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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Law K, Garcia ERM, Hastad C, Murray D, Urriola PE, Gomez A. Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period. J Anim Sci Biotechnol 2024; 15:33. [PMID: 38431668 PMCID: PMC10909285 DOI: 10.1186/s40104-024-00993-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/07/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Nursery pigs undergo stressors in the post-weaning period that result in production and welfare challenges. These challenges disproportionately impact the offspring of primiparous sows compared to those of multiparous counterparts. Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes. Therefore, the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbiome and performance in response to a prebiotic post-weaning. At weaning, piglets were allotted into three treatment groups: a standard nursery diet including pharmacological doses of Zn and Cu (Con), a group fed a commercial prebiotic only (Preb) based on an Aspergillus oryzae fermentation extract, and a group fed the same prebiotic plus Zn and Cu (Preb + ZnCu). RESULTS Although there were no differences in vaginal microbiome composition between primiparous and multiparous sows, fecal microbiome composition was different (R2 = 0.02, P = 0.03). The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 postweaning (P < 0.01), with differences in community composition observed at d 21 (R2 = 0.03, P = 0.04). When analyzing the effects of maternal parity within each treatment, only the Preb diet triggered significant microbiome distinctions between primiparous and multiparous offspring (d 21: R2 = 0.13, P = 0.01; d 42: R2 = 0.19, P = 0.001). Compositional differences in pig fecal microbiomes between treatments were observed only at d 21 (R2 = 0.12, P = 0.001). Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb + ZnCu group. CONCLUSIONS Nursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract, with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups. These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.
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Affiliation(s)
- Kayla Law
- Department of Animal Science, University of Minnesota, 1364 Eckles Avenue, Saint Paul, MN, 55108, USA
| | | | - Chad Hastad
- New Fashion Pork, 164 Industrial Parkway, Jackson, MN, 56143, USA
| | - Deborah Murray
- New Fashion Pork, 164 Industrial Parkway, Jackson, MN, 56143, USA
| | - Pedro E Urriola
- Department of Animal Science, University of Minnesota, 1364 Eckles Avenue, Saint Paul, MN, 55108, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, 1364 Eckles Avenue, Saint Paul, MN, 55108, USA.
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Satora M, Magdziarz M, Rząsa A, Rypuła K, Płoneczka-Janeczko K. Insight into the intestinal microbiome of farrowing sows following the administration of garlic (Allium sativum) extract and probiotic bacteria cultures under farming conditions. BMC Vet Res 2020; 16:442. [PMID: 33187511 PMCID: PMC7666521 DOI: 10.1186/s12917-020-02659-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
Background Due to the tendency to reduce antibiotic use in humans and animals, more attention is paid to feed additives as their replacement. Crucial role of feed additives is to improve the health status, production efficiency and performance. In this original research, we estimate the potential influence of garlic (Allium sativum) extract and probiotic formula including Enterococcus faecium, Lactobacillus rhamnosus and Lactobacillus fermentum on the intestinal microbiota of sows, using the next generation sequencing method (NGS). Results Our results indicate that the overall species richness as well as the composition of swine gut microbiota may be shaped by regular feeding with supplemented additives. On the Family and Genus level both additives (garlic extract and probiotics) seem to decrease microbiome diversity and richness. However, when it comes to garlic supplementation, we found the opposite trend on the Species level. Conclusions The analysis of the selected microbial function indicates that both additives used in this study (garlic extract and composition of probiotics) seem to create a greater metabolic potential than estimated in a control group of sows. A general trend of losing or decreasing members of pathogenic species in the swine microbiome seems to occur in relation to both supplemented additives. In the prevention of some bacterial diseases supplemented additives could be considered for future use.
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Affiliation(s)
- Marta Satora
- Department of Epizootiology with Clinic for Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Plac Grunwaldzki 45, Wrocław, Poland
| | - Marcin Magdziarz
- Hugo Steinhaus Center, Faculty of Pure and Applied Mathematics, Wrocław University of Science and Technology, Wyspianskiego 27, Wrocław, Poland
| | - Anna Rząsa
- Department of Immunology, Pathophysiology and Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Norwida 31, Wrocław, Poland
| | - Krzysztof Rypuła
- Department of Epizootiology with Clinic for Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Plac Grunwaldzki 45, Wrocław, Poland
| | - Katarzyna Płoneczka-Janeczko
- Department of Epizootiology with Clinic for Birds and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Plac Grunwaldzki 45, Wrocław, Poland.
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