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Wayop IYA, de Vet E, Leerlooijer JN, Wagenaar JA, Speksnijder DC. Using Implementation Mapping to develop an intervention program to support veterinarians' adherence to the guideline on Streptococcus suis clinical practice in weaned pigs. PLoS One 2024; 19:e0299905. [PMID: 38635508 PMCID: PMC11025762 DOI: 10.1371/journal.pone.0299905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/17/2024] [Indexed: 04/20/2024] Open
Abstract
Streptococcus suis (S. suis) infections in weaned pigs are common and responsible for a high consumption of antimicrobials, and their presence is assumed to be multi-factorial. A specific evidence-based veterinary guideline to support the control of S. suis in weaned pigs was developed for veterinary practitioners in the Netherlands in 2014. Adherence to the S. suis clinical practice guideline helps veterinary practitioners to prevent and control the disease in a systematical approach and thereby improve antimicrobial stewardship and contribute to the prevention of antimicrobial resistance in animals and humans. The impact of such a clinical practice guideline on (animal) disease management depends not only on its content, but also largely on the extent to which practitioners adhere to the clinical guideline in practice. When the S. suis guideline was published, no specific activities were undertaken to support veterinarians' uptake and implementation, thereby contributing to suboptimal adherence in clinical practice. As the S. suis guideline was comprehensively written by veterinary experts following an evidence-based approach, our aim was not to judge the (scientific) quality of the guideline but to study the possibility to improve the currently low adherence of this guideline in veterinary practice. This paper describes the systematic development, using Implementation Mapping, of a theory-based intervention program to support swine veterinarians' adherence to the S. suis guideline. The knowledge, skills, beliefs about capabilities, and beliefs about consequences domains are addressed in the program, which includes seven evidence-based methods (modelling, tailoring, feedback, discussion, persuasive communication, active learning, and self-monitoring) for use in program activities such as a peer-learning meeting and an e-learning module. The intervention program has been developed for practicing swine veterinarians, lasts eight months, and is evaluated through a stepped-wedge design. The Implementation Mapping approach ensured that all relevant adopters and implementers were involved, and that outcomes, determinants (influencing factors), and objectives were systematically discussed.
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Affiliation(s)
- Isaura Y. A. Wayop
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Emely de Vet
- Consumption and Healthy Lifestyles Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Joanne N. Leerlooijer
- Knowledge, Technology and Innovation, Wageningen University and Research, Wageningen, The Netherlands
| | - Jaap A. Wagenaar
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - David C. Speksnijder
- Faculty of Veterinary Medicine, Department Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- University Farm Animal Clinic ULP, Harmelen, The Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Dankittipong N, Broek JVD, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS. Prev Vet Med 2024; 225:106156. [PMID: 38402649 DOI: 10.1016/j.prevetmed.2024.106156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10-3 to 2.5∙10-3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10-3 and 0.8∙10-3, increasing to 0.9∙10-3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 - 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 - 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 - 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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Schwartzman JA, Lebreton F, Salamzade R, Shea T, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo ILBC, Sgardioli BF, Prichula J, Guedes Frazzon AP, Giribet G, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, Gilmore MS. Global diversity of enterococci and description of 18 previously unknown species. Proc Natl Acad Sci U S A 2024; 121:e2310852121. [PMID: 38416678 DOI: 10.1073/pnas.2310852121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/06/2023] [Indexed: 03/01/2024] Open
Abstract
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.
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Affiliation(s)
- Julia A Schwartzman
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Biology, University of Southern California, Los Angeles, CA 90089
| | - Francois Lebreton
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Rauf Salamzade
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Melissa J Martin
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Katharina Schaufler
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- University of Greifswald, Institute of Pharmacy, Greifswald 17489, Germany
- Kiel University and University Medical Center Schleswig-Holstein, Institute of Infection Medicine, Kiel 24105, Germany
| | - Aysun Urhan
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Thomas Abeel
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft 2628XE, The Netherlands
| | - Ilana L B C Camargo
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Bruna F Sgardioli
- Laboratório de Epidemiologia e Microbiologia Moleculares, Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos - SP 13566-590, Brazil
| | - Janira Prichula
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Federal University of Health Sciences of Porto Alegre, Porto Alegre - RS 90050-170, Brazil
| | - Ana Paula Guedes Frazzon
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre - RS, 90010-150, Brazil
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Daria Van Tyne
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA 15213
| | | | - Charles J Innis
- New England Aquarium, Animal Health Department and Anderson Cabot Center for Ocean Life, Boston, MA 02110
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Ryan M Whipple
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Michael S Gilmore
- Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA 02144
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
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5
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Rubio-Garcia A, Zomer AL, Guo R, Rossen JWA, van Zeijl JH, Wagenaar JA, Luiken REC. Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation. PLoS One 2023; 18:e0295072. [PMID: 38051704 DOI: 10.1371/journal.pone.0295072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
Animal rehabilitation centres provide a unique opportunity to study the microbiome of wild animals because subjects will be handled for their treatment and can therefore be sampled longitudinally. However, rehabilitation may have unintended consequences on the animals' microbiome because of a less varied and suboptimal diet, possible medical treatment and exposure to a different environment and human handlers. Our study describes the gut microbiome of two large seal cohorts, 50 pups (0-30 days old at arrival) and 23 weaners (more than 60 days old at arrival) of stranded harbour seals admitted for rehabilitation at the Sealcentre Pieterburen in the Netherlands, and the effect of rehabilitation on it. Faecal samples were collected from all seals at arrival, two times during rehabilitation and before release. Only seals that did not receive antimicrobial treatment were included in the study. The average time in rehabilitation was 95 days for the pups and 63 days for the weaners. We observed that during rehabilitation, there was an increase in the relative abundance of some of the Campylobacterota spp and Actinobacteriota spp. The alpha diversity of the pups' microbiome increased significantly during their rehabilitation (p-value <0.05), while there were no significant changes in alpha diversity over time for weaners. We hypothesize that aging is the main reason for the observed changes in the pups' microbiome. At release, the sex of a seal pup was significantly associated with the microbiome's alpha (i.e., Shannon diversity was higher for male pups, p-value <0.001) and beta diversity (p-value 0.001). For weaners, variation in the microbiome composition (beta diversity) at release was partly explained by sex and age of the seal (p-values 0.002 and 0.003 respectively). We mainly observed variables known to change the gut microbiome composition (e.g., age and sex) and conclude that rehabilitation in itself had only minor effects on the gut microbiome of seal pups and seal weaners.
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Affiliation(s)
- Ana Rubio-Garcia
- Veterinary and Research Department, Sealcentre Pieterburen, Pieterburen, The Netherlands
- Division of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary Medicine, Utrecht, The Netherlands
| | - Aldert L Zomer
- Division of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary Medicine, Utrecht, The Netherlands
| | - Ruoshui Guo
- Division of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary Medicine, Utrecht, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States of America
- Laboratory of Clinical Microbiology and Infectious Diseases & Isala Academy, Isala hospital, Zwolle, The Netherlands
| | - Jan H van Zeijl
- Department of Medical Microbiology Friesland and Noordoostpolder, Certe, Leeuwarden, The Netherlands
| | - Jaap A Wagenaar
- Division of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary Medicine, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Roosmarijn E C Luiken
- Division of Infectious Diseases and Immunology, Utrecht University Faculty of Veterinary Medicine, Utrecht, The Netherlands
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Morgan AL, Woolhouse ME, Wagenaar JA, van Bunnik BA. Modelling the effects of antibiotic usage in livestock on human salmonellosis. One Health 2023; 17:100639. [PMID: 38024252 PMCID: PMC10665166 DOI: 10.1016/j.onehlt.2023.100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotic usage in livestock has been suggested as a driver of antimicrobial resistance in human and livestock populations. This has contributed to the implementation of stewardship programs to curtail usage of antibiotics in livestock. However, the consequences of antibiotic curtailment in livestock on human health are poorly understood. There is the potential for increases in the carriage of pathogens such as Salmonella spp. in livestock, and subsequent increases in human foodborne disease. We use a mathematical model fitted to four case studies, ampicillin and tetracycline usage in fattening pig and broiler poultry populations, to explore the impact of curtailing antibiotic usage in livestock on salmonellosis in humans. Increases in the daily incidence of salmonellosis and a decrease in the proportion of resistant salmonellosis were identified following curtailment of antibiotic usage in livestock. The extent of these increases in human foodborne disease ranged from negligible, to controllable through interventions to target the farm-to-fork pathway. This study provides a motivating example of one plausible scenario following curtailment of antibiotic usage in livestock and suggests that a focus on ensuring good farm-to-fork hygiene and livestock biosecurity is sufficient to mitigate the negative human health consequences of antibiotic stewardship in livestock populations.
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Affiliation(s)
- Alex L.K. Morgan
- Centre for Immunity, Infection & Evolution and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Mark E.J. Woolhouse
- Centre for Immunity, Infection & Evolution and School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jaap A. Wagenaar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Wageningen Bioveterinary Research, Lelystad, Netherlands
- WHO Collaborating Center for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
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7
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Rattigan R, Wajda L, Vlasblom AA, Wolfe A, Zomer AL, Duim B, Wagenaar JA, Lawlor PG. Safety Evaluation of an Intranasally Applied Cocktail of Lactococcus lactis Strains in Pigs. Animals (Basel) 2023; 13:3442. [PMID: 38003060 PMCID: PMC10668741 DOI: 10.3390/ani13223442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Three Lactococcus lactis strains from the nasal microbiota of healthy pigs were identified as candidates for reducing MRSA in pigs. The safety of nasal administration of a cocktail of these strains was examined in new-born piglets. Six days pre-farrowing, twelve sows were assigned to the placebo or cocktail group (n = 6/group). After farrowing, piglets were administered with either 0.5 mL of the placebo or the cocktail to each nostril. Health status and body weight were monitored at regular time points. Two piglets from three sows/treatment group were euthanised at 24 h, 96 h and 14 d after birth, and conchae, lung and tonsil samples were collected for histopathological and gene expression analysis. Health scores were improved in the cocktail group between d1-5. Body weight and daily gains did not differ between groups. Both groups displayed histological indications of euthanasia and inflammation in the lungs, signifying the findings were not treatment related. The expression of pBD2, TLR9 and IL-1β in the nasal conchae differed between groups, indicating the cocktail has the potential to modulate immune responses. In summary, the L. lactis cocktail was well tolerated by piglets and there was no negative impact on health scores, growth or lung histopathology indicating that it is safe for administration to new-born piglets.
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Affiliation(s)
- Ruth Rattigan
- Teagasc Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 County Cork, Ireland
| | - Lukasz Wajda
- Teagasc Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 County Cork, Ireland
| | - Abel A. Vlasblom
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Alan Wolfe
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Aldert L. Zomer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Birgitta Duim
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Peadar G. Lawlor
- Teagasc Pig Development Department, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, P61 C996 County Cork, Ireland
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Dankittipong N, Alderliesten JB, Van den Broek J, Dame-Korevaar MA, Brouwer MSM, Velkers FC, Bossers A, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Prev Vet Med 2023; 219:105998. [PMID: 37647719 DOI: 10.1016/j.prevetmed.2023.105998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria comparable to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed over 12 pens on the day of hatch (day 0). On day 5, half of the 10 remaining chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). To evaluate the effect of antibiotic treatment, amoxicillin was given twice daily in drinking water in 6 of the 12 pens from days 2-6. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or by other differences between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2-6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jesse B Alderliesten
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - M Anita Dame-Korevaar
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Alex Bossers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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Stege PB, Hordijk J, Sandholt AKS, Zomer AL, Viveen MC, Rogers MRC, Salomons M, Wagenaar JA, Mughini-Gras L, Willems RJL, Paganelli FL. Gut Colonization by ESBL-Producing Escherichia coli in Dogs Is Associated with a Distinct Microbiome and Resistome Composition. Microbiol Spectr 2023; 11:e0006323. [PMID: 37404183 PMCID: PMC10434115 DOI: 10.1128/spectrum.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The gut microbiome of humans and animals acts as a reservoir of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC). Dogs are known for having a high prevalence of ESBL-EC in their gut microbiota, although their ESBL-EC carrier status often shifts over time. We hypothesized that the gut microbiome composition of dogs is implicated in ESBL-EC colonization status. Therefore, we assessed whether ESBL-EC carriage in dogs is associated with changes in the gut microbiome and resistome. Fecal samples were collected longitudinally from 57 companion dogs in the Netherlands every 2 weeks for a total of 6 weeks (n = 4 samples/dog). Carriage of ESBL-EC was determined through selective culturing and PCR and in line with previous studies, we observed a high prevalence of ESBL-EC carriage in dogs. Using 16s rRNA gene profiling we found significant associations between detected ESBL-EC carriage and an increased abundance of Clostridium sensu stricto 1, Enterococcus, Lactococcus, and the shared genera of Escherichia-Shigella in the dog microbiome. A resistome capture sequencing approach (ResCap) furthermore, revealed associations between detected ESBL-EC carriage and the increased abundance of the antimicrobial resistance genes: cmlA, dfrA, dhfR, floR, and sul3. In summary, our study showed that ESBL-EC carriage is associated with a distinct microbiome and resistome composition. IMPORTANCE The gut microbiome of humans and animals is an important source of multidrug resistant pathogens, including beta-lactamase-producing Escherichia coli (ESBL-EC). In this study, we assessed if the carriage of ESBL-EC in dogs was associated with changes in gut composition of bacteria and antimicrobial resistant genes (ARGs). Therefore, stool samples from 57 dogs were collected every 2 weeks for a total of 6 weeks. Sixty eight percent of the dogs carried ESBL-EC during at least one of the time points analyzed. By investigating the gut microbiome and resistome composition, we observed specific changes at time points when dogs were colonized with ESBL-EC compared to time points whenESBL-EC were not detected. In conclusion, our study highlights the importance to study the microbial diversity in companion animals, as gut colonization of particular antimicrobial resistant bacteria might be an indication of a changed microbial composition that is associated with the selection of particular ARGs.
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Affiliation(s)
- Paul B. Stege
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Joost Hordijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arnar K. S. Sandholt
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Marco C. Viveen
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Malbert R. C. Rogers
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Moniek Salomons
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, Utrecht, The Netherlands
| | - Rob J. L. Willems
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
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10
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Schwartzman JA, Lebreton F, Salamzade R, Martin MJ, Schaufler K, Urhan A, Abeel T, Camargo IL, Sgardioli BF, Prichula J, Frazzon APG, Van Tyne D, Treinish G, Innis CJ, Wagenaar JA, Whipple RM, Manson AL, Earl AM, Gilmore MS. Global diversity of enterococci and description of 18 novel species. bioRxiv 2023:2023.05.18.540996. [PMID: 37293047 PMCID: PMC10245769 DOI: 10.1101/2023.05.18.540996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Enterococci are commensal gut microbes of most land animals. They diversified over hundreds of millions of years adapting to evolving hosts and host diets. Of over 60 known enterococcal species, Enterococcus faecalis and E. faecium uniquely emerged in the antibiotic era among leading causes of multidrug resistant hospital-associated infection. The basis for the association of particular enterococcal species with a host is largely unknown. To begin deciphering enterococcal species traits that drive host association, and to assess the pool of Enterococcus-adapted genes from which known facile gene exchangers such as E. faecalis and E. faecium may draw, we collected 886 enterococcal strains from nearly 1,000 specimens representing widely diverse hosts, ecologies and geographies. This provided data on the global occurrence and host associations of known species, identifying 18 new species in the process expanding genus diversity by >25%. The novel species harbor diverse genes associated with toxins, detoxification, and resource acquisition. E. faecalis and E. faecium were isolated from a wide diversity of hosts highlighting their generalist properties, whereas most other species exhibited more restricted distributions indicative of specialized host associations. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades as well as genes associated with range expansion, such as B-vitamin biosynthesis and flagellar motility. Collectively, this work provides an unprecedentedly broad and deep view of the genus Enterococcus, potential threats to human health, and new insights into its evolution.
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Affiliation(s)
- Julia A. Schwartzman
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Department of Biology, University of Southern California, Los Angeles, CA, USA
| | - Francois Lebreton
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rauf Salamzade
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Melissa J. Martin
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Katharina Schaufler
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- University of Greifswald, Institute of Pharmacy, Greifswald, Germany
- Kiel University and University Medical Center Schleswig-Holstein, Institute of Infection Medicine, Kiel, Germany
| | - Aysun Urhan
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Thomas Abeel
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ilana L.B.C Camargo
- Laboratório de Epidemiologia e Microbiologia Moleculares (LEMiMo), Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Bruna F. Sgardioli
- Laboratório de Epidemiologia e Microbiologia Moleculares (LEMiMo), Departamento de Física e Ciências Interdisciplinares, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Janira Prichula
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Ana Paula Guedes Frazzon
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Department of Microbiology, Immunology and Parasitology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Daria Van Tyne
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
| | | | | | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Ryan M. Whipple
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael S. Gilmore
- Departments of Ophthalmology and Microbiology, Mass Eye and Ear, and Harvard Medical School, Boston, MA,USA
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11
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Duijvestijn MBHM, Schuurman NNMP, Vernooij JCM, van Leeuwen MAJM, Bosch BJ, van den Brand JMA, Wagenaar JA, van Kuppeveld FJM, Egberink HF, Verhagen JH. Serological Survey of Retrovirus and Coronavirus Infections, including SARS-CoV-2, in Rural Stray Cats in The Netherlands, 2020-2022. Viruses 2023; 15:1531. [PMID: 37515217 PMCID: PMC10385588 DOI: 10.3390/v15071531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Stray cats can host (zoonotic) viral pathogens and act as a source of infection for domestic cats or humans. In this cross-sectional (sero)prevalence study, sera from 580 stray cats living in 56 different cat groups in rural areas in The Netherlands were collected from October 2020 to July 2022. These were used to investigate the prevalence of the cat-specific feline leukemia virus (FeLV, n = 580), the seroprevalence of the cat-specific feline viruses feline immunodeficiency virus (FIV, n = 580) and feline coronavirus (FCoV, n = 407), and the zoonotic virus severe acute respiratory coronavirus-2 (SARS-CoV-2, n = 407) using enzyme-linked immunosorbent assays (ELISAs). ELISA-positive results were confirmed using Western blot (FIV) or pseudovirus neutralization test (SARS-CoV-2). The FIV seroprevalence was 5.0% (95% CI (Confidence Interval) 3.4-7.1) and ranged from 0-19.0% among groups. FIV-specific antibodies were more often detected in male cats, cats ≥ 3 years and cats with reported health problems. No FeLV-positive cats were found (95% CI 0.0-0.6). The FCoV seroprevalence was 33.7% (95% CI 29.1-38.5) and ranged from 4.7-85.7% among groups. FCoV-specific antibodies were more often detected in cats ≥ 3 years, cats with reported health problems and cats living in industrial areas or countryside residences compared to cats living at holiday parks or campsites. SARS-CoV-2 antibodies against the subunit 1 (S1) and receptor binding domain (RBD) protein were detected in 2.7% (95% CI 1.4-4.8) of stray cats, but sera were negative in the pseudovirus neutralization test and therefore were considered SARS-CoV-2 suspected. Our findings suggest that rural stray cats in The Netherlands can be a source of FIV and FCoV, indicating a potential risk for transmission to other cats, while the risk for FeLV is low. However, suspected SARS-CoV-2 infections in these cats were uncommon. We found no evidence of SARS-CoV-2 cat-to-cat spread in the studied stray cat groups and consider the likelihood of spillover to humans as low.
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Affiliation(s)
- Mirjam B H M Duijvestijn
- Clinical Infectiology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Nancy N M P Schuurman
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Johannes C M Vernooij
- Division of Farm Animal Health, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, The Netherlands
| | | | - Berend-Jan Bosch
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Judith M A van den Brand
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Clinical Infectiology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Herman F Egberink
- Clinical Infectiology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Josanne H Verhagen
- Clinical Infectiology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Section of Virology, Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
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12
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van der Graaf-van Bloois L, Chen H, Wagenaar JA, Zomer AL. Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping. Microb Genom 2023; 9. [PMID: 37130055 DOI: 10.1099/mgen.0.001007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Vibrio parahaemolyticus is an important food-borne human pathogen and presents immunogenic surface polysaccharides, which can be used to distinguish problematic and disease-causing lineages. V. parahaemolyticus is divided in 16 O-serotypes (O-antigen) and 71 K-serotypes (K-antigen). Agglutination tests are still the gold standard for serotyping, but many V. parahaemolyticus isolates are not typable by agglutination. An alternative for agglutination tests is genotyping using whole-genome sequencing data, by which K- and O- genotypes have been curated and identified previously for other clinically relevant organisms with the software tool Kaptive. In this study, V. parahaemolyticus isolates were serotyped and sequenced, and all known and several novel O- and K-loci were identified. We developed Kaptive databases for all O- and K-loci after manual curation of the loci. In our study, we could genotype the O- and K-loci of 98 and 93 % of the genomes, respectively, with a Kaptive confidence score higher than 'none'. The newly developed Kaptive databases with the identified V. parahaemolyticus O- and K-loci can be used to identify the O- and K-genotypes of V. parahaemolyticus isolates from genome sequences.
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Affiliation(s)
- Linda van der Graaf-van Bloois
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Hongyou Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, PR China
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Aldert L Zomer
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
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13
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Anwar Sani R, Wagenaar JA, Dinar TEHA, Sunandar S, Nurbiyanti N, Suandy I, Pertela G, Jahja EJ, Purwanto B, van Geijlswijk IM, Speksnijder DC. The comparison and use of tools for quantification of antimicrobial use in Indonesian broiler farms. Front Vet Sci 2023; 10:1092302. [PMID: 36968477 PMCID: PMC10036347 DOI: 10.3389/fvets.2023.1092302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/02/2023] [Indexed: 03/12/2023] Open
Abstract
IntroductionIndonesia has a large broiler industry with extensive antimicrobial use (AMU) according to empirical evidence. However, there are no quantitative data of on-farm AMU. Quantification of AMU at farm level is crucial to guide interventions on antimicrobial stewardship (AMS). The objective of this study was to compare on-farm AMU monitoring methods, to assess which monitoring method is best suited to gain insight in the quantitative AMU at farm level in medium-scale Indonesian broiler farms.MethodAMU was calculated using four different indicators—mg/PCU (mass-based), TFUDDindo (Treatment Frequency of Used Daily Dose, dose-based), TFDDDvet (Treatment Frequency of Defined Daily Dose, dose-based), and TFcount − based (count-based)—for the total AMU of 98 production cycles with an average length of 30 days.ResultsBroilers were exposed to an average of 10 days of antimicrobial treatments per production cycle, whereas 60.8% of the antimicrobials belonged to the Highest Priority Critically Important Antimicrobials (HPCIAs). For each pair of indicators, the Spearman rank correlation coefficient was calculated to assess if the production cycles were ranked consistently in increasing AMU across the different indicators. The correlation varied between 0.4 and 0.8.DiscussionThis study illustrates the considerable difference in the ranking of AMU between the different indicators. In a setting comparable to medium-scale broiler farms in Indonesia, where resources are scarce and there is no professional oversight, the TFcount − based method is best suitable. Before implementing an AMU monitoring method, careful consideration of the use-indicators is paramount to achieve fair benchmarking.
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Affiliation(s)
- Rianna Anwar Sani
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jaap A. Wagenaar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Wageningen Bioveterinary Research, Lelystad, Netherlands
- WHO Collaborating Center for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
| | - Tagrid E. H. A. Dinar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Sunandar Sunandar
- Center for Indonesian Veterinary Analytical Studies (CIVAS), Bogor, Indonesia
| | - Nofita Nurbiyanti
- Center for Indonesian Veterinary Analytical Studies (CIVAS), Bogor, Indonesia
| | - Imron Suandy
- Ministry of Agriculture of the Republic of Indonesia, Jakarta, Indonesia
| | - Gian Pertela
- Laboratory Services and Surveillance Department, PT Medion Farma Jaya, Bandung, Indonesia
| | - Elvina J. Jahja
- Animal Health Department, PT Medion Farma Jaya, Bandung, Indonesia
| | - Budi Purwanto
- Technical Education and Consultation Department, PT Medion Ardhika Bhakti, Bandung, Indonesia
| | | | - Ingeborg M. van Geijlswijk
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - David C. Speksnijder
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- WHO Collaborating Center for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, Netherlands
- University Farm Animal Clinic, Harmelen, Netherlands
- *Correspondence: David C. Speksnijder
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14
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van der Graaf-van Bloois L, Duim B, Looft T, Veldman KT, Zomer AL, Wagenaar JA. Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution. Microb Genom 2023; 9. [PMID: 36862577 PMCID: PMC10132061 DOI: 10.1099/mgen.0.000934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Campylobacter fetus is a pathogen, which is primarily associated with fertility problems in sheep and cattle. In humans, it can cause severe infections that require antimicrobial treatment. However, knowledge on the development of antimicrobial resistance in C. fetus is limited. Moreover, the lack of epidemiological cut-off values (ECOFFs) and clinical breakpoints for C. fetus hinders consistent reporting about wild-type and non-wild-type susceptibility. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus and to determine the C. fetus resistome [the collection of all antimicrobial resistance genes (ARGs) and their precursors] to describe the genomic basis of antimicrobial resistance in C. fetus isolates over time. Whole-genome sequences of 295 C. fetus isolates, including isolates that were isolated in the period 1939 till the mid 1940s, before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers, and phenotypic antimicrobial susceptibility was obtained for a selection of 47 isolates. C. fetus subspecies fetus (Cff) isolates showed multiple phenotypic antimicrobial resistances compared to C. fetus subspecies venerealis (Cfv) isolates that were only intrinsic resistant to nalidixic acid and trimethoprim. Cff isolates showed elevated minimal inhibitory concentrations for cefotaxime and cefquinome that were observed in isolates from 1943 onwards, and Cff isolates contained gyrA substitutions, which conferred resistance to ciprofloxacin. Resistances to aminoglycosides, tetracycline and phenicols were linked to acquired ARGs on mobile genetic elements. A plasmid-derived tet(O) gene in a bovine Cff isolate in 1999 was the first mobile genetic element observed, followed by detection of mobile elements containing tet(O)-aph(3')-III and tet(44)-ant(6)-Ib genes, and a plasmid from a single human isolate in 2003, carrying aph(3')-III-ant(6)-Ib and a chloramphenicol resistance gene (cat). The presence of ARGs in multiple mobile elements distributed among different Cff lineages highlights the risk for spread and further emergence of AMR in C. fetus. Surveillance for these resistances requires the establishment of ECOFFs for C. fetus.
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Affiliation(s)
- Linda van der Graaf-van Bloois
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Torey Looft
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Aldert L Zomer
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands
| | - Jaap A Wagenaar
- Department Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective / WOAH Reference Laboratory for Campylobacteriosis, Utrecht/Lelystad, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
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15
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Naing SY, Duim B, Broens EM, Schweitzer V, Zomer A, van der Graaf-van Bloois L, van der Meer C, Stellingwerff L, Fluit AC, Wagenaar JA. Molecular Characterization and Clinical Relevance of Taxonomic Reassignment of Staphylococcus schleiferi Subspecies into Two Separate Species, Staphylococcus schleiferi and Staphylococcus coagulans. Microbiol Spectr 2023; 11:e0467022. [PMID: 36853031 PMCID: PMC10101015 DOI: 10.1128/spectrum.04670-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
Staphylococcus schleiferi is an opportunistic pathogen in humans and dogs. Recent taxonomic reassignment of its subspecies (S. schleiferi subsp. schleiferi and S. schleiferi subsp. coagulans) into two separate species (S. schleiferi and S. coagulans) lacks supporting data for diagnostic implications and clinical relevance. We aimed to confirm the reclassification of S. schleiferi by using genomic and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data for a large set of isolates from humans and animals to investigate their molecular epidemiology and clinical relevance. Routine MALDI-TOF analysis and Illumina sequencing were performed on 165 S. schleiferi isolates from the Netherlands. With 33 publicly available genomes, the study included 198 genomes from 149 dogs, 34 humans, and 15 other sources. The Type Strain Genome Server was used to identify species in the genomes, and the MALDI-TOF MS database was extended to improve species differentiation. MALDI-TOF did not discriminate between S. schleiferi and S. coagulans. Genome phylogeny distinguished the two species in two monophyletic clusters. S. schleiferi isolates originated from humans, while S. coagulans isolates were found in animals and three human isolates clustering with the animal isolates. The sialidase B gene (nanB) was a unique marker gene for S. schleiferi, whereas the chrA gene was exclusive for S. coagulans. The mecA gene was exclusively detected in S. coagulans, as were the lnu(A), blaZ, erm(B/C), tet(O/M), and aac(6')-aph(2'') genes. The MALDI-TOF database extension did not improve differentiation between the two species. Even though our whole-genome sequencing-based approach showed clear differentiation between these two species, it remains critical to identify S. schleiferi and S. coagulans correctly in routine diagnostics. IMPORTANCE This study clearly shows that S. schleiferi is a concern in human hospital settings, whereas S. coagulans predominantly causes infections in animals. S. coagulans is more resistant to antibiotics and can sometimes transmit to humans via exposure to infected dogs. Even though genome-based methods can clearly differentiate the two species, current diagnostic methods used routinely in clinical microbiology laboratories cannot distinguish the two bacterial species.
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Affiliation(s)
- Soe Yu Naing
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Birgitta Duim
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Els M. Broens
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Valentijn Schweitzer
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Aldert Zomer
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Coby van der Meer
- Certe Medical Microbiology Friesland and Noordoostpolder, Leeuwarden, the Netherlands
| | - Luutsen Stellingwerff
- Certe Medical Microbiology Friesland and Noordoostpolder, Leeuwarden, the Netherlands
| | - Ad C. Fluit
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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16
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Theelen MJP, Luiken REC, Wagenaar JA, Sloet van Oldruitenborgh-Oosterbaan MM, Rossen JWA, Schaafstra FJWC, van Doorn DA, Zomer AL. Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome. Microbiome 2023; 11:33. [PMID: 36850017 PMCID: PMC9969626 DOI: 10.1186/s40168-023-01465-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids. METHODS In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples. RESULTS Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later. CONCLUSIONS Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.
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Affiliation(s)
- Mathijs J. P. Theelen
- Department of Clinical Sciences (Equine Sciences), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112, 3584 CM Utrecht, the Netherlands
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Roosmarijn E. C. Luiken
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | | | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, the Netherlands
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Ste #1100, Salt Lake City, Utah 84112 USA
| | - Femke J. W. C. Schaafstra
- HAS University of Applied Sciences, Onderwijsboulevard 221, 5223 DE ‘s-Hertogenbosch, the Netherlands
- Department of Population Health Sciences (Farm Animal Health), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands
| | - David A. van Doorn
- Department of Clinical Sciences (Equine Sciences), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 112, 3584 CM Utrecht, the Netherlands
- Department of Population Health Sciences (Farm Animal Health), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, 3584 CL Utrecht, the Netherlands
| | - Aldert L. Zomer
- Department of Biomolecular Health Sciences (Infectious Diseases and Immunology), Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, 3584 CL Utrecht, the Netherlands
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17
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Wayop IYA, de Vet E, Wagenaar JA, Speksnijder DC. Why Veterinarians (Do Not) Adhere to the Clinical Practice Streptococcus suis in Weaned Pigs Guideline: A Qualitative Study. Antibiotics (Basel) 2023; 12:antibiotics12020320. [PMID: 36830232 PMCID: PMC9952329 DOI: 10.3390/antibiotics12020320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The Netherlands has been very successful in the last decade in reducing antimicrobial use in animals. On about a quarter of farms, antimicrobial use in weaned pigs remains relatively high. As Streptococcus suis (S. suis) infections are responsible for a high consumption of antimicrobials, a specific veterinary guideline to control S. suis was developed, but seemed to be poorly adopted by veterinarians. Guided by the theoretical domains framework, the aim of this study was to identify determinants influencing veterinarians' adherence to this guideline. We interviewed 13 pig veterinarians. Interviewees described multiple approaches to managing S. suis problems and adherence to the guideline. Mentioned determinants could be categorized into 12 theoretical domains. The following six domains were mentioned in all interviews: knowledge, skills, beliefs about capabilities, beliefs about consequences, social influences, and environmental context and resources. The insights derived from this study are relevant for understanding factors influencing veterinarians' adoption of scientific evidence and guidelines and can be used to develop evidence-based implementation strategies for veterinary guidelines.
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Affiliation(s)
- Isaura Y. A. Wayop
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Emely de Vet
- Consumption and Healthy Lifestyles Group, Wageningen University and Research, 6700 EW Wageningen, The Netherlands
| | - Jaap A. Wagenaar
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - David C. Speksnijder
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- University Farm Animal Clinic ULP, Reijerscopse Overgang 1, 3481 LZ Harmelen, The Netherlands
- Correspondence:
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18
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Kardomatea N, Hopman NEM, van Geijlswijk IM, Portengen L, Wagenaar JA, Heederik DJJ, Broens EM. Quantifying topical antimicrobial use before and during participation in an antimicrobial stewardship programme in Dutch companion animal clinics. PLoS One 2023; 18:e0283956. [PMID: 37053211 PMCID: PMC10101466 DOI: 10.1371/journal.pone.0283956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
The emergence of bacterial strains resistant to topical antimicrobials in both human and veterinary medicine has raised concerns over retaining the efficacy of these preparations. Yet, little information is available regarding the use of topical antimicrobials in either sector for planning targeted interventions. This study aims to quantify the use of topical antimicrobials in 44 Dutch companion animal clinics before and during their participation in an antimicrobial stewardship programme (ASP), to explore the effect of the intervention on topical antimicrobial use (AMU). Hence, prescription and clinic animal population data, collected from July 2012 until June 2018 were used. Specifically, the period from July 2012 until June 2015 was defined as pre-intervention period, whereas clinics started to participate in the ASP from March 2016 onwards. As quantification metric, the Defined Daily Dose for Animals (DDDA) was used and a mixed effect times series model with auto-regression was applied to monthly topical AMU data. The intervention effect was modelled using a step function with a change in (linear) time trend and clinic characteristics, as potential determinants of topical AMU, were assessed using a multivariable regression model. A seasonal pattern was identified, in the pre-intervention period, where topical AMU was highest in July-August and lowest in February-March. In addition, total topical AMU appeared to significantly decrease over time in the pre-intervention period and the proportion of dogs in the clinic was positively associated with topical AMU. The intervention effect was significant only for second line and for skin product AMU. This study demonstrates that during participation in an ASP, second line and skin product AMU decreased in Dutch companion animal clinics. Additionally, this study demonstrates the existence of a seasonal effect and a decrease in topical AMU over time already before introduction of a targeted intervention.
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Affiliation(s)
- Nafsika Kardomatea
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nonke E M Hopman
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ingeborg M van Geijlswijk
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lützen Portengen
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dick J J Heederik
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Els M Broens
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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19
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Kannekens‐Jager MM, de Rooij MMT, de Groot Y, Biesbroeck E, de Jong MK, Pijnacker T, Smit LAM, Schuurman N, Broekhuizen‐Stins MJ, Zhao S, Duim B, Langelaar MFM, Stegeman A, Kooistra HS, Radstake C, Egberink HF, Wagenaar JA, Broens EM. SARS-CoV-2 infection in dogs and cats is associated with contact to COVID-19-positive household members. Transbound Emerg Dis 2022; 69:4034-4040. [PMID: 36163676 PMCID: PMC9538208 DOI: 10.1111/tbed.14713] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/25/2022] [Accepted: 09/21/2022] [Indexed: 02/07/2023]
Abstract
Several domestic and wild animal species are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Reported (sero)prevalence in dogs and cats vary largely depending on the target population, test characteristics, geographical location and time period. This research assessed the prevalence of SARS-CoV-2-positive cats and dogs (PCR- and/or antibody positive) in two different populations. Dogs and cats living in a household with at least one confirmed COVID-19-positive person (household (HH) study; 156 dogs and 152 cats) and dogs and cats visiting a veterinary clinic (VC) (VC study; 183 dogs and 140 cats) were sampled and tested for presence of virus (PCR) and antibodies. Potential risk factors were evaluated and follow-up of PCR-positive animals was performed to determine the duration of virus shedding and to detect potential transmission between pets in the same HH. In the HH study, 18.8% (27 dogs, 31 cats) tested SARS-CoV-2 positive (PCR- and/or antibody positive), whereas in the VC study, SARS-CoV-2 prevalence was much lower (4.6%; six dogs, nine cats). SARS-CoV-2 prevalence amongst dogs and cats was significantly higher in the multi-person HHs with two or more COVID-19-positive persons compared with multi-person HHs with only one COVID-19-positive person. In both study populations, no associations could be identified between SARS-CoV-2 status of the animal and health status, age or sex. During follow-up of PCR-positive animals, no transmission to other pets in the HH was observed despite long-lasting virus shedding in cats (up to 35 days). SARS-CoV-2 infection in dogs and cats appeared to be clearly associated with reported COVID-19-positive status of the HH. Our study supports previous findings and suggests a very low risk of pet-to-human transmission within HHs, no severe clinical signs in pets and a negligible pet-to-pet transmission between HHs.
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Affiliation(s)
- Marleen M. Kannekens‐Jager
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Myrna M. T. de Rooij
- Department of Population Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Yasmina de Groot
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Elena Biesbroeck
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Marja K. de Jong
- Department of Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Tera Pijnacker
- Department of Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Lidwien A. M. Smit
- Department of Population Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Nancy Schuurman
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Marian J. Broekhuizen‐Stins
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Shan Zhao
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Birgitta Duim
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Merel F. M. Langelaar
- Department of Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Arjan Stegeman
- Department of Population Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Hans S. Kooistra
- Department of Clinical SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Carien Radstake
- Stray Cat Foundation NetherlandsNieuw BeijerlandThe Netherlands
| | - Herman F. Egberink
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Jaap A. Wagenaar
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Els M. Broens
- Department of Biomolecular Health Sciences, Faculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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20
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Wegener A, Duim B, van der Graaf-van Bloois L, Zomer AL, Visser CE, Spaninks M, Timmerman AJ, Wagenaar JA, Broens EM. Within-Household Transmission and Bacterial Diversity of Staphylococcus pseudintermedius. Pathogens 2022; 11:pathogens11080850. [PMID: 36014971 PMCID: PMC9415945 DOI: 10.3390/pathogens11080850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 12/05/2022] Open
Abstract
Staphylococcus pseudintermedius can be transmitted between dogs and their owners and can cause opportunistic infections in humans. Whole genome sequencing was applied to identify the relatedness between isolates from human infections and isolates from dogs in the same households. Genome SNP diversity and distribution of plasmids and antimicrobial resistance genes identified related and unrelated isolates in both households. Our study shows that within-host bacterial diversity is present in S. pseudintermedius, demonstrating that multiple isolates from each host should preferably be sequenced to study transmission dynamics.
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Affiliation(s)
- Alice Wegener
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
- Correspondence:
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
| | - Caroline E. Visser
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, 1105 AZ Amsterdam, The Netherlands;
| | - Mirlin Spaninks
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands;
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands
| | - Els M. Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (A.W.); (L.v.d.G.-v.B.); (A.L.Z.); (A.J.T.); (J.A.W.); (E.M.B.)
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21
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Veldhuis FL, Nijsse R, Wagenaar JA, Arkesteijn G, Kooyman FNJ. Variation in haplotypes in single cysts of assemblages C and D, but not of assemblage E of Giardia duodenalis. BMC Microbiol 2022; 22:166. [PMID: 35754024 PMCID: PMC9235224 DOI: 10.1186/s12866-022-02581-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
Background Giardia duodenalis, a single-celled intestinal parasite, is divided into eight assemblages (A-H), with differences in host specificity. Giardia duodenalis reproduces asexually and cycles between the binucleated trophozoite (4 N) and the infectious cyst with four nuclei (16 N). Interaction between the nuclei is limited. Therefore, genetic drift causes differences in genetic make-up between the non-daughter nuclei; the allelic sequence heterozygosity (ASH). The ASH is low (0.01%—0.0023%) for the related assemblages A and E, higher (0.43–0.53) for assemblage B and much higher (0.74% -0.89%) for the assemblage C and D at the root of the phylogenetic tree. The heterozygosity in assemblage F, in the same clade as assemblage A and E, was unknown. The heterozygosity in the sequences of the gdh and dis3 genes was used as proxy for the ASH and whole genome amplification of single cysts followed by cloning and Sanger sequencing of dis3 fragment could reveal the genetic variation within the cyst. The aim of the study was to determine the level of heterozygosity within pooled and single cysts of different assemblages. Results The heterozygosity in gdh and dis3 was determined in pooled cysts of the assemblages A to F. Heterozygosity in the isolates of the assemblages C (n = 2) and D (n = 1) ranged from 0.41% to 0.82% for gdh and dis3 and no heterozygosity was found in the isolates of the assemblages A (n = 4), E (n = 3) and F (n = 3). The heterozygosity in assemblage B (n = 7) was intermediate (0% to 0.62%). Next, the number of haplotypes of dis3 was determined for single cysts of assemblages C, D and E. In the assemblages C and D, two to four haplotypes were found per cyst, while in assemblage E only one haplotype was identified. Conclusions Having high heterozygosity is characteristic for the assemblages C and D, while having a low heterozygosity is characteristic for the clade with the assemblages A, E and F. Presence of more than 1 haplotype per cyst in assemblage C and D suggests differences between the non-daughter nuclei, in contrast to the one haplotype in assemblage E.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02581-3.
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Affiliation(s)
- Floor L Veldhuis
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rolf Nijsse
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ger Arkesteijn
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frans N J Kooyman
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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22
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Takai S, Ohashi M, Suzuki Y, Sasaki Y, Kakuda T, Broens EM, Wagenaar JA, van Duijkeren E. Virulence plasmids in clinical isolates of Rhodococcus equi from sick foals in the Netherlands. Lett Appl Microbiol 2022; 75:908-912. [PMID: 35707941 DOI: 10.1111/lam.13769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/30/2022]
Abstract
Clinical samples from 123 foals with suspected rhodococcosis submitted to the Veterinary Microbiological Diagnostic Centre of the Faculty of Veterinary Medicine between 1993 and 2006 were tested for the presence of the virulence gene vapA. Of the 123 samples, 120 were vapA-positive and 3 vapA-negative Rhodococcus equi were isolated. The 120 vapA-positive R. equi were isolated from 70 tracheal wash, 19 lung tissues, 7 lymph nodes, 6 synovial fluids, 13 abscesses or pus and single isolates from the uterus, gut, cerebrospinal fluid, abdomen fluid and faeces. Of the 120 isolates, 46 were from Dutch warmblood horses, 23 from Friesian horses, 14 from Trotters, 4 from Holsteiners, 3 from Arab breed, 2 from ponies, 1 from a Welsh pony and 27 from undefined breed horses. Using plasmid profile analysis of the 120 isolates, 117 isolates contained the 85-kb type I plasmid, 2 contained the 87-kb type I plasmid and 1 contained the novel 52-kb non-mobilizable virulence plasmid reported recently. These results showed that the virulent R. equi strains harbouring a virulence plasmid of 85-kb type I or 87-kb type I, which have been detected in clinical isolates from five European countries, are widespread in the Netherlands. This is the first report of plasmid types of clinical R. equi isolates in the Netherlands.
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Affiliation(s)
- S Takai
- Department of Animal Hygiene, School of Veterinary Medicine and Animal Sciences, Kitasato University, Towada, Aomori, Japan
| | - M Ohashi
- Department of Animal Hygiene, School of Veterinary Medicine and Animal Sciences, Kitasato University, Towada, Aomori, Japan
| | - Y Suzuki
- Department of Animal Hygiene, School of Veterinary Medicine and Animal Sciences, Kitasato University, Towada, Aomori, Japan
| | - Y Sasaki
- Department of Animal Hygiene, School of Veterinary Medicine and Animal Sciences, Kitasato University, Towada, Aomori, Japan
| | - T Kakuda
- Department of Animal Hygiene, School of Veterinary Medicine and Animal Sciences, Kitasato University, Towada, Aomori, Japan
| | - E M Broens
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, the Netherlands
| | - J A Wagenaar
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, the Netherlands
| | - E van Duijkeren
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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23
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Luiken RE, Heederik DJ, Scherpenisse P, Van Gompel L, van Heijnsbergen E, Greve GD, Jongerius-Gortemaker BG, Tersteeg-Zijderveld MH, Fischer J, Juraschek K, Skarżyńska M, Zając M, Wasyl D, Wagenaar JA, Smit LA, Wouters IM, Mevius DJ, Schmitt H. Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries. Environ Res 2022; 208:112715. [PMID: 35033551 DOI: 10.1016/j.envres.2022.112715] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Livestock feces with antimicrobial resistant bacteria reaches the farm floor, manure pit, farm land and wider environment by run off and aerosolization. Little research has been done on the role of dust in the spread of antimicrobial resistance (AMR) in farms. Concentrations and potential determinants of antimicrobial resistance genes (ARGs) in farm dust are at present not known. Therefore in this study absolute ARG levels, representing the levels people and animals might be exposed to, and relative abundances of ARGs, representing the levels in the bacterial population, were quantified in airborne farm dust using qPCR. Four ARGs were determined in 947 freshly settled farm dust samples, captured with electrostatic dustfall collectors (EDCs), from 174 poultry (broiler) and 159 pig farms across nine European countries. By using linear mixed modeling, associations with fecal ARG levels, antimicrobial use (AMU) and farm and animal related parameters were determined. Results show similar relative abundances in farm dust as in feces and a significant positive association (ranging between 0.21 and 0.82) between the two reservoirs. AMU in pigs was positively associated with ARG abundances in dust from the same stable. Higher biosecurity standards were associated with lower relative ARG abundances in poultry and higher relative ARG abundances in pigs. Lower absolute ARG levels in dust were driven by, among others, summer season and certain bedding materials for poultry, and lower animal density and summer season for pigs. This study indicates different pathways that contribute to shaping the dust resistome in livestock farms, related to dust generation, or affecting the bacterial microbiome. Farm dust is a large reservoir of ARGs from which transmission to bacteria in other reservoirs can possibly occur. The identified determinants of ARG abundances in farm dust can guide future research and potentially farm management policy.
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Affiliation(s)
- Roosmarijn Ec Luiken
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands.
| | - Dick Jj Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Eri van Heijnsbergen
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | | | | | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Strasse 8-10, 10589, Berlin, Germany
| | - Katharina Juraschek
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Strasse 8-10, 10589, Berlin, Germany
| | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute (PIWet), Partyzantów 57, 24-100, Puławy, Poland
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute (PIWet), Partyzantów 57, 24-100, Puławy, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute (PIWet), Partyzantów 57, 24-100, Puławy, Poland
| | - Jaap A Wagenaar
- Department Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221RA, Lelystad, the Netherlands
| | - Lidwien Am Smit
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands
| | - Dik J Mevius
- Department Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221RA, Lelystad, the Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584CM, Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721MA, Bilthoven, the Netherlands
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24
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Sanders P, Mevius D, Veldman K, van Geijlswijk I, Wagenaar JA, Bonten M, Heederik D. Comparison of different antimicrobial use indicators and antimicrobial resistance data in food-producing animals. JAC Antimicrob Resist 2022; 3:dlab172. [PMID: 35224492 PMCID: PMC8569442 DOI: 10.1093/jacamr/dlab172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Objectives To explore the effects of using different indicators to quantify antimicrobial usage (AMU) in livestock and compare outcomes with antimicrobial resistance (AMR) data. Methods Three indicators were used to quantify AMU, two indicators in which the denominator varied: defined daily doses per average mass of the animals present per year (DDD/AY) and defined daily doses per population correction unit (DDD/PCU) and one in which the numerator varied: milligrams of active ingredient per PCU (mg/PCU). AMU was compared with antimicrobial resistance data from the national monitoring programme from 2013 to 2018 with the proportion of Escherichia coli isolates fully susceptible to a predefined panel of antimicrobials for the broiler, dairy cattle and pig farming livestock sectors in the Netherlands. Results The ranking of livestock sectors differs between sectors when using different indicators to express AMU. Dairy cattle rank lowest when expressing AMU in DDD/AY, followed by pigs and broilers corresponding to the rankings of the sectors for AMR. When changing the denominator to PCU, the ranking in AMU is reversed: use ranks highest in dairy cattle and lowest broilers. Conclusions Using different denominators in AMU indicators has a major impact on measured use. This might result in misinterpretation of effects of interventions on AMU and the associations of AMU with AMR across animal sectors. From an epidemiological perspective, indicators that take into account time at risk of exposure to antimicrobials are to be preferred and reflect the AMR risk most accurately.
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Affiliation(s)
- Pim Sanders
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands
| | - Dik Mevius
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Inge van Geijlswijk
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,Pharmacy Department, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marc Bonten
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Heederik
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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25
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Dankittipong N, Fischer EAJ, Swanenburg M, Wagenaar JA, Stegeman AJ, de Vos CJ. Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms. Antibiotics (Basel) 2022; 11:antibiotics11020281. [PMID: 35203883 PMCID: PMC8868399 DOI: 10.3390/antibiotics11020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022] Open
Abstract
Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.
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Affiliation(s)
- Natcha Dankittipong
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
- Correspondence:
| | - Egil A. J. Fischer
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Manon Swanenburg
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
| | - Jaap A. Wagenaar
- Department Biomolecular Health Science, Infectious Diseases & Immunology, Utrecht University, Androclusgebouw, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Arjan J. Stegeman
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Clazien J. de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
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26
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Naing SY, Hordijk J, Duim B, Broens EM, van der Graaf-van Bloois L, Rossen JW, Robben JH, Leendertse M, Wagenaar JA, Zomer AL. Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands. Pathogens 2022; 11:pathogens11020123. [PMID: 35215067 PMCID: PMC8875366 DOI: 10.3390/pathogens11020123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 01/27/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.
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Affiliation(s)
- Soe Yu Naing
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Els M. Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - John W. Rossen
- Department of Medical Microbiology, University Medical Center, University of Groningen, 9700 AB Groningen, The Netherlands;
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Joris H. Robben
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands;
| | - Masja Leendertse
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (S.Y.N.); (J.H.); (B.D.); (E.M.B.); (L.v.d.G.-v.B.); (M.L.); (J.A.W.)
- Correspondence:
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27
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Yang D, Heederik DJJ, Scherpenisse P, Van Gompel L, Luiken REC, Wadepohl K, Skarżyńska M, Van Heijnsbergen E, Wouters IM, Greve GD, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld M, Portengen L, Juraschek K, Fischer J, Zając M, Wasyl D, Wagenaar JA, Mevius DJ, Smit LAM, Schmitt H. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1883-1893. [PMID: 35466367 PMCID: PMC9244224 DOI: 10.1093/jac/dkac133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples. Conclusions qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.
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Affiliation(s)
| | - Dick J J Heederik
- 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
| | - 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
| | - Katharina Wadepohl
- Außenstelle für Epidemiologie, Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - 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
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Monique Tersteeg-Zijderveld
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lützen Portengen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - 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
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - 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
| | - 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
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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28
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Yang D, Heederik DJJ, Mevius DJ, Scherpenisse P, Luiken REC, Van Gompel L, Skarżyńska M, Wadepohl K, Chauvin C, Van Heijnsbergen E, Wouters IM, Greve GD, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld M, Zając M, Wasyl D, Juraschek K, Fischer J, Wagenaar JA, Smit LAM, Schmitt H. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:969-978. [PMID: 35061866 PMCID: PMC8969523 DOI: 10.1093/jac/dkac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives The occurrence and zoonotic potential of antimicrobial resistance (AMR) in pigs and broilers has been studied intensively in past decades. Here, we describe AMR levels of European pig and broiler farms and determine the potential risk factors. Methods We collected faeces from 181 pig farms and 181 broiler farms in nine European countries. Real-time quantitative PCR (qPCR) was used to quantify the relative abundance of four antimicrobial resistance genes (ARGs) [aph(3′)-III, erm(B), sul2 and tet(W)] in these faeces samples. Information on antimicrobial use (AMU) and other farm characteristics was collected through a questionnaire. A mixed model using country and farm as random effects was performed to evaluate the relationship of AMR with AMU and other farm characteristics. The correlation between individual qPCR data and previously published pooled metagenomic data was evaluated. Variance component analysis was conducted to assess the variance contribution of all factors. Results The highest abundance of ARG was for tet(W) in pig faeces and erm(B) in broiler faeces. In addition to the significant positive association between corresponding ARG and AMU levels, we also found on-farm biosecurity measures were associated with relative ARG abundance in both pigs and broilers. Between-country and between-farm variation can partially be explained by AMU. Different ARG targets may have different sample size requirements to represent the overall farm level precisely. Conclusions qPCR is an efficient tool for targeted assessment of AMR in livestock-related samples. The AMR variation between samples was mainly contributed to by between-country, between-farm and within-farm differences, and then by on-farm AMU.
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Affiliation(s)
- Dongsheng Yang
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Corresponding author. E-mail:
| | - Dick J. J. Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 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
| | - Peter Scherpenisse
- 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
| | - Liese Van Gompel
- 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 Wadepohl
- Außenstelle für Epidemiologie, Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Claire Chauvin
- ANSES, Epidemiology, Health and Welfare Unit, Paris, France
| | - 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
| | - Gerdit D. Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Monique Tersteeg-Zijderveld
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Dariusz Wasyl
- 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
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Lidwien A. M. Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - 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
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Abstract
Antimicrobial-resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know whether the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole-genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single-copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict whether the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial taxa, including Campylobacter, Escherichia coli and Salmonella, and has a taxon agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as a standalone tool and via a web interface.
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Affiliation(s)
- Linda van der Graaf-van Bloois
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Aldert L Zomer
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands.,WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from an One Health Perspective/OIE Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands
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Joosten P, Sarrazin S, Chauvin C, Moyano G, Wadepohl K, Van Gompel L, Wagenaar JA, Dewulf J. Assigning Defined Daily/Course Doses for Antimicrobials in Turkeys to Enable a Cross-Country Quantification and Comparison of Antimicrobial Use. Antibiotics (Basel) 2021; 10:antibiotics10080971. [PMID: 34439021 PMCID: PMC8388960 DOI: 10.3390/antibiotics10080971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) threatens our public health and is mainly driven by antimicrobial usage (AMU). For this reason the World Health Organization calls for detailed monitoring of AMU over all animal sectors involved. Therefore, we aimed to quantify AMU on turkey farms. First, turkey-specific Defined Daily Dose (DDDturkey) was determined. These were compared to the broiler alternative from the European Surveillance of Veterinary Antimicrobial Consumption (DDDvet), that mention DDDvet as a proxy for other poultry species. DDDturkey ranged from being 81.5% smaller to 48.5% larger compared to its DDDvet alternative for broilers. Second, antimicrobial treatments were registered on 60 turkey farms divided over France, Germany and Spain between 2014 and 2016 (20 flocks per country). Afterwards, AMU was quantified using treatment incidence (TI) per 100 days. TI expresses the percentage of the rearing period that the turkeys were treated with a standard dose of antimicrobials. Minimum, median and maximum TI at flock level and based on DDDturkey = 0.0, 10.0 and 65.7, respectively. Yet, a huge variation in amounts of antimicrobials used at flock level was observed, both within and between countries. Seven farms (12%) did not use any antimicrobials. Aminopenicillins, polymyxins, and fluoroquinolones were responsible for 72.2% of total AMU. The proportion of treating farms peaked on week five of the production cycle (41.7%), and 79.4% of the total AMU was administered in the first half of production. To conclude, not all DDDvet values for broilers can be applied to turkeys. Additionally, the results of AMU show potential for reducing and improving AMU on turkey farms, especially concerning the usage of critically important antimicrobials.
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Affiliation(s)
- Philip Joosten
- Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (S.S.); (J.D.)
- Correspondence: ; Tel.: +32-(0)-92647548
| | - Steven Sarrazin
- Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (S.S.); (J.D.)
| | - Claire Chauvin
- Anses, French Agency for Food, Environmental and Occupational Health and Safety, 22440 Ploufragan, France;
| | - Gabriel Moyano
- Departamento de Sanidad Animal y Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Katharina Wadepohl
- Institute of Food Quality and Safety, University of Veterinary Medicine Hannover, 49456 Bakum, Germany;
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, The Netherlands;
| | - Jaap A. Wagenaar
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - Jeroen Dewulf
- Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; (S.S.); (J.D.)
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van Dijk MA, Engelsma MY, Visser VX, Keur I, Holtslag ME, Willems N, Meij BP, Willemsen PT, Wagenaar JA, Roest HI, Broens EM. Transboundary Spread of Brucella canis through Import of Infected Dogs, the Netherlands, November 2016-December 2018. Emerg Infect Dis 2021; 27:1783-1788. [PMID: 34152959 PMCID: PMC8237882 DOI: 10.3201/eid2707.201238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Brucella canis had not been isolated in the Netherlands until November 2016, when it was isolated from a dog imported from Romania. Including this case, 16 suspected cases were notified to the authorities during the following 25 months. Of these 16 dogs, 10 were seropositive; tracking investigations found another 8 seropositive littermates. All seropositive animals were rescue dogs imported from Eastern Europe. B. canis was cultured from urine, blood, and other specimens collected from the dogs. Genotyping of isolates revealed clustering by litter and country. Isolating B. canis in urine indicates that shedding should be considered when assessing the risk for zoonotic transmission. This case series proves introduction of B. canis into a country to which it is not endemic through import of infected dogs from B. canis-endemic areas, posing a threat to the naive autochthonous dog population and humans.
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Wegener A, Damborg P, Guardabassi L, Moodley A, Mughini-Gras L, Duim B, Wagenaar JA, Broens EM. Specific staphylococcal cassette chromosome mec (SCCmec) types and clonal complexes are associated with low-level amoxicillin/clavulanic acid and cefalotin resistance in methicillin-resistant Staphylococcus pseudintermedius. J Antimicrob Chemother 2021; 75:508-511. [PMID: 31846043 PMCID: PMC9297311 DOI: 10.1093/jac/dkz509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/01/2019] [Accepted: 11/08/2019] [Indexed: 01/28/2023] Open
Abstract
Background Staphylococcus pseudintermedius is a common pathogen in dogs and methicillin resistance has emerged over recent decades. According to the current guidelines, S. pseudintermedius displaying oxacillin resistance should be reported as resistant to all β-lactams. Objectives To identify possible associations between β-lactam resistance levels and clonal complexes (CCs) and/or staphylococcal cassette chromosome mec (SCCmec) types in methicillin-resistant S. pseudintermedius (MRSP). Methods MICs of oxacillin, penicillin, ampicillin, amoxicillin/clavulanic acid and cefalotin were determined by broth microdilution for 86 clinical canine MRSP isolates from Denmark and the Netherlands. PCR and sequencing were used for SCCmec typing and MLST. Results Isolates belonged to CC71 (n = 36), CC258 (n = 33), CC45 (n = 11), CC68 (n = 1) and five singleton STs. SCCmecII-III was exclusively found in CC71 and SCCmecIV was significantly associated with CC258. SCCmecV and non-typeable SCCmec types occurred in 4 and 14 isolates, respectively. SCCmecIV was associated with lower MICs of oxacillin (<2 mg/L), ampicillin (<8 mg/L) and amoxicillin/clavulanic acid (<4 mg/L) and with susceptibility to cefalotin (<4 mg/L). All isolates harbouring SCCmecV were susceptible to cefalotin as well. Conclusions SCCmec types were associated with different CCs and with either high- or low-level resistance to different β-lactams. The finding of amoxicillin/clavulanic acid (20%) and cefalotin (70%) in vitro susceptibility across all CCs might have clinical implications, since amoxicillin/clavulanic acid and first-generation cephalosporins are first-choice antibiotics for treatment of S. pseudintermedius infections. Pharmacokinetic/pharmacodynamic and clinical outcome studies are warranted to evaluate the in vivo efficacy of these β-lactams for treatment of MRSP infections.
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Affiliation(s)
- Alice Wegener
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter Damborg
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Pathobiology and Population Sciences, The Royal Veterinary College, North Mymms, UK
| | - Arshnee Moodley
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Lapo Mughini-Gras
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Els M Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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33
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Zhao S, Schuurman N, Li W, Wang C, Smit LAM, Broens EM, Wagenaar JA, van Kuppeveld FJM, Bosch BJ, Egberink H. Serologic Screening of Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Cats and Dogs during First Coronavirus Disease Wave, the Netherlands. Emerg Infect Dis 2021; 27:1362-1370. [PMID: 33900184 PMCID: PMC8084487 DOI: 10.3201/eid2705.204055] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect many animal species, including minks, cats, and dogs. To gain insights into SARS-CoV-2 infections in cats and dogs, we developed and validated a set of serologic assays, including ELISA and virus neutralization. Evaluation of samples from animals before they acquired coronavirus disease and samples from cats roaming SARS-CoV-2–positive mink farms confirmed the suitability of these assays for specific antibody detection. Furthermore, our findings exclude SARS-CoV-2 nucleocapsid protein as an antigen for serologic screening of cat and dog samples. We analyzed 500 serum samples from domestic cats and dogs in the Netherlands during April–May 2020. We showed 0.4% of cats and 0.2% of dogs were seropositive. Although seroprevalence in cats and dogs that had unknown SARS-CoV-2 exposure was low during the first coronavirus disease wave, our data stress the need for development of continuous serosurveillance for SARS-CoV-2 in these 2 animal species.
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van den Bunt G, Fluit AC, Spaninks MP, Timmerman AJ, Geurts Y, Kant A, Scharringa J, Mevius D, Wagenaar JA, Bonten MJM, van Pelt W, Hordijk J. Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household. J Antimicrob Chemother 2021; 75:342-350. [PMID: 31711228 PMCID: PMC6966097 DOI: 10.1093/jac/dkz462] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/06/2019] [Accepted: 10/10/2019] [Indexed: 11/21/2022] Open
Abstract
Background ESBL-producing Enterobacteriaceae (ESBL-E) are observed in many reservoirs. Pets might play an important role in the dissemination of ESBL-E to humans since they live closely together. Objectives To identify prevalence, risk factors, molecular characteristics, persistence and acquisition of ESBL-E in dogs and cats, and co-carriage in human–pet pairs belonging to the same household. Methods In a nationwide study, one person per household was randomly invited to complete a questionnaire and to submit a faecal sample. Dog and cat owners were invited to also submit a faecal sample from their pet. Repeated sampling after 1 and 6 months was performed in a subset. ESBL-E were obtained through selective culture and characterized by WGS. Logistic regression analyses and random forest models were performed to identify risk factors. Results The prevalence of ESBL-E carriage in these cohorts was 3.8% (95% CI: 2.7%–5.4%) for human participants (n=550), 10.7% (95% CI: 8.3%–13.7%) for dogs (n=555) and 1.4% (95% CI: 0.5%–3.8%) for cats (n=285). Among animals, blaCTX-M-1 was most abundant, followed by blaCTX-M-15. In dogs, persistence of carriage was 57.1% at 1 month and 42.9% at 6 months. Eating raw meat [OR: 8.8, 95% CI: 4.7–16.4; population attributable risk (PAR): 46.5%, 95% CI: 41.3%–49.3%] and dry food (OR: 0.2, 95% CI: 0.1–0.5; PAR: 56.5%, 95% CI: 33.2%–66.6%) were predictors for ESBL-E carriage in dogs. Human–dog co-carriage was demonstrated in five households. Human–cat co-carriage was not observed. Conclusions ESBL-E prevalence was higher in dogs than in humans and lowest in cats. The main risk factor for ESBL-E carriage was eating raw meat. Co-carriage in dogs and household members was uncommon.
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Affiliation(s)
- G van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - M P Spaninks
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - A J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Y Geurts
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - A Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - D Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - W van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hopman NEM, Wagenaar JA, van Geijlswijk IM, Broens EM. Development and Pilot of an Interactive Online Course on Antimicrobial Stewardship in Companion Animals. Antibiotics (Basel) 2021; 10:antibiotics10050610. [PMID: 34065607 PMCID: PMC8161360 DOI: 10.3390/antibiotics10050610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/06/2021] [Accepted: 05/17/2021] [Indexed: 11/28/2022] Open
Abstract
A holistic approach to antimicrobial use (AMU) and prescribing is needed to combat the problem of antimicrobial resistance (AMR). Previously, an antimicrobial stewardship programme (ASP) was developed, introduced, and evaluated in 44 Dutch companion animal clinics, which resulted in an optimization of AMU. As a follow-up to this, an online course was developed to promote awareness of AMU, AMR, and responsible antimicrobial prescribing. The aim of this paper is to describe the development and pilot, including evaluation, of this course, which will be disseminated more widely among Dutch companion animal veterinarians. The interactive programme consists of a major e-learning component and two online, face-to-face meetings. The course comprises five different parts corresponding with five consecutive weeks. Theory on several topics is offered, for example on AMU and AMR in general, Dutch regulations and guidelines on veterinary AMU, behavioural change, and possible methods to quantify AMU. Additionally, several assignments are offered, for example to reflect upon one’s own current antimicrobial prescribing behaviour. Interactive discussion and peer-to-peer learning are promoted. Since September 2020, the course has been offered in a pilot phase, and the feedback is promising. Evaluation of the pilot phase will result in recommendations for further optimization and dissemination.
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Affiliation(s)
- Nonke E. M. Hopman
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (J.A.W.); (E.M.B.)
- Correspondence:
| | - Jaap A. Wagenaar
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (J.A.W.); (E.M.B.)
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Ingeborg M. van Geijlswijk
- IRAS Veterinary Pharmacology and Therapeutics Group, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 106, 3584 CM Utrecht, The Netherlands;
| | - Els M. Broens
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Yalelaan 1, 3584 CL Utrecht, The Netherlands; (J.A.W.); (E.M.B.)
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Van Gompel L, Dohmen W, Luiken REC, Bouwknegt M, Heres L, van Heijnsbergen E, Jongerius-Gortemaker BGM, Scherpenisse P, Greve GD, Tersteeg-Zijderveld MHG, Wadepohl K, Ribeiro Duarte AS, Muñoz-Gómez V, Fischer J, Skarżyńska M, Wasyl D, Wagenaar JA, Urlings BAP, Dorado-García A, Wouters IM, Heederik DJJ, Schmitt H, Smit LAM. Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers. Ann Work Expo Health 2021; 64:125-137. [PMID: 31883001 PMCID: PMC9194797 DOI: 10.1093/annweh/wxz098] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 01/05/2023] Open
Abstract
Objectives Slaughterhouse staff is occupationally exposed to antimicrobial resistant bacteria. Studies reported high antimicrobial resistance gene (ARG) abundances in slaughter pigs. This cross-sectional study investigated occupational exposure to tetracycline (tetW) and macrolide (ermB) resistance genes and assessed determinants for faecal tetW and ermB carriage among pig slaughterhouse workers. Methods During 2015–2016, 483 faecal samples and personal questionnaires were collected from workers in a Dutch pig abattoir, together with 60 pig faecal samples. Human dermal and respiratory exposure was assessed by examining 198 carcass, 326 gloves, and 33 air samples along the line, next to 198 packed pork chops to indicate potential consumer exposure. Samples were analyzed by qPCR (tetW, ermB). A job exposure matrix was created by calculating the percentage of tetW and ermB positive carcasses or gloves for each job position. Multiple linear regression models were used to link exposure to tetW and ermB carriage. Results Workers are exposed to tetracycline and macrolide resistance genes along the slaughter line. Tetw and ermB gradients were found for carcasses, gloves, and air filters. One packed pork chop contained tetW, ermB was non-detectable. Human faecal tetW and ermB concentrations were lower than in pig faeces. Associations were found between occupational tetW exposure and human faecal tetW carriage, yet, not after model adjustments. Sampling round, nationality, and smoking were determinants for ARG carriage. Conclusion We demonstrated clear environmental tetracycline and macrolide resistance gene exposure gradients along the slaughter line. No robust link was found between ARG exposure and human faecal ARG carriage.
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Affiliation(s)
- Liese Van Gompel
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Wietske Dohmen
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | | | - Eri van Heijnsbergen
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Betty G M Jongerius-Gortemaker
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Katharina Wadepohl
- Field Station for Epidemiology, University of Veterinary Medicine Hannover Foundation, Bakum, Germany
| | - Ana Sofia Ribeiro Duarte
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Jennie Fischer
- German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße, Berlin, Germany
| | | | - Dariusz Wasyl
- National Veterinary Research Institute (PIWet), Puławy, Poland
| | - Jaap A Wagenaar
- Wageningen, Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology (I&I), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Alejandro Dorado-García
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Centre for Infectious Disease Control (RIVM), National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Duarte ASR, Röder T, Van Gompel L, Petersen TN, Hansen RB, Hansen IM, Bossers A, Aarestrup FM, Wagenaar JA, Hald T. Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures. Front Microbiol 2021; 11:601407. [PMID: 33519742 PMCID: PMC7843941 DOI: 10.3389/fmicb.2020.601407] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomics can unveil the genetic content of the total microbiota in different environments, such as food products and the guts of humans and livestock. It is therefore considered of great potential to investigate the transmission of foodborne hazards as part of source-attribution studies. Source-attribution of antimicrobial resistance (AMR) has traditionally relied on pathogen isolation, while metagenomics allows investigating the full span of AMR determinants. In this study, we hypothesized that the relative abundance of fecal resistome components can be associated with specific reservoirs, and that resistomes can be used for AMR source-attribution. We used shotgun-sequences from fecal samples of pigs, broilers, turkeys- and veal calves collected across Europe, and fecal samples from humans occupationally exposed to livestock in one country (pig slaughterhouse workers, pig and broiler farmers). We applied both hierarchical and flat forms of the supervised classification ensemble algorithm Random Forests to classify resistomes into corresponding reservoir classes. We identified country-specific and -independent AMR determinants, and assessed the impact of country-specific determinants when attributing AMR resistance in humans. Additionally, we performed a similarity percentage analysis with the full spectrum of AMR determinants to identify resistome signatures for the different reservoirs. We showed that the number of AMR determinants necessary to attribute a resistome into the correct reservoir increases with a larger reservoir heterogeneity, and that the impact of country-specific resistome signatures on prediction varies between countries. We predicted a higher occupational exposure to AMR determinants among workers exposed to pigs than among those exposed to broilers. Additionally, results suggested that AMR exposure on pig farms was higher than in pig slaughterhouses. Human resistomes were more similar to pig and veal calves’ resistomes than to those of broilers and turkeys, and the majority of these resistome dissimilarities can be explained by a small set of AMR determinants. We identified resistome signatures for each individual reservoir, which include AMR determinants significantly associated with on-farm antimicrobial use. We attributed human resistomes to different livestock reservoirs using Random Forests, which allowed identifying pigs as a potential source of AMR in humans. This study thus demonstrates that it is possible to apply metagenomics in AMR source-attribution.
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Affiliation(s)
- Ana Sofia Ribeiro Duarte
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Timo Röder
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Nordahl Petersen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Inge Marianne Hansen
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Frank M Aarestrup
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Tine Hald
- Division of Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs Lyngby, Denmark
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Mulder AC, Franz E, de Rijk S, Versluis MAJ, Coipan C, Buij R, Müskens G, Koene M, Pijnacker R, Duim B, Bloois LVDGV, Veldman K, Wagenaar JA, Zomer AL, Schets FM, Blaak H, Mughini-Gras L. Tracing the animal sources of surface water contamination with Campylobacter jejuni and Campylobacter coli. Water Res 2020; 187:116421. [PMID: 32992147 DOI: 10.1016/j.watres.2020.116421] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Campylobacter jejuni and C. coli, the primary agents of human bacterial gastroenteritis worldwide, are widespread in surface water. Several animal sources contribute to surface water contamination with Campylobacter, but their relative contributions thus far remained unclear. Here, the prevalence, genotype diversity, and potential animal sources of C. jejuni and C. coli strains in surface water in the Netherlands were investigated. It was also assessed whether the contribution of the different animal sources varied according to surface water type (i.e. agricultural water, surface water at discharge points of wastewater treatment plants [WWTPs], and official recreational water), season, and local livestock (poultry, pig, ruminant) density. For each surface water type, 30 locations spread over six areas with either high or low density of poultry, ruminants, or pigs, were sampled once every season in 2018-2019. Campylobacter prevalence was highest in agricultural waters (77%), and in autumn and winter (74%), and lowest in recreational waters (46%) and in summer (54%). In total, 76 C. jejuni and 177 C. coli water isolates were whole-genome sequenced. Most C. coli water isolates (78.5%) belonged to hitherto unidentified clones when using the seven-locus sequence type (ST) scheme, while only 11.8% of the C. jejuni isolates had unidentified STs. The origin of these isolates, as defined by core-genome multi-locus sequence typing (cgMLST), was inferred by comparison with Campylobacter strain collections from meat-producing poultry, laying hens, adult cattle, veal calves, small ruminants, pigs, and wild birds. Water isolates were mainly attributed to wild birds (C. jejuni: 60.0%; C. coli: 93.7%) and meat-producing poultry (C. jejuni: 18.9%; C. coli: 5.6%). Wild bird contribution was high among isolates from recreational waters and WWTP discharge points, and in areas with low poultry (C. coli) or high ruminant (C. jejuni) densities. The contribution of meat-producing poultry was high in areas with high density of poultry, springtime, agricultural waters and WWTP discharge points. While wild birds and poultry were the main contributors to Campylobacter contamination in surface water, their contribution differed significantly by water type, season, and local poultry and ruminant densities.
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Affiliation(s)
- Annemieke C Mulder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands.
| | - Eelco Franz
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Sharona de Rijk
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Moyke A J Versluis
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
| | - Claudia Coipan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Ralph Buij
- Wageningen Environmental Research (WENR), Wageningen University & Research (WUR), Droevendaalsesteeg 3-3 A, 6708 PB, Wageningen, The Netherlands
| | - Gerard Müskens
- Wageningen Environmental Research (WENR), Wageningen University & Research (WUR), Droevendaalsesteeg 3-3 A, 6708 PB, Wageningen, The Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Houtribweg 39, 8221 RA, Lelystad, The Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology (I&I), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands; WHO Collaborating Centre for Campylobacter / OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology (I&I), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands; WHO Collaborating Centre for Campylobacter / OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Houtribweg 39, 8221 RA, Lelystad, The Netherlands
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Houtribweg 39, 8221 RA, Lelystad, The Netherlands; Department of Infectious Diseases and Immunology (I&I), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands; WHO Collaborating Centre for Campylobacter / OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology (I&I), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands; WHO Collaborating Centre for Campylobacter / OIE Reference Laboratory for Campylobacteriosis, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
| | - Franciska M Schets
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Hetty Blaak
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Postbus 1, 3720 BA Bilthoven Bilthoven, Utrecht, The Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Yalelaan 1, De Uithof, 3584 CL, Utrecht, The Netherlands
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Uiterwijk M, Mughini-Gras L, Nijsse R, Wagenaar JA, Ploeger HW, Kooyman FNJ. Giardia duodenalis multi-locus genotypes in dogs with different levels of synanthropism and clinical signs. Parasit Vectors 2020; 13:605. [PMID: 33267878 PMCID: PMC7709413 DOI: 10.1186/s13071-020-04496-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In dogs, infections with Giardia duodenalis are mainly caused by assemblages C and D, but also by the potentially zoonotic assemblages A and B. The aims of this study were to assess differences in assemblages (i) between dogs living mainly in close proximity to humans (synanthropic dogs) versus dogs living mainly among other dogs, (ii) between samples of dogs with or without loose stool, and (iii) related to the amount of cysts shedding. METHODS One hundred eighty-nine qPCR Giardia positive fecal samples of dogs originating from four groups (household, sheltered, hunting, and dogs for which a veterinarian sent a fecal sample to a diagnostic laboratory) were used for genotyping. For this, multi-locus genotyping of beta-giardin, triose phosphate isomerase, and glutamate dehydrogenase and genotyping of SSU rDNA gene fragments were performed. Fecal consistency was scored (loose or non-loose stool), and cysts per gram of feces were determined with qPCR. RESULTS Assemblage D was the most prevalent in all groups, followed by the other canid assemblage C. Also, mixed C/D was common. In two (synanthropic) household dogs, the potentially zoonotic assemblage AI was present. Although occurrence of assemblage AI in household dogs was not significantly different from dogs living among other dogs (sheltered and hunting dogs), it was significantly higher compared to dogs for which a sample was sent to a diagnostic laboratory. Dogs with assemblage D shed significantly more cysts than dogs with other assemblages (except for mixed C/D results) or dogs in which no assemblage could be determined. None of the assemblages was significantly associated with loose stool. CONCLUSION Not only do dogs mainly shed the canid Giardia duodenalis assemblages D and/or C, the numbers of cysts per gram for the canid assemblage D were also higher than for the potential zoonotic assemblage AI. Based on the assemblages shed by dogs, the risk to public health posed by dogs is estimated to be low, even though the dogs that shed AI were synanthropic household dogs. Loose stool in infected dogs was not associated with any particular Giardia assemblage.
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Affiliation(s)
- Mathilde Uiterwijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Present Address: National Reference Laboratory, The Netherlands Food and Consumer Product Safety Authority (NVWA), Centre for Monitoring of Vectors (CMV), Wageningen, The Netherlands
| | - Lapo Mughini-Gras
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rolf Nijsse
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Harm W. Ploeger
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frans N. J. Kooyman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Mughini-Gras L, Pijnacker R, Coipan C, Mulder AC, Fernandes Veludo A, de Rijk S, van Hoek AHAM, Buij R, Muskens G, Koene M, Veldman K, Duim B, van der Graaf-van Bloois L, van der Weijden C, Kuiling S, Verbruggen A, van der Giessen J, Opsteegh M, van der Voort M, Castelijn GAA, Schets FM, Blaak H, Wagenaar JA, Zomer AL, Franz E. Sources and transmission routes of campylobacteriosis: A combined analysis of genome and exposure data. J Infect 2020; 82:216-226. [PMID: 33275955 DOI: 10.1016/j.jinf.2020.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/13/2020] [Accepted: 09/26/2020] [Indexed: 01/24/2023]
Abstract
OBJECTIVES To determine the contributions of several animal and environmental sources of human campylobacteriosis and identify source-specific risk factors. METHODS 1417 Campylobacter jejuni/coli isolates from the Netherlands in 2017-2019 were whole-genome sequenced, including isolates from human cases (n = 280), chickens/turkeys (n = 238), laying hens (n = 56), cattle (n = 158), veal calves (n = 49), sheep/goats (n = 111), pigs (n = 110), dogs/cats (n = 100), wild birds (n = 62), and surface water (n = 253). Questionnaire-based exposure data was collected. Source attribution was performed using core-genome multilocus sequence typing. Risk factors were determined on the attribution estimates. RESULTS Cases were mostly attributed to chickens/turkeys (48.2%), dogs/cats (18.0%), cattle (12.1%), and surface water (8.5%). Of the associations identified, never consuming chicken, as well as frequent chicken consumption, and rarely washing hands after touching raw meat, were risk factors for chicken/turkey-attributable infections. Consuming unpasteurized milk or barbecued beef increased the risk for cattle-attributable infections. Risk factors for infections attributable to environmental sources were open water swimming, contact with dog faeces, and consuming non-chicken/turkey avian meat like game birds. CONCLUSIONS Poultry and cattle are the main livestock sources of campylobacteriosis, while pets and surface water are important non-livestock sources. Foodborne transmission is only partially consistent with the attributions, as frequency and alternative pathways of exposure are significant.
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Affiliation(s)
- Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
| | - Roan Pijnacker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Claudia Coipan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Annemieke C Mulder
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Sharona de Rijk
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela H A M van Hoek
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ralph Buij
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Gerard Muskens
- Wageningen Environmental Research (WER), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research (WBVR), Wageningen University & Research (WUR), Lelystad, the Netherlands
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Coen van der Weijden
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands
| | - Sjoerd Kuiling
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Anjo Verbruggen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joke van der Giessen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marieke Opsteegh
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Menno van der Voort
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Greetje A A Castelijn
- Wageningen Food Safety Research (WFSR), Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Franciska M Schets
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hetty Blaak
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Aldert L Zomer
- Department of Infectious Diseases and Immunology (I&I), Utrecht University & WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Flipse J, Duim B, Wallinga JA, de Wijkerslooth LRH, van der Graaf-van Bloois L, Timmerman AJ, Zomer AL, Veldman KT, Wagenaar JA, Bloembergen P. A Case of Persistent Diarrhea in a Man with the Molecular Detection of Various Campylobacter species and the First Isolation of candidatus Campylobacter infans. Pathogens 2020; 9:E1003. [PMID: 33265947 PMCID: PMC7761484 DOI: 10.3390/pathogens9121003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
A man with a well-controlled HIV infection, previously diagnosed with lymphogranuloma venereum and treated for Hodgkin's lymphoma, was suffering from chronic diarrhea. He travelled to Indonesia in the month prior to the start of complaints. Over a 15-month period, sequences related to Campylobactertroglodytis/upsaliensis, C. pinnepediorum/mucosalis/concisus and C. hominis were detected by 16S rRNA qPCR-based assays in various stool samples and in a colon biopsy. Culture revealed the first isolation of "candidatus Campylobacter infans", a species identified recently by molecular methods only. The patient was treated with azithromycin, ciprofloxacin and tetracycline. To identify potential continuous exposure of the patient to Campylobacter, stool samples of the partner and the cat of the patient were analyzed and C. pinnepediorum/mucosalis/concisus and C. helveticus, respectively, were detected. The diversity in detected species in this immunocompromised patient with a lack of repeatedly consistent findings resulted in the conclusion that not any of the Campylobacter species was the primary cause of the clinical condition. This study shows the challenges in detection and interpretation of diagnostic results regarding Campylobacter.
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Affiliation(s)
- Jacky Flipse
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
| | - Birgitta Duim
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Janny A. Wallinga
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
| | | | - Linda van der Graaf-van Bloois
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Arjen J. Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
| | - Kees T. Veldman
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands; (L.v.d.G.-v.B.); (A.J.T.); (A.L.Z.); (J.A.W.)
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, 3584 CL Utrecht, The Netherlands
- Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands;
| | - Peter Bloembergen
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Clinics, 8025 AB Zwolle, The Netherlands; (J.A.W.); (P.B.)
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Ortega-Paredes D, de Janon S, Villavicencio F, Ruales KJ, De La Torre K, Villacís JE, Wagenaar JA, Matheu J, Bravo-Vallejo C, Fernández-Moreira E, Vinueza-Burgos C. Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador. Front Vet Sci 2020; 7:547843. [PMID: 33324692 PMCID: PMC7724036 DOI: 10.3389/fvets.2020.547843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL blaCTX-M-55, blaCTX-M-3, blaCTX-M-15, blaCTX-M-65, blaCTX-M-27, and blaCTX-M-14 were the most prevalent ESBL genes while blaCMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.
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Affiliation(s)
- David Ortega-Paredes
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
| | - Sofía de Janon
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
| | - Fernando Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Katherine Jaramillo Ruales
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Kenny De La Torre
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - José E Villacís
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador.,Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jorge Matheu
- Department of Food Safety and Zoonoses, World Health Organization, Geneva, Switzerland
| | - Camila Bravo-Vallejo
- Hospital General del Sur Quito-Instituto Ecuatoriano de Seguridad Social (IESS), Quito, Ecuador
| | | | - Christian Vinueza-Burgos
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
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44
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Foster G, Baily JL, Howie F, Brownlow AC, Wagenaar JA, Gilbert MJ, Miller WG, Byrne BA, Clothier KA, Schmitt T, Patterson T, Reid RJ, Dagleish MP. Campylobacter pinnipediorum subsp. caledonicus and C. pinnipediorum subsp. pinnipediorum recovered from abscesses in pinnipeds. Dis Aquat Organ 2020; 142:41-46. [PMID: 33210610 DOI: 10.3354/dao03544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Campylobacter pinnipediorum was described recently for isolates recovered from pinnipeds. The novel species was further split into 2 subspecies based on host and geography, with C. pinnipediorum subsp. pinnipediorum recovered from otariid seals in California (USA) and C. pinnipediorum subsp. caledonicus recovered from phocid seals in Scotland. We report details of the infections of 7 pinnipeds from which C. pinnipediorum was isolated: C. pinnipediorum subsp. caledonicus was isolated from 2 harbour seals Phoca vitulina and a single grey seal Halichoerus grypus, and C. pinnipediorum subsp. pinnipediorum was isolated from California sea lions Zalophus californianus. Six of the isolates were recovered from samples collected at post-mortem investigation. In 2 of the Scottish seals and in 3 of the California seals, C. pinnipediorum was the sole bacterial isolate recovered from abscesses present and suggests they may have resulted from conspecific or intraspecific bite wounds.
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Affiliation(s)
- Geoffrey Foster
- SRUC Veterinary Services, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
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45
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Luiken REC, Van Gompel L, Bossers A, Munk P, Joosten P, Hansen RB, Knudsen BE, García-Cobos S, Dewulf J, Aarestrup FM, Wagenaar JA, Smit LAM, Mevius DJ, Heederik DJJ, Schmitt H. Farm dust resistomes and bacterial microbiomes in European poultry and pig farms. Environ Int 2020; 143:105971. [PMID: 32738764 DOI: 10.1016/j.envint.2020.105971] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust. OBJECTIVES We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored. METHODS In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool. RESULTS The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study. CONCLUSION Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.
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Affiliation(s)
- Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands.
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Patrick Munk
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Philip Joosten
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | | | - Berith E Knudsen
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, PO Box 30.001, 9700 RB Groningen, the Netherlands
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - Frank M Aarestrup
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Dik J Mevius
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721MA Bilthoven, the Netherlands
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46
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Van Gompel L, Luiken REC, Hansen RB, Munk P, Bouwknegt M, Heres L, Greve GD, Scherpenisse P, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld MHG, García-Cobos S, Dohmen W, Dorado-García A, Wagenaar JA, Urlings BAP, Aarestrup FM, Mevius DJ, Heederik DJJ, Schmitt H, Bossers A, Smit LAM. Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study. Environ Int 2020; 143:105939. [PMID: 32679392 DOI: 10.1016/j.envint.2020.105939] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND By studying the entire human faecal resistome and associated microbiome, the diversity and abundance of faecal antimicrobial resistance genes (ARGs) can be comprehensively characterized. Prior culture-based studies have shown associations between occupational exposure to livestock and carriage of specific antimicrobial resistant bacteria. Using shotgun metagenomics, the present study investigated 194 faecal resistomes and bacteriomes from humans occupationally exposed to ARGs in livestock (i.e. pig and poultry farmers, employees and family members and pig slaughterhouse workers) and a control population (Lifelines cohort) in the Netherlands. In addition, we sought to identify determinants for the human resistome and bacteriome composition by applying a combination of multivariate (NMDS, PERMANOVA, SIMPER and DESeq2 analysis) and multivariable regression analysis techniques. RESULTS Pig slaughterhouse workers and pig farmers carried higher total ARG abundances in their stools compared to broiler farmers and control subjects. Tetracycline, β-lactam and macrolide resistance gene clusters dominated the resistome of all studied groups. No significant resistome alpha diversity differences were found among the four populations. However, the resistome beta diversity showed a separation of the mean resistome composition of pig and pork exposed workers from broiler farmers and controls, independent of their antimicrobial use. We demonstrated differences in resistome composition between slaughter line positions, pig versus poultry exposed workers, as well as differences between farmers and employees versus family members. In addition, we found a significant correlation between the bacteriome and resistome, and significant differences in the bacteriome composition between and within the studied subpopulations. Finally, an in-depth analysis of pig and poultry farms - of which also farm livestock resistomes were analysed - showed positive associations between the number of on-farm working hours and human faecal AMR loads. CONCLUSION We found that the total normalized faecal ARG carriage was larger in persons working in the Dutch pork production chain compared to poultry farmers and controls. Additionally, we showed significant differences in resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. The number of on-farm working hours and the farm type (pig or broiler) that persons live or work on are determinants for the human faecal resistome. Overall, our results may suggest direct or indirect livestock contact as a determinant for human ARG carriage. Future studies should further focus on the connection between the human and livestock resistome (i.e. transmission routes) to substantiate the evidence for livestock-associated resistome acquisition.
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Affiliation(s)
- Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands.
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Rasmus B Hansen
- Intomics A/S, Lottenborgvej 26, 2800 Kongens Lyngby, Denmark
| | - Patrick Munk
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | | | - Lourens Heres
- Vion Food Group, Boseind 15, 5281 RM Boxtel, the Netherlands
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Betty G M Jongerius-Gortemaker
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Monique H G Tersteeg-Zijderveld
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, 9713 GZ Groningen, the Netherlands
| | - Wietske Dohmen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Alejandro Dorado-García
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | | | - Frank M Aarestrup
- Section for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721MA Bilthoven, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
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Mejía L, Medina JL, Bayas R, Salazar CS, Villavicencio F, Zapata S, Matheu J, Wagenaar JA, González-Candelas F, Vinueza-Burgos C. Genomic Epidemiology of Salmonella Infantis in Ecuador: From Poultry Farms to Human Infections. Front Vet Sci 2020; 7:547891. [PMID: 33134346 PMCID: PMC7550756 DOI: 10.3389/fvets.2020.547891] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/20/2020] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is one of the most important foodborne pathogens around the world. In the last years, S. enterica serovar Infantis has become an important emerging pathogen in many countries, often as multidrug resistant clones. To understand the importance of S. enterica in the broiler industry in Ecuador, we performed a study based on phenotypic and WGS data of isolates from poultry farms, chicken carcasses and humans. We showed a high prevalence of S. enterica in poultry farms (41.4%) and chicken carcasses (55.5%), but a low prevalence (1.98%) in human samples. S. Infantis was shown to be the most prevalent serovar with a 98.2, 97.8, and 50% in farms, foods, and humans, respectively, presenting multidrug resistant patterns. All sequenced S. Infantis isolates belonged to ST32. For the first time, a pESI-related megaplasmid was identified in Ecuadorian samples. This plasmid contains genes of antimicrobial resistance, virulence factors, and environmental stress tolerance. Genomic analysis showed a low divergence of S. Infantis strains in the three analyzed components. The results from this study provide important information about genetic elements that may help understand the molecular epidemiology of S. Infantis in Ecuador.
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Affiliation(s)
- Lorena Mejía
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain
| | - José Luis Medina
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria, Universidad Central del Ecuador, Quito, Ecuador
| | - Rosa Bayas
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Carolina Satan Salazar
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Fernando Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Sonia Zapata
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jorge Matheu
- Department of Food Safety and Zoonoses, World Health Organization (WHO), Geneva, Switzerland
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research (WBVR), Lelystad, Netherlands
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology, University of Valencia, Valencia, Spain.,Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.,CIBER (Centro de Investigación Biomédica en Red) in Epidemiology and Public Health, Valencia, Spain
| | - Christian Vinueza-Burgos
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria, Universidad Central del Ecuador, Quito, Ecuador
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hordijk J, Fischer EAJ, van Werven T, Sietsma S, Van Gompel L, Timmerman AJ, Spaninks MP, Heederik DJJ, Nielen M, Wagenaar JA, Stegeman A. Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms. J Antimicrob Chemother 2020; 74:1531-1538. [PMID: 30753489 PMCID: PMC6524482 DOI: 10.1093/jac/dkz035] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 11/30/2018] [Accepted: 01/14/2019] [Indexed: 01/10/2023] Open
Abstract
Objectives To explore the dynamics of faecal ESBL/AmpC shedding in dairy cattle and farmers, a study was conducted to examine changes in shedding by individual animals, as well as environmental exposure, and to study the association between antimicrobial use (AMU) and ESBL/AmpC shedding. Methods The study comprised a cross-sectional survey of 20 farms and a 1 year follow-up of 10 farms. Faecal samples were cultured by both direct inoculation on MacConkey agar + 1 mg/L cefotaxime (MC+) and enrichment in LB-broth + 1 mg/L cefotaxime with subsequent inoculation on MC+. Dust samples were collected using electrostatic dustfall collectors (EDCs). Human faecal samples were collected by the farmers. Presence of ESBL/AmpC genes was screened for by PCR and sequencing. Using mixed effects logistic regression, ORs were determined and population-attributable fractions (PAFs) calculated subsequently. Results In Phase 1, 8/20 farms were positive for ESBL/AmpC and, with 2 negative farms, were selected for Phase 2. Transient shedding of dominant allele variants was observed in the animals. EDCs and human faecal samples did not reflect what was observed in the animals. AMU was related to shedding of ESBLs in the next sampling moment [OR 14.6 (95% CI 3.0–80.0)] and the PAF of AMU was 0.36 (95% CI 0.08–0.77). Calves fed with colostrum from cows on dry-off therapy was not a risk factor [OR 1.7 (95% CI 0.7–4.9, P = 0.28)]. Conclusions The presence of ESBL/AmpC could only be partly explained by AMU. No link was shown between shedding in cattle and humans or the environment. Interventions should focus on prevention of introduction.
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Affiliation(s)
- Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Egil A J Fischer
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Tine van Werven
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,University Farm Animal Practice (ULP), Harmelen, The Netherlands
| | - Steven Sietsma
- University Farm Animal Practice (ULP), Harmelen, The Netherlands
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Arjen J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mirlin P Spaninks
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mirjam Nielen
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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50
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Van Gompel L, Luiken REC, Sarrazin S, Munk P, Knudsen BE, Hansen RB, Bossers A, Aarestrup FM, Dewulf J, Wagenaar JA, Mevius DJ, Schmitt H, Heederik DJJ, Dorado-García A, Smit LAM. The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries. J Antimicrob Chemother 2020; 74:865-876. [PMID: 30649386 DOI: 10.1093/jac/dky518] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe. METHODS A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM). RESULTS Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models. CONCLUSIONS Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.
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Affiliation(s)
- Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands
| | - Steven Sarrazin
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - Patrick Munk
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, Kongens Lyngby, Denmark
| | - Berith E Knudsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, Kongens Lyngby, Denmark
| | | | - Alex Bossers
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Houtribweg 39, RA, Lelystad, The Netherlands
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, Kongens Lyngby, Denmark
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Houtribweg 39, RA, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, CL, Utrecht, The Netherlands
| | - Dik J Mevius
- Wageningen Bioveterinary Research, Houtribweg 39, RA, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, CL, Utrecht, The Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands.,Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, MA, Bilthoven, The Netherlands
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands
| | - Alejandro Dorado-García
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, CM Utrecht, The Netherlands
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