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Millar N, Dufour S, Lardé H, Massé J, De Lagarde M, Archambault M, Fairbrother JM, Roy JP, Belloc C, Francoz D, Aenishaenslin C. Redefining on-farm practices: The perceived effect of a responsible antimicrobial use regulation on dairy farmers. J Dairy Sci 2024; 107:6913-6929. [PMID: 38762113 DOI: 10.3168/jds.2024-24667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/30/2024] [Indexed: 05/20/2024]
Abstract
The global food animal industry faces a growing concern regarding antimicrobial resistance (AMR), primarily driven by the use of antimicrobials (AM) for the treatment, control, and prevention of diseases. Addressing this challenge requires promoting responsible antimicrobial use (AMU) practices. In 2019, the province of Québec, Canada, took a significant step by implementing a regulation that limits the use of AM of very high importance for human medicine (category I AM as defined by Health Canada) in the food animal industry. However, the implementation of such regulation can significantly influence behavioral shifts among producers, contributing to the wider effort against AMR. Therefore, the objective of this observational study was to describe the perceived changes in dairy producers' knowledge and on-farm practices following the implementation of this regulation, using a cohort design. Data collection involved administering questionnaires to 87 dairy producers from 3 regions of the province of Québec (Estrie, Montérégie, Centre-Du-Québec) before (2017-2018) and after (2020-2021) the implementation of the regulation. The questionnaires explored the descriptive characteristics of farms, the knowledge of producers about the categorization of AM, the on-farm treatment practices, and the perceived effects of the regulation. Statistical analysis included t-tests and McNemar tests to compare the paired data obtained using the 2 questionnaires. The results indicated an increase in the knowledge score (the number of AM correctly categorized by the producers by their importance for human medicine) after the implementation of the regulation, suggesting an improved understanding of the categorization of AM based on their importance for human medicine. Trends in AMU practices for treating clinical mastitis and reproductive diseases suggested that category I AM were less likely to be reported as the primary treatment after the regulation, whereas category II AM were more often reported as primary treatment. Adoption of the selective dry cow therapy method significantly increased, whereas the use of teat sealants remained unchanged. Moreover, producers had divergent perceptions regarding the effect of the regulation on the cure rates and disease frequencies. This disparity emphasizes the need for comprehensive data collection to discern the risks associated with such regulatory shifts. The study acknowledges several limitations, including the potential for recall bias, confirmation bias, and desirability bias. Despite these limitations, this study shows that implementing regulations to encourage responsible AMU drives positive transformations in producers' knowledge and on-farm practices. This underscores the pivotal effect of proactive interventions in combating the escalating threat of AMR within the global food animal industry.
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Affiliation(s)
- Nikky Millar
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Centre de recherche en santé publique, Université de Montréal et Centre intégré de santé et de services sociaux du Québec du Centre-Sud-de-l'Île-de-Montréal, Montréal, H2L 4M1 QC, Canada; Regroupement FRQNT Op+lait, Saint-Hyacinthe, J2S 2M2 QC, Canada.
| | - Simon Dufour
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Regroupement FRQNT Op+lait, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Hélène Lardé
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, PO Box 334 Basseterre, St. Kitts, West Indies
| | - Jonathan Massé
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Regroupement FRQNT Op+lait, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Maud De Lagarde
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; WOAH Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Marie Archambault
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - John Morris Fairbrother
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; WOAH Reference Laboratory for Escherichia coli, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Swine and Poultry Infectious Research Center (CRIPA-FQRNT), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Jean-Philippe Roy
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, J2S 2M2 QC, Canada; Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Catherine Belloc
- Biologie, Épidémiologie et Analyses de risque en santé animale (BIOEPAR), ONIRIS-INRAE, 44300 Nantes, France
| | - David Francoz
- Regroupement FRQNT Op+lait, Saint-Hyacinthe, J2S 2M2 QC, Canada; Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada
| | - Cécile Aenishaenslin
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Groupe de recherche en épidémiologie des zoonoses et santé publique (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, J2S 2M2 QC, Canada; Centre de recherche en santé publique, Université de Montréal et Centre intégré de santé et de services sociaux du Québec du Centre-Sud-de-l'Île-de-Montréal, Montréal, H2L 4M1 QC, Canada
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Usein CR, Oprea M, Dinu S, Popa LI, Cristea D, Militaru CM, Ghiță A, Costin M, Popa IL, Croitoru A, Bologa C, Rusu LC. Shiga Toxin-Producing Escherichia coli Strains from Romania: A Whole Genome-Based Description. Microorganisms 2024; 12:1469. [PMID: 39065242 PMCID: PMC11278934 DOI: 10.3390/microorganisms12071469] [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: 06/19/2024] [Revised: 07/05/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The zoonotic Shiga toxin-producing Escherichia coli (STEC) group is unanimously regarded as exceptionally hazardous for humans. This study aimed to provide a genomic perspective on the STEC recovered sporadically from humans and have a foundation of internationally comparable data. Fifty clinical STEC isolates, representing the culture-confirmed infections reported by the STEC Reference Laboratory between 2016 and 2023, were subjected to whole-genome sequencing (WGS) analysis and sequences were interpreted using both commercial and public free bioinformatics tools. The WGS analysis revealed a genetically diverse population of STEC dominated by non-O157 serogroups commonly reported in human STEC infections in the European Union. The O26:H11 strains of ST21 lineage played a major role in the clinical disease resulting in hospitalisation and cases of paediatric HUS in Romania surpassing the O157:H7 strains. The latter were all clade 7 and mostly ST1804. Notably, among the Romanian isolates was a stx2a-harbouring cryptic clade I strain associated with a HUS case, stx2f- and stx2e-positive strains, and hybrid strains displaying a mixture of intestinal and extraintestinal virulence genes were found. As a clearer picture emerges of the STEC strains responsible for infections in Romania, further surveillance efforts are needed to uncover their prevalence, sources, and reservoirs.
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Affiliation(s)
- Codruța-Romanița Usein
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Mihaela Oprea
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Sorin Dinu
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Laura-Ioana Popa
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Daniela Cristea
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Cornelia-Mădălina Militaru
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Andreea Ghiță
- Cantacuzino National Military Medical Institute of Research and Development, 050096 Bucharest, Romania; (M.O.); (S.D.); (L.-I.P.); (D.C.); (C.-M.M.); (A.G.)
| | - Mariana Costin
- Emergency Clinical Hospital for Children “M.S. Curie”, 041451 Bucharest, Romania; (M.C.); (I.-L.P.); (A.C.); (C.B.)
- Discipline Pediatrics—Emergency Clinical Hospital for Children M.S. Curie, University of Medicine and Pharmacy “Carol Davila” Bucharest, 050474 Bucharest, Romania
| | - Ionela-Loredana Popa
- Emergency Clinical Hospital for Children “M.S. Curie”, 041451 Bucharest, Romania; (M.C.); (I.-L.P.); (A.C.); (C.B.)
- Discipline Pediatrics—Emergency Clinical Hospital for Children M.S. Curie, University of Medicine and Pharmacy “Carol Davila” Bucharest, 050474 Bucharest, Romania
| | - Anca Croitoru
- Emergency Clinical Hospital for Children “M.S. Curie”, 041451 Bucharest, Romania; (M.C.); (I.-L.P.); (A.C.); (C.B.)
- Discipline Pediatrics—Emergency Clinical Hospital for Children M.S. Curie, University of Medicine and Pharmacy “Carol Davila” Bucharest, 050474 Bucharest, Romania
| | - Cristina Bologa
- Emergency Clinical Hospital for Children “M.S. Curie”, 041451 Bucharest, Romania; (M.C.); (I.-L.P.); (A.C.); (C.B.)
| | - Lavinia-Cipriana Rusu
- National Centre for Communicable Diseases Prevention and Control, National Public Health Institute, 050463 Bucharest, Romania;
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Narimisa N, Razavi S, Masjedian Jazi F. Prevalence of antibiotic resistance in Salmonella Typhimurium isolates originating from Iran: a systematic review and meta-analysis. Front Vet Sci 2024; 11:1388790. [PMID: 38860007 PMCID: PMC11163077 DOI: 10.3389/fvets.2024.1388790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Objective Antibiotic resistance in Salmonella represents a significant global public health concern. Among various serovars, Salmonella enterica serovar Typhimurium is prevalent in multiple countries. This study aims to conduct a systematic review and meta-analysis to evaluate the pattern of antibiotic resistance in S. Typhimurium isolates from diverse sources in Iran. Methods We conducted a comprehensive and systematic search for relevant articles until December 2023 in the following databases: PubMed, Scopus, Web of Science, and SID. The collected data were analyzed using Stata software version 17. Results Eighteen studies examined the pattern of antibiotic resistance in S. Typhimurium for various antibiotics in Iran. Piperacillin and tetracycline exhibited the highest resistance rates, at 79 and 60% respectively, while cefixime and ceftriaxone had the lowest resistance rates at 0%. Conclusion Our findings indicate a high level of antibiotic resistance among the studied antibiotics. This high level of antibiotic resistance raises concerns and underscores the necessity for monitoring the use of antibiotics. Moreover, resistance to these antibiotics was more prevalent in samples isolated from animals compared to other sources. This highlights the importance of animal screening to detect the presence of drug-resistant isolates, with the ultimate goal of reducing antibiotic resistance and preventing the transmission of resistant strains to humans.
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Affiliation(s)
| | | | - Faramarz Masjedian Jazi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Munk P, Yang D, Röder T, Maier L, Petersen TN, Duarte ASR, Clausen PTLC, Brinch C, Van Gompel L, Luiken R, Wagenaar JA, Schmitt H, Heederik DJJ, Mevius DJ, Smit LAM, Bossers A, Aarestrup FM. The European livestock resistome. mSystems 2024; 9:e0132823. [PMID: 38501800 PMCID: PMC11019871 DOI: 10.1128/msystems.01328-23] [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: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.
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Affiliation(s)
- Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Dongsheng Yang
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Leonie Maier
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | | | | | | | - Christian Brinch
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Roosmarijn Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dick J. J. Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - Dik J. Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Lidwien A. M. Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
| | - EFFORT ConsortiumGravelandHaitskeGonzalez-ZornBrunoMoyanoGabrielSandersPascalChauvinClaireBattistiAntonioDewulfJeroenWadepohlKatharinaWasylDariuszSkarzyńskaMagdalenaZajacMagdalenaPękala-SafińskaAgnieszkaDaskalovHristoStärkKatharina D. C.
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, The Netherlands, Utrecht
- Wageningen Bioveterinary Research, Wageningen University & Research, Lelystad, The Netherlands
| | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
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Oliveira RP, da Silva JS, da Silva GC, Rosa JN, Bazzolli DMS, Mantovani HC. Prevalence and characteristics of ESBL-producing Escherichia coli in clinically healthy pigs: implications for antibiotic resistance spread in livestock. J Appl Microbiol 2024; 135:lxae058. [PMID: 38444193 DOI: 10.1093/jambio/lxae058] [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: 12/15/2023] [Revised: 01/31/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
AIM This study aimed to compare and characterize the resistance profile and the presence of extended-spectrum beta-lactamase (ESBL) related genes in Escherichia coli isolated from healthy finishing pigs fed with or without antibiotics in their diets. METHODS AND RESULTS A total of 27 ceftiofur-resistant E. coli isolates were obtained from 96 healthy pigs. The antibiotic resistance profile was tested, and all 27 isolates were classified as multidrug-resistant (MDR). A high proportion of isolates were resistant to cephalosporins, ampicillin, ciprofloxacin, and tetracyclines. The ESBL production was observed in 85% of isolates by double-disc synergy test. The MDR-E. coli isolates harbored ESBL genes, such as blaTEM, blaCTX-M-1, blaCTX-M-2, and blaCTX-M-8,25. In addition, other antibiotics resistance genes (ARGs) were also detected, such as sul2, ant(3″)-I, tetA, and mcr-1. The mobilization of the blaCTX-M gene was confirmed for nine E. coli isolates by conjugation assays. The presence of blaCTX-M on mobile genetic elements in these isolates was demonstrated by Southern blot hybridization, and the resistance to cephalosporins was confirmed in the transconjugants. Our results indicate the prevalence of CTX-M-producing E. coli strains harboring mobile genetic elements in the normal microbiota of healthy pigs. CONCLUSIONS These findings highlight the significance of ESBL genes as a global health concern in livestock and the potential spread of antimicrobial resistance to other members of the gastrointestinal tract microbiota.
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Affiliation(s)
- Rúzivia Pimentel Oliveira
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Laboratory of Molecular Genetics of Bacteria, Instituto de Biotecnologia Aplicada à Agropecuária (Bioagro), Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Juliana Soares da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Giarlã Cunha da Silva
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Jéssica Nogueira Rosa
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Denise Mara Soares Bazzolli
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Laboratory of Molecular Genetics of Bacteria, Instituto de Biotecnologia Aplicada à Agropecuária (Bioagro), Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Hilario C Mantovani
- Department of Microbiology, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, WI, United States
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Hou X, Yang J, Xie J, Zhu S, Zhang Z. Diversity and Antibiotic Resistance of Triticale Seed-Borne Bacteria on the Tibetan Plateau. Microorganisms 2024; 12:650. [PMID: 38674594 PMCID: PMC11052201 DOI: 10.3390/microorganisms12040650] [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: 02/17/2024] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The Tibetan Plateau is located in southwestern China. It has many important ecological functions, such as biodiversity protection, and is an important grassland agroecosystem in China. With the development of modern agriculture and animal husbandry, antibiotics are widely used to treat humans and livestock, and antibiotics cannot be fully metabolised by both. Antibiotics eventually find their way into the environment, affecting other parts of grassland agroecosystems. Triticale (Triticosecale wittmack) is an artificial hybrid forage that can be used for both grain and forage. This study revealed the diversity of seedborne bacteria in triticale on the Tibetan Plateau and the resistance of the bacteria to nine antibiotics. It identified 37 representative strains and successfully obtained the spliced sequences of 36 strains of the bacteria, which were clustered into 5 phyla and 16 genera. Among them, 18 strains showed resistance to at least one of the 9 antibiotics, and the colony-forming unit (CFU) abundance of antibiotic-resistant bacteria (ARB) accounted for 45.38% of the total samples. Finally, the bacterial motility and biofilm formation ability were measured, and their correlation with bacterial resistance was analysed. The results showed that the bacterial resistance did not have an absolute positive correlation with the motility or biofilm formation ability.
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Affiliation(s)
| | | | | | | | - Zhenfen Zhang
- Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China; (X.H.); (J.Y.); (J.X.); (S.Z.)
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7
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Manishimwe R, Ndayisenga B, Habimana R, Mwikarago IE, Habiyaremye T, Ndindibije JP, Shyaka A, Kabatende J, Habyalimana V, Karangwa C, Bienvenu E. Importation trends in antibiotics for veterinary use in Rwanda: A retrospective study between 2019 and 2021. PLoS One 2024; 19:e0299917. [PMID: 38451985 PMCID: PMC10919585 DOI: 10.1371/journal.pone.0299917] [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: 07/19/2023] [Accepted: 02/17/2024] [Indexed: 03/09/2024] Open
Abstract
Estimating antibiotic consumption in animals is fundamental to guiding decision-making and research on controlling the emergence and spread of antibiotic-resistant bacteria in humans, animals, and the environment. This study aimed to establish importation trends of antibiotics for veterinary use in Rwanda between 2019 and 2021. Data was collected from the Rwanda Food and Drugs Authority's database. Quantities of imported antibiotic active ingredients were computed using the information extracted from the issued import licenses. These quantities were subsequently adjusted per animal biomass. In total, 35,291.4 kg of antibiotics were imported into Rwanda between 2019 and 2021, with an annual mean of 11,763.8 ± 1,486.9 kg. The adjustment of imported quantities of antibiotics per animal biomass revealed that 29.1 mg/kg, 24.3 mg/kg, and 30.3 mg/kg were imported in 2019, 2020, and 2021 respectively. A slight but not statistically significant decline in antibiotic importation was noted in 2020 (p-value = 0.547). Most of the imported antibiotics were indicated to be used in food-producing animals (35,253.8 kg or 99.9% of the imported antibiotics). Tetracyclines (17,768.6 kg or 50.3%), followed by sulfonamides (7,865.0 kg or 22.3%) and aminoglycosides (4,071.1 kg or 11.5%), were the most imported antibiotics over the studied period. It was noted that 78.9% of the imported antibiotics were categorized as highly important antimicrobials for human medicine. This study established a generalized overview of the importation of antibiotics for veterinary use in Rwanda. These results can serve as guidance for the control of antibiotic misuse. They can be used to make a correlation between antibiotic importation, antibiotic consumption, and the occurrence of antibiotic resistance in the country.
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Affiliation(s)
| | | | | | | | | | | | - Anselme Shyaka
- Center for One Health, University of Global Health Equity, Butaro, Rwanda
| | - Joseph Kabatende
- World Health Organization, Regional Office for Africa, Brazzaville, Republic of the Congo
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Londoño-Carmona J, Blandón-Escobar S, Montoya-Zuluaga J, Betancourt-Chaves P, Castillo-Moreno S, Arboleda-Múnera C, Vallejo-Timarán D. Antibiotic residues and microbial contamination in pasteurized whole milk intended for human consumption. Vet World 2024; 17:720-727. [PMID: 38680139 PMCID: PMC11045524 DOI: 10.14202/vetworld.2024.720-727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/28/2024] [Indexed: 05/01/2024] Open
Abstract
Background and Aim Milk contamination for human consumption is one of the biggest concerns worldwide. To prevent milk contamination, it is important to implement sustainable production practices that ensure animal health and guarantee veterinary drugs have been used properly. This study aimed to detect antibiotic residues and microbial contamination in commercially available pasteurized whole milk intended for human consumption. Materials and Methods We conducted a cross-sectional study on all brands of pasteurized milk (n = 17) for human consumption in Medellín, Colombia, from February 30 to April 30, 2022. Six milk samples of each brand were collected every 15 days, resulting in 102 samples. IDEXX SNAPduo™ ST Plus test (IDEXX Laboratories Inc, Maine, USA) was used to detect cephalosporins residues to detect beta-lactam and tetracyclines. We detected mesophilic aerobic bacteria and coliforms using Chromocult Coliform Agar® (Merck KGaA, Darmstadt, Germany) and Plate-Count Agar® (Merck KGaA), respectively. Results Beta-lactam residues were found in 24.4% of the brands. No tetracyclines or cephalosporins were detected. Mesophilic aerobic bacteria and coliform contamination were detected in 42.6% and 12.8% of the brands, respectively. No fecal coliform contamination was detected. Conclusion This study demonstrated the presence of antibiotic residues and microbial contamination in commercially available pasteurized whole milk intended for human consumption in the study area, highlighting its potential public health implications.
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Affiliation(s)
- Juan Londoño-Carmona
- Center of Natural and Renewable Resources, La Salada. National Learning Service – SENA, Research Group La Salada, Government of Colombia. Caldas, Colombia
| | - Sandra Blandón-Escobar
- Center of Natural and Renewable Resources, La Salada. National Learning Service – SENA, Research Group La Salada, Government of Colombia. Caldas, Colombia
| | - John Montoya-Zuluaga
- Veterinary Medicine and Animal Sciences Faculty, Research Group GIsCA, University Vision de las Americas, Medellín, Colombia
| | - Patricia Betancourt-Chaves
- Veterinary Medicine and Animal Sciences Faculty, Research Group GIsCA, University Vision de las Americas, Medellín, Colombia
| | - Sara Castillo-Moreno
- Veterinary Medicine and Animal Sciences Faculty, Research Group GIsCA, University Vision de las Americas, Medellín, Colombia
| | - Carlos Arboleda-Múnera
- Veterinary Medicine and Animal Sciences Faculty, Research Group GIsCA, University Vision de las Americas, Medellín, Colombia
| | - Darío Vallejo-Timarán
- Colombian Agricultural Research Corporation – AGROSAVIA. Obonuco Research Center, Pasto, Colombia
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9
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Gao FZ, He LY, Liu YS, Zhao JL, Zhang T, Ying GG. Integrating global microbiome data into antibiotic resistance assessment in large rivers. WATER RESEARCH 2024; 250:121030. [PMID: 38113599 DOI: 10.1016/j.watres.2023.121030] [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: 11/06/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Rivers are important in spreading antimicrobial resistance (AMR). Assessing AMR risk in large rivers is challenged by large spatial scale and numerous contamination sources. Integrating river resistome data into a global framework may help addressing this difficulty. Here, we conducted an omics-based assessment of AMR in a large river (i.e. the Pearl River in China) with global microbiome data. Results showed that antibiotic resistome in river water and sediment was more diversified than that in other rivers, with contamination levels in some river reaches higher than global baselines. Discharge of WWTP effluent and landfill waste drove AMR prevalence in the river, and the resistome level was highly associated with human and animal sources. Detection of 54 risk rank I ARGs and emerging mobilizable mcr and tet(X) highlighted AMR risk in the river reaches with high human population density and livestock pollution. Florfenicol-resistant floR therein deserved priority concerns due to its high detection frequency, dissimilar phylogenetic distance, mobilizable potential, and presence in multiple pathogens. Co-sharing of ARGs across taxonomic ranks implied their transfer potentials in the community. By comparing with global genomic data, we found that Burkholderiaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were important potential ARG-carrying bacteria in the river, and WHO priority carbapenem-resistant Enterobacteriaceae, A. baumannii and P. aeruginosa should be included in future surveillance. Collectively, the findings from this study provide an omics-benchmarked assessment strategy for public risk associated with AMR in large rivers.
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Affiliation(s)
- Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Jian-Liang Zhao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou, China; School of Environment, South China Normal University, University Town, Guangzhou, China.
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10
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Odey TOJ, Tanimowo WO, Afolabi KO, Jahid IK, Reuben RC. Antimicrobial use and resistance in food animal production: food safety and associated concerns in Sub-Saharan Africa. Int Microbiol 2024; 27:1-23. [PMID: 38055165 PMCID: PMC10830768 DOI: 10.1007/s10123-023-00462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023]
Abstract
The use of antimicrobials in food animal (FA) production is a common practice all over the world, with even greater usage and dependence in the developing world, including Sub-Saharan Africa (SSA). However, this practice which serves obvious economic benefits to producers has raised public health concerns over the last decades, thus driving the selection and dissemination of antimicrobial resistance and adversely impacting food safety and environmental health. This review presents the current and comprehensive antimicrobial usage practices in food animal production across SSA. We further highlighted the overall regional drivers as well as the public health, environmental, and economic impact of antimicrobial use in the production of food animals. Antimicrobial use is likely to increase with even exacerbated outcomes unless cost-effective, safe, and sustainable alternatives to antibiotics, especially probiotics, prebiotics, bacteriocins, antimicrobial peptides, bacteriophages, vaccines, etc. are urgently advocated for and used in food animal production in SSA. These, in addition to the implementation of strong legislation on antimicrobial use, and improved hygiene will help mitigate the public health concerns associated with antimicrobial use in food animals and improve the well-being and safety of food animals and their products.
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Affiliation(s)
- Timothy Obiebe Jason Odey
- Department of Biological Sciences, Faculty of Natural, Applied, and Health Sciences, Anchor University, Lagos, Nigeria
| | - Williams Omotola Tanimowo
- Department of Biological Sciences, Faculty of Natural, Applied, and Health Sciences, Anchor University, Lagos, Nigeria
| | - Kayode Olayinka Afolabi
- Department of Biological Sciences, Faculty of Natural, Applied, and Health Sciences, Anchor University, Lagos, Nigeria
- Pathogenic Yeasts Research Group, Department of Microbiology and Biochemistry, University of The Free State, Bloemfontein, South Africa
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Rine Christopher Reuben
- Department of Biological Sciences, Faculty of Natural, Applied, and Health Sciences, Anchor University, Lagos, Nigeria.
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
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11
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Oliveira A, Dias C, Oliveira R, Almeida C, Fuciños P, Sillankorva S, Oliveira H. Paving the way forward: Escherichia coli bacteriophages in a One Health approach. Crit Rev Microbiol 2024; 50:87-104. [PMID: 36608263 DOI: 10.1080/1040841x.2022.2161869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
Escherichia coli is one of the most notorious pathogens for its ability to adapt, colonize, and proliferate in different habitats through a multitude of acquired virulence factors. Its presence affects the food-processing industry and causes food poisoning, being also a major economic burden for the food, agriculture, and health sectors. Bacteriophages are emerging as an appealing strategy to mitigate bacterial pathogens, including specific E. coli pathovars, without exerting a deleterious effect on humans and animals. This review globally analyzes the applied research on E. coli phages for veterinary, food, and human use. It starts by describing the pathogenic E. coli pathotypes and their relevance in human and animal context. The idea that phages can be used as a One Health approach to control and interrupt the transmission routes of pathogenic E. coli is sustained through an exhaustive revision of the recent literature. The emerging phage formulations, genetic engineering and encapsulation technologies are also discussed as a means of improving phage-based control strategies, with a particular focus on E. coli pathogens.
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Affiliation(s)
- Ana Oliveira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Carla Dias
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Ricardo Oliveira
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vairão, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Carina Almeida
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vairão, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Pablo Fuciños
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Sanna Sillankorva
- INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga, Portugal
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
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12
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Zhao C, Wang Y, Mulchandani R, Van Boeckel TP. Global surveillance of antimicrobial resistance in food animals using priority drugs maps. Nat Commun 2024; 15:763. [PMID: 38278814 PMCID: PMC10817973 DOI: 10.1038/s41467-024-45111-7] [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: 06/21/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Antimicrobial resistance (AMR) in food animals is a growing threat to animal health and potentially to human health. In resource-limited settings, allocating resources to address AMR can be guided with maps. Here, we mapped AMR prevalence in 7 antimicrobials in Escherichia coli and nontyphoidal Salmonella species across low- and middle-income countries (LIMCs), using 1088 point-prevalence surveys in combination with a geospatial model. Hotspots of AMR were predicted in China, India, Brazil, Chile, and part of central Asia and southeastern Africa. The highest resistance prevalence was for tetracycline (59% for E. coli and 54% for nontyphoidal Salmonella, average across LMICs) and lowest for cefotaxime (33% and 19%). We also identified the antimicrobial with the highest probability of resistance exceeding critical levels (50%) in the future (1.7-12.4 years) for each 10 × 10 km pixel on the map. In Africa and South America, 78% locations were associated with penicillins or tetracyclines crossing 50% resistance in the future. In contrast, in Asia, 77% locations were associated with penicillins or sulphonamides. Our maps highlight diverging geographic trends of AMR prevalence across antimicrobial classes, and can be used to target AMR surveillance in AMR hotspots for priority antimicrobial classes.
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Affiliation(s)
- Cheng Zhao
- Health Geography and Policy Group, ETH Zürich, Zürich, Switzerland
| | - Yu Wang
- Health Geography and Policy Group, ETH Zürich, Zürich, Switzerland
| | | | - Thomas P Van Boeckel
- Health Geography and Policy Group, ETH Zürich, Zürich, Switzerland.
- One Health Trust, Washington DC, USA.
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium.
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13
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Nomoto R, Osawa K, Kinoshita S, Kitagawa K, Nakanishi N, Sarassari R, Raharjo D, Fujisawa M, Kuntaman K, Shirakawa T. Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia. Microorganisms 2024; 12:199. [PMID: 38258025 PMCID: PMC10819989 DOI: 10.3390/microorganisms12010199] [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: 12/05/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial agents are administered to humans and livestock, and bacterial antimicrobial resistance (AMR) and antimicrobial agents are released into the environment. In this study, to investigate the trend of AMR in humans, livestock, and the environment, we performed a metagenomic analysis of multidrug-resistant bacteria with CHROMagar ESBL in environmental river water samples, which were collected using syringe filter units from waters near hospitals, downtown areas, residential areas, and water treatment plants in Surabaya, Indonesia. Our results showed that Acinetobacter, Pseudomonas, Aeromonas, Enterobacter, Escherichia, and Klebsiella grew in CHROMagar ESBL; they were most frequently detected in water samples from rivers surrounding hospitals contaminated with various AMR genes (ARGs) in high levels. These results identified bacteria as ARG reservoirs and revealed that hospitals could be sources for various ARGs disseminated into the environment. In conclusion, this study details a novel metagenomic analysis of collected bacteria in environmental water samples using a syringe filter unit for an AMR epidemiological study based on the One Health approach.
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Affiliation(s)
- Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe 650-0046, Japan; (R.N.); (N.N.)
| | - Kayo Osawa
- Department of Medical Technology, Kobe Tokiwa University, Kobe 653-0838, Japan
| | - Shohiro Kinoshita
- Division of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe 650-0017, Japan; (S.K.); (K.K.); (T.S.)
| | - Koichi Kitagawa
- Division of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe 650-0017, Japan; (S.K.); (K.K.); (T.S.)
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe 650-0046, Japan; (R.N.); (N.N.)
| | - Rosantia Sarassari
- Department of Microbiology, Faculty of Medicine, Airlangga University, Surabaya 60132, Indonesia; (R.S.); (K.K.)
| | - Dadik Raharjo
- Institute of Tropical Disease, Airlangga University, Surabaya 60286, Indonesia;
| | - Masato Fujisawa
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
| | - Kuntaman Kuntaman
- Department of Microbiology, Faculty of Medicine, Airlangga University, Surabaya 60132, Indonesia; (R.S.); (K.K.)
- Institute of Tropical Disease, Airlangga University, Surabaya 60286, Indonesia;
| | - Toshiro Shirakawa
- Division of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe 650-0017, Japan; (S.K.); (K.K.); (T.S.)
- Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan;
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14
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Thorn AV, Aarestrup FM, Munk P. Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis. Microbiol Spectr 2024; 12:e0241323. [PMID: 38084973 PMCID: PMC10783016 DOI: 10.1128/spectrum.02413-23] [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: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.
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Affiliation(s)
- Alix Vincent Thorn
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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15
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Piña-González AM, Castelán-Sánchez HG, Hurtado-Ramírez JM, López-Leal G. Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species. Microbiol Spectr 2024; 12:e0279523. [PMID: 38088548 PMCID: PMC10782988 DOI: 10.1128/spectrum.02795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/12/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.
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Affiliation(s)
- Adán Manuel Piña-González
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Hugo G. Castelán-Sánchez
- Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Humanidades, Ciudad de México, México
| | | | - Gamaliel López-Leal
- Laboratorio de Biología Computacional y Virómica Integrativa, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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16
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Dittoe DK, Anderson RC, Poole TL, Crippen TL, Harvey RB, Ricke SC. Chlortetracycline Concentration Impact on Salmonella Typhimurium Sustainability in the Presence of Porcine Gastrointestinal Tract Bacteria Maintained in Continuous Culture. Pathogens 2023; 12:1454. [PMID: 38133337 PMCID: PMC10748003 DOI: 10.3390/pathogens12121454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Concern exists that the continued use of antibiotics in animal feeds may lead to an increased prevalence of resistant bacteria within the host animal's gastrointestinal tract. To evaluate the effect of chlortetracycline on the persistence of Salmonella enterica serotype Typhimurium within a diverse population of porcine cecal bacteria, we cultured a mixed population of cecal bacteria without or with added chlortetracycline. When grown at a 24 h vessel turnover rate, chlortetracycline-susceptible S. Typhimurium exhibited more than 2.5 times faster (p < 0.05) disappearance rates than theoretically expected (0.301 log10 colony-forming unit/mL per day) but did not differ whether treated or not with 55 mg of chlortetracycline/L. Chlortetracycline-resistant S. Typhimurium was not recovered from any of these cultures. When the mixed cultures were inoculated with a chlortetracycline-resistant S. Typhimurium, rates of disappearance were nearly two times slower (p < 0.05) than those observed earlier with chlortetracycline-susceptible S. Typhimurium, and cultures persisted at >2 log10 colony-forming units/mL for up to 14 days of treatment with 110 mg of chlortetracycline/L. Under the conditions of this study, chlortetracycline-resistant S. Typhimurium was competitively enabled to persist longer within the mixed populations of porcine gut bacteria than chlortetracycline-susceptible S. Typhimurium, regardless of the presence or absence of added chlortetracycline.
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Affiliation(s)
- Dana K. Dittoe
- Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA;
| | - Robin C. Anderson
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (R.C.A.); (T.L.P.); (T.L.C.); (R.B.H.)
| | - Toni L. Poole
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (R.C.A.); (T.L.P.); (T.L.C.); (R.B.H.)
| | - Tawni L. Crippen
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (R.C.A.); (T.L.P.); (T.L.C.); (R.B.H.)
| | - Roger B. Harvey
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, TX 77845, USA; (R.C.A.); (T.L.P.); (T.L.C.); (R.B.H.)
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
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17
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Morgan AL, Woolhouse ME, Wagenaar JA, van Bunnik BA. Modelling the effects of antibiotic usage in livestock on human salmonellosis. One Health 2023; 17:100639. [PMID: 38024252 PMCID: PMC10665166 DOI: 10.1016/j.onehlt.2023.100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotic usage in livestock has been suggested as a driver of antimicrobial resistance in human and livestock populations. This has contributed to the implementation of stewardship programs to curtail usage of antibiotics in livestock. However, the consequences of antibiotic curtailment in livestock on human health are poorly understood. There is the potential for increases in the carriage of pathogens such as Salmonella spp. in livestock, and subsequent increases in human foodborne disease. We use a mathematical model fitted to four case studies, ampicillin and tetracycline usage in fattening pig and broiler poultry populations, to explore the impact of curtailing antibiotic usage in livestock on salmonellosis in humans. Increases in the daily incidence of salmonellosis and a decrease in the proportion of resistant salmonellosis were identified following curtailment of antibiotic usage in livestock. The extent of these increases in human foodborne disease ranged from negligible, to controllable through interventions to target the farm-to-fork pathway. This study provides a motivating example of one plausible scenario following curtailment of antibiotic usage in livestock and suggests that a focus on ensuring good farm-to-fork hygiene and livestock biosecurity is sufficient to mitigate the negative human health consequences of antibiotic stewardship in livestock populations.
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Affiliation(s)
- Alex L.K. Morgan
- Centre for Immunity, Infection & Evolution and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Mark E.J. Woolhouse
- Centre for Immunity, Infection & Evolution and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jaap A. Wagenaar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Wageningen Bioveterinary Research, Lelystad, Netherlands
- WHO Collaborating Center for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
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18
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Kenneth MJ, Koner S, Hsu GJ, Chen JS, Hsu BM. A review on the effects of discharging conventionally treated livestock waste to the environmental resistome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122643. [PMID: 37775024 DOI: 10.1016/j.envpol.2023.122643] [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: 06/09/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.
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Affiliation(s)
- Mutebi John Kenneth
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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Glassmeyer ST, Burns EE, Focazio MJ, Furlong ET, Gribble MO, Jahne MA, Keely SP, Kennicutt AR, Kolpin DW, Medlock Kakaley EK, Pfaller SL. Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies. GEOHEALTH 2023; 7:e2022GH000716. [PMID: 38155731 PMCID: PMC10753268 DOI: 10.1029/2022gh000716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 12/30/2023]
Abstract
The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.
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Affiliation(s)
- Susan T. Glassmeyer
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | | | - Michael J. Focazio
- Retired, Environmental Health ProgramEcosystems Mission AreaU.S. Geological SurveyRestonVAUSA
| | - Edward T. Furlong
- Emeritus, Strategic Laboratory Sciences BranchLaboratory & Analytical Services DivisionU.S. Geological SurveyDenverCOUSA
| | - Matthew O. Gribble
- Gangarosa Department of Environmental HealthRollins School of Public HealthEmory UniversityAtlantaGAUSA
| | - Michael A. Jahne
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Scott P. Keely
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Alison R. Kennicutt
- Department of Civil and Mechanical EngineeringYork College of PennsylvaniaYorkPAUSA
| | - Dana W. Kolpin
- U.S. Geological SurveyCentral Midwest Water Science CenterIowa CityIAUSA
| | | | - Stacy L. Pfaller
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
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20
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Ishengoma VL, Amachawadi RG, Tokach MD, Shi X, Kang Q, Goodband RD, DeRouchey J, Woodworth J, Nagaraja TG. Impact of In-Feed versus In-Water Chlortetracycline and Tiamulin Administrations on Fecal Prevalence and Antimicrobial Susceptibilities of Campylobacter in a Population of Nursery Pigs. Microorganisms 2023; 11:2876. [PMID: 38138021 PMCID: PMC10745678 DOI: 10.3390/microorganisms11122876] [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: 10/19/2023] [Revised: 11/19/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is a major public health concern in the US and around the world. Campylobacter is an important foodborne pathogen that resides in the gut of pigs and is shed in feces, with the potential to be transmitted to humans. In pigs, the oral route, either in-feed or in-water, is by far the most common route of administration of antimicrobials. Because the distribution of the antibiotic in the gut and the dosages are different, the impact of in-feed vs. in-water administration of antibiotics on the development of AMR is likely to be different. Therefore, a study was conducted to compare in-feed vs. in-water administrations of chlortetracycline (CTC) and/or tiamulin on fecal prevalence and AMR profiles of Campylobacter among weaned nursery piglets. A total of 1,296 weaned piglets, allocated into 48 pens (27 piglets per pen), were assigned randomly to six treatment groups: Control (no antibiotic), in-feed CTC, in-water CTC, in-feed tiamulin, in-water tiamulin, or in-feed CTC and tiamulin. Fecal samples were collected randomly from 5 piglets from each pen during the pre-treatment (days 0, 7), treatment (days 14, 21), and post-treatment (days 28, 35) phases. Bacterial isolations and species identifications were conducted by culture and PCR, respectively. The microbroth dilution method with SensititreTM plates was used to determine the antimicrobial susceptibility and resistance of Campylobacter isolates. The results on resistance were interpreted based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cutoff values for Campylobacter. The overall prevalence of Campylobacter was 18.2% (262/1440). Speciation of Campylobacter isolates by PCR indicated the prevalence of only two species: Campylobacter hyointestinalis (17.9%; 258/1440) and C. coli (0.3%; 4/1440). Campylobacter isolates were resistant to tetracycline (98.5%), ciprofloxacin (89.3%), and nalidixic acid (60.3%). Neither the antibiotic nor the route of administration had an effect (p > 0.05) on the prevalence of AMR Campylobacter in the feces of piglets.
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Affiliation(s)
- Victor L. Ishengoma
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Raghavendra G. Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA;
| | - Mike D. Tokach
- Department of Animal Sciences & Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA; (M.D.T.); (R.D.G.); (J.D.); (J.W.)
| | - Xiaorong Shi
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (X.S.); (T.G.N.)
| | - Qing Kang
- Department of Statistics, College of Arts and Sciences, Kansas State University, Manhattan, KS 66506, USA;
| | - Robert D. Goodband
- Department of Animal Sciences & Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA; (M.D.T.); (R.D.G.); (J.D.); (J.W.)
| | - Joel DeRouchey
- Department of Animal Sciences & Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA; (M.D.T.); (R.D.G.); (J.D.); (J.W.)
| | - Jason Woodworth
- Department of Animal Sciences & Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA; (M.D.T.); (R.D.G.); (J.D.); (J.W.)
| | - Tiruvoor G. Nagaraja
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (X.S.); (T.G.N.)
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21
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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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22
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Che M, Birk T, Hansen LT. Prevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark. Antibiotics (Basel) 2023; 12:1602. [PMID: 37998804 PMCID: PMC10668726 DOI: 10.3390/antibiotics12111602] [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: 09/03/2023] [Revised: 10/27/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22). Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.
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Affiliation(s)
- Meiyao Che
- National Food Institute, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Tina Birk
- Department of Technology, University College Copenhagen, 2300 Copenhagen, Denmark;
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23
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Guenin MJ, Studnitz M, Molia S. Interventions to change antimicrobial use in livestock: A scoping review and an impact pathway analysis of what works, how, for whom and why. Prev Vet Med 2023; 220:106025. [PMID: 37776605 DOI: 10.1016/j.prevetmed.2023.106025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 07/25/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Antimicrobial resistance (AMR) is a public health threat responsible for 700,000 deaths per year worldwide. Antimicrobial use (AMU) in livestock contributes to AMR in animal and public health. Therefore, it is essential to implement effective interventions towards better AMU in livestock. However, there is a lack of evidence to inform decision-makers of what works, how, for whom and why and how effective interventions can be adapted to different contexts. We conducted a scoping review and an impact pathway analysis to systematically map the research done in this area and to inform evidence-based and context-appropriate policies. We followed the PRISMA-ScR requirements and searched Web of Science, PubMed and Scopus databases to identify studies in English or French languages, in open access and published between 2000 and 2022. We selected thirty references addressing twenty-eight different interventions that were successful in changing AMU in livestock. We used an impact pathway logic model as an analytic framework to guide the technical aspects of the scoping review process and to identify the complex relationships between outputs, outcomes, impacts and contextual factors. A majority of interventions managed to improve AMU by changing herd and health management practices (ni=18). We identified intermediate outcomes including change in the veterinarian-farmer relationship (ni=7), in knowledge and perception (ni=6), and in motivation and confidence (ni=1). Twenty-two studies recorded positive impacts on animal health and welfare (ni=11), technical performances (ni=9), economic performances (ni=4) and AMR reduction (ni=4). Interventions implemented different strategies including herd and health management support (ni=20), norms and standards (ni=11), informational and educational measures (ni=10), economic support (ni=5). Studies were mainly in European countries and in pig and large ruminants farming. Most interventions targeted farmers or veterinarians but we identified other major and influential actors including authority and governmental organizations, academics and research, organization of producers or veterinarians, herd advisors and technicians, laboratories, and public opinion. Key success factors were knowledge and perception (ni=14), social factors (ni=13), intervention characteristics (ni=11), trajectory and ecosystem of change (ni=11), economic factors (ni=9), herd and health status (ni=8), data access and monitoring (ni=4). This review describes a paucity of impact assessment of interventions towards better AMU in livestock. There is no one-size-fits-all transition pathway but we inform decision-makers about the most successful interventions that work, how, for whom and why. The impact pathway analysis provided a holistic view of the successful change processes and the complex relationships between outputs, outcomes, impacts and contexts.
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Affiliation(s)
| | - Merete Studnitz
- International Centre for Research in Organic Food Systems, DK-8830 Tjele, Denmark
| | - Sophie Molia
- UMR ASTRE, Université de Montpellier, CIRAD, INRAE, Montpellier, France
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24
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Jensen EEB, Sedor V, Eshun E, Njage P, Otani S, Aarestrup FM. The resistomes of rural and urban pigs and poultry in Ghana. mSystems 2023; 8:e0062923. [PMID: 37737585 PMCID: PMC10654090 DOI: 10.1128/msystems.00629-23] [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: 06/15/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.
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Affiliation(s)
| | - Victoria Sedor
- Veterinary Services Department, Ministry of Food and Agriculture, National Food Safety Laboratory, Accra, Ghana
| | - Emmanuel Eshun
- Veterinary Services Department, Ministry of Food and Agriculture, National Food Safety Laboratory, Accra, Ghana
| | - Patrick Njage
- Technical University of Denmark, Kemitorvet, Denmark
| | - Saria Otani
- Technical University of Denmark, Kemitorvet, Denmark
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25
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Dankittipong N, Alderliesten JB, Van den Broek J, Dame-Korevaar MA, Brouwer MSM, Velkers FC, Bossers A, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Prev Vet Med 2023; 219:105998. [PMID: 37647719 DOI: 10.1016/j.prevetmed.2023.105998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria comparable to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed over 12 pens on the day of hatch (day 0). On day 5, half of the 10 remaining chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). To evaluate the effect of antibiotic treatment, amoxicillin was given twice daily in drinking water in 6 of the 12 pens from days 2-6. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or by other differences between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2-6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jesse B Alderliesten
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - M Anita Dame-Korevaar
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Alex Bossers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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26
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Wang B, Xu J, Wang Y, Stirling E, Zhao K, Lu C, Tan X, Kong D, Yan Q, He Z, Ruan Y, Ma B. Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301980. [PMID: 37424042 PMCID: PMC10502870 DOI: 10.1002/advs.202301980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.
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Affiliation(s)
- Binhao Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
| | - Yiling Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Erinne Stirling
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganizationAdelaide5064Australia
- School of Biological SciencesThe University of AdelaideAdelaide5005Australia
| | - Kankan Zhao
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Caiyu Lu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Xiangfeng Tan
- Institute of Digital AgricultureZhejiang Academy of Agricultural SciencesHangzhou310021P. R. China
- Xianghu LaboratoryHangzhouZhejiang311200P. R. China
| | - Dedong Kong
- Institute of Digital AgricultureZhejiang Academy of Agricultural SciencesHangzhou310021P. R. China
- Xianghu LaboratoryHangzhouZhejiang311200P. R. China
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519080P. R. China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519080P. R. China
| | - Yunjie Ruan
- Institute of Agricultural Bio‐Environmental EngineeringCollege of Bio‐SystemsEngineering and Food ScienceZhejiang UniversityHangzhou310058P. R. China
- The Rural Development AcademyZhejiang UniversityHangzhou310058P. R. China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
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27
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Raut R, Maharjan P, Fouladkhah AC. Practical Preventive Considerations for Reducing the Public Health Burden of Poultry-Related Salmonellosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6654. [PMID: 37681794 PMCID: PMC10487474 DOI: 10.3390/ijerph20176654] [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: 04/25/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
With poultry products as one of the leading reservoirs for the pathogen, in a typical year in the United States, it is estimated that over one million individuals contract non-typhoidal Salmonella infections. Foodborne outbreaks associated with Salmonella infections in poultry, thus, continue to remain a significant risk to public health. Moreover, the further emergence of antimicrobial resistance among various serovars of Salmonella is an additional public health concern. Feeding-based strategies (such as use of prebiotics, probiotics, and/or phytobiotics as well as essential oils), non-feeding-based strategies (such as use of bacteriophages, vaccinations, and in ovo strategies), omics tools and surveillance for identifying antibiotic-resistance genes, post-harvest application of antimicrobials, and biosecurity measures at poultry facilities are practical interventions that could reduce the public health burden of salmonellosis and antibiotic resistance associated with poultry products. With the escalating consumption of poultry products around the globe, the fate, prevalence, and transmission of Salmonella in agricultural settings and various poultry-processing facilities are major public health challenges demanding integrated control measures throughout the food chain. Implementation of practical preventive measures discussed in the current study could appreciably reduce the public health burden of foodborne salmonellosis associated with poultry products.
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Affiliation(s)
- Rabin Raut
- Cooperative Extension Program, Tennessee State University, Nashville, TN 37209, USA;
- Public Health Microbiology Laboratory, Tennessee State University, Nashville, TN 37209, USA
| | - Pramir Maharjan
- Cooperative Extension Program, Tennessee State University, Nashville, TN 37209, USA;
| | - Aliyar Cyrus Fouladkhah
- Public Health Microbiology Laboratory, Tennessee State University, Nashville, TN 37209, USA
- Public Health Microbiology FoundationSM, Nashville, TN 37209, USA
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Konteh SA, Bangura (Turay) FI, Leno A, Satyanarayana S, Nair D, Bah MA, Saidu S, Sellu-Sallu D, Gborie SR, Kamara SM, Jalloh AT, Kanu JS, Kamara KN, Moiwo MM, Dsani E, Nantima N. Improvement in the Surveillance System for Livestock Diseases and Antimicrobial Use Following Operational Research Studies in Sierra Leone January-March 2023. Trop Med Infect Dis 2023; 8:408. [PMID: 37624345 PMCID: PMC10459562 DOI: 10.3390/tropicalmed8080408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
In Sierra Leone, two operational research (OR) studies in 2019 and 2021 showed deficiencies in the data being captured by the Integrated Animal Disease Surveillance and Reporting (IADSR) system. This third OR study was conducted in 2023 to assess whether the second OR study's results and recommendations were disseminated with the key stakeholders, the uptake of the recommendations, improvements in data capture in the IADSR system, and to describe the data on livestock disease and antimicrobial use. In 2022, on seven occasions, the authors of the second OR study disseminated the study's findings. Of the four recommendations, the one on improving laboratory infrastructure for confirmation of animal disease was not implemented. The district animal health weekly surveillance reports received through the IADSR system were sustained at 88% between the second (2021) and third (2023) studies. In both studies, the proportion of sick animals receiving antibiotics (25%) remained the same, but the use of "critically important antimicrobials for veterinary use" declined from 77% (in 2021) to 69% (in 2023). The IADSR system has improved considerably in providing information on animal health and antibiotic use, and sequential OR studies have played a key role in its improvement.
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Affiliation(s)
- Samuel Alie Konteh
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Fatmata Isatu Bangura (Turay)
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Amara Leno
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Srinath Satyanarayana
- Center for Operational Research, International Union Against TB and Lung Disease (The Union), 75006 Paris, France; (S.S.); (D.N.)
| | - Divya Nair
- Center for Operational Research, International Union Against TB and Lung Disease (The Union), 75006 Paris, France; (S.S.); (D.N.)
| | - Mohamed Alpha Bah
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Salam Saidu
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - David Sellu-Sallu
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Sahr Raymond Gborie
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Sorie Mohamed Kamara
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Amadu Tejan Jalloh
- Livestock and Veterinary Services Division, Ministry of Agriculture and Forestry, Youyi Building, Brooked, Freetown 00232, Sierra Leone (A.L.); (M.A.B.); (S.S.); (D.S.-S.); (S.R.G.); (S.M.K.); (A.T.J.)
| | - Joseph Sam Kanu
- National Disease Surveillance Program, Directorate of Health Security and Emergencies, Ministry of Health and Sanitation, Sierra Leone National Public Health Emergency Operations Centre, Cockerill, Wilkinson Road, Freetown 00232, Sierra Leone; (J.S.K.); (K.N.K.)
- College of Medicine and Allied Health Sciences (COMAHS), University of Sierra Leone (USL), Tower Hill, Freetown 00232, Sierra Leone
| | - Kadijatu Nabie Kamara
- National Disease Surveillance Program, Directorate of Health Security and Emergencies, Ministry of Health and Sanitation, Sierra Leone National Public Health Emergency Operations Centre, Cockerill, Wilkinson Road, Freetown 00232, Sierra Leone; (J.S.K.); (K.N.K.)
| | - Matilda Mattu Moiwo
- Joint Medical Unit, Ministry of Defense, Republic of Sierra Leone Armed Forces, Freetown 00232, Sierra Leone
| | - Esther Dsani
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Freetown 00232, Sierra Leone; (E.D.)
| | - Noelina Nantima
- Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations (FAO), Freetown 00232, Sierra Leone; (E.D.)
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Fredriksen S, de Warle S, van Baarlen P, Boekhorst J, Wells JM. Resistome expansion in disease-associated human gut microbiomes. MICROBIOME 2023; 11:166. [PMID: 37507809 PMCID: PMC10386251 DOI: 10.1186/s40168-023-01610-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome. RESULTS The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer. CONCLUSIONS Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.
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Affiliation(s)
- Simen Fredriksen
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands.
| | - Stef de Warle
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Jos Boekhorst
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Jerry M Wells
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands.
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Byarugaba DK, Wokorach G, Alafi S, Erima B, Najjuka F, Mworozi EA, Kibuuka H, Wabwire-Mangen F. Whole Genome Sequencing Reveals High Genetic Diversity, Diverse Repertoire of Virulence-Associated Genes and Limited Antibiotic Resistance Genes among Commensal Escherichia coli from Food Animals in Uganda. Microorganisms 2023; 11:1868. [PMID: 37630428 PMCID: PMC10457813 DOI: 10.3390/microorganisms11081868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 08/27/2023] Open
Abstract
Commensal Escherichia coli with broad repertoire of virulence and antimicrobial resistance (AMR) genes pose serious public health risks as reservoirs of AMR and virulence. This study undertook whole genome characterization of commensal E. coli from food-producing animals in Uganda to investigate their genome variability (resistome and virulome). We established that the E. coli had high genomic diversity with 38 sequence types, 24 FimH types, and 33 O-antigen serotypes randomly distributed within three phylogroups (A, B1, and E). A greater proportion (≥93.65%) of the E. coli were resistant to amoxicillin/clavulanate and ampicillin antibiotics. The isolates were AmpC beta-lactamase producers dominated by blaEC-15 (71.88%) and tet(A) (20.31%) antimicrobial resistant genes besides a diverse armory of virulence-associated genes in the class of exotoxin, adhesins, iron uptake, and serine protease autotransporters which varied by host species. Cattle were found to be the major source of E. coli carrying Shiga toxin genes, whereas swine was the main source of E. coli carrying colicin-like Usp toxin gene. The study underscores the importance of livestock as the carrier of E. coli with antimicrobial resistance and a large repertoire of virulence traits with a potential of causing disease in animals and humans by acquiring more genetic traits.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- Gulu University Multifunctional Research Laboratories, Gulu P.O. Box 166, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Edison A. Mworozi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (G.W.); (S.A.); (B.E.); (H.K.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Nüesch-Inderbinen M, Biggel M, Haussmann A, Treier A, Heyvaert L, Cernela N, Stephan R. Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter. Front Microbiol 2023; 14:1150070. [PMID: 37389336 PMCID: PMC10301837 DOI: 10.3389/fmicb.2023.1150070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Background Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes. Objective This study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland. Methods A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). Results Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium. Conclusion Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.
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Affiliation(s)
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Adrian Haussmann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Lore Heyvaert
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, University of Ghent, Ghent, Belgium
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Duarte ASR, Marques AR, Andersen VD, Korsgaard HB, Mordhorst H, Møller FD, Petersen TN, Vigre H, Hald T, Aarestrup FM. Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018. Euro Surveill 2023; 28:2200678. [PMID: 37199989 PMCID: PMC10197494 DOI: 10.2807/1560-7917.es.2023.28.20.2200678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023] Open
Abstract
BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.
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Affiliation(s)
- Ana Sofia R Duarte
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Ana Rita Marques
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Vibe D Andersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Helle B Korsgaard
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Hanne Mordhorst
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frederik D Møller
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Thomas N Petersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Håkan Vigre
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Tine Hald
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
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Han N, Li J, Wan P, Pan Y, Xu T, Xiong W, Zeng Z. Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine. Antibiotics (Basel) 2023; 12:antibiotics12050825. [PMID: 37237728 DOI: 10.3390/antibiotics12050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020-2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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Moura P, Sandberg M, Høg BB, Niza-Ribeiro J, Nielsen EO, Alban L. Characterisation of antimicrobial usage in Danish pigs in 2020. Front Vet Sci 2023; 10:1155811. [PMID: 37180070 PMCID: PMC10167271 DOI: 10.3389/fvets.2023.1155811] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
Introduction Denmark is one of the world's largest exporters of pigs and pig meat, so the sector plays an important role in the national antimicrobial use (AMU). The Danish government has run antimicrobial stewardship programs in collaboration with the pig industry for more than 25 years. These have resulted in substantial overall reductions in total AMU and limiting the use of fluoroquinolones, the 3rd and 4th generation cephalosporines and the polymyxin colistin. To understand where further reductions in AMU could take place, it is necessary to investigate which antimicrobials are being used, how, and for which reasons. Materials and methods We characterized the AMU in the Danish pig sector in 2020, providing new analytical insights based on data retrieved from the VetStat database. The AMU data were segmented into classes, routes of administration, treatment indications and age groups, and interpreted as an outcome of the interventions taken. We evaluated the current AMU regarding choice of antimicrobial class. Moreover, we discussed how to further improve the antimicrobial stewardship in Danish pig production to achieve additional reductions without jeopardizing animal welfare. Where relevant, two pig veterinary specialists were consulted. Results In 2020, 43.3 mg antimicrobials per population correction unit (PCU) were ascribed to the Danish pig sector. There was practically no use of fluoroquinolones, 3rd and 4th generation cephalosporins and polymyxins. Weaners related to 45% of the total AMU in pigs when measured in tonnes and 81% when measured in defined animal daily doses, of these 76% were ascribed to gastrointestinal indications and overall, 83% were administered perorally. Conclusion To enable further reductions in AMU, it should be investigated how and when to replace group treatments (e.g., all animals in section or a pen) with individual treatments. Moreover, prevention of disease and promotion of animal health should be prioritized, e.g., through focus on feed, vaccination, biosecurity, and disease eradication.
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Affiliation(s)
- Pedro Moura
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Marianne Sandberg
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Birgitte Borck Høg
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - João Niza-Ribeiro
- Departamento de Estudo de Populações, ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal
| | | | - Lis Alban
- Department for Food Safety, Veterinary Issues and Risk Analysis, Danish Agriculture and Food Council, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Upadhyaya N, Karki S, Rana S, Elsohaby I, Tiwari R, Oli M, Paudel S. Trend of Antimicrobial Use in Food-Producing Animals from 2018 to 2020 in Nepal. Animals (Basel) 2023; 13:ani13081377. [PMID: 37106940 PMCID: PMC10135152 DOI: 10.3390/ani13081377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance is a global public health problem and is primarily driven by the widespread overuse of antibiotics. However, antimicrobial use data in animals are not readily available due to the absence of a national database in many developing countries, including Nepal. This study was conducted to estimate the quantities of antimicrobials available in Nepal as an indicator of their use in food-producing animals between 2018 and 2020. Data were collected through surveys targeting major stakeholders: (i) the Department of Drug Administration (DDA), the Government of Nepal (GoN) for the authorized antimicrobials for veterinary use in Nepal, (ii) veterinary pharmaceuticals for antimicrobials produced in Nepal, (iii) the DDA and Veterinary Importers Association for antimicrobials bought by veterinary drug importers, and (iv) the Department of Customs, GoN, for antibiotics sourced through customs. Data showed that in the 3 years, a total of 96 trade names, comprising 35 genera of antibiotics representing 10 classes, were either produced or imported in Nepal. In total, 91,088 kg, 47,694 kg, and 45,671 kg of active ingredients of antimicrobials were available in 2018, 2019, and 2020, respectively. None of the antibiotics were intended for growth promotion, but were primarily for therapeutic purposes. Oxytetracycline, tilmicosin, and sulfadimidine were among the most-used antibiotics in Nepal in 2020. Oxytetracycline was primarily intended for parenteral application, whereas tilmicosin was solely for oral use. Sulfadimidine was available for oral use, except for a small proportion for injection purposes. Aminoglycosides, fluroquinolones, nitrofurans, sulfonamides, and tetracyclines were mostly produced locally, whereas cephalosporins, macrolides and "other" classes of antimicrobials were imported. Amphenicols and penicillins were exclusively imported and nitrofurans were produced locally only. In general, except for tetracyclines, the volume of antimicrobials produced locally and/or imported in 2020 was lower than that in 2018, which corresponded to a decreasing trend in total antimicrobials available. Furthermore, the subsequent years have seen a decrease in the use of critically important antibiotics, particularly class I antibiotics. Finally, this study has firstly established a benchmark for future monitoring of antimicrobial usage in food-producing animals in Nepal. These data are useful for risk analysis, planning, interpreting resistance surveillance data, and evaluating the effectiveness of prudent use, efforts, and mitigation strategies.
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Affiliation(s)
- Nabin Upadhyaya
- Veterinary Standards and Drug Regulatory Laboratory, Budhanilakantha, Kathmandu 44600, Nepal
| | - Surendra Karki
- Food and Agriculture Organization of the United Nations, Emergency Center for Transboundary Animal Diseases, Lalitpur 44700, Nepal
| | - Sujan Rana
- Department of Livestock Services, Hariharbhawan, Lalitpur 44700, Nepal
| | - Ibrahim Elsohaby
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
- Centre for Applied One Health Research and Policy Advice (OHRP), City University of Hong Kong, Hong Kong SAR, China
| | - Ramanandan Tiwari
- Ministry of Agriculture and Livestock Development Nepal, Singhadurbar, Kathmandu 44600, Nepal
| | - Manoj Oli
- Tulsipur Municipality, Tulsipur, Dang 22412, Nepal
| | - Surya Paudel
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
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Zhang W, Wang J, Zhu L, Wang J, Mao S, Yan X, Wen S, Wang L, Dong Z, Kim YM. New insights into the effects of antibiotics and copper on microbial community diversity and carbon source utilization. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023:10.1007/s10653-023-01491-1. [PMID: 36939996 DOI: 10.1007/s10653-023-01491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Residual antibiotics (ABs) and heavy metals (HMs) are continuously released from soil, reflecting their intensive use and contamination of water and soil, posing an environmental problem of great concern. Relatively few studies exist of the functional diversity of soil microorganisms under the combined action of ABs and HMs. To address this deficiency, BIOLOG ECO microplates and the Integrated Biological Responses version 2 (IBRv2) method were used to comprehensively explore the effects of single and combined actions of copper (Cu) and enrofloxacin (ENR), oxytetracycline (OTC), and sulfadimidine (SM2) on the soil microbial community. The results showed that the high concentration (0.80 mmol/kg) compound group had a significant effect on average well color development (AWCD) and OTC showed a dose-response relationship. The results of IBRv2 analysis showed that the single treatment group of ENR or SM2 had a significant effect on soil microbial communities, and the IBRv2 of E1 was 5.432. Microbes under ENR, SM2, and Cu stress had more types of available carbon sources, and all treatment groups were significantly more enriched with microorganisms having D-mannitol and L-asparagine as carbon sources. This study confirms that the combined effects of ABs and HMs can inhibit or promote the function of soil microbial communities. In addition, this paper will provide new insights into IBRv2 as an effective method to evaluate the impacts of contaminants on soil health.
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Affiliation(s)
- Wenjie Zhang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jinhua Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China.
| | - Lusheng Zhu
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Jun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Shushuai Mao
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Xiaojing Yan
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Shengfang Wen
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Lanjun Wang
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Zikun Dong
- Key Laboratory of Agricultural Environment in Universities of Shandong, College of Resources and Environment, Shandong Agricultural University, 61 Daizong Road, Taian, 271018, People's Republic of China
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-Gu, Seoul, 04763, Republic of Korea
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Cabello FC, Millanao AR, Lozano-Muñoz I, Godfrey HP. Misunderstandings and misinterpretations: Antimicrobial use and resistance in salmon aquaculture. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36934450 DOI: 10.1111/1758-2229.13147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The exponential growth of aquaculture over the past 30 years has been accompanied by a parallel increase in the use of antimicrobials. This widespread use has had negative effects on animal, human and environmental health and affected the biodiversity of the environments where aquaculture takes place. Results showing these harmful effects have been resisted and made light of by the aquaculture industry and their scientific supporters through introduction of misunderstandings and misinterpretations of concepts developed in the evolution, genetics, and molecular epidemiology of antimicrobial resistance. We focus on a few of the most obvious scientific shortcomings and biases of two recent attempts to minimise the negative impacts of excessive antimicrobial use in Chilean salmon aquaculture on human and piscine health and on the environment. Such open debate is critical to timely implementation of effective regulation of antimicrobial usage in salmon aquaculture in Chile, if the negative local and worldwide impacts of this usage are to be avoided.
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Affiliation(s)
- Felipe C Cabello
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | - Ana R Millanao
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ivonne Lozano-Muñoz
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Henry P Godfrey
- Department of Pathology (retired), New York Medical College, Valhalla, New York, USA
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Bunduruș IA, Balta I, Ștef L, Ahmadi M, Peț I, McCleery D, Corcionivoschi N. Overview of Virulence and Antibiotic Resistance in Campylobacter spp. Livestock Isolates. Antibiotics (Basel) 2023; 12:antibiotics12020402. [PMID: 36830312 PMCID: PMC9952398 DOI: 10.3390/antibiotics12020402] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Campylobacter remains the most prevalent foodborne pathogen bacterium responsible for causing gastroenteritis worldwide. Specifically, this pathogen colonises a ubiquitous range of environments, from poultry, companion pets and livestock animals to humans. The bacterium is uniquely adaptable to various niches, leading to complicated gastroenteritis and, in some cases, difficult to treat due to elevated resistance to certain antibiotics. This increased resistance is currently detected via genomic, clinical or epidemiological studies, with the results highlighting worrying multi-drug resistant (MDR) profiles in many food and clinical isolates. The Campylobacter genome encodes a rich inventory of virulence factors offering the bacterium the ability to influence host immune defences, survive antimicrobials, form biofilms and ultimately boost its infection-inducing potential. The virulence traits responsible for inducing clinical signs are not sufficiently defined because several populations have ample virulence genes with physiological functions that reflect their pathogenicity differences as well as a complement of antimicrobial resistance (AMR) systems. Therefore, exhaustive knowledge of the virulence factors associated with Campylobacter is crucial for collecting molecular insights into the infectivity processes, which could pave the way for new therapeutical targets to combat and control the infection and mitigate the spread of MDR bacteria. This review provides an overview of the spread and prevalence of genetic determinants associated with virulence and antibiotic resistance from studies performed on livestock animals. In addition, we have investigated the relevant coincidental associations between the prevalence of the genes responsible for pathogenic virulence, horizontal gene transfer (HGT) and transmissibility of highly pathogenic Campylobacter strains.
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Affiliation(s)
- Iulia Adelina Bunduruș
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Igori Balta
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Lavinia Ștef
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Mirela Ahmadi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - Ioan Peț
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
| | - David McCleery
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
| | - Nicolae Corcionivoschi
- Faculty of Bioengineering of Animal Resources, University of Life Sciences King Mihai I from Timisoara, 300645 Timisoara, Romania
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK
- Correspondence: (D.M.); (N.C.)
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Nüesch-Inderbinen M, Heyvaert L, Treier A, Zurfluh K, Cernela N, Biggel M, Stephan R. High occurrence of Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae harbouring oxazolidinone resistance genes in raw meat-based diets for companion animals - a public health issue, Switzerland, September 2018 to May 2020. Euro Surveill 2023; 28:2200496. [PMID: 36757316 PMCID: PMC9912375 DOI: 10.2807/1560-7917.es.2023.28.6.2200496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and meat thereof, but few studies have analysed their occurrence in raw meat-based diets (RMBDs) for pets.AimWe aimed to examine how far RMBDs may represent a source of bacteria with oxazolidinone resistance genes.MethodsFifty-nine samples of different types of RMBDs from 10 suppliers (three based in Germany, seven in Switzerland) were screened for florfenicol-resistant Gram-positive bacteria using a selective culture medium. Isolates were phenotypically and genotypically characterised.ResultsA total of 27 Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae isolates were obtained from 24 of the 59 samples. The optrA, poxtA, and cfr genes were identified in 24/27, 6/27 and 5/27 isolates, respectively. Chloramphenicol and linezolid minimum inhibitory concentrations (MICs) ranged from 24.0 mg/L-256.0 mg/L, and 1.5 mg/L-8.0 mg/L, respectively. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoints, 26 of 27 isolates were resistant to chloramphenicol (MICs ≥ 32 mg/L), and two were resistant to linezolid (MICs ≥ 8 mg/L). Multilocus sequence typing analysis of the 17 E. faecalis isolates identified 10 different sequence types (ST)s, with ST593 (n = 4 isolates) and ST207 (n = 2 isolates) occurring more than once, and two novel STs (n = 2 isolates). E. faecium isolates belonged to four different STs (168, 264, 822, and 1846).ConclusionThe high occurrence in our sample of Gram-positive bacteria harbouring genes encoding resistance to the critical antimicrobial linezolid is of concern since such bacteria may spread from companion animals to humans upon close contact between pets and their owners.
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Affiliation(s)
| | - Lore Heyvaert
- Department Veterinary and Biosciences, Faculty Veterinary Medicine, University of Ghent, Ghent, Belgium
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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40
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Mulchandani R, Wang Y, Gilbert M, Van Boeckel TP. Global trends in antimicrobial use in food-producing animals: 2020 to 2030. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001305. [PMID: 36963007 PMCID: PMC10021213 DOI: 10.1371/journal.pgph.0001305] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/02/2022] [Indexed: 02/04/2023]
Abstract
Use of antimicrobials in farming has enabled the growth of intensive animal production and helped in meeting the global increase in demand for animal protein. However, the widespread use of veterinary antimicrobials drives antimicrobial resistance, with important consequences for animal health, and potentially human health. Global monitoring of antimicrobial use is essential: first, to track progress in reducing the reliance of farming on antimicrobials. Second, to identify countries where antimicrobial-stewardship efforts should be targeted to curb antimicrobial resistance. Data on usage of antimicrobials in food animals were collected from 42 countries. Multivariate regression models were used in combination with projections of animal counts for cattle, sheep, chicken, and pigs from the Food and Agriculture Organization to estimate global antimicrobial usage of veterinary antimicrobials in 2020 and 2030. Maps of animal densities were used to identify geographic hotspots of antimicrobial use. In each country, estimates of antimicrobial use (tonnes) were calibrated to match continental-level reports of antimicrobial use intensity (milligrams per kilogram of animal) from the World Organization for Animal Health, as well as country-level reports of antimicrobial use from countries that made this information publicly available. Globally, antimicrobial usage was estimated at 99,502 tonnes (95% CI 68,535-198,052) in 2020 and is projected, based on current trends, to increase by 8.0% to 107,472 tonnes (95% CI: 75,927-202,661) by 2030. Hotspots of antimicrobial use were overwhelmingly in Asia (67%), while <1% were in Africa. Findings indicate higher global antimicrobial usage in 2030 compared to prior projections that used data from 2017; this is likely associated with an upward revision of antimicrobial use in Asia/Oceania (~6,000 tonnes) and the Americas (~4,000 tonnes). National-level reporting of antimicrobial use should be encouraged to better evaluate the impact of national policies on antimicrobial use levels.
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Affiliation(s)
| | - Yu Wang
- Health Geography and Policy Group, ETH Zürich, Zurich, Switzerland
| | - Marius Gilbert
- Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium
- Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Thomas P. Van Boeckel
- Health Geography and Policy Group, ETH Zürich, Zurich, Switzerland
- Center for Diseases Dynamics, Economics, and Policy, New Delhi, India
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The Marginal Abatement Cost of Antimicrobials for Dairy Cow Mastitis: A Bioeconomic Optimization Perspective. Vet Sci 2023; 10:vetsci10020092. [PMID: 36851396 PMCID: PMC9962292 DOI: 10.3390/vetsci10020092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Maintaining udder health is the primary indication for antimicrobial use (AMU) in dairy production, and modulating this application is a key factor in decreasing AMU. Defining the optimal AMU and the associated practical rules is challenging since AMU interacts with many parameters. To define the trade-offs between decreased AMU, labor and economic performance, the bioeconomic stochastic simulation model DairyHealthSim (DHS)© was applied to dairy cow mastitis management and coupled to a mean variance optimization model and marginal abatement cost curve (MACC) analysis. The scenarios included three antimicrobial (AM) treatment strategies at dry-off, five types of general barn hygiene practices, five milking practices focused on parlor hygiene levels and three milk withdrawal strategies. The first part of economic results showed similar economic performances for the blanked dry-off strategy and selective strategy but demonstrated the trade-off between AMU reduction and farmers' workload. The second part of the results demonstrated the optimal value of the animal level of exposure to AM (ALEA). The MACC analysis showed that reducing ALEA below 1.5 was associated with a EUR 10,000 loss per unit of ALEA on average for the farmer. The results call for more integrative farm decision processes and bioeconomic reasoning to prompt efficient public interventions.
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Bahaddad SA, Almalki MHK, Alghamdi OA, Sohrab SS, Yasir M, Azhar EI, Chouayekh H. Bacillus Species as Direct-Fed Microbial Antibiotic Alternatives for Monogastric Production. Probiotics Antimicrob Proteins 2023; 15:1-16. [PMID: 35092567 PMCID: PMC8799964 DOI: 10.1007/s12602-022-09909-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2022] [Indexed: 01/18/2023]
Abstract
Antibiotic growth promoters have been utilized for long time at subtherapeutic levels as feed supplements in monogastric animal rations. Because of their side-effects such as antibiotic resistance, reduction of beneficial bacteria in the gut, and dysbiosis, it is necessary to look for non-therapeutic alternatives. Probiotics play an important role as the key substitutes to antibacterial agents due to their many beneficial effects on the monogastric animal host. For instance, enhancement of the gut microbiota balance can contribute to improvement of feed utilization efficiency, nutrients absorption, growth rate, and economic profitability of livestock. Probiotics are defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host." They are available in diverse forms for use as feed supplements. Their utilization as feed additives assists in good digestion of feed ingredients and hence, making the nutrients available for promoting growth. Immunity can also be enhanced by supplementing probiotics to monogastrics diets. Moreover, probiotics can help in improving major meat quality traits and countering a variety of monogastric animals infectious diseases. A proper selection of the probiotic strains is required in order to confer optimal beneficial effects. The present review focuses on the general functional, safety, and technological screening criteria for selection of ideal Bacillus probiotics as feed supplements as well as their mechanism of action and beneficial effects on monogastric animals for improving production performance and health status.
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Affiliation(s)
- Shifa A Bahaddad
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Meshal H K Almalki
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Sayed S Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Hichem Chouayekh
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia.
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Cao H, Bougouffa S, Park TJ, Lau A, Tong MK, Chow KH, Ho PL. Sharing of Antimicrobial Resistance Genes between Humans and Food Animals. mSystems 2022; 7:e0077522. [PMID: 36218363 PMCID: PMC9765467 DOI: 10.1128/msystems.00775-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 12/25/2022] Open
Abstract
The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread. IMPORTANCE Antimicrobial resistance (AMR) has proven to be a global public health concern. To conquer this increasingly worrying trend, an overarching, One Health approach has been used that brings together different sectors, but the fundamental knowledge of the relationship between humans, food animals, and their environments is not mature yet or is lacking in some aspect. With swine and chicken as examples of food animals, a large global data set of over 1,000 human and food animal gut metagenomes was analyzed with a focus on acquired antibiotic resistance genes (ARGs) associated with mobile genetic elements (MGEs) to answer this question. Outputs from this work open a new avenue to further our understanding of ARG transferability in food animals. It is a necessary milestone to better equip governmental agencies to monitor and pre-empt antibiotic resistance hot spots. This work will assist and give guidance on how to decipher other links within any One Health initiatives with expected positive feedback to human health.
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Affiliation(s)
- Huiluo Cao
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, People’s Republic of China
| | - Salim Bougouffa
- Computational Bioscience Research Center and Bioscience Core Lab, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tae-Jin Park
- HME Healthcare Co., Ltd., Suwon-si, Gyeonggi-do, Republic of Korea
| | - Andes Lau
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, People’s Republic of China
| | - Man-Ki Tong
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, People’s Republic of China
| | - Kin-Hung Chow
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, People’s Republic of China
| | - Pak-Leung Ho
- Carol Yu Center for Infection and Department of Microbiology, University of Hong Kong, Hong Kong, People’s Republic of China
- Department of Microbiology, Queen Mary Hospital, Hong Kong, People’s Republic of China
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Günther T, Kramer-Schadt S, Fuhrmann M, Belik V. Environmental factors associated with the prevalence of ESBL/AmpC-producing Escherichia coli in wild boar (Sus scrofa). Front Vet Sci 2022; 9:980554. [PMID: 36311652 PMCID: PMC9608181 DOI: 10.3389/fvets.2022.980554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/26/2022] [Indexed: 11/04/2022] Open
Abstract
Antimicrobial resistances (AMR) in bacteria, such as ESBL/AmpC-producing E. coli, are a burden to human and animal health. This burden is mainly driven by the consumption and release of antimicrobial substances into the environment. The pollution and contamination of habitats by AMR in bacteria and antimicrobial substances can lead to the transmission of bacterial AMR to wildlife. Therefore, it is necessary to understand the transmission cycle of antibiotics and resistant bacteria between humans, and animals as well as their occurrences in the environment. Environmental factors associated with the occurrence of bacterial AMR in wildlife can lead to a better understanding of the distribution of bacterial AMR in humans and animals using One Health approaches. Here, we analyzed data gathered in the framework of the German zoonoses monitoring program in 2016 and 2020 using spatiotemporal statistics to identify relevant environmental factors (e.g., livestock density, climatic variables, and human density) in association with the spatial distribution of ESBL/AmpC-producing E. coli. For this purpose, we developed a generic data integration and analysis pipeline to link spatially explicit environmental factors to the monitoring data. Finally, we built a binomial generalized linear mixed model (GLMM) to determine the factors associated with the spatial distribution of ESBL/AmpC-producing E. coli. In 2016 and 2020, 807 fecal samples from hunted wild boar (Sus scrofa L.) were randomly taken in 13 federal states and selectively analyzed for ESBL/AmpC-producing E. coli. Forty-eight isolates were identified in 12 German federal states, with an overall prevalence of 6%. We observed an almost three times higher probability of ESBL/AmpC-producing E. coli isolates in wild boar in counties with high cattle densities (OR = 2.57, p ≤ 0.01). Furthermore, we identified a seasonal effect in areas with high precipitation during the off-hunting seasons (OR = 2.78, p = 0.025) and low precipitation throughout the years (OR = 0.42, p = 0.025). However, due to the low amount of identified isolates, confidence intervals were wide, indicating a high level of uncertainty. This suggests that further studies on smaller scales need to be conducted with multiannual data and improved metadata, e.g., on the location, the hunting procedure, and species characteristics to be collected during field sampling.
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Affiliation(s)
- Taras Günther
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany,System Modeling Group, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany,*Correspondence: Taras Günther
| | - Stephanie Kramer-Schadt
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany,Institute of Ecology, Technical University of Berlin, Berlin, Germany
| | - Marcel Fuhrmann
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vitaly Belik
- System Modeling Group, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
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Ding Q, Gao J, Ding X, Huang D, Zhao Y, Yang M. Consumers' knowledge, attitude, and behavior towards antimicrobial resistance and antimicrobial use in food production in China. Front Public Health 2022; 10:1015950. [PMID: 36211698 PMCID: PMC9540231 DOI: 10.3389/fpubh.2022.1015950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/31/2022] [Indexed: 01/27/2023] Open
Abstract
Background Antimicrobial resistance (AMR) can be induced by overuse or misuse of antimicrobials. Few researches were involved in consumers' knowledge and attitude toward antimicrobial use (AMU) in food production. This study was designed to investigate the knowledge and awareness, perception, and attitude of Chinese consumers toward AMU in food production. Their behavior, purchase intention of antimicrobial-free food products, and confidence in information sources were also investigated. Methods As a descriptive cross-sectional study, an online electronic survey questionnaire was conducted between February 25 and March 8, 2022, involving 1,065 consumers in China. Factor analysis was conducted to identify underlying patterns of the attitudes and information sources. Spearman correlations were employed to determine the relationship between knowledge, attitudes and the intention to pay extra. The differences in knowledge and attitudes were performed by independent t-test and one-way analysis of variance (ANOVA) test, and the difference in intention was performed by Chi-square test, when compared with demographic factors. Results The findings showed that even though 75.0% of them heard of AMR, and 48.2% knew the definition of AMR, the level of consumers' knowledge of AMU in farming production and food regulations in China was not high (48.9% of participants replied correctly). About half viewed AMU and AMR as a potential risk to their health. Of these participants, 61.3% claimed that they were more likely looking for specific information about AMU on food packaging, and 58.3% changed their eating or cooking habits due to the concern. In addition, 79.8% were willing to pay extra for antimicrobial-free food products. Information sources from professionals and authorities were considered more accurate than those from media, the internet, word of mouth, and others. Conclusions Chinese consumers had insufficient knowledge and neutral attitudes about AMU in farming production and food regulations in China. A large proportion of the participants were willing to purchase antimicrobial-free food products. Most of them obtained related information from the media. This study highlighted the importance of updated education and effective communication with consumers in China. It helps to develop the reliable foodborne AMR surveillance system along food chain and improve government communication and consumer awareness.
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Affiliation(s)
- Qianyun Ding
- Department of 'A', The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jiuzhi Gao
- National Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Dan Huang
- Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, China,Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunfeng Zhao
- Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, China,Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Yunfeng Zhao
| | - Min Yang
- Center of Clinical Big Data and Analytics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China,Department of Nutrition and Food Hygiene, School of Public Health, Zhejiang University School of Medicine, Hangzhou, China,*Correspondence: Min Yang
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Comparison of Antimicrobial Resistances in Escherichia coli from Conventionally and Organic Farmed Poultry from Germany. Antibiotics (Basel) 2022; 11:antibiotics11101282. [PMID: 36289940 PMCID: PMC9598375 DOI: 10.3390/antibiotics11101282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, resistance rates in Escherichia coli from organic and conventional poultry in Germany were compared. Isolates were randomly collected from organic and conventional broiler and turkey flocks at the farm and from turkey meat at retail. Resistance testing was performed as prescribed by Commission implementing decision 2013/652/EU. Logistic regression analyses were performed for the resistance to the different antimicrobials. Overall, resistance rates for the antimicrobials tested were lower in E. coli from organic than from conventionally raised animals. In turkeys, the percentage of isolates susceptible to all antimicrobials tested from animals and meat was twice as high from organic than from conventional origin (~50% vs. <25%). In broilers, the percentage of susceptible isolates from organic farms was five times higher than from conventional farms (70.1% vs. 13.3%) and resistance to three or more classes of antimicrobials was 1.7- to 5.0-fold more common in isolates from conventional farms. The differences between organic and conventional farming were more pronounced in broilers than in turkeys. More studies on turkeys are needed to determine whether this difference is confirmed.
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47
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Selected Antimicrobial Peptides Inhibit In Vitro Growth of Campylobacter spp. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Campylobacter is a major cause of acute human diarrheal illness. Broiler chickens constitute a primary reservoir for C. jejuni leading to human infection. Consequently, there is a need for developing novel intervention methods. Antimicrobial peptides (AMP) are small proteins which have evolved in most lifeforms to provide defense against microbial infections. To date, over 3000 AMP have been discovered; however, few of them have been analyzed specifically for ability to kill campylobacters. We selected and evaluated a set of 11 unique chemically synthesized AMP for ability to inhibit growth of C. jejuni. Six of the AMP we tested produced zones of inhibition on lawns of C. jejuni. These AMP included: NRC-13, RL-37, Temporin L, Cecropin–Magainin, Dermaseptin, and C12K-2β12. In addition, MIC were determined for Cecropin–Magainin, RL-37 and C12K-2β12 against 15 isolates of Campylobacter representing the three most common pathogenic strains. MIC for campylobacters were approximately 3.1 µg/mL for AMP RL-37 and C12K-2β12. MIC were slightly higher for the Cecropin–Magainin AMP in the range of 12.5 to 100 µg/mL. These AMP are attractive subjects for future study and potential in vivo delivery to poultry to reduce Campylobacter spp. populations.
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Lv C, Shang J, Zhang W, Sun B, Li M, Guo C, Zhou N, Guo X, Huang S, Zhu Y. Dynamic antimicrobial resistant patterns of Escherichia coli from healthy poultry and swine over 10 years in Chongming Island, Shanghai. Infect Dis Poverty 2022; 11:98. [PMID: 36114584 PMCID: PMC9482194 DOI: 10.1186/s40249-022-01025-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is one of the greatest threats to animal and public health. Here, we conducted a dynamic surveillance of Escherichia coli on Chongming Island in Shanghai during 2009-2021 to identify the characteristics and trends of Chongming's AMR pandemic. METHODS Rectal (cloaca) swabs from four poultry and nine swine farms (Chongming Island, 2009-2021) were collected for E. coli strains acquisition. The micro-broth dilution method was used to test antimicrobial susceptibility of E. coli isolates against 10 antimicrobial classes including 15 antimicrobials. Utilizing generalized linear mixed models (GLMMs) and co-occurrence analyses, we further explored the multiple-drug-resistance (MDR) combinations and dynamic patterns of E. coli over 10 years in two food animals. RESULTS Total of 863 MDR isolates were found among 945 collected E. coli isolates, 337 from poultry and 608 from swine. Both isolates exhibited high resistant rates (> 70%) to tetracyclines, phenicols, sulfonamides, penicillins, and aminoglycosides (only in swine). The resistant rates of swine isolates to penicillins, aminoglycosides, tetracyclines, phenicols, and polymyxins were significantly higher than those of poultry isolates, whereas resistance to fluoroquinolones was reversed. Resistance to polymyxins decreased similarly in swine (42.4% in 2009 to 0.0% in 2021) and poultry isolates (from 16.5% to 0.0%). However, resistance to other seven antimicrobial classes (excluding carbapenems and penicillins) declined dramatically in swine isolates, particularly fluoroquinolones (from 80.5% to 14.4%), and tendencies of resistance to the seven classes showed markedly divergent patterns in poultry isolates. Using Poisson GLMMs, the AMR carriage since 2016 was significantly lower than that of 2009 (odds ratio < 1), indicating a decline in the risk of MDR emergence. Furthermore, despite the highly diverse MDR profiles, co-occurrence analysis identified two prominent MDR clusters of penicillins-phenicols-fluoroquinolones in poultry and aminoglycosides-tetracyclines-sulfonamides-phenicols in swine. CONCLUSIONS Our study uncovered vastly distinct AMR patterns and dynamic tendencies of poultry and swine E. coli isolates from Chongming. Meanwhile, Chongming's AMR status has ameliorated, as indicated by the decline in antimicrobials prevalence (particularly in swine), lower likelihood of MDR emergence and low carbapenem-, cephalosporin-, and polymyxin resistance. Importantly, this surveillance results are the vital basis for future policy development in Chongming and Shanghai.
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Affiliation(s)
- Chao Lv
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Jun Shang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai, 201103, China
| | - Wengang Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai, 201103, China
| | - Bingqing Sun
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai, 201103, China
| | - Min Li
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Chaoyi Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Nan Zhou
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
| | - Shixin Huang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai, 201103, China.
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
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Marutescu LG, Jaga M, Postolache C, Barbuceanu F, Milita NM, Romascu LM, Schmitt H, de Roda Husman AM, Sefeedpari P, Glaeser S, Kämpfer P, Boerlin P, Topp E, Gradisteanu Pircalabioru G, Chifiriuc MC, Popa M. Insights into the impact of manure on the environmental antibiotic residues and resistance pool. Front Microbiol 2022; 13:965132. [PMID: 36187968 PMCID: PMC9522911 DOI: 10.3389/fmicb.2022.965132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
The intensive use of antibiotics in the veterinary sector, linked to the application of manure-derived amendments in agriculture, translates into increased environmental levels of chemical residues, AR bacteria (ARB) and antibiotic resistance genes (ARG). The aim of this review was to evaluate the current evidence regarding the impact of animal farming and manure application on the antibiotic resistance pool in the environment. Several studies reported correlations between the prevalence of clinically relevant ARB and the amount and classes of antibiotics used in animal farming (high resistance rates being reported for medically important antibiotics such as penicillins, tetracyclines, sulfonamides and fluoroquinolones). However, the results are difficult to compare, due to the diversity of the used antimicrobials quantification techniques and to the different amounts and types of antibiotics, exhibiting various degradation times, given in animal feed in different countries. The soils fertilized with manure-derived products harbor a higher and chronic abundance of ARB, multiple ARG and an enriched associated mobilome, which is also sometimes seen in the crops grown on the amended soils. Different manure processing techniques have various efficiencies in the removal of antibiotic residues, ARB and ARGs, but there is only a small amount of data from commercial farms. The efficiency of sludge anaerobic digestion appears to be dependent on the microbial communities composition, the ARB/ARG and operating temperature (mesophilic vs. thermophilic conditions). Composting seems to reduce or eliminate most of antibiotics residues, enteric bacteria, ARB and different representative ARG in manure more rapidly and effectively than lagoon storage. Our review highlights that despite the body of research accumulated in the last years, there are still important knowledge gaps regarding the contribution of manure to the AMR emergence, accumulation, spread and risk of human exposure in countries with high clinical resistance rates. Land microbiome before and after manure application, efficiency of different manure treatment techniques in decreasing the AMR levels in the natural environments and along the food chain must be investigated in depth, covering different geographical regions and countries and using harmonized methodologies. The support of stakeholders is required for the development of specific best practices for prudent – cautious use of antibiotics on farm animals. The use of human reserve antibiotics in veterinary medicine and of unprescribed animal antimicrobials should be stopped and the use of antibiotics on farms must be limited. This integrated approach is needed to determine the optimal conditions for the removal of antibiotic residues, ARB and ARG, to formulate specific recommendations for livestock manure treatment, storage and handling procedures and to translate them into practical on-farm management decisions, to ultimately prevent exposure of human population.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
| | - Mihaela Jaga
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | | | - Florica Barbuceanu
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Nicoleta Manuela Milita
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Luminita Maria Romascu
- Research Institute of University of Bucharest, Bucharest, Romania
- The Institute for Diagnostic and Animal Health (IDSA), Bucharest, Romania
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Heike Schmitt
- National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | | | - Stefanie Glaeser
- Institute for Applied Microbiology Heinrich-Buff-Ring, Justus-Liebig University, Gießen, Germany
| | - Peter Kämpfer
- Institute for Applied Microbiology Heinrich-Buff-Ring, Justus-Liebig University, Gießen, Germany
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Department of Biology, Agriculture and Agri-Food Canada, University of Western Ontario, London, ON, Canada
| | - Gratiela Gradisteanu Pircalabioru
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- *Correspondence: Gratiela Gradisteanu Pircalabioru,
| | - Mariana Carmen Chifiriuc
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- The Romanian Academy, Bucharest, Romania
- Mariana Carmen Chifiriuc,
| | - Marcela Popa
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest, Bucharest, Romania
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Assessing the role of internet in reducing overuse of livestock antibiotics by utilizing combination of novel damage control and 2-SLS approaches: Risk, responsibility, and action. Prev Vet Med 2022; 208:105754. [PMID: 36099702 DOI: 10.1016/j.prevetmed.2022.105754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022]
Abstract
Reducing farmers' overuse of livestock antibiotics is very essential to ensure food, environment, and public health safety. Currently, the "internet + " has emerged as a new initiative to stimulate the development of rural industries by alleviating farmers' information constraints, lack of skills, and knowledge deficiencies. However, very few studies have focused on this issue, and studies specifically focused on the role of the Internet in reducing the overuse of livestock antibiotics are still very limited. To fill this existing research gap, this study aims to investigate the role of the Internet in reducing the overuse of livestock antibiotics using data of 426 farmers based in three provinces, including the Hebei, Henan, and Hubei provinces of China. To analyze the collected data, we first employ a damage control model to estimate the marginal productivity of farmer use of livestock antibiotics and then use a two-stage least squares (2SLS) approach to assess the role of the Internet in reducing antibiotic overuse. The findings of our study show that the marginal productivity of farmers' use of livestock antibiotics by farmers is 0.0079 (approaching 0), indicating that the overuse of antibiotics has become the realistic response of farmers. Our results further reveal that the Internet has a significant inhibitory effect on the overuse of livestock antibiotics by farmers. The Internet can reduce the use of antibiotics by 1.3147 yuan/head by improving your knowledge and skills about antibiotics. The further findings of our study reveal that the educational level and organizational participation of farmers are also important driving factors to reduce the overuse of livestock antibiotics. Furthermore, the findings of this study validate the role of gender, age, and educational level in the non-linear effect of the Internet on farmers' overuse of antibiotics. In conclusion, the findings of this study provide insight for policy makers in motivating farmers to reduce antibiotic overuse by strengthening rural internet infrastructure, implementing skill training, improving supervision, and establishing an incentive mechanism for the standard use of antibiotics.
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