMC10719582 DOI: 10.1016/j.wroa.2023.100203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 12/17/2023]
Abstract
Scarcity of freshwater for agriculture has led to increased utilization of treated wastewater (TWW), establishing it as a significant and reliable source of irrigation water. However, years of research indicate that if not managed adequately, TWW may deleteriously affect soil functioning and plant productivity, and pose a hazard to human and environmental health. This review leverages the experience of researchers, stakeholders, and policymakers from Israel, the United-States, and Europe to present a holistic, multidisciplinary perspective on maximizing the benefits from municipal TWW use for irrigation. We specifically draw on the extensive knowledge gained in Israel, a world leader in agricultural TWW implementation. The first two sections of the work set the foundation for understanding current challenges involved with the use of TWW, detailing known and emerging agronomic and environmental issues (such as salinity and phytotoxicity) and public health risks (such as contaminants of emerging concern and pathogens). The work then presents solutions to address these challenges, including technological and agronomic management-based solutions as well as source control policies. The concluding section presents suggestions for the path forward, emphasizing the importance of improving links between research and policy, and better outreach to the public and agricultural practitioners. We use this platform as a call for action, to form a global harmonized data system that will centralize scientific findings on agronomic, environmental and public health effects of TWW irrigation. Insights from such global collaboration will help to mitigate risks, and facilitate more sustainable use of TWW for food production in the future.
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Affiliation(s)
- David Yalin
- A Department of Earth and Planetary Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Hillary A. Craddock
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Shmuel Assouline
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Evyatar Ben Mordechay
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Ben-Gal
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization (ARO) – The Volcani Institute, Gilat Reseach Center, Israel
| | - Nirit Bernstein
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | | | - Benny Chefetz
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering, NIREAS-International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - Bernd M. Gawlik
- Ocean and Water Unit, Joint Research Centre, European Commission, Ispra, Italy
| | - Kerry A. Hamilton
- The School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Leron Khalifa
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Isaya Kisekka
- Department of Land Air and Water Resources, University of California, Davis, California, USA
| | - Iftach Klapp
- Institute of Agricultural engineering, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | | | - Daniel Kurtzman
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Guy J. Levy
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Roberta Maffettone
- Ocean and Water Unit, Joint Research Centre, European Commission, Ispra, Italy
| | - Sixto Malato
- CIEMAT-Plataforma Solar de Almería, Ctra. Sen´es km 4, 04200 Tabernas, Almería, Spain
| | - Célia M. Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Kyriakos Manoli
- NIREAS-International Water Research Center, University of Cyprus, Nicosia, Cyprus
| | - Orah F. Moshe
- Department of Soil Conservation, Soil Erosion Research Center, Ministry of Agriculture, Rishon LeZion, Israel
| | - Andrew Rimelman
- PG Environmental. 1113 Washington Avenue, Suite 200. Golden, CO 80401, USA
| | - Luigi Rizzo
- Water Science and Technology (WaSTe) Group, Department of Civil Engineering, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - David L. Sedlak
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Maya Shnit-Orland
- Extension Service, Ministry of Agriculture and Rural Development, Israel
| | - Eliav Shtull-Trauring
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
| | - Jorge Tarchitzky
- The Robert H Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Clinton Williams
- US Arid-Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, USA
| | - Jean McLain
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agriculture Research Organization (ARO) – The Volcani Institute, Rishon LeZion, Israel
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7
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Li M, Chen L, Zhao F, Tang J, Bu Q, Feng Q, Yang L. An innovative risk evaluation method on soil pathogens in urban-rural ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132286. [PMID: 37595464 DOI: 10.1016/j.jhazmat.2023.132286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
The presence and reproduction of pathogens in soil environment have significant negative impacts on soil security and human health in urban-rural ecosystem. Rapid urbanization has dramatically changed the land use, soil ecosystems, and the presence of pathogens in soil environment, however, the risk associated with soil pathogens remains unknown. Identifying the potential risk of pathogens in soils in urban-rural ecosystem has become an urgent issue. In this study, we established a risk evaluation method for soil pathogens based on analytic hierarchy process and entropy methods to quantitatively estimate the potential risk of soil pathogens to children and adults in urban-rural ecosystem. The abundance and species number of soil pathogens, network structure of soil microbial community, and human exposure factors were considered with 12 indicators to establish the risk evaluation system. The results revealed that 19 potential pathogenic bacteria were detected in soils within a typical urban-rural ecosystem. Substantial differences were observed in both abundance and species of soil pathogens as well as network structure of soil microbial community from urban to rural areas. Urban areas exhibited relatively lower levels of soil pathogenic abundance, but the microbial network was considerably unstable. Rural areas supported relatively higher levels of soil pathogenic abundance and stable microbial networks. Notably, peri-urban areas showed relatively unstable microbial networks alongside higher levels of soil pathogenic abundance compared to other areas. The risk evaluation of soil pathogens for both adults and children showed that peri-urban areas presented the highest potential risk, with children being more susceptible than adults to threats posed by soil pathogens in both urban and peri-urban areas. The established evaluation system provides an innovative approach for quantifying risk of soil pathogens at regional scale and can be used as a reference for preventing soil pathogens contamination and enhancing soil health in areas with intense human activities.
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Affiliation(s)
- Min Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liding Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangkai Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Jianfeng Tang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qingwei Bu
- School of Chemical & Environmental Engineering, China University of Mining & Technology-Beijing, Beijing 100083, China
| | - Qingyu Feng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Kim S, Pachepsky Y, Micallef SA, Rosenberg Goldstein R, Sapkota AR, Hashem F, Parveen S, Kniel KE, Sharma M. Temporal stability of Salmonella enterica and Listeria monocytogenes in surface waters used for irrigation in the Mid-Atlantic United States. J Food Prot 2023; 86:100058. [PMID: 37005038 DOI: 10.1016/j.jfp.2023.100058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023]
Abstract
Enteric bacterial pathogen levels can influence the suitability of irrigation water sources for fruits and vegetables. We hypothesize that stable spatial patterns of Salmonella enterica and Listeria monocytogenes levels may exist across surface water sources in the Mid-Atlantic U.S. Water samples were collected at four streams and two pond sites in the mid-Atlantic U.S. over 2 years, biweekly during the fruit and vegetable growing seasons, and once a month during nongrowing seasons. Two stream sites and one pond site had significantly different mean concentrations in growing and nongrowing seasons. Stable spatial patterns were determined for relative differences between the site concentrations and average concentration of both pathogens across the study area. Mean relative differences were significantly different from zero at four of the six sites for S. enterica and three of six sites for L. monocytogenes. There was a similarity between the mean relative difference distribution between sites over growing season, nongrowing season, and the entire observation period. Mean relative differences were determined for temperature, oxidation-reduction potential, specific electrical conductance, pH, dissolved oxygen, turbidity, and cumulative rainfall. A moderate-to-strong Spearman correlation (rs > 0.657) was found between spatial patterns of S. enterica and 7-day rainfall, and between relative difference patterns of L. monocytogenes and temperature (rs = 0.885) and dissolved oxygen (rs = -0.885). Persistence in ranking sampling sites by the concentrations of the two pathogens was also observed. Finding spatially stable patterns in pathogen concentrations highlights spatiotemporal dynamics of these microorganisms across the study area can facilitate the design of an effective microbial water quality monitoring program for surface irrigation water.
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Affiliation(s)
- Seongyun Kim
- United States Department of Agriculture, Northeast Area, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, USA; Department of Environmental System Engineering, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Yakov Pachepsky
- United States Department of Agriculture, Northeast Area, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, USA.
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Rachel Rosenberg Goldstein
- Maryland Institute of Applied and Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Amy R Sapkota
- Maryland Institute of Applied and Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Fawzy Hashem
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, USA
| | - Salina Parveen
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, USA
| | - Kalmia E Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Manan Sharma
- United States Department of Agriculture, Northeast Area, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, MD, USA
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9
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Malayil L, Ramachandran P, Chattopadhyay S, Allard SM, Bui A, Butron J, Callahan MT, Craddock HA, Murray R, East C, Sharma M, Kniel K, Micallef S, Hashem F, Gerba CP, Ravishankar S, Parveen S, May E, Handy E, Kulkarni P, Anderson-Coughlin B, Craighead S, Gartley S, Vanore A, Duncan R, Foust D, Haymaker J, Betancourt W, Zhu L, Mongodin EF, Sapkota A, Pop M, Sapkota AR. Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15019-15033. [PMID: 36194536 PMCID: PMC9632240 DOI: 10.1021/acs.est.2c02281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.
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Affiliation(s)
- Leena Malayil
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Padmini Ramachandran
- Office
of Regulatory Science, Division of Microbiology, United States Food and Drug Administration, HFS-712, 5001 Campus Drive, College Park, Maryland 20740, United States
| | - Suhana Chattopadhyay
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Sarah M. Allard
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Anthony Bui
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Jicell Butron
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mary Theresa Callahan
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Hillary A. Craddock
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Rianna Murray
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Cheryl East
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Manan Sharma
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Kalmia Kniel
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shirley Micallef
- Department
of Plant Science and Landscape Agriculture, University of Maryland, College
Park, Maryland 20740, United States
| | - Fawzy Hashem
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Charles P. Gerba
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Sadhana Ravishankar
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Salina Parveen
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric May
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Eric Handy
- Northeast
Area, Beltsville Agriculture Research Center, Environmental Microbiology
and Food Safety Laboratory, Agriculture
Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, United States
| | - Prachi Kulkarni
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Brienna Anderson-Coughlin
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Shani Craighead
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Samantha Gartley
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Adam Vanore
- Department
of Animal and Food Sciences, University
of Delaware, Newark, Delaware 19716, United States
| | - Rico Duncan
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Derek Foust
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Joseph Haymaker
- Department
of Agriculture and Resource Sciences, University
of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Walter Betancourt
- Department
of Environmental Science, University of
Arizona, Tucson, Arizona 85719, United States
| | - Libin Zhu
- School
of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Emmanuel F. Mongodin
- Institute
for Genome Sciences, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Amir Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
| | - Mihai Pop
- Department
of Computer Science and Center for Bioinformatics and Computational
Biology, University of Maryland, College Park, Maryland 20742, United States
| | - Amy R. Sapkota
- Maryland
Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland 20740, United States
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10
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Listeria monocytogenes in Irrigation Water: An Assessment of Outbreaks, Sources, Prevalence, and Persistence. Microorganisms 2022; 10:microorganisms10071319. [PMID: 35889038 PMCID: PMC9323950 DOI: 10.3390/microorganisms10071319] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
As more fresh fruits and vegetables are needed to meet the demands of a growing population, growers may need to start depending on more varied sources of water, including environmental, recycled, and reclaimed waters. Some of these sources might be susceptible to contamination with microbial pathogens, such as Listeria monocytogenes. Surveys have found this pathogen in water, soil, vegetation, and farm animal feces around the world. The frequency at which this pathogen is present in water sources is dependent on multiple factors, including the season, surrounding land use, presence of animals, and physicochemical water parameters. Understanding the survival duration of L. monocytogenes in specific water sources is important, but studies are limited concerning this environment and the impact of these highly variable factors. Understanding the pathogen’s ability to remain infectious is key to understanding how L. monocytogenes impacts produce outbreaks and, ultimately, consumers’ health.
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