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Mikulski D, Juśkiewicz J, Ognik K, Fotschki B, Tykałowski B, Jankowski J. Gastrointestinal response to the early administration of antimicrobial agents in growing turkeys infected with Escherichia coli. Poult Sci 2024; 103:103720. [PMID: 38652949 PMCID: PMC11063517 DOI: 10.1016/j.psj.2024.103720] [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: 12/05/2023] [Revised: 03/13/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
This study investigated the effects of the early administration of enrofloxacin (E) or doxycycline (D) for the first 5 consecutive days of life, or the continuous administration of the coccidiostat monensin (M) throughout the rearing period on gastrointestinal function in turkeys infected with avian pathogenic Escherichia coli (APEC) in an early or later stage of rearing. Experiment 1 lasted 21 d, and turkeys in groups E, D, and M were infected with APEC on d 15. Experiment 2 lasted 56 d, and it had a factorial arrangement of treatments where birds in groups E, D, and M were infected with APEC on d 15 or d 50. In both experiments, control groups (C) consisted of infected and uninfected birds without antibiotic or coccidiostat administration. On d 21 (Experiment 1) and d 56 (Experiment 2), 8 birds from each subgroup were killed, and the ileal and cecal digesta were sampled to analyze the activity of bacterial enzymes and the concentrations of short-chain fatty acids (SCFA). The experimental treatments did not affect the final body weight or body weight gain of birds. Both experiments demonstrated that APEC contributed to an increase in ammonia levels of the cecal digesta (means from 2 experiments: 0.311 vs. 0.225 mg/g in uninfected birds) and ileal pH (6.79 vs. 6.00) and viscosity (2.43 vs. 1.83 mPa⋅s). Moreover, the E. coli challenge enhanced the extracellular activity of several cecal bacterial enzymes, especially in older turkeys infected with APEC in a later stage of life. The continuous administration of monensin throughout the rearing period resulted in a weaker gastrointestinal response in older birds, compared with the other 2 antibiotics administered for the first 5 d of life. The results of the study are inconclusive as both desirable and undesirable effects of preventive early short-term antibiotic therapy were observed in turkeys, including normalization of ileal viscosity and cecal ammonia concentration (positive effect), and disruption in cecal SCFA production (negative effect).
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Affiliation(s)
- Dariusz Mikulski
- Department of Poultry Science and Apiculture, University of Warmia and Mazury in Olsztyn, Olsztyn 10-719, Poland
| | - Jerzy Juśkiewicz
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-748 Olsztyn, Poland.
| | - Katarzyna Ognik
- Department of Biochemistry and Toxicology, University of Life Sciences, Lublin 20-950, Poland
| | - Bartosz Fotschki
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, 10-748 Olsztyn, Poland
| | - Bartłomiej Tykałowski
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn 10-719, Poland
| | - Jan Jankowski
- Department of Poultry Science and Apiculture, University of Warmia and Mazury in Olsztyn, Olsztyn 10-719, Poland
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Zicarelli F, Iommelli P, Musco N, Wanapat M, Lotito D, Lombardi P, Infascelli F, Tudisco R. Growth Performance of Buffalo Calves in Response to Different Diets with and without Saccharomyces cerevisiae Supplementation. Animals (Basel) 2024; 14:1245. [PMID: 38672393 PMCID: PMC11047708 DOI: 10.3390/ani14081245] [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: 03/11/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of the present trial was to evaluate the growth performance of buffalo calves fed on diets characterized by different forage/concentrate ratios, with or without Saccharomyces cerevisiae supplementation (CBS 493.94, Yea-Sacc®). Twenty-four male buffalo calves (mean age of 145.1 ± 16.1 days; mean weight of 108.0 ± 18.7 kg) were assigned randomly to 4 groups, homogeneous in age, that were fed four different diets: diet 1, F:C ratio 50:50; diet 2, F:C ratio 30:70; diet 3, F:C ratio 50:50 + Yea-Sacc®; and diet 4, F:C ratio 30:70 + Yea-Sacc®. Buffalo calves were individually weighted before the start of the experiment and the data were used as a covariate, being taken monthly until the end of the trial. Dry matter intake (DMI), daily weight gain (DWG) and feed conversion ratio (FCR) were calculated. The differences in diets composition significantly (p < 0.01) affected all these parameters. In particular, the animals fed diet 1 and diet 3 showed higher values of DWG (0.91 and 0.88 g/d vs. 0.68 and 0.66 for group 2 and 4) and DMI (5.8 and 5.3 kg/d, respectively) compared to the other groups (4.3 and 4.4 kg/d for group 2 and 4), as well as a higher final body weight (370.5 and 334.1 kg for group 1 and 3 vs. 272.8 and 273.1 kg of group 2 and 4, respectively). Indeed, the supplementation with Yea-Sacc® at the dosage of 1 × 10E8 did not affect buffaloes' growth performance.
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Affiliation(s)
- Fabio Zicarelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Piera Iommelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Nadia Musco
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Daria Lotito
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Pietro Lombardi
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Federico Infascelli
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
| | - Raffaella Tudisco
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy; (F.Z.); (P.I.); (D.L.); (P.L.); (F.I.); (R.T.)
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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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Silva A, Silva V, Dapkevicius MDLE, Azevedo M, Cordeiro R, Pereira JE, Valentão P, Falco V, Igrejas G, Caniça M, Poeta P. Unveiling Antibiotic Resistance, Clonal Diversity, and Biofilm Formation in E. coli Isolated from Healthy Swine in Portugal. Pathogens 2024; 13:305. [PMID: 38668260 PMCID: PMC11054063 DOI: 10.3390/pathogens13040305] [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: 02/26/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
Escherichia coli, a commensal microorganism found in the gastrointestinal tract of human and animal hosts, plays a central role in agriculture and public health. Global demand for animal products has promoted increased pig farming, leading to growing concerns about the prevalence of antibiotic-resistant E. coli strains in swine populations. It should be noted that a significant portion of antibiotics deployed in swine management belong to the critically important antibiotics (CIA) class, which should be reserved for human therapeutic applications. This study aimed to characterize the prevalence of antibiotic resistance, genetic diversity, virulence characteristics, and biofilm formation of E. coli strains in healthy pigs from various farms across central Portugal. Our study revealed high levels of antibiotic resistance, with resistance to tetracycline, ampicillin, tobramycin, and trimethoprim-sulfamethoxazole. Multidrug resistance is widespread, with some strains resistant to seven different antibiotics. The ampC gene, responsible for broad-spectrum resistance to cephalosporins and ampicillin, was widespread, as were genes associated with resistance to sulfonamide and beta-lactam antibiotics. The presence of high-risk clones, such as ST10, ST101, and ST48, are a concern due to their increased virulence and multidrug resistance profiles. Regarding biofilm formation, it was observed that biofilm-forming capacity varied significantly across different compartments within pig farming environments. In conclusion, our study highlights the urgent need for surveillance and implementation of antibiotic management measures in the swine sector. These measures are essential to protect public health, ensure animal welfare, and support the swine industry in the face of the growing global demand for animal products.
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Affiliation(s)
- Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Maria de Lurdes Enes Dapkevicius
- IITAA—Institute of Agricultural and Environmental Research and Technology, University of the Azores (UAc), 9700-042 Angra do Heroísmo, Portugal
| | - Mónica Azevedo
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4049-021 Porto, Portugal; (M.A.)
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Rui Cordeiro
- Intergados, SA, Av. de Olivença, S/N, 2870-108 Montijo, Portugal;
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Patrícia Valentão
- Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Universidade do Porto, 2829-516 Caparica, Portugal; (P.V.)
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Virgílio Falco
- Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Universidade do Porto, 2829-516 Caparica, Portugal; (P.V.)
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Universidade of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Manuela Caniça
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4049-021 Porto, Portugal; (M.A.)
- CIISA—Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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Hassan IZ, Qekwana DN, Naidoo V. Prevalence of colistin resistance and antibacterial resistance in commensal Escherichia coli from chickens: An assessment of the impact of regulatory intervention in South Africa. Vet Med Sci 2024; 10:e1315. [PMID: 37929776 PMCID: PMC10766030 DOI: 10.1002/vms3.1315] [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: 07/22/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a global health problem largely due to the overuse of antimicrobials. In recognition of this, the World Health Assembly in 2015 agreed on a global action plan to tackle AMR. Following the global emergence of the mcr-1-associated colistin resistance gene in the livestock industry in 2016, several countries including South Africa restricted the veterinary use of colistin as the gene threatens the clinical utility of the drug. This study is a follow-up to the restriction in place in order to evaluate the impact of such policy adoption. OBJECTIVE To assess the prevalence of antibacterial resistance (ABR), and the mcr-1 colistin resistance gene in broiler chicken over a 2-year period, as a follow-up to the veterinary ban on colistin use in South Africa. METHODS A total of 520 swab samples were obtained during 2019 (March-April) and 2020 (February-March), from healthy broiler chicken carcasses (n = 20) and chicken droppings in transport crates (n = 20) at various poultry abattoirs (N = 7) in the Gauteng province of South Africa. Escherichia coli organisms were isolated and subjected to a panel of 24 antibacterials using the MicroScan machine. Screening for mcr-1 colistin resistance gene was undertaken using PCR. RESULT Four hundred and thirty-eight (438) E. coli strains were recovered and none demonstrated phenotypic resistance towards colistin, amikacin, carbapenems, tigecycline and piperacillin/tazobactam. The mcr-1 gene was not detected in any of the isolates tested. Resistances to the aminoglycosides (0%-9.8%) and fluoroquinolones (0%-18.9%) were generally low. Resistances to ampicillin (32%-39.3%) and trimethoprim/sulphamethoxazole (30.6%-3.6%) were fairly high. A significant (p < 0.05) increase in cephalosporins and cephamycin resistance was noted in the year 2020 (February-March) when compared with the year 2019 (March-April). CONCLUSION The absence of mcr-1 gene and colistin resistance suggests that mitigation strategies adopted were effective and clearly demonstrated the significance of regulatory interventions in reducing resistance to critical drugs. Despite the drawback in regulatory framework such as free farmers access to antimicrobials OTC and a dual registration system in place, there is a general decline in the prevalence of ABR when the present data are compared with the last national veterinary surveillance on AMR (SANVAD 2007). To further drive resistance down, mitigation strategies should focus on strengthening regulatory framework, the withdrawal of OTC dispensing of antimicrobials, capping volumes of antimicrobials, banning growth promoters and investing on routine surveillance/monitoring of AMR and antimicrobial consumption.
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Affiliation(s)
- Ibrahim Z. Hassan
- Department of Paraclinical SciencesFaculty of Veterinary ScienceUniversity of PretoriaPretoriaSouth Africa
- Present address:
DSI/NWU Preclinical Drug Development PlatformNorth‐West UniversityPotchefstroomSouth Africa
| | - Daniel N. Qekwana
- Department of Paraclinical SciencesFaculty of Veterinary ScienceUniversity of PretoriaPretoriaSouth Africa
| | - Vinny Naidoo
- Department of Paraclinical SciencesFaculty of Veterinary ScienceUniversity of PretoriaPretoriaSouth Africa
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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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Deza-Cruz I, Vilar MJ, Velasova M, AbuOun M, Anjum MF, Smith RP. Antimicrobial resistance of Escherichia coli in the UK: comparison of single vs. pooled samples from healthy pigs. Lett Appl Microbiol 2023; 76:ovad123. [PMID: 37942558 DOI: 10.1093/lambio/ovad123] [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: 04/18/2023] [Revised: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
This study compared the antimicrobial resistance (AMR) of Escherichia coli detected from single samples vs. pooled samples at herd level. The national monitoring dataset included isolates from one sample per pig holding, whereas the research study included isolates from pooled samples of 10 pigs per holding. In both datasets, caecal samples were collected from healthy pigs randomly selected at slaughterhouses and plated on non-selective and antibiotic selective media. Resistance against a panel of nine antibiotics was compared between datasets by generalized linear mixed effects models (GLMMs) and by bootstrapped generalized linear model (GLM) to account for pooling. The highest proportion of resistant E. coli was observed against tetracycline and ampicillin in both datasets. In non-selective media, single and pooled samples showed similar results, but the bootstrapped GLM detected significantly lower resistance to ciprofloxacin and nalidixic acid in the national dataset. In selective media, a significantly greater proportion of resistant isolates was observed in the research dataset for ceftazidime (OR: 0.05, 95%CI = 0.01-0.42) and nalidixic acid (OR: 0.15, 95%CI = 0.05-0.51). The results suggest that one sample per holding provides similar information on AMR at herd level as pooled samples for most of the tested antibiotics, although less resistance to ciprofloxacin, ceftazidime, and nalidixic acid was detected.
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Affiliation(s)
- Iñaki Deza-Cruz
- Department of Veterinary Epidemiology and Public Health, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, United Kingdom
| | - María J Vilar
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Martina Velasova
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey KT15 3NB, United Kingdom
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Xu Y, Zhu L, Chen S, Wu H, Li R, Li J, Yuan J, Wen T, Xue C, Shen Q. Risk assessment and dissemination mechanism of antibiotic resistance genes in compost. ENVIRONMENT INTERNATIONAL 2023; 178:108126. [PMID: 37562342 DOI: 10.1016/j.envint.2023.108126] [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: 06/19/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/12/2023]
Abstract
In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.
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Affiliation(s)
- Yifei Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lin Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shanguo Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Haiyan Wu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ruiqi Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jing Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Green Intelligent Fertilizer Innovation, MARD, Sinong Bio-organic Fertilizer Institute, Nanjing 210000, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China.
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9
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Shrestha RD, Agunos A, Gow SP, Deckert AE, Varga C. Decrease in the prevalence of antimicrobial resistance in Escherichia coli isolates of Canadian turkey flocks driven by the implementation of an antimicrobial stewardship program. PLoS One 2023; 18:e0282897. [PMID: 37486902 PMCID: PMC10365295 DOI: 10.1371/journal.pone.0282897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/25/2023] [Indexed: 07/26/2023] Open
Abstract
The emergence of antimicrobial-resistant organisms at the human-animal-environment interface has raised global concern prompting governments and various stakeholders to take action. As a part of the stewardship initiative, Canadian turkey producers have implemented an antimicrobial use (AMU) strategy to manage antimicrobial resistance (AMR) in their sector. This study evaluated farm-level AMU and AMR data collected between 2016 and 2021 in major turkey-producing provinces/regions through the Canadian Integrated Program for Antimicrobial Resistance Surveillance to assess the progress of the strategy by characterizing the prevalence of homologous and multidrug resistance (MDR) in Escherichia coli isolated from turkeys. Multivariable mixed-effect logistic regression models assessed temporal and provincial/regional variations in AMR and MDR. Negative binomial regression models examined the temporal and regional variations in the total AMU. The total AMU (measured in mg/kg turkey biomass) significantly decreased in all provinces/regions in 2020 and 2021. Escherichia coli isolates from turkey flocks showed a significant decrease in resistance to gentamicin, sulfisoxazole, and tetracyclines during the six-year study period, consistent with the timing of the AMU reduction strategy. The prevalence of MDR isolates was significantly lower in 2020 and 2021 compared to 2016. Higher prevalence was observed in the Western region compared to Québec and Ontario. Two common AMR patterns were identified: ampicillin-streptomycin-tetracyclines and streptomycin-sulfisoxazole-tetracyclines. These AMR patterns indicate possible cross-resistances (same class), co-selection (unrelated classes) for resistance, or potential carryover of resistance determinants from previous production cycles. The decreasing prevalence of resistance to homologous antimicrobials, MDR, and AMU quantity are suggestive that the turkey sector's AMU strategy is achieving its desired impact. However, antimicrobials previously eliminated for preventive use in turkey flocks and the use of highly important antimicrobials in human medicine suggest that the AMU reduction strategy should be monitored and re-evaluated periodically to mitigate the emergence of MDR bacteria and safeguard animal and public health.
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Affiliation(s)
- Rima D Shrestha
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Agnes Agunos
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Sheryl P Gow
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Saskatoon, Saskatchewan, Canada
| | - Anne E Deckert
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
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10
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Silva A, Silva V, Pereira JE, Maltez L, Igrejas G, Valentão P, Falco V, Poeta P. Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals. Antibiotics (Basel) 2023; 12:1061. [PMID: 37370379 DOI: 10.3390/antibiotics12061061] [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: 04/30/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.
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Affiliation(s)
- Adriana Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - José Eduardo Pereira
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, No. 228, 4050-313 Porto, Portugal
| | - Virgílio Falco
- Chemistry Research Centre (CQ-VR), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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11
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Merle R, Weise S, Gorisek L, Baer J, Robé C, Friese A, Jensen KC. The therapy frequency of antibiotics and phenotypical resistance of Escherichia coli in calf rearing sites in Germany. Front Vet Sci 2023; 10:1152246. [PMID: 37275609 PMCID: PMC10233112 DOI: 10.3389/fvets.2023.1152246] [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: 01/27/2023] [Accepted: 04/26/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction The association between antibiotic use and the occurrence of resistant bacteria is a global health problem and is subject to enormous efforts at national and international levels. Within the scope of the study "KAbMon", the resistance situation as well as the use of antibiotics in calf rearing farms in Germany was investigated. We hypothesized that the levels of resistance are associated with certain calf keeping farm types, such as pre-weaned calf farms, animal groups, and therapy frequency. Methods In total, 95 calf keeping farms were visited between October 2019 and April 2021. At each farm, up to three pooled fecal samples (10 freshly released feces each) were collected. One sample was taken in the youngest calf group, another in the oldest calf group, and one in the hospital box, if available. Escherichia coli was isolated from non-selective MacConkey agar. The therapy frequency reflects the average number of treatment days per calf in a half-year, while the resistance score is the sum of the relative minimum inhibitory concentration per substance over all 10 tested substances. Results The 1781 isolates from 178 samples showed high resistance rates against sulfamethoxazole (82%), tetracycline (49%), and ampicillin (40%). High resistance scores were mainly found in pre-weaned calf farms (purchasing calves from 2 weeks of life) and in the youngest animals. The therapy frequency showed an almost linear relationship with the resistance scores, and the age at purchase was negatively related to the resistance score. Discussion The high use of antimicrobials of young calves might be associated with a high risk for infectious diseases and might indicate that the current system of crowding 14-day-old calves from different farms in one group is not optimal. Further efforts are necessary to educate and motivate the calf keepers to ensure highest levels of hygiene and management as well as animal welfare conditions and to increase animal health.
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Affiliation(s)
- Roswitha Merle
- Department Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Susann Weise
- Department Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Lisa Gorisek
- Department Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
| | - Jorinde Baer
- Department Veterinary Medicine, Institute of Animal and Environmental Hygiene, Freie Universität Berlin, Berlin, Germany
| | - Caroline Robé
- Department Veterinary Medicine, Institute of Animal and Environmental Hygiene, Freie Universität Berlin, Berlin, Germany
| | - Anika Friese
- Department Veterinary Medicine, Institute of Animal and Environmental Hygiene, Freie Universität Berlin, Berlin, Germany
| | - Katharina Charlotte Jensen
- Department Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Freie Universität Berlin, Berlin, Germany
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12
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Whole Genome Sequencing (WGS) Analysis of Virulence and AMR Genes in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli from Animal and Environmental Samples in Four Italian Swine Farms. Antibiotics (Basel) 2022; 11:antibiotics11121774. [PMID: 36551431 PMCID: PMC9774568 DOI: 10.3390/antibiotics11121774] [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: 08/29/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Whole genome sequencing (WGS) is a powerful tool to analyze bacterial genomes rapidly, and can be useful to study and detect AMR genes. We carried out WGS on a group of Escherichia coli (n = 30), sampled from healthy animals and farm environment in four pigsties in northern Italy. Two × 250bp paired end sequencing strategy on Illumina MiSeq™ was used. We performed in silico characterization of E. coli isolates through the web tools provided by the Center for Genomic Epidemiology (cge.cbs.dtu.dk/services/) to study AMR and virulence genes. Bacterial strains were further analyzed to detect phenotypic antimicrobial susceptibility against several antimicrobials. Data obtained from WGS were compared to phenotypic results. All 30 strains were MDR, and they were positive for the genes blaCTX-M and blaTEM as verified by PCR. We observed a good concordance between phenotypic and genomic results. Different AMR determinants were identified (e.g., qnrS, sul, tet). Potential pathogenicity of these strains was also assessed, and virulence genes were detected (e.g., etsC, gad, hlyF, iroN, iss), mostly related to extraintestinal E. coli pathotypes (UPEC/APEC). However, enterotoxin genes, such as astA, ltcA and stb were also identified, indicating a possible hybrid pathogenic nature. Various replicons associated to plasmids, previously recovered in pathogenic bacteria, were identified (e.g., IncN and IncR plasmid), supporting the hypothesis that our strains were pathogenic. Eventually, through WGS it was possible to confirm the phenotypic antibiotic resistance results and to appreciate the virulence side of our ESBL-producing E. coli. These findings highlight the need to monitor commensal E. coli sampled from healthy pigs considering a One Health perspective.
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13
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De Jong A, El Garch F, Hocquet D, Prenger-Berninghoff E, Dewulf J, Migura-Garcia L, Perrin-Guyomard A, Veldman KT, Janosi S, Skarzynska M, Simjee S, Moyaert H, Rose M. European-wide antimicrobial resistance monitoring in commensal Escherichia coli isolated from healthy food animals between 2004 and 2018. J Antimicrob Chemother 2022; 77:3301-3311. [PMID: 36203261 DOI: 10.1093/jac/dkac318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/31/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To describe the susceptibility of Escherichia coli to medically important antibiotics, collected over four periods (2004-2006, 2008-2009, 2013-2014, 2017-2018), from food-producing animals at slaughter. METHODS Intestinal contents from cattle, pigs and broilers were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; one sample/animal/farm) for isolation of Escherichia coli; antimicrobial susceptibilities were centrally determined by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation. RESULTS In total, 10 613 E. coli strains were recovered. In broilers, resistance percentages were the lowest (P ≤ 0.01) in the latest time period. A significant decrease in MDR over time was also observed for broilers and a tendency for a decrease for pigs. Resistance to meropenem and tigecycline was absent, and resistance to azithromycin was 0.2%-2.0%. Also, low resistance to third-generation cephalosporins (1.1%-7.4%) was detected in broilers. Resistance to colistin varied between 0.1%-4.8%. E. coli from broilers showed high resistance to ciprofloxacin (7.3%-23.3%), whereas for cattle and pigs this was 0.2%-2.5%. Low/moderate resistance to chloramphenicol (9.3%-21.3%) and gentamicin (0.9%-7.0%) was observed in pigs and broilers. The highest resistance was noted for ampicillin (32.7%-65.3%), tetracycline (41.3%-67.5%), trimethoprim (32.0%-35.7%) and trimethoprim/sulfamethoxazole (27.5%-49.7%) from pigs and broilers, with marked country differences. MDR peaked in pigs and broilers with 24 and 26 phenotypes, with 21.9%-26.2% and 18.7%-34.1% resistance, respectively. CONCLUSIONS In this pan-EU survey antibiotic susceptibility of commensal E. coli varied largely between antibiotics, animal species and countries. Resistance to critically important antibiotics for human medicine was absent or low, except for ciprofloxacin in broilers and ampicillin in pigs and broilers.
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Affiliation(s)
- Anno De Jong
- EASSA Study Group, c/o CEESA, 168, Av. de Tervueren, Brussels, Belgium
| | - Farid El Garch
- EASSA Study Group, c/o CEESA, 168, Av. de Tervueren, Brussels, Belgium.,Vetoquinol S.A., Lure, France
| | - Didier Hocquet
- Infection Control Unit, University Hospital of Besançon, CHU Besançon, France.,UMR 6249, Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Department of Veterinary Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Lourdes Migura-Garcia
- IRTA-UAB Mixed Research Unit in Animal Health, Centre de Recerca en Sanitat Animal (CReSA), Barcelona, Spain.,IRTA, Animal Health Programme, CReSA, OIE Collaborating Centre, Campus de la Universitat Autònoma de Barcelona, Spain
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Szilard Janosi
- Laboratory of Bacteriology, National Food Chain Safety Office, Budapest, Hungary
| | - Magdalena Skarzynska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Shabbir Simjee
- EASSA Study Group, c/o CEESA, 168, Av. de Tervueren, Brussels, Belgium.,Elanco Animal health, Basingstoke, UK
| | - Hilde Moyaert
- EASSA Study Group, c/o CEESA, 168, Av. de Tervueren, Brussels, Belgium.,Zoetis, Zaventem, Belgium
| | - Markus Rose
- EASSA Study Group, c/o CEESA, 168, Av. de Tervueren, Brussels, Belgium.,MSD Animal Health Innovation GmbH, Schwabenheim, Germany
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14
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Distribution and Characterization of Antimicrobial Resistant Pathogens in a Pig Farm, Slaughterhouse, Meat Processing Plant, and in Retail Stores. Microorganisms 2022; 10:microorganisms10112252. [DOI: 10.3390/microorganisms10112252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
The emergence of antibiotic resistance in foodborne pathogens isolated from meat pro-ducts and their producing environment has been an increasing and leading threat to public health. The aim of the study was to identify pathogens and their antimicrobial resistance isolated from pig production to pork meat distribution phases. Through this study, food spoilage and foodborne or clinical pathogenic bacteria were isolated and identified from pork (belly and neck) meat product and its related environmental samples that include pig swabs, diets, feces, liquid manure, workers’ gloves, dust fan swabs, carcass swabs, floor swabs, and drain water in the affiliated farm, slaughterhouse, meat processing plant, and in retail stores. All carcasses at the slaughterhouse and meat products at the meat processing plant were tracked from pigs at a targeted farm. Nine different selective media agars were used to effectively isolate various pathogenic bacteria. A total of 283 presumptive pathogenic bacteria isolated from 126 samples were selected and identified using MALDI-ToF MS. Twenty-three important foodborne pathogens were identified, and some of them, Shiga-toxin-producing E. coli (STEC), Listeria monocytogenes, Staphylococcus aureus, and Yersinia enterocolitica, were further confirmed using PCR. The PFGE patterns of 12 STEC isolates were grouped by sample source or site. All the foodborne pathogens used in the study were not resistant to amoxicillin/clavulanate, ciprofloxacin, and gentamicin, whereas some of the STEC, L. monocytogenes, and S. aureus isolates were resistant to various antibiotics, including ampicillin, erythromycin, tetracycline, and vancomycin. The most common antimicrobial resistance pattern in the pathogenic STEC isolates was AMP-KAN-STR-SXT-TET. Consequently, this study provides valuable information for the distribution of antimicrobial-resistant pathogens along the pork meat production chain and can assist farmers and stakeholders to develop a systematic strategy for reducing the current emergence and spread of antimicrobial resistance in the different phases of pig production and distribution.
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15
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Han L, Liu XW, Zang T, Ren H, Liang DS, Bai SC, Li C, Liao XP, Liu YH, Zhang C, Sun J. H2S responsive PEGylated poly (lipoic acid) with ciprofloxacin for targeted therapy of Salmonella. J Control Release 2022; 351:896-906. [DOI: 10.1016/j.jconrel.2022.09.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022]
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16
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Pham VH, Abbas W, Huang J, Guo F, Zhang K, Kong L, Zhen W, Guo Y, Wang Z. Dietary coated essential oil and organic acid mixture supplementation improves health of broilers infected with avian pathogenic Escherichia coli. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 12:245-262. [PMID: 36712401 PMCID: PMC9868345 DOI: 10.1016/j.aninu.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 01/19/2023]
Abstract
Colibacillosis caused by avian pathogenic Escherichia coli (APEC) is a very prevalent disease in poultry farms in China. The exploration of effective non-antibiotic substances is of great significance for the control of APEC infections. This experiment evaluated the efficacy of coated essential oil and organic acid (EOA) supplementation to prevent E. coli O78 infection in broiler chickens. A total of 288 one-day-old male broiler chicks were randomly distributed into 4 groups with 6 replicates per group. Chickens were fed a diet either supplemented with EOA (500 mg/kg feed) or not, and either uninfected or infected with E. coli O78 intratracheally. Results showed that E. coli O78 infection reduced body weight gain, increased mortality and the ratio of feed to gain along with cecal and liver E. coli load, damaged gut mucosa, induced local and systemic inflammation, and altered cecal microbial composition, diversity and function (P < 0.05). Supplemental EOA improved feed conversion efficiency, lowered gross lesion scores and cecal E. coli population, enhanced intestinal goblet cells and serum IgG concentration, and tended to decrease serum IL-12 production (P < 0.05). Essential oil and organic acid addition downregulated IFN-γ mRNA, tended to decrease mucin-2 mRNA levels while upregulating IL-10 mRNA, and tended to increase ZO-1 gene expression in the jejuna of infected birds at 7 d after E. coli O78 challenge (P < 0.05). The 16S rRNA gene sequencing indicated that both EOA addition and E. coli O78 challenge altered the diversity and composition of the cecal microbiota community. Furthermore, infected birds fed EOA showed decreased Bacteroidetes and genus Lactobacillus abundance compared with the infected control. LEfSe analysis showed that Firmicutes, Ruminococcaceae, Clostridiales, Clostridia, Lactobacillus, Lactobacilaceae, and cc-115 were enriched in the non-infected but EOA-treated group (P < 0.05). Collectively, dietary EOA supplementation could mildly alleviate E. coli-induced gut injury and inflammation.
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Affiliation(s)
- Van Hieu Pham
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China,Faculty of Animal Science and Veterinary Medicine, Thai Nguyen University Agriculture and Forestry, Thai Nguyen, Viet Nam
| | - Waseem Abbas
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinyu Huang
- Menon Animal Nutrition Technology Co. Ltd., Shanghai, 201807, China
| | - Fangshen Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kaichen Zhang
- Tengzhou Heyi Food Co. Ltd., Zaozhuang, 277000, China
| | - Linhua Kong
- Tengzhou Heyi Food Co. Ltd., Zaozhuang, 277000, China
| | - Wenrui Zhen
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhong Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China,Corresponding author.
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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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Vinayamohan PG, Locke SR, Portillo-Gonzalez R, Renaud DL, Habing GG. Antimicrobial Use and Resistance in Surplus Dairy Calf Production Systems. Microorganisms 2022; 10:1652. [PMID: 36014070 PMCID: PMC9413162 DOI: 10.3390/microorganisms10081652] [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: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Surplus calves, which consist predominately of male calves born on dairy farms, are an underrecognized source of antimicrobial-resistant (AMR) pathogens. Current production systems for surplus calves have important risk factors for the dissemination of pathogens, including the high degree of commingling during auction and transportation and sometimes inadequate care early in life. These circumstances contribute to an increased risk of respiratory and other infectious diseases, resulting in higher antimicrobial use (AMU) and the development of AMR. Several studies have shown that surplus calves harbor AMR genes and pathogens that are resistant to critically important antimicrobials. This is a potential concern as the resistant pathogens and genes can be shared between animal, human and environmental microbiomes. Although knowledge of AMU and AMR has grown substantially in dairy and beef cattle systems, comparable studies in surplus calves have been mostly neglected in North America. Therefore, the overall goal of this narrative review is to summarize the existing literature regarding AMU and AMR in surplus dairy calf production, highlight the management practices contributing to the increased AMU and the resulting AMR, and discuss potential strategies and barriers for improved antimicrobial stewardship in surplus calf production systems.
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Affiliation(s)
- Poonam G. Vinayamohan
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Samantha R. Locke
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Rafael Portillo-Gonzalez
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - David L. Renaud
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Gregory G. Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA
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19
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Becker J, Perreten V, Schüpbach-Regula G, Stucki D, Steiner A, Meylan M. Associations of antimicrobial use with antimicrobial susceptibility at the calf level in bacteria isolated from the respiratory and digestive tracts of veal calves before slaughter. J Antimicrob Chemother 2022; 77:2859-2866. [PMID: 35962594 PMCID: PMC9525080 DOI: 10.1093/jac/dkac246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Antimicrobial drugs are frequently administered in veal calves, but investigations on associations with antimicrobial susceptibility of bacteria are scarce and convey partly contradictory findings. The aim of this study was to investigate associations of antimicrobial use (AMU) during the fattening period with antimicrobial susceptibility shortly before slaughter. Methods Detailed treatment data of 1905 veal calves from 38 farms were collected prospectively during monthly farm visits for 1 year (n = 1864 treatments, n = 535 visits); 1582 Escherichia coli, 1059 Pasteurella multocida and 315 Mannheimia haemolytica were isolated from rectal and nasopharyngeal swabs collected before slaughter and subjected to antimicrobial susceptibility testing by microdilution. Associations of antimicrobial treatments with resistant isolates were investigated at the calf level. Results Associations of AMU with antimicrobial resistance were observed using generalized linear models. For E. coli, the odds of being resistant were increased with increased AMU (OR 1.36 when number of treatments >1, P = 0.066). Use of tetracyclines was associated with resistance to tetracycline (OR 1.86, P < 0.001) and use of penicillins was associated with resistance to ampicillin (OR 1.66, P = 0.014). No significant associations were observed for P. multocida (use of aminoglycosides: OR 3.66 for resistance to spectinomycin, P = 0.074). For M. haemolytica, the odds of being resistant were increased with increased AMU (OR 4.63, P < 0.001), and use of tetracyclines was associated with resistance to tetracycline (OR 6.49, P < 0.001). Conclusions Occurrence of resistant bacteria shortly before slaughter was associated with AMU in veal calves. Prudent and appropriate use may contribute to limit the selection of resistant bacteria on veal farms.
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Affiliation(s)
- Jens Becker
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012 Bern, Switzerland
| | - Gertraud Schüpbach-Regula
- Veterinary Public Health Institute, Vetsuisse Faculty, University of Bern, Schwarzenburgstrasse 161, 3097 Liebefeld, Switzerland
| | - Dimitri Stucki
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - Adrian Steiner
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
| | - Mireille Meylan
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3012 Bern, Switzerland
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20
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Shrestha RD, Agunos A, Gow SP, Deckert AE, Varga C. Associations between antimicrobial resistance in fecal Escherichia coli isolates and antimicrobial use in Canadian turkey flocks. Front Microbiol 2022; 13:954123. [PMID: 35966666 PMCID: PMC9372513 DOI: 10.3389/fmicb.2022.954123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance (AMR) in enteric bacteria continues to be detected in turkey flocks and retail products worldwide, including in Canada. However, studies assessing linkages between on-farm antimicrobial use (AMU) and the development of AMR are lacking. This study aims to identify AMU characteristics that impact the development of AMR in the indicator bacteria Escherichia coli in turkey flocks, building on the Canadian Integrated Program for Antimicrobial Resistance Surveillance methodology for farm-level AMU and AMR data integration. Two analytic approaches were used: (1) multivariable mixed-effects logistic regression models examined associations between AMU (any route, route-specific, and route-disease-specific indication) summarized as the number of defined daily doses in animals using Canadian standards ([nDDDvetCA]/1,000 kg-animal-days at risk) and AMR and (2) multivariable mixed-effects Poisson regression models studied the linkages between AMU and the number of classes to which an E. coli isolate was resistant (nCRE. coli). A total of 1,317 E. coli isolates from a network of 16 veterinarians and 334 turkey producers across the five major turkey-producing provinces in Canada between 2016 and 2019 were used. Analysis indicated that AMR emerged with the use of related antimicrobials (e.g., tetracycline use-tetracycline resistance), however, the use of unrelated antimicrobial classes was also impacting AMR (e.g., aminoglycosides/streptogramins use-tetracycline resistance). As for studying AMU-nCRE. coli linkages, the most robust association was between the parenteral aminoglycosides use and nCRE. coli, though in-feed uses of four unrelated classes (bacitracin, folate pathway inhibitors, streptogramins, and tetracyclines) appear to be important, indicating that ongoing uses of these classes may slow down the succession from multidrug-resistant to a more susceptible E. coli populations. The analysis of AMU (route and disease-specific)-AMR linkages complemented the above findings, suggesting that treatment of certain diseases (enteric, late-stage septicemic conditions, and colibacillosis) are influential in the development of resistance to certain antimicrobial classes. The highest variances were at the flock level indicating that stewardship actions should focus on flock-level infection prevention practices. This study added new insights to our understanding of AMU-AMR linkages in turkeys and is useful in informing AMU stewardship in the turkey sector. Enhanced surveillance using sequencing technologies are warranted to explain molecular-level determinants of AMR.
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Affiliation(s)
- Rima D. Shrestha
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Agnes Agunos
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Sheryl P. Gow
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Saskatoon, SK, Canada
| | - Anne E. Deckert
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Csaba Varga,
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21
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Chowdhury G, Ramamurthy T, Das B, Ghosh D, Okamoto K, Miyoshi SI, Dutta S, Mukhopadhyay AK. Characterization of NDM-5 Carbapenemase-Encoding Gene ( bla NDM-5) - Positive Multidrug Resistant Commensal Escherichia coli from Diarrheal Patients. Infect Drug Resist 2022; 15:3631-3642. [PMID: 35837541 PMCID: PMC9275505 DOI: 10.2147/idr.s364526] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose The multidrug resistance Enterobacteriaceae cause many serious infections resulting in prolonged hospitalization, increased treatment charges and mortality rate. In this study, we characterized bla NDM-5-positive multidrug resistance commensal Escherichia coli (CE) isolated from diarrheal patients in Kolkata, India. Methods Three CE strains were isolated from diarrheal stools, which were negative for different pathogroups of diarrheagenic E. coli (DEC). The presence of carbapenemases encoding genes and other antimicrobial resistance genes (ARGs) was detected using PCR. The genetic arrangement adjoining bla NDM-5 was investigated by plasmid genome sequencing. The genetic relatedness of the strains was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) methods. Results In addition to colistin, the bla NDM-5-positive CE strains showed resistance to most of the antibiotics. Higher MICs were detected for ciprofloxacin (>32 mg/L) and imipenem (8 mg/L). Molecular typing revealed that three CE strains belonged to two different STs (ST 101 and ST 648) but they were 95% similar in the PFGE analysis. Screening for ARGs revealed that CE strains harbored Int-1, bla TEM, blaC TX-M3, bla OXA-1, bla OXA-7, bla OXA-9, tetA, strA, aadA1, aadB, sul2, floR, mph(A), and aac(6´)-Ib-cr. In conjugation experiment, transfer frequencies ranged from 2.5×10-3 to 8.4x10-5. The bla NDM-5 gene was located on a 94-kb pNDM-TC-CE-89 type plasmid, which is highly similar to the IncFII plasmid harboring an IS26-IS30-bla NDM-5-ble MBL-trpF-dsbd-IS91-dhps structure. Conclusion To the best of our knowledge, this is the first report on carbapenem resistance involving the bla NDM-5 gene in CE from diarrheal patients. The circulation of bla NDM-5 gene in CE is worrisome, since it has the potential to transfer bla NDM-5 gene to other enteric pathogens.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Bhabatosh Das
- Department of Infection and Immunology, Translational Health Science and Technology Institute, Faridabad, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Keinosuke Okamoto
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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22
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Suwono B, Eckmanns T, Kaspar H, Tenhagen BA. A Joint Regional Analysis of Resistance Combinations in Escherichia coli in Humans and Different Food-Producing Animal Populations in Germany Between 2014 and 2017. Front Public Health 2022; 10:823613. [PMID: 35757609 PMCID: PMC9218088 DOI: 10.3389/fpubh.2022.823613] [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: 11/27/2021] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
A joint comparative regional analysis of different resistance combinations across human and veterinary medicine has not been previously conducted in Germany. This study analyses 16 resistance combinations from four antibiotics in E. coli from different human and food-producing animal populations in three German regions: East, North West and South West. The E. coli data were collected from the three national surveillance and monitoring systems for antimicrobial resistance (AMR) bacteria in humans (ARS), food-safety (Zoonosis Monitoring) and animal pathogens (GERM-Vet) from January 2014 to December 2017. Analyses were performed using cluster analysis (hierarchical clustering, average linkage) in R. We included data from 537,215 E. coli isolates from human clinical isolates, from clinical as well as non-clinical isolates from food-producing animals and from food. The majority of the data originated from the North West region. There were two main clusters built on 54 different human and animal populations. We observed close similarities of resistance combinations in human isolates from the different regions within the same human populations from outpatient cares, general wards and ICUs. These resistance combinations clustered separately from non-clinical isolates from broilers, turkeys, cattle and pigs; except for some of clinical isolates from these populations which clustered closely to isolates from human populations. Frequently, the resistance combinations in E. coli isolates from farms clustered closely to the resistance combinations in isolates from slaughterhouses from broilers and turkeys over all regions. However, the resistance combinations in E. coli isolates from retail meat populations tended to cluster separately within their respective populations in between all regions.
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Affiliation(s)
- Beneditta Suwono
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany.,Department Infectious Disease Epidemiology, Unit Healthcare-Associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Tim Eckmanns
- Department Infectious Disease Epidemiology, Unit Healthcare-Associated Infections, Surveillance for Antibiotic Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Heike Kaspar
- Unit Antibiotic Resistance Monitoring, German Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department Biological Safety, Unit Epidemiology, Zoonoses and Antimicrobial Resistance, German Federal Institute for Risk Assessment, Berlin, Germany
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23
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Kusi J, Ojewole CO, Ojewole AE, Nwi-Mozu I. Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications. Antibiotics (Basel) 2022; 11:antibiotics11060821. [PMID: 35740227 PMCID: PMC9219700 DOI: 10.3390/antibiotics11060821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 01/03/2023] Open
Abstract
Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC's National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.
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Affiliation(s)
- Joseph Kusi
- Department of Environmental Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Campus Box 1099, Edwardsville, IL 62026, USA; (C.O.O.); (A.E.O.)
- Correspondence:
| | - Catherine Oluwalopeye Ojewole
- Department of Environmental Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Campus Box 1099, Edwardsville, IL 62026, USA; (C.O.O.); (A.E.O.)
| | - Akinloye Emmanuel Ojewole
- Department of Environmental Sciences, Southern Illinois University Edwardsville, 44 Circle Drive, Campus Box 1099, Edwardsville, IL 62026, USA; (C.O.O.); (A.E.O.)
| | - Isaac Nwi-Mozu
- Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA;
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Epidemiological Prevalence of Phenotypical Resistances and Mobilised Colistin Resistance in Avian Commensal and Pathogenic E. coli from Denmark, France, The Netherlands, and the UK. Antibiotics (Basel) 2022; 11:antibiotics11050631. [PMID: 35625275 PMCID: PMC9137498 DOI: 10.3390/antibiotics11050631] [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: 04/04/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/10/2023] Open
Abstract
Colistin has been used for the treatment of non-invasive gastrointestinal infections caused by avian pathogenic E. coli (APEC). The discovery of mobilised colistin resistance (mcr) in E. coli has instigated a One Health approach to minimise colistin use and the spread of resistance. The aim of this study was to compare colistin susceptibility of APECs (collected from Denmark n = 25 and France n = 39) versus commensal E. coli (collected from the Netherlands n = 51 and the UK n = 60), alongside genetic (mcr-1−5) and phenotypic resistance against six other antimicrobial classes (aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulphonamides/trimethoprim, tetracyclines). Minimum inhibitory concentration (MIC) values were determined using a broth microdilution method (EUCAST guidelines), and phenotypic resistance was determined using disk diffusion. Colistin MIC values of APEC were significantly lower than those for commensals by 1 dilution (p < 0.0001, Anderson-Darling test), and differences in distributions were observed between countries. No isolate carried mcr-1−5. Three phenotypically resistant isolates were identified in 2/62 APEC and 1/111 commensal isolates. Gentamicin or gentamicin−ceftriaxone co-resistance was observed in two of these isolates. This study showed a low prevalence of phenotypic colistin resistance, with no apparent difference in colistin resistance between commensal E. coli strains and APEC strains.
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Antibiotic consumption is a major driver of antibiotic resistance in calves raised on Italian cow-calf beef farms. Res Vet Sci 2022; 145:71-81. [DOI: 10.1016/j.rvsc.2022.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/30/2021] [Accepted: 01/12/2022] [Indexed: 12/24/2022]
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Mesa-Varona O, Boone I, Flor M, Eckmanns T, Kaspar H, Grobbel M, Tenhagen BA. Comparison of Consumption Data and Phenotypical Antimicrobial Resistance in E. coli Isolates of Human Urinary Samples and of Weaning and Fattening Pigs from Surveillance and Monitoring Systems in Germany. Antibiotics (Basel) 2021; 11:antibiotics11010028. [PMID: 35052905 PMCID: PMC8772873 DOI: 10.3390/antibiotics11010028] [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: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/23/2022] Open
Abstract
Antimicrobial resistance (AMR) data from humans are mostly collected from clinical isolates, whereas from livestock data also exist from colonizing pathogens. In Germany, livestock data are collected from clinical and nonclinical isolates. We compared resistance levels of clinical and nonclinical isolates of Escherichia coli from weaning and fattening pigs with clinical outpatient isolates of humans from urban and rural areas. We also studied the association of AMR with available antimicrobial use (AMU) data from humans and pigs. Differences between rural and urban isolates were minor and did not affect the comparison between human and pig isolates. We found higher resistance levels to most antimicrobials in human isolates compared to nonclinical isolates of fattening pigs. Resistance to ampicillin, however, was significantly more frequent in clinical isolates of fattening pigs and in clinical and nonclinical isolates of weaning pigs compared to isolates from humans. The opposite was observed for ciprofloxacin. Co-trimoxazole resistance proportions were higher in clinical isolates of weaning and fattening pigs as compared to isolates from humans. Resistance proportions were higher in clinical isolates than in nonclinical isolates from pigs of the same age group and were also higher in weaner than in fattening pigs. Significant associations of AMU and AMR were found for gentamicin resistance and aminoglycoside use in humans (borderline) and for ampicillin resistance in clinical isolates and penicillin use in fattening pigs. In summary, we found significant differences between isolates from all populations, requiring more detailed analyses supported by molecular data and better harmonized data on AMU and AMR.
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Affiliation(s)
- Octavio Mesa-Varona
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.F.); (M.G.); (B.-A.T.)
- Correspondence:
| | - Ides Boone
- Department for Infectious Disease Epidemiology, Robert Koch Institute (RKI), 13353 Berlin, Germany; (I.B.); (T.E.)
| | - Matthias Flor
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.F.); (M.G.); (B.-A.T.)
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute (RKI), 13353 Berlin, Germany; (I.B.); (T.E.)
| | - Heike Kaspar
- Federal Office of Consumer Protection and Food Safety (BVL), Reference Laboratories, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Department Method Standardization, 12277 Berlin, Germany;
| | - Mirjam Grobbel
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.F.); (M.G.); (B.-A.T.)
| | - Bernd-Alois Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.F.); (M.G.); (B.-A.T.)
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Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part I, Methodology Development. Pathogens 2021; 10:pathogens10111492. [PMID: 34832647 PMCID: PMC8618382 DOI: 10.3390/pathogens10111492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
This study explores methodologies for the data integration of antimicrobial use (AMU) and antimicrobial resistance (AMR) results within and across three food animal species, surveyed at the farm-level by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The approach builds upon existing CIPARS methodology and principles from other AMU and AMR surveillance systems. Species level data integration involved: (1) standard CIPARS descriptive and temporal analysis of AMU/AMR, (2) synthesis of results, (3) selection of AMU and AMR outcomes for integration, (4) selection of candidate AMU indicators to enable comparisons of AMU levels between species and simultaneous assessment of AMU and AMR trends, (5) exploration of analytic options for studying associations between AMU and AMR, and (6) interpretation and visualization. The multi-species integration was also completed using the above approach. In addition, summarized reporting of internationally-recognized indicators of AMR (i.e., AMR adjusted for animal biomass) and AMU (mg/population correction unit, mg/kg animal biomass) is explored. It is envisaged that this approach for species and multi-species AMU-AMR data integration will be applied to the annual CIPARS farm-level data and progressively developed over time to inform AMU-AMR integrated surveillance best practices for further enhancement of AMU stewardship actions.
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Agunos A, Gow SP, Deckert AE, Léger DF. Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part II, Application. Pathogens 2021; 10:pathogens10111491. [PMID: 34832646 PMCID: PMC8621420 DOI: 10.3390/pathogens10111491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 11/16/2022] Open
Abstract
Using the methodology developed for integrated analysis and reporting of antimicrobial use (AMU) and antimicrobial resistance (AMR) data, farm-level surveillance data were synthesized and integrated to assess trends and explore potential AMU and AMR associations. Data from broiler chicken flocks (n = 656), grower-finisher pig herds (n = 462) and turkey flocks (n = 339) surveyed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) at the farm-level (2015-2019) were used. The analyses showed a reduction in mean flock/herd level number of defined daily doses using Canadian standards (nDDDvetCA) adjusted for kg animal biomass that coincided with the decline in % resistance in the three species. This was noted in most AMU-AMR pairs studied except for ciprofloxacin resistant Campylobacter where resistance continued to be detected (moderate to high levels) despite limited fluoroquinolone use. Noteworthy was the significantly negative association between the nDDDvetCA/kg animal biomass and susceptible Escherichia coli (multispecies data), an early indication that AMU stewardship actions are having an impact. However, an increase in the reporting of diseases in recent years was observed. This study highlighted the value of collecting high-resolution AMU surveillance data with animal health context at the farm-level to understand AMR trends, enable data integration and measure the impact of AMU stewardship actions.
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Affiliation(s)
- Agnes Agunos
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
- Correspondence: ; Tel.: +1-519-4007895
| | - Sheryl P. Gow
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Saskatoon, SK S7N 5B4, Canada;
| | - Anne E. Deckert
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
| | - David F. Léger
- Center for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada; (A.E.D.); (D.F.L.)
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 13: Diaminopyrimidines: trimethoprim. EFSA J 2021; 19:e06865. [PMID: 34729093 PMCID: PMC8546793 DOI: 10.2903/j.efsa.2021.6865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The specific concentrations of trimethoprim in non-target feed for food-producing animals below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for trimethoprim was estimated. Uncertainties and data gaps associated to the levels reported were addressed. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. No suitable data for the assessment were available. It was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC for trimethoprim.
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Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries. Antibiotics (Basel) 2021; 10:antibiotics10070820. [PMID: 34356741 PMCID: PMC8300668 DOI: 10.3390/antibiotics10070820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3′-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.
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Hesp A, Veldman K, Brouwer MSM, Wagenaar JA, Mevius D, van Schaik G. Latent class analysis to assess whole-genome sequencing versus broth microdilution for monitoring antimicrobial resistance in livestock. Prev Vet Med 2021; 193:105406. [PMID: 34147959 DOI: 10.1016/j.prevetmed.2021.105406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) monitoring in animals is performed in commensal Escherichia coli, and other microorganisms relevant for human or veterinary health. Due to advances in the field and major reductions in cost, it is expected that whole-genome sequencing (WGS)-based antimicrobial susceptibility testing (AST) will (partly) replace culture-based AST. So far, no studies have been performed without using culture-based AST as the gold standard. Our aim was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility testing of commensal E. coli by WGS-based AST versus culture-based AST as this test does not assume a gold standard. OpenBUGS was used to model two independent tests in three animal populations (N = 150, 50 bacterial isolates per population): veal calves, pigs, and broilers. This resulted in the first estimation of sensitivity and specificity of WGS-based AST versus culture-based AST to detect AMR without a gold standard. Both methods had high sensitivity (>0.92, lowest limit probability interval: 0.76) and specificity was generally high for both methods for all antimicrobial classes except for aminoglycosides and macrolides. We compared WGS results for different length and identity settings (%) of gene alignment and found few differences between the 60/90, 90/90 and 95/95 settings. We recommend to further investigate sensitivity and specificity of WGS-based AST by means of latent class analysis, especially for low-prevalent resistance.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Kees Veldman
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Gerdien van Schaik
- Royal GD, Deventer, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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Coaching Belgian and Dutch Broiler Farmers Aimed at Antimicrobial Stewardship and Disease Prevention. Antibiotics (Basel) 2021; 10:antibiotics10050590. [PMID: 34067541 PMCID: PMC8156534 DOI: 10.3390/antibiotics10050590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
A reduction in antimicrobial use (AMU) is needed to curb the increase in antimicrobial resistance in broiler production. Improvements in biosecurity can contribute to a lower incidence of disease and thereby lower the need for AMU. However, veterinary advice related to AMU reduction or biosecurity is often not complied with, and this has been linked to the attitudes of farmers. Behavior change promoted by coaching may facilitate uptake and compliance regarding veterinary advice. Thirty broiler farms in Belgium and the Netherlands with high AMU were included in this study for 13 months. For each farmer, the attitude towards AMU reduction was quantified using an adjusted Awareness, Desire, Knowledge, Ability, and Reinforcement (ADKAR®) change management model, and farm biosecurity was assessed with the Biocheck.UGent™ tool. Subsequently, farmers were coached to improve disease prevention and antimicrobial stewardship. After the individual coaching of farmers, there was a change in their attitudes regarding AMU, reflected by an increase in ADKAR® scores. Biosecurity levels improved by around 6% on average, and AMU was reduced by 7% on average without negative effects on performance parameters. Despite these improvements, no significant association could be found between higher ADKAR® scores and lower AMU. Further investigation into sociological models is needed as a tool to reduce AMU in livestock production.
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Skarżyńska M, Zaja C M, Bomba A, Bocian Ł, Kozdruń W, Polak M, Wia Cek J, Wasyl D. Antimicrobial Resistance Glides in the Sky-Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential. Front Microbiol 2021; 12:656223. [PMID: 33897669 PMCID: PMC8062882 DOI: 10.3389/fmicb.2021.656223] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global health concerns; therefore, the identification of AMR reservoirs and vectors is essential. Attention should be paid to the recognition of potential hazards associated with wildlife as this field still seems to be incompletely explored. In this context, the role of free-living birds as AMR carriers is noteworthy. Therefore, we applied methods used in AMR monitoring, supplemented by colistin resistance screening, to investigate the AMR status of Escherichia coli from free-living birds coming from natural habitats and rescue centers. Whole-genome sequencing (WGS) of strains enabled to determine resistance mechanisms and investigate their epidemiological relationships and virulence potential. As far as we know, this study is one of the few that applied WGS of that number (n = 71) of strains coming from a wild avian reservoir. The primary concerns arising from our study relate to resistance and its determinants toward antimicrobial classes of the highest priority for the treatment of critical infections in people, e.g., cephalosporins, quinolones, polymyxins, and aminoglycosides, as well as fosfomycin. Among the numerous determinants, bla CTX-M-15, bla CMY-2, bla SHV-12, bla TEM-1B, qnrS1, qnrB19, mcr-1, fosA7, aac(3)-IIa, ant(3")-Ia, and aph(6)-Id and chromosomal gyrA, parC, and parE mutations were identified. Fifty-two sequence types (STs) noted among 71 E. coli included the global lineages ST131, ST10, and ST224 as well as the three novel STs 11104, 11105, and 11194. Numerous virulence factors were noted with the prevailing terC, gad, ompT, iss, traT, lpfA, and sitA. Single E. coli was Shiga toxin-producing. Our study shows that the clonal spread of E. coli lineages of public and animal health relevance is a serious avian-associated hazard.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Magdalena Zaja C
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Łukasz Bocian
- Department of Epidemiology and Risk Assessment, National Veterinary Research Institute, Puławy, Poland
| | - Wojciech Kozdruń
- Department of Poultry Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Marcin Polak
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jarosław Wia Cek
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.,Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries. Microorganisms 2021; 9:microorganisms9040678. [PMID: 33805983 PMCID: PMC8064350 DOI: 10.3390/microorganisms9040678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022] Open
Abstract
Livestock data on antimicrobial resistance (AMR) are commonly collected from bacterial populations of clinical and non-clinical isolates. In contrast to data on non-clinical isolates from livestock, data on clinical isolates are not harmonized in Europe. The Normalized Resistance Interpretation (NRI) method was applied to overcome the lack of harmonization of laboratory methods and interpretation rules between monitoring systems. Statistical analyses were performed to identify associations between the isolate type (clinical vs. non-clinical) and resistance to four antimicrobials (ampicillin, tetracycline, gentamicin, and nalidixic acid) per animal category in Germany and France. Additional statistical analyses comparing clinical and non-clinical isolates were performed with the available data on the same antimicrobial panel and animal categories from the UK and Norway. Higher resistance prevalence was found in clinical isolates compared to non-clinical isolates from calves to all antimicrobials included in Germany and France. It was also found for gentamicin in broilers from France. In contrast, in broilers and turkeys from Germany and France and in broilers from the UK, a higher resistance level to ampicillin and tetracycline in non-clinical isolates was encountered. This was also found in resistance to gentamicin in isolates from turkeys in Germany. Resistance differed within countries and across years, which was partially in line with differences in antimicrobial use patterns. Differences in AMR between clinical and non-clinical isolates of Escherichia coli are associated with animal category (broiler, calf, and turkey) and specific antimicrobials. The NRI method allowed comparing results of non-harmonized AMR systems and might be useful until international harmonization is achieved.
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Mencía-Ares O, Argüello H, Puente H, Gómez-García M, Manzanilla EG, Álvarez-Ordóñez A, Carvajal A, Rubio P. Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. is influenced by production system, antimicrobial use, and biosecurity measures on Spanish pig farms. Porcine Health Manag 2021; 7:27. [PMID: 33741079 PMCID: PMC7980634 DOI: 10.1186/s40813-021-00206-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/11/2021] [Indexed: 01/23/2023] Open
Abstract
Background Antimicrobial resistance (AMR) is a global public health threat consequence of antimicrobial use (AMU) in human and animal medicine. In food-producing animals factors such as management, husbandry or biosecurity may impact AMU. Organic and extensive Iberian swine productions are based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the AMR in indicator bacteria. Here, we evaluate the usefulness of commensal Escherichia coli and Enterococcus spp. isolates as AMR bioindicators when comparing 37 Spanish pig farms from both intensive and organic-extensive production systems, considering the effect of AMU and biosecurity measures, the last only on intensive farms. Results The production system was the main factor contributing to explain the AMR differences in E. coli and Enterococcus spp. In both bacteria, the pansusceptible phenotype was more common (p < 0.001) on organic-extensive farms when compared to intensive herds. The microbiological resistance in commensal E. coli was, for most of the antimicrobials evaluated, significantly higher (p < 0.05) on intensive farms. In enterococci, the lincosamides usage revealed the association between AMR and AMU, with an increase in the AMR for erythromycin (p < 0.01), quinupristin-dalfopristin (p < 0.01) and the multidrug-resistant (MDR) phenotype (p < 0.05). The biosecurity measures implemented on intensive farms influenced the AMR of these bioindicators, with a slightly lower resistance to sulfamethoxazole (p < 0.01) and the MDR phenotype (p < 0.05) in E. coli isolated from farms with better cleaning and disinfection protocols. On these intensive farms, we also observed that larger herds had a higher biosecurity when compared to smaller farms (p < 0.01), with no significant associations between AMU and the biosecurity scores. Conclusions Overall, this study evidences that the production system and, to a lesser extent, the biosecurity measures, contribute to the AMR development in commensal E. coli and Enterococcus spp., with antimicrobial usage as the main differential factor, and demonstrates the potential value of these bacteria as bioindicators on pig farms in AMR surveillance programs.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain.
| | - Héctor Argüello
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Héctor Puente
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Manuel Gómez-García
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Edgar G Manzanilla
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Ireland.,School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Faculty of Veterinary, Universidad de León, León, Spain.,Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Ana Carvajal
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
| | - Pedro Rubio
- Department of Animal Health, Faculty of Veterinary, Universidad de León, León, Spain
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Mesa-Varona O, Kaspar H, Grobbel M, Tenhagen BA. Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017. PLoS One 2020; 15:e0243772. [PMID: 33306730 PMCID: PMC7732064 DOI: 10.1371/journal.pone.0243772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/28/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3-0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73-0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56-15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29-0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26-0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29-0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR.
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Affiliation(s)
- Octavio Mesa-Varona
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Heike Kaspar
- Department Method Standardisation, Reference Laboratories, Resistance to Antibiotics, Berlin, Germany
- Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Mirjam Grobbel
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Sjöström K, Hickman RA, Tepper V, Olmos Antillón G, Järhult JD, Emanuelson U, Fall N, Sternberg Lewerin S. Antimicrobial Resistance Patterns in Organic and Conventional Dairy Herds in Sweden. Antibiotics (Basel) 2020; 9:E834. [PMID: 33233471 PMCID: PMC7700389 DOI: 10.3390/antibiotics9110834] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 01/24/2023] Open
Abstract
Monitoring antimicrobial resistance (AMR) and use (AMU) is important for control. We used Escherichia coli from healthy young calves as an indicator to evaluate whether AMR patterns differ between Swedish organic and conventional dairy herds and whether the patterns could be related to AMU data. Samples were taken twice, in 30 organic and 30 conventional dairy herds. Selective culturing for Escherichia coli, without antibiotics and with nalidixic acid or tetracycline, was used to estimate the proportions of resistant isolates. Microdilution was used to determine the minimum inhibitory concentrations (MICs) for thirteen antimicrobial substances. AMU data were based on collection of empty drug packages. Less than 8% of the bacterial growth on non-selective plates was also found on selective plates with tetracycline, and 1% on plates with nalidixic acid. Despite some MIC variations, resistance patterns were largely similar in both periods, and between organic and conventional herds. For most substances, only a few isolates were classified as resistant. The most common resistances were against ampicillin, streptomycin, sulfamethoxazole, and tetracycline. No clear association with AMU could be found. The lack of difference between organic and conventional herds is likely due to a generally good animal health status and consequent low AMU in both categories.
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Affiliation(s)
- Karin Sjöström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; (K.S.); (G.O.A.); (U.E.); (N.F.)
| | - Rachel A. Hickman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, 751 23 Uppsala, Sweden; (R.A.H.); (V.T.)
| | - Viktoria Tepper
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, 751 23 Uppsala, Sweden; (R.A.H.); (V.T.)
- Institute of Environmental Engineering, ETH, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
| | - Gabriela Olmos Antillón
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; (K.S.); (G.O.A.); (U.E.); (N.F.)
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University Hospital, 751 85 Uppsala, Sweden;
| | - Ulf Emanuelson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; (K.S.); (G.O.A.); (U.E.); (N.F.)
| | - Nils Fall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; (K.S.); (G.O.A.); (U.E.); (N.F.)
| | - Susanna Sternberg Lewerin
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Yang D, Van Gompel L, Luiken REC, Sanders P, Joosten P, van Heijnsbergen E, Wouters IM, Scherpenisse P, Chauvin C, Wadepohl K, Greve GD, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld MHG, Soumet C, Skarżyńska M, Juraschek K, Fischer J, Wasyl D, Wagenaar JA, Dewulf J, Schmitt H, Mevius DJ, Heederik DJJ, Smit LAM. Association of antimicrobial usage with faecal abundance of aph(3')-III, ermB, sul2 and tetW resistance genes in veal calves in three European countries. Int J Antimicrob Agents 2020; 56:106131. [PMID: 32763373 DOI: 10.1016/j.ijantimicag.2020.106131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND High antimicrobial use (AMU) and antimicrobial resistance (AMR) in veal calves remain a source of concern. As part of the EFFORT project, the association between AMU and the abundance of faecal antimicrobial resistance genes (ARGs) in veal calves in three European countries was determined. METHODS In 2015, faecal samples of veal calves close to slaughter were collected from farms located in France, Germany and the Netherlands (20 farms in France, 20 farms in the Netherlands and 21 farms in Germany; 25 calves per farm). Standardized questionnaires were used to record AMU and farm characteristics. In total, 405 faecal samples were selected for DNA extraction and quantitative polymerase chain reaction to quantify the abundance (16S normalized concentration) of four ARGs [aph(3')-III, ermB, sul2 and tetW] encoding for resistance to frequently used antimicrobials in veal calves. Multiple linear mixed models with random effects for country and farm were used to relate ARGs to AMU and farm characteristics. RESULTS A significant positive association was found between the use of trimethoprim/sulfonamides and the concentration of sul2 in faeces from veal calves. A higher weight of calves on arrival at the farm was negatively associated with aph(3')-III and ermB. Lower concentrations of aph(3')-III were found at farms with non-commercial animals present. Furthermore, farms using only water for the cleaning of stables had a significantly lower abundance of faecal ermB and tetW compared with other farms. CONCLUSION A positive association was found between the use of trimethoprim/sulfonamides and the abundance of sul2 in faeces in veal calves. Additionally, other relevant risk factors associated with ARGs in veal calves were identified, such as weight on arrival at the farm and cleaning practices.
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Affiliation(s)
- Dongsheng Yang
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Pim Sanders
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Philip Joosten
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Eri van Heijnsbergen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Claire Chauvin
- ANSES, Epidemiology, Health and Welfare Unit, Paris, France
| | - Katharina Wadepohl
- Außenstelle für Epidemiologie, Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | | | | | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Katharina Juraschek
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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