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Pandey P, Gaa ME, Huo J, Okada Y, Lee KY, Giat S, Li X, Zhang R, Pandey P. Determining the prevalence of Escherichia coli, Salmonella, and shiga toxin-producing Escherichia coli in manure of dairy lagoons. J Appl Microbiol 2024; 135:lxae103. [PMID: 38664008 DOI: 10.1093/jambio/lxae103] [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: 01/03/2024] [Revised: 03/11/2024] [Accepted: 04/20/2024] [Indexed: 06/04/2024]
Abstract
AIM The aim of this study was to determine the prevalence of microbial pathogens in manure of dairy lagoons in California. METHODS AND RESULTS To determine pathogens in dairy manure stored in anaerobic lagoons of dairy farm, an extensive field study was conducted across California to sample manure from 20 dairy farms. Samples were analyzed to determine the prevalence of indicator Escherichia coli, Shiga toxin producing E. coli (STEC), Salmonella, and E. coli O157: H7. To test the E. coli, STEC, and Salmonella, we used agar culture-based method followed by polymerase chain reaction (PCR) method. In addition, a real- time PCR based method was used to determine the presence of E coli O157: H7. Study demonstrated that the prevalence of Salmonella in manure sample is lower than E. coli. The presence of Salmonella was found in 2.26% of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, ∼11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. CONCLUSION These findings demonstrate that indicator E. coli are abundantly present in anaerobic lagoons. However, the presence of STEC, and Salmonella is substantially low.
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Affiliation(s)
- Prachi Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
| | - Megan Elise Gaa
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Jiang Huo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Yu Okada
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Katie Yen Lee
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Sharon Giat
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Xunde Li
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Ruihong Zhang
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
| | - Pramod Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States
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Hilaire SS, Chen C, Pan Z, Radolinski J, Stewart RD, Maguire RO, Xia K. Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14972-14981. [PMID: 35839145 DOI: 10.1021/acs.est.2c00981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.
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Affiliation(s)
- Sheldon S Hilaire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Zhizhen Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jesse Radolinski
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Ecology, University of Innsbruck, Innsbruck 6020, Austria
| | - Ryan D Stewart
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rory O Maguire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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Dollmann S, Vermeulen L, de Roda Husman AM. Untangling the Governance of Public Health Aspects of Manure in The Netherlands. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182312472. [PMID: 34886196 PMCID: PMC8656784 DOI: 10.3390/ijerph182312472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/12/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
The Netherlands is one of the most densely populated countries in terms of people and livestock and is the second largest exporter of agricultural products worldwide. As a result, the Netherlands has a manure surplus. Excess application of manure can lead to environmental problems; therefore, manure needs to be treated and discharged. Manure can contain zoonotic pathogens, but whether exposure to manure and manure treatment also poses a risk to public health is still unknown. This study analysed the regulations, relevant actors, and responsibilities in the complex system of manure and public health in the Netherlands. Interviews and system mapping have demonstrated interlinkages between environmental, economic, and health aspects. Constraints and opportunities for public health protection have been identified. This study reveals the complexity of the Dutch manure policy, its scattered responsibilities, the challenge to deal with uncertainties, and, most importantly, the need for a microbial risk assessment in order to adequately communicate and manage possible risks to protect the health of animals, the environment, and people.
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Affiliation(s)
- Sophia Dollmann
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (L.V.); (A.M.d.R.H.)
- Correspondence:
| | - Lucie Vermeulen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (L.V.); (A.M.d.R.H.)
| | - Ana Maria de Roda Husman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands; (L.V.); (A.M.d.R.H.)
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
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Xu S, Schwinghamer T, Sura S, Cessna AJ, Zvomuya F, Zaheer R, Larney FJ, McAllister TA. Degradation of antimicrobial resistance genes within stockpiled beef cattle feedlot manure. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:1093-1106. [PMID: 34605371 DOI: 10.1080/10934529.2021.1965416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Degradation of antimicrobial resistance genes (ARG) in manure from beef cattle administered (kg-1 feed) 44 mg of chlortetracycline (CTC), 44 mg of chlortetracycline plus sulfamethazine (CTCSMZ), 11 mg of tylosin (TYL), or no antimicrobials (Control) was examined. Manure was stockpiled and quantitative PCR (qPCR) was used to assess tetracycline [tet(C), (L), (M), (W)], erythromycin [erm(A), (B), (F), (X)], and sulfamethazine [sul(1), (2)] ARG and 16S rDNA. After 102 d, copies of all ARG decreased by 0.3 to 1.5 log10 copies (g dry matter)-1. Temperature in the interior of piles averaged ≥ 55 °C for 10 d, except for CTCSMZ, but did not reach 55 °C at pile exteriors. Compared to Control, CTCSMZ increased (P < 0.05) tet(C), tet(M), tet(W), sul(1), and sul(2) in stockpiled manure. Copies of 16S rDNA remained higher (P < 0.05) in CTCSMZ than Control for the first 26 d. Levels of most ARG did not differ between the interior and exterior of stockpiles. Our results suggest that stockpiled manure would still introduce ARG to land upon manure application, but at levels lower than if manure was applied fresh.
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Affiliation(s)
- Shanwei Xu
- Alberta Agriculture and Forestry, Lethbridge, Alberta, Canada
| | - Tim Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Srinivas Sura
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Allan J Cessna
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Francis Zvomuya
- Department of Soil Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Francis J Larney
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
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Wang Y, Pandey PK, Kuppu S, Pereira R, Aly S, Zhang R. Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion. PLoS One 2021; 16:e0254836. [PMID: 34432793 PMCID: PMC8386849 DOI: 10.1371/journal.pone.0254836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.
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Affiliation(s)
- Yi Wang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- Department of Biological and Agricultural Engineering, University of California-Davis, Davis, California, United States of America
| | - Pramod K. Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
- * E-mail:
| | - Sundaram Kuppu
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Richard Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Sharif Aly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America
| | - Ruihong Zhang
- Department of Biological and Agricultural Engineering, University of California-Davis, Davis, California, United States of America
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Rodriguez C, Taminiau B, García-Fuentes E, Daube G, Korsak N. Listeria monocytogenes dissemination in farming and primary production: Sources, shedding and control measures. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Factors contributing to Listeria monocytogenes transmission and impact on food safety. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Augustin M, Sanguansri L, Fox E, Cobiac L, Cole M. Recovery of wasted fruit and vegetables for improving sustainable diets. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16244896. [PMID: 31817253 PMCID: PMC6950033 DOI: 10.3390/ijerph16244896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/30/2019] [Accepted: 12/01/2019] [Indexed: 01/08/2023]
Abstract
The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies
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Chen C, Pankow CA, Oh M, Heath LS, Zhang L, Du P, Xia K, Pruden A. Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments. ENVIRONMENT INTERNATIONAL 2019; 128:233-243. [PMID: 31059918 DOI: 10.1016/j.envint.2019.04.043] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 05/12/2023]
Abstract
Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21 × unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33-fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibiotic-manure-amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.
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Affiliation(s)
- Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Christine A Pankow
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - Min Oh
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA 24061, United States
| | - Pang Du
- Department of Statistics, Virginia Tech, Blacksburg, VA 24061, United States
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States.
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, United States
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Ashekuzzaman SM, Richards K, Ellis S, Tyrrel S, O'Leary E, Griffiths B, Ritz K, Fenton O. Risk Assessment of E. coli Survival Up to the Grazing Exclusion Period After Dairy Slurry, Cattle Dung, and Biosolids Application to Grassland. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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