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Scicchitano D, Leuzzi D, Babbi G, Palladino G, Turroni S, Laczny CC, Wilmes P, Correa F, Leekitcharoenphon P, Savojardo C, Luise D, Martelli P, Trevisi P, Aarestrup FM, Candela M, Rampelli S. Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. Anim Microbiome 2024; 6:17. [PMID: 38555432 PMCID: PMC10981832 DOI: 10.1186/s42523-024-00305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment. RESULTS In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe. CONCLUSIONS Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.
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Affiliation(s)
- Daniel Scicchitano
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Daniela Leuzzi
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Paul Wilmes
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Pierluigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Marco Candela
- Fano Marine Center, Fano, Italy.
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Simone Rampelli
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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2
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Garofalo C, Cesaro C, Milanović V, Belleggia L, Matricardi T, Osimani A, Aquilanti L, Cardinali F, Rampanti G, Simoni S, Vignaroli C, Brenciani A, Pasquini M, Trombetta MF. Search for carbapenem-resistant bacteria and carbapenem resistance genes along swine food chains in Central Italy. PLoS One 2024; 19:e0296098. [PMID: 38181018 PMCID: PMC10769077 DOI: 10.1371/journal.pone.0296098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 01/07/2024] Open
Abstract
The presence of carbapenem-resistant bacteria and carbapenem resistance genes (CRGs) in livestock is increasing. To evaluate the presence of carbapenemase-producing Enterobacteriaceae (CPE) and the main CRGs along swine food chains of the Marche Region (Central Italy), samples of faeces, feed, and animal-food derived products were collected from seven small/medium, medium, and large-scale pig farms. A total of 191 samples were analysed using a culture-dependent method, with the aim of isolating CPE. Isolates were analysed for their resistance to carbapenems using a modified Hodge test and the microdilution method for the minimum inhibitory concentration (MIC) determination. Moreover, the extraction of microbial DNA from each sample was performed to directly detect selected CRGs via qPCR. Among the 164 presumptive resistant isolates, only one strain from a liver sample, identified as Aeromonas veronii, had an ertapenem MIC of 256 μg/mL and carried a carbapenemase- (cphA) and a β-lactamase- (blaOXA-12) encoding genes. A low incidence of CRGs was found; only nine and four faecal samples tested positive for blaNDM-1 and blaOXA-48, respectively. Overall, the importance of monitoring CPE and CRGs in livestock and their food chains should be stressed to control all potential non-human CPE and CRGs reservoirs and to determine safety levels for human health.
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Affiliation(s)
- Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Cristiana Cesaro
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Luca Belleggia
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Tullia Matricardi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Federica Cardinali
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Giorgia Rampanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Serena Simoni
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche, Ancona, Italy
| | - Carla Vignaroli
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA), Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Brenciani
- Dipartimento di Scienze Biomediche e Sanità Pubblica (DSBSP), Università Politecnica delle Marche, Ancona, Italy
| | - Marina Pasquini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
| | - Maria Federica Trombetta
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
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3
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O’Neill L, Manzanilla EG, Ekhlas D, Leonard FC. Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract. Antibiotics (Basel) 2023; 12:1616. [PMID: 37998818 PMCID: PMC10669415 DOI: 10.3390/antibiotics12111616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.
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Affiliation(s)
- Lorcan O’Neill
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Edgar García Manzanilla
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
| | - Daniel Ekhlas
- Pig Development Department, Teagasc, The Irish Food and Agriculture Authority, Moorepark, Fermoy, Co Cork P61 C996, Ireland; (E.G.M.); (D.E.)
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin D15 DY05, Ireland
| | - Finola C. Leonard
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland;
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4
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Andrade L, P Ryan M, P Burke L, Hynds P, Weatherill J, O'Dwyer J. Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121970. [PMID: 37343911 DOI: 10.1016/j.envpol.2023.121970] [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: 01/30/2023] [Revised: 05/08/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.
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Affiliation(s)
- Luisa Andrade
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland.
| | - Michael P Ryan
- Department of Applied Sciences, Technological University of the Shannon Midwest, Moylish, Ireland
| | - Liam P Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Paul Hynds
- Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Sustainability and Health Institute, Technological University Dublin, Dublin 7, Ireland
| | - John Weatherill
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Jean O'Dwyer
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; Irish Centre for Research in Applied Geosciences, University College Dublin, Dublin, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
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5
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Shay JA, Haniford LSE, Cooper A, Carrillo CD, Blais BW, Lau CHF. Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods. ENVIRONMENTAL MICROBIOME 2023; 18:25. [PMID: 36991496 PMCID: PMC10052294 DOI: 10.1186/s40793-023-00482-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample's metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods. RESULT A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (> 300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n = 10; ground meat, n = 26) and their corresponding bacterial enrichment cultures (n = 36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition. CONCLUSIONS For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.
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Affiliation(s)
- Julie A Shay
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Laura S E Haniford
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Ashley Cooper
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Burton W Blais
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
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6
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Zaidi SEZ, Zaheer R, Poulin-Laprade D, Scott A, Rehman MA, Diarra M, Topp E, Domselaar GV, Zovoilis A, McAllister TA. Comparative Genomic Analysis of Enterococci across Sectors of the One Health Continuum. Microorganisms 2023; 11:microorganisms11030727. [PMID: 36985300 PMCID: PMC10052687 DOI: 10.3390/microorganisms11030727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Enterococci are Gram-positive bacteria that can be isolated from a variety of environments including soil, water, plants, and the intestinal tract of humans and animals. Although they are considered commensals in humans, Enterococcus spp. are important opportunistic pathogens. Due to their presence and persistence in diverse environments, Enterococcus spp. are ideal for studying antimicrobial resistance (AMR) from the One Health perspective. We undertook a comparative genomic analysis of the virulome, resistome, mobilome, and the association between the resistome and mobilome of 246 E. faecium and 376 E. faecalis recovered from livestock (swine, beef cattle, poultry, dairy cattle), human clinical samples, municipal wastewater, and environmental sources. Comparative genomics of E. faecium and E. faecalis identified 31 and 34 different antimicrobial resistance genes (ARGs), with 62% and 68% of the isolates having plasmid-associated ARGs, respectively. Across the One Health continuum, tetracycline (tetL and tetM) and macrolide resistance (ermB) were commonly identified in E. faecium and E. faecalis. These ARGs were frequently associated with mobile genetic elements along with other ARGs conferring resistance against aminoglycosides [ant(6)-la, aph(3′)-IIIa], lincosamides [lnuG, lsaE], and streptogramins (sat4). Study of the core E. faecium genome identified two main clades, clade ‘A’ and ‘B’, with clade A isolates primarily originating from humans and municipal wastewater and carrying more virulence genes and ARGs related to category I antimicrobials. Overall, despite differences in antimicrobial usage across the continuum, tetracycline and macrolide resistance genes persisted in all sectors.
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Affiliation(s)
- Sani-e-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Dominic Poulin-Laprade
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 1Z3, Canada
| | - Andrew Scott
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Moussa Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, MB R3E 3R2, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Correspondence:
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Gaire TN, Scott HM, Noyes NR, Ericsson AC, Tokach MD, Menegat MB, Vinasco J, Roenne B, Ray T, Nagaraja TG, Volkova VV. Age influences the temporal dynamics of microbiome and antimicrobial resistance genes among fecal bacteria in a cohort of production pigs. Anim Microbiome 2023; 5:2. [PMID: 36624546 PMCID: PMC9830919 DOI: 10.1186/s42523-022-00222-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The pig gastrointestinal tract hosts a diverse microbiome, which can serve to select and maintain a reservoir of antimicrobial resistance genes (ARG). Studies suggest that the types and quantities of antimicrobial resistance (AMR) in fecal bacteria change as the animal host ages, yet the temporal dynamics of AMR within communities of bacteria in pigs during a full production cycle remains largely unstudied. RESULTS A longitudinal study was performed to evaluate the dynamics of fecal microbiome and AMR in a cohort of pigs during a production cycle; from birth to market age. Our data showed that piglet fecal microbial communities assemble rapidly after birth and become more diverse with age. Individual piglet fecal microbiomes progressed along similar trajectories with age-specific community types/enterotypes and showed a clear shift from E. coli/Shigella-, Fusobacteria-, Bacteroides-dominant enterotypes to Prevotella-, Megaspheara-, and Lactobacillus-dominated enterotypes with aging. Even when the fecal microbiome was the least diverse, the richness of ARGs, quantities of AMR gene copies, and counts of AMR fecal bacteria were highest in piglets at 2 days of age; subsequently, these declined over time, likely due to age-related competitive changes in the underlying microbiome. ARGs conferring resistance to metals and multi-compound/biocides were detected predominately at the earliest sampled ages. CONCLUSIONS The fecal microbiome and resistome-along with evaluated descriptors of phenotypic antimicrobial susceptibility of fecal bacteria-among a cohort of pigs, demonstrated opposing trajectories in diversity primarily driven by the aging of pigs.
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Affiliation(s)
- Tara N. Gaire
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - H. Morgan Scott
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Noelle R. Noyes
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - Aaron C. Ericsson
- grid.134936.a0000 0001 2162 3504Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211 USA
| | - Michael D. Tokach
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Mariana B. Menegat
- grid.36567.310000 0001 0737 1259Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506 USA
| | - Javier Vinasco
- grid.264756.40000 0004 4687 2082Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Boyd Roenne
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Tui Ray
- grid.17635.360000000419368657Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - T. G. Nagaraja
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Victoriya V. Volkova
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
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8
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Holman DB, Kommadath A, Tingley JP, Abbott DW. Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes. Microbiol Spectr 2022; 10:e0238022. [PMID: 35880887 PMCID: PMC9431278 DOI: 10.1128/spectrum.02380-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/20/2022] Open
Abstract
Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. IMPORTANCE Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.
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Affiliation(s)
- Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Arun Kommadath
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Jeffrey P. Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - D. Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
- Department of Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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Gaire TN, Odland C, Zhang B, Ray T, Doster E, Nerem J, Dee S, Davies P, Noyes N. The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs. MICROBIOME 2022; 10:118. [PMID: 35922873 PMCID: PMC9351240 DOI: 10.1186/s40168-022-01312-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups. RESULTS Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials. CONCLUSIONS The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.
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Affiliation(s)
- Tara N Gaire
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Carissa Odland
- Pipestone Veterinary Services, Pipestone, Minnesota, USA
| | - Bingzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tui Ray
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Enrique Doster
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joel Nerem
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Scott Dee
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Peter Davies
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
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Monger XC, Saucier L, Gilbert AA, Vincent AT. Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses. MethodsX 2022; 9:101716. [PMID: 35601955 PMCID: PMC9118172 DOI: 10.1016/j.mex.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Stabilization of faecal samples improves the integrity of extracted DNA. Microbiome results are affected by sample stabilization. Results are similar for samples that were stabilized when frozen, to samples that were stabilized before freezing.
Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals’ microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80°C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing.
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Wu Z, Ren Y, Liang Y, Huang L, Yang Y, Zafar A, Hasan M, Yang F, Shu X. Synthesis, Characterization, Immune Regulation, and Antioxidative Assessment of Yeast-Derived Selenium Nanoparticles in Cyclophosphamide-Induced Rats. ACS OMEGA 2021; 6:24585-24594. [PMID: 34604640 PMCID: PMC8482516 DOI: 10.1021/acsomega.1c03205] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Indexed: 05/05/2023]
Abstract
This article introduces an environmentally friendly and more economical method for preparing red selenium nanoparticles (Se-NPs) with high stability, good biocompatibility, and narrow size using yeast as a bio-reducing agent with high antioxidant, immune regulation, and low toxicity than inorganic and organic Se. The yeast-derived Se-NPs were characterized by scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The results revealed spherical-shaped particles of Se-NPs with an average diameter of 71.14 ± 18.17 nm, an amorphous structure, and surface enhancement with an organic shell layer, that provide precise geometry and stability in the formation of bio-inert gray or black Se-NPs instead of red Se-NPs. Furthermore, the addition of 0.3-0.8 mg/kg Se-NPs in the feed significantly improved the health of mice. As Se-NPs stimulated the oxidative state of mice, it significantly increased the level of GSH-Px, SOD, and AOC, and decreased the level of MDA. The yeast-derived Se-NPs alleviated the immunosuppression induced by cyclophosphamide, whereas protected the liver, spleen, and kidney of mice, stimulated the humoral immune potential of the mice, and significantly increased the levels of I g M, IgA, and I g G. These results indicated that the yeast-derived Se-NPs, as a trace element feed additive, increased the defense of the animal against oxidative stress and infectious diseases and therefore Se-NPs can be used as a potential antibiotic substitute for animal husbandry.
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Affiliation(s)
- Ziqian Wu
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Yanli Ren
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Yuejuan Liang
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Liting Huang
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Yuanting Yang
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Ayesha Zafar
- Department
of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
| | - Murtaza Hasan
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University, Bahawalpur 63100, Pakistan
| | - Fujie Yang
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
| | - Xugang Shu
- School
of Chemistry and Chemical Engineering, Zhongkai
University of Agriculture and Engineering, Guangzhou 510225, Guangdong Province, P.R. China
- Guangdong
Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong Province 510225, China
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Moor J, Aebi S, Rickli S, Mostacci N, Overesch G, Oppliger A, Hilty M. Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study. Int J Antimicrob Agents 2021; 58:106382. [PMID: 34157404 DOI: 10.1016/j.ijantimicag.2021.106382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 05/31/2021] [Accepted: 06/12/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environment. METHODS On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture, and clonal relationships and resistance genes were derived from whole genome sequencing data. RESULTS Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n=7 farms, 22.6%) and horizontal gene transfer (n=1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n=10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment. CONCLUSIONS Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.
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Affiliation(s)
- Julia Moor
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Susanne Rickli
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Nadezda Mostacci
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Gudrun Overesch
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Anne Oppliger
- Unisante, Department of Occupational and Environmental Health, University of Lausanne, Lausanne, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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