145 results on '"Wagenaar, Jaap A"'
Search Results
2. Campylobacter fetus Plasmid Diversity: Comparative Analysis of Fully Sequenced Plasmids and Proposed Classification Scheme.
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Pena-Fernández, Nerea, Bloois, Linda van der Graaf-van, Duim, Birgitta, Zomer, Aldert, Wagenaar, Jaap A, Ocejo, Medelin, Lavín, Jose Luís, Collantes-Fernández, Esther, Hurtado, Ana, and Aduriz, Gorka
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MOBILE genetic elements ,WHOLE genome sequencing ,DNA-binding proteins ,PLASMIDS ,DRUG resistance in microorganisms - Abstract
Campylobacter fetus is an animal pathogen that contains 2 mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv) including its biovar intermedius that exhibit different biochemical traits and differences in pathogenicity. Although plasmids are important in the horizontal transfer of antimicrobial resistance genes and virulence factors, C. fetus plasmids are understudied. Here, the closed sequences of 12 plasmids from Spanish C. fetus isolates were compared with the publicly available DNA sequences of C. fetus plasmids and other members of the Campylobacterales order. Sizes of C. fetus plasmids from Spanish isolates ranged between 4 and 50 kb and most of them (10/12) were potentially conjugative. Comparative analysis of the plasmids' gene content revealed a close genetic relationship between the plasmids of C. fetus isolated in Spain and those from other geographical regions, while being clearly distinct from plasmids of other Campylobacter species. Furthermore, C. fetus plasmids were grouped into two main clusters regardless of their geographic location or lineage. The distribution pattern of relaxase, replicase, and single-stranded DNA binding SSB protein encoding genes showed a clustering comparable to that resulting from plasmid whole gene content analysis, suggesting its potential use for the classification of C. fetus plasmids. Most of the larger plasmids harbored mobile genetic elements. These results can help to better understand the evolutionary dynamics and pathogenic implications of C. fetus plasmids. [ABSTRACT FROM AUTHOR]
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- 2024
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3. The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens.
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Vlasblom, Abel A., Duim, Birgitta, Patel, Shriram, Luiken, Roosmarijn E. C., Crespo-Piazuelo, Daniel, Eckenberger, Julia, Huseyin, Chloe E., Lawlor, Peadar G., Elend, Christian, Wagenaar, Jaap A., Claesson, Marcus J., and Zomer, Aldert L.
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- 2024
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4. Extended period of selection for antimicrobial resistance due to recirculation of persistent antimicrobials in broilers.
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Swinkels, Aram F, Berendsen, Bjorn J A, Fischer, Egil A J, Zomer, Aldert L, and Wagenaar, Jaap A
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DRUG resistance in bacteria ,ESCHERICHIA coli ,DRUG resistance in microorganisms ,ANIMAL behavior ,FLUOROQUINOLONES - Abstract
Objectives Antimicrobials can select for antimicrobial-resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable, recirculation of subinhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens. Methods The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (unstable), doxycycline or enrofloxacin (stable). Antimicrobials were extracted from the faecal samples and were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by using Escherichia coli as indicator microorganism. Results Up to 37 days after treatment, doxycycline and enrofloxacin had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the amoxicillin treatment. The amoxicillin treatment showed a significant difference (P ≤ 0.01 and P ≤ 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic resistance and a significant difference (P ≤ 0.05 and P ≤ 0.0001) in genotypic resistance throughout the trial. Furthermore, enrofloxacin treatment resulted in a complete non-WT E. coli population but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations. Conclusions Based on our findings, we suggest that persistence of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock. [ABSTRACT FROM AUTHOR]
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- 2024
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5. A coaching approach to strengthen farm management teams to reduce antimicrobial use in Dutch high usage pig farms: a 2 year intervention study.
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Prinsen, Heleen, Huifang Deng, Heederik, Dick, Wagenaar, Jaap A., Speksnijder, David C., and Dohmen, Wietske
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SWINE farms ,FARM management ,PIGLETS ,BIOSECURITY ,SWINE - Abstract
The use of antimicrobials in the pig sector in the Netherlands has been reduced by more than 70% over the last decade. However, there is still a considerable number of pig farms that have not been able to lower their antimicrobial usage (AMU) to a sufficiently low level, comparable to the majority of the other pig farms. Therefore, an intervention study was initiated to lower on-farm antimicrobial use in which 45 pig farms with high AMU were recruited. These farms were coached over a period of 2 years whereby different management interventions were introduced. During the 2-year study period a significant reduction of 13 and 17% in total AMU was seen in weaned piglets and fattening pigs respectively. The introduction of coaching as well as multiple management interventions were (univariably) associated with the decrease in AMU. After mutual adjustment of coaching and individual interventions, the association between coaching and AMU became substantially weaker, indicating that coaching and interventions were interrelated and specific interventions explained the reduction in AMU. In conclusion, a coaching effect was observed in this study, with an effect on AMU through specific interventions. More insights are needed regarding the role and effects of coaching on the influence on the management team comprising the farmer, veterinarian and (feed) advisor, and interventions implemented. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Azole Resistance in Veterinary Clinical Aspergillus fumigatus Isolates in the Netherlands.
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van Dijk, Marloes A. M., Buil, Jochem B., Tehupeiory-Kooreman, Marlou, Broekhuizen, Marian J., Broens, Els M., Wagenaar, Jaap A., and Verweij, Paul E.
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Aspergillus fumigatus is a saprophytic fungal pathogen that causes opportunistic infections in animals and humans. Azole resistance has been reported globally in human A. fumigatus isolates, but the prevalence of resistance in isolates from animals is largely unknown. A retrospective resistance surveillance study was performed using a collection of clinical A. fumigatus isolates from various animal species collected between 2015 and 2020. Agar-based azole resistance screening of all isolates was followed by in vitro antifungal susceptibility testing and cyp51A gene sequencing of the azole-resistant isolates. Over the 5 year period 16 (11.3%) of 142 A. fumigatus culture-positive animals harbored an azole-resistant isolate. Resistant isolates were found in birds (15%; 2/13), cats (21%; 6/28), dogs (8%; 6/75) and free-ranging harbor porpoise (33%; 2/6). Azole-resistance was cyp51A mediated in all isolates: 81.3% (T-67G/)TR
34 /L98H, 12.5% TR46 /Y121F/T289A. In one azole-resistant A. fumigatus isolate a combination of C(-70)T/F46Y/C(intron7)T/C(intron66)T/M172V/E427K single-nucleotide polymorphisms in the cyp51A gene was found. Of the animals with an azole-resistant isolate and known azole exposure status 71.4% (10/14) were azole naive. Azole resistance in A. fumigatus isolates from animals in the Netherlands is present and predominantly cyp51A TR-mediated, supporting an environmental route of resistance selection. Our data supports the need to include veterinary isolates in resistance surveillance programs. Veterinarians should consider azole resistance as a reason for therapy failure when treating aspergillosis and consider resistance testing of relevant isolates. [ABSTRACT FROM AUTHOR]- Published
- 2024
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7. Using Implementation Mapping to develop an intervention program to support veterinarians' adherence to the guideline on Streptococcus suis clinical practice in weaned pigs.
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Wayop, Isaura Y. A., de Vet, Emely, Leerlooijer, Joanne N., Wagenaar, Jaap A., and Speksnijder, David C.
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STREPTOCOCCUS suis ,VETERINARIANS ,SWINE ,ACTIVE learning ,ANTIMICROBIAL stewardship - 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. [ABSTRACT FROM AUTHOR]
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- 2024
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8. The European livestock resistome.
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Munk, Patrick, Dongsheng Yang, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Ribeiro Duarte, Ana Sofia, Clausen, Philip T. L. C., Brinch, Christian, Van Gompe, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A., Schmitt, Heike, Heederik, Dick J. J., Mevius, Dik J., Smit, Lidwien A. M., Bossers, Alex, and Aarestrup, Frank M.
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- 2024
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9. Global diversity of enterococci and description of 18 previously unknown species.
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Schwartzman, Julia A., Lebreton, Francois, Salamzade, Rauf, Shea, Terrance, Martin, Melissa J., Schaufler, Katharina, Urhan, Aysun, Abeel, Thomas, Camargo, Ilana L. B. C., Sgardioli, Bruna F., Prichula, Janira, Guedes Frazzon, Ana Paula, Giribet, Gonzalo, Van Tyne, Daria, Treinish, Gregg, Innis, Charles J., Wagenaar, Jaap A., Whipple, Ryan M., Manson, Abigail L., and Earl, Ashlee M.
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ENTEROCOCCUS ,ENTEROCOCCUS faecalis ,SPECIES ,ENTEROCOCCUS faecium ,HUMAN microbiota ,SPECIES diversity - 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 unprecedented^ 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. [ABSTRACT FROM AUTHOR]
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- 2024
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10. Pola Penggunaan Anti Mikrob pada Peternakan Mandiri Ayam Broiler di Kabupaten Bogor.
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Sunandar, Suandy, Imron, Nurbiyanti, Nofita, Arief, Riana Aryani, Rachmawati, Annisa Devi, Pertela, Gian, Purwanto, Budi, Daradjat, Hanan, Speksnijder, David, Sani, Rianna Anwar, Dinar, Tagrid, Putri Naipospos, Tri Satya, and Wagenaar, Jaap
- Abstract
Copyright of Acta Vet Indones. The Indonesian Veterinary Journal / Jurnal Acta Veterinaria Indonesiana is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2024
11. Characterising the gut microbiome of stranded harbour seals (Phoca vitulina) in rehabilitation.
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Rubio-Garcia, Ana, Zomer, Aldert L., Guo, Ruoshui, Rossen, John W. A., van Zeijl, Jan H., Wagenaar, Jaap A., and Luiken, Roosmarijn E. C.
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HARBOR seal ,GUT microbiome ,REHABILITATION centers ,REHABILITATION ,HUMAN ecology - 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. [ABSTRACT FROM AUTHOR]
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- 2023
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12. Safety Evaluation of an Intranasally Applied Cocktail of Lactococcus lactis Strains in Pigs.
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Rattigan, Ruth, Wajda, Lukasz, Vlasblom, Abel A., Wolfe, Alan, Zomer, Aldert L., Duim, Birgitta, Wagenaar, Jaap A., and Lawlor, Peadar G.
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LACTOCOCCUS lactis ,SWINE ,INTRANASAL administration ,LUNGS ,PIGLETS ,GENE expression ,COCKTAILS - Abstract
Simple Summary: In this study, the safety of an intranasally applied cocktail of Lactococcus lactis was evaluated in new-born pigs. Prior to farrowing, twelve sows were assigned to either a placebo or cocktail group. Immediately after farrowing, either the placebo or cocktail was applied to both nostrils of all piglets in the corresponding group. Piglet health and growth were monitored at regular intervals, and on three occasions piglets were necropsied and samples were collected from the respiratory tract to identify any changes caused by the treatment. The results show that the cocktail did not negatively impact piglet growth or health, nor did it cause histological changes in the nasal conchae, tonsils or lung tissues; but it did alter the gene expression of pBD2, TLR9 and IL-1β in the nasal conchae. These findings indicate the cocktail is safe for administration to pigs. 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. [ABSTRACT FROM AUTHOR]
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- 2023
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13. Serological Survey of Retrovirus and Coronavirus Infections, including SARS-CoV-2, in Rural Stray Cats in The Netherlands, 2020–2022.
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Duijvestijn, Mirjam B. H. M., Schuurman, Nancy N. M. P., Vernooij, Johannes C. M., van Leeuwen, Michelle A. J. M., Bosch, Berend-Jan, van den Brand, Judith M. A., Wagenaar, Jaap A., van Kuppeveld, Frank J. M., Egberink, Herman F., and Verhagen, Josanne H.
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RETROVIRUS diseases ,SARS-CoV-2 ,COVID-19 ,FELINE leukemia virus ,CATS ,ENZYME-linked immunosorbent assay - 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. [ABSTRACT FROM AUTHOR]
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- 2023
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14. Quantifying topical antimicrobial use before and during participation in an antimicrobial stewardship programme in Dutch companion animal clinics.
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Kardomatea, Nafsika, Hopman, Nonke E. M., van Geijlswijk, Ingeborg M., Portengen, Lützen, Wagenaar, Jaap A., Heederik, Dick J. J., and Broens, Els M.
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PETS ,ANTIMICROBIAL stewardship ,VETERINARY medicine ,ANIMAL populations ,PARTICIPATION ,CLINICS - 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. [ABSTRACT FROM AUTHOR]
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- 2023
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15. Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome.
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Theelen, Mathijs J. P., Luiken, Roosmarijn E. C., Wagenaar, Jaap A., Sloet van Oldruitenborgh-Oosterbaan, Marianne M., Rossen, John W. A., Schaafstra, Femke J. W. C., van Doorn, David A., and Zomer, Aldert L.
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ORAL drug administration ,GUT microbiome ,HOSPITAL admission & discharge ,SHOTGUN sequencing ,LONGITUDINAL method ,HOSPITAL care - 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. -NEQ1286BccpFJdhcRCuNy Video Abstract [ABSTRACT FROM AUTHOR]
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- 2023
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16. Why Veterinarians (Do Not) Adhere to the Clinical Practice Streptococcus suis in Weaned Pigs Guideline: A Qualitative Study.
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Wayop, Isaura Y. A., de Vet, Emely, Wagenaar, Jaap A., and Speksnijder, David C.
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STREPTOCOCCUS suis ,VETERINARIANS ,SWINE ,SOCIAL influence ,QUALITATIVE research - 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. [ABSTRACT FROM AUTHOR]
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- 2023
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17. Biosecurity and antimicrobial use in broiler farms across nine European countries: toward identifying farm-specific options for reducing antimicrobial usage.
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Mallioris, Panagiotis, Teunis, Gijs, Lagerweij, Giske, Joosten, Philip, Dewulf, Jeroen, Wagenaar, Jaap A., Stegeman, Arjan, Mughini-Gras, Lapo, and consortium, the EFFORT
- Abstract
Broiler chickens are among the main livestock sectors worldwide. With individual treatments being inapplicable, contrary to many other animal species, the need for antimicrobial use (AMU) is relatively high. AMU in animals is known to drive the emergence and spread of antimicrobial resistance (AMR). High farm biosecurity is a cornerstone for animal health and welfare, as well as food safety, as it protects animals from the introduction and spread of pathogens and therefore the need for AMU. The goal of this study was to identify the main biosecurity practices associated with AMU in broiler farms and to develop a statistical model that produces customised recommendations as to which biosecurity measures could be implemented on a farm to reduce its AMU, including a cost-effectiveness analysis of the recommended measures. AMU and biosecurity data were obtained cross-sectionally in 2014 from 181 broiler farms across nine European countries (Belgium, Bulgaria, Denmark, France, Germany, Italy, the Netherlands, Poland and Spain). Using mixed-effects random forest analysis (Mix-RF), recursive feature elimination was implemented to determine the biosecurity measures that best predicted AMU at the farm level. Subsequently, an algorithm was developed to generate AMU reduction scenarios based on the implementation of these measures. In the final Mix-RF model, 21 factors were present: 10 about internal biosecurity, 8 about external biosecurity and 3 about farm size and productivity, with the latter showing the largest (Gini) importance. Other AMU predictors, in order of importance, were the number of depopulation steps, compliance with a vaccination protocol for non-officially controlled diseases, and requiring visitors to check in before entering the farm. K -means clustering on the proximity matrix of the final Mix-RF model revealed that several measures interacted with each other, indicating that high AMU levels can arise for various reasons depending on the situation. The algorithm utilised the AMU predictive power of biosecurity measures while accounting also for their interactions, representing a first step toward aiding the decision-making process of veterinarians and farmers who are in need of implementing on-farm biosecurity measures to reduce their AMU. [ABSTRACT FROM AUTHOR]
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- 2023
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18. Variation in haplotypes in single cysts of assemblages C and D, but not of assemblage E of Giardia duodenalis.
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Veldhuis, Floor L., Nijsse, Rolf, Wagenaar, Jaap A., Arkesteijn, Ger, and Kooyman, Frans N. J.
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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. [ABSTRACT FROM AUTHOR]
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- 2022
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19. Biosecurity and antimicrobial use in broiler farms across nine European countries: toward identifying farm-specific options for reducing antimicrobial usage.
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Mallioris, Panagiotis, Teunis, Gijs, Lagerweij, Giske, Joosten, Philip, Dewulf, Jeroen, Wagenaar, Jaap A., Stegeman, Arjan, Mughini-Gras, Lapo, the EFFORT consortium, Graveland, H., Schmitt, H., Mevius, D., van Essen, A., Gonzalez-Zorn, B., Moyano, G., Sanders, P., Chauvin, C., David, J., Battisti, A., and Caprioli, A.
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Broiler chickens are among the main livestock sectors worldwide. With individual treatments being inapplicable, contrary to many other animal species, the need for antimicrobial use (AMU) is relatively high. AMU in animals is known to drive the emergence and spread of antimicrobial resistance (AMR). High farm biosecurity is a cornerstone for animal health and welfare, as well as food safety, as it protects animals from the introduction and spread of pathogens and therefore the need for AMU. The goal of this study was to identify the main biosecurity practices associated with AMU in broiler farms and to develop a statistical model that produces customised recommendations as to which biosecurity measures could be implemented on a farm to reduce its AMU, including a cost-effectiveness analysis of the recommended measures. AMU and biosecurity data were obtained cross-sectionally in 2014 from 181 broiler farms across nine European countries (Belgium, Bulgaria, Denmark, France, Germany, Italy, the Netherlands, Poland and Spain). Using mixed-effects random forest analysis (Mix-RF), recursive feature elimination was implemented to determine the biosecurity measures that best predicted AMU at the farm level. Subsequently, an algorithm was developed to generate AMU reduction scenarios based on the implementation of these measures. In the final Mix-RF model, 21 factors were present: 10 about internal biosecurity, 8 about external biosecurity and 3 about farm size and productivity, with the latter showing the largest (Gini) importance. Other AMU predictors, in order of importance, were the number of depopulation steps, compliance with a vaccination protocol for non-officially controlled diseases, and requiring visitors to check in before entering the farm. K -means clustering on the proximity matrix of the final Mix-RF model revealed that several measures interacted with each other, indicating that high AMU levels can arise for various reasons depending on the situation. The algorithm utilised the AMU predictive power of biosecurity measures while accounting also for their interactions, representing a first step toward aiding the decision-making process of veterinarians and farmers who are in need of implementing on-farm biosecurity measures to reduce their AMU. [ABSTRACT FROM AUTHOR]
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- 2022
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20. SARS‐CoV‐2 infection in dogs and cats is associated with contact to COVID‐19‐positive household members.
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Kannekens‐Jager, Marleen M., de Rooij, Myrna M. T., de Groot, Yasmina, Biesbroeck, Elena, de Jong, Marja K., Pijnacker, Tera, Smit, Lidwien A. M., Schuurman, Nancy, Broekhuizen‐Stins, Marian J., Zhao, Shan, Duim, Birgitta, Langelaar, Merel F. M., Stegeman, Arjan, Kooistra, Hans S., Radstake, Carien, Egberink, Herman F., Wagenaar, Jaap A., and Broens, Els M.
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PETS ,SARS-CoV-2 ,DOGS ,PLANT viruses ,CATS - 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. [ABSTRACT FROM AUTHOR]
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- 2022
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21. Hubungan Penggunaan Antimikroba terhadap Resistansi pada Peternakan Unggas Broiler Mandiri di Kabupaten Bogor .
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Nurbiyanti, Nofita, Suandy, Imron, Sunandar, Arief, Riana Aryani, Allamanda, Putik, Pertela, Gian, Purwanto, Budi, Daradjat, Hanan, Triwijayanti, Nuraini, Rahayu, Kanti Puji, Susanti, Oli, Desitania, Riska, Sani, Rianna Anwar, Speksnijder, David, Dinar, Tagrid, Putri Naipospos, Tri Satya, and Wagenaar, Jaap
- Abstract
Copyright of Acta Vet Indones. The Indonesian Veterinary Journal / Jurnal Acta Veterinaria Indonesiana is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2022
22. Within-Household Transmission and Bacterial Diversity of Staphylococcus pseudintermedius.
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Wegener, Alice, Duim, Birgitta, van der Graaf-van Bloois, Linda, Zomer, Aldert L., Visser, Caroline E., Spaninks, Mirlin, Timmerman, Arjen J., Wagenaar, Jaap A., and Broens, Els M.
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BACTERIAL diversity ,WHOLE genome sequencing ,STAPHYLOCOCCUS ,OPPORTUNISTIC infections ,INFECTIOUS disease transmission ,PLASMIDS - 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. [ABSTRACT FROM AUTHOR]
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- 2022
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23. Antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe.
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Yang, Dongsheng, Heederik, Dick J J, Scherpenisse, Peter, Gompel, Liese Van, Luiken, Roosmarijn E C, Wadepohl, Katharina, Skarżyńska, Magdalena, Heijnsbergen, Eri Van, Wouters, Inge M, Greve, Gerdit D, Jongerius-Gortemaker, Betty G M, Tersteeg-Zijderveld, Monique, Portengen, Lützen, Juraschek, Katharina, Fischer, Jennie, Zając, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A, Mevius, Dik J, and Smit, Lidwien A M
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MEAT ,CATTLE ,POULTRY ,CROSS-sectional method ,ANIMAL experimentation ,ANTI-infective agents ,RNA ,SWINE ,FECES ,GENES ,RESEARCH funding ,DRUG resistance in microorganisms ,ANTIBIOTICS ,ANIMALS ,PHARMACODYNAMICS - 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. [ABSTRACT FROM AUTHOR]- Published
- 2022
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24. Risk factors for the abundance of antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) in pig and broiler faeces in nine European countries.
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Yang, Dongsheng, Heederik, Dick J. J., Mevius, Dik J., Scherpenisse, Peter, Luiken, Roosmarijn E. C., Gompel, Liese Van, Skarżyńska, Magdalena, Wadepohl, Katharina, Chauvin, Claire, Heijnsbergen, Eri Van, Wouters, Inge M., Greve, Gerdit D., Jongerius-Gortemaker, Betty G. M., Tersteeg-Zijderveld, Monique, Zając, Magdalena, Wasyl, Dariusz, Juraschek, Katharina, Fischer, Jennie, Wagenaar, Jaap A., and Smit, Lidwien A. M.
- 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. [ABSTRACT FROM AUTHOR]- Published
- 2022
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25. Comparison of different antimicrobial use indicators and antimicrobial resistance data in food-producing animals.
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Sanders, Pim, Mevius, Dik, Veldman, Kees, van Geijlswijk, Inge, Wagenaar, Jaap A., Bonten, Marc, and Heederik, Dick
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- 2021
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26. Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets.
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Patel, Shriram, Vlasblom, Abel A., Verstappen, Koen M., Zomer, Aldert L., Fluit, Ad C., Rogers, Malbert R. C., Wagenaar, Jaap A., Claesson, Marcus J., and Duimb, Birgitta
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- 2021
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27. Transboundary Spread of Brucella canis through Import of Infected Dogs, the Netherlands, November 2016-December 2018.
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van Dijk, Marloes A. M., Engelsma, Marc Y., Visser, Vanessa X. N., Keur, Ingrid, Holtslag, Marjolijn E., Willems, Nicole, Meij, Björn P., Willemsen, Peter T. J., Wagenaar, Jaap A., Roest, Hendrik I. J., and Broens, Els M.
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CANIS ,DOGS ,BRUCELLA ,RESCUE dogs ,DOG rescue ,DOG diseases ,BRUCELLOSIS ,GRAM-negative aerobic bacteria ,ANIMALS - 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. [ABSTRACT FROM AUTHOR]
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- 2021
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28. Serologic Screening of Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Cats and Dogs during First Coronavirus Disease Wave, the Netherlands.
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Shan Zhao, Schuurman, Nancy, Wentao Li, Chunyan Wang, Smit, Lidwien A. M., Broens, Els M., Wagenaar, Jaap A., van Kuppeveld, Frank J. M., Bosch, Berend-Jan, Egberink, Herman, Zhao, Shan, Li, Wentao, and Wang, Chunyan
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COVID-19 ,DOGS ,CATS ,SARS-CoV-2 ,ANIMAL species - 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. [ABSTRACT FROM AUTHOR]
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- 2021
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29. Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants – Identification of Reservoir Resistome Signatures.
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Duarte, Ana Sofia Ribeiro, Röder, Timo, Van Gompel, Liese, Petersen, Thomas Nordahl, Hansen, Rasmus Borup, Hansen, Inge Marianne, Bossers, Alex, Aarestrup, Frank M., Wagenaar, Jaap A., and Hald, Tine
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METAGENOMICS ,DRUG resistance in microorganisms ,RESERVOIRS ,RANDOM forest algorithms ,SWINE ,OCCUPATIONAL exposure - 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. [ABSTRACT FROM AUTHOR]
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- 2021
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30. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America.
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Castellanos, L. Ricardo, van der Graaf-van Bloois, Linda, Donado-Godoy, Pilar, Veldman, Kees, Duarte, Francisco, Acuña, María T., Jarquín, Claudia, Weill, François-Xavier, Mevius, Dik J., Wagenaar, Jaap A., Hordijk, Joost, and Zomer, Aldert L.
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SALMONELLA enterica serovar Typhi ,DRUG resistance in microorganisms ,SALMONELLA enterica ,PRINCIPAL components analysis ,POULTRY ,TREE populations - Abstract
Salmonella enterica serovar Paratyphi B variant Java sequence type 28 is prevalent in poultry and poultry meat. We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. Phylogenetic time trees and effective population sizes (Ne) showed separate clustering of strains from Latin America and Europe. The separation is estimated to have occurred during the 1980s. Ne of strains increased sharply in Europe around 1995 and in Latin America around 2005. Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. Regardless of the evolutionary separation, similar features of resistance to β-lactams and quinolones/fluoroquinolones indicated parallel evolution of antimicrobial resistance in both regions. [ABSTRACT FROM AUTHOR]
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- 2020
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31. Leptospira infection and shedding in dogs in Thailand.
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Altheimer, Kerstin, Jongwattanapisan, Prapaporn, Luengyosluechakul, Supol, Pusoonthornthum, Rosama, Prapasarakul, Nuvee, Kurilung, Alongkorn, Broens, Els M., Wagenaar, Jaap A., Goris, Marga G. A., Ahmed, Ahmed A., Pantchev, Nikola, Reese, Sven, and Hartmann, Katrin
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LEPTOSPIRA ,IMMUNOGLOBULIN M ,ENZYME-linked immunosorbent assay ,IMMUNOGLOBULIN G ,DOGS ,EMERGING infectious diseases ,ZOONOSES - Abstract
Background: Leptospirosis is a widespread zoonosis and has been recognized as a re-emerging infectious disease in humans and dogs, but prevalence of Leptospira shedding in dogs in Thailand is unknown. The aim of this study was to determine urinary shedding of Leptospira in dogs in Thailand, to evaluate antibody prevalence by microscopic agglutination test (MAT) and enzyme-linked immunosorbent assay (ELISA), and to assess risk factors for Leptospira infection. In Northern, Northeastern, and Central Thailand, 273 stray (n = 119) or client-owned (n = 154) dogs from rural (n = 139) or urban (n = 134) areas were randomly included. Dogs that had received antibiotics within 4 weeks prior to sampling were excluded. No dog had received vaccination against Leptospira. Urine was evaluated by real-time polymerase chain reaction (PCR) specific for lipL32 gene of pathogenic Leptospira. Additionally, urine was cultured for 6 months in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium. Antibodies were measured by ELISA and MAT against 24 serovars belonging to 15 serogroups and 1 undesignated serogroup. Risk factor analysis was performed with backwards stepwise selection based on Wald. Results: Twelve of 273 (4.4%; 95% confidence interval (CI): 2.0–6.8%) urine samples were PCR-positive. In 1/273 dogs (0.4%; 95% CI: 0.01–1.1%) Leptospira could be cultured from urine. MAT detected antibodies in 33/273 dogs (12.1%; 95% CI: 8.2–16.0%) against 19 different serovars (Anhoa, Australis, Ballum, Bataviae, Bratislava, Broomi, Canicola, Copenhageni, Coxi, Grippotyphosa, Haemolytica, Icterohaemorrhagiae, Khorat, Paidjan, Patoc, Pyrogenes, Rachmati, Saxkoebing, Sejroe). In 111/252 dogs (44.0%; 95% CI: 37.9–50.2%) immunoglobulin M (IgM) and/or immunoglobulin G (IgG) antibodies were found by ELISA. Female dogs had a significantly higher risk for Leptospira infection (p = 0.023). Conclusions: Leptospira shedding occurs in randomly sampled dogs in Thailand, with infection rates comparable to those of Europe and the USA. Therefore, the potential zoonotic risk should not be underestimated and use of Leptospira vaccines are recommended. [ABSTRACT FROM AUTHOR]
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- 2020
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32. Occupational Exposure and Carriage of Antimicrobial Resistance Genes (tetW, ermB) in Pig Slaughterhouse Workers.
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Gompel, Liese Van, Dohmen, Wietske, Luiken, Roosmarijn E C, Bouwknegt, Martijn, Heres, Lourens, Heijnsbergen, Eri van, Jongerius-Gortemaker, Betty G M, Scherpenisse, Peter, Greve, Gerdit D, Tersteeg-Zijderveld, Monique H G, Wadepohl, Katharina, Duarte, Ana Sofia Ribeiro, Muñoz-Gómez, Violeta, Fischer, Jennie, Skarżyńska, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A, Urlings, Bert A P, Dorado-García, Alejandro, and Wouters, Inge M
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FECAL analysis ,DRUG resistance in microorganisms ,FOOD industry ,GENES ,MACROLIDE antibiotics ,POLYMERASE chain reaction ,QUESTIONNAIRES ,SWINE ,TETRACYCLINE ,OCCUPATIONAL hazards ,ENVIRONMENTAL exposure ,MULTIPLE regression analysis ,CROSS-sectional method - 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. [ABSTRACT FROM AUTHOR]
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- 2020
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33. 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.
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Wegener, Alice, Damborg, Peter, Guardabassi, Luca, Moodley, Arshnee, Mughini-Gras, Lapo, Duim, Birgitta, Wagenaar, Jaap A, and Broens, Els M
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OXACILLIN ,CLAVULANIC acid ,AMOXICILLIN ,METHICILLIN-resistant staphylococcus aureus ,CHROMOSOMES ,STAPHYLOCOCCUS ,METHICILLIN resistance ,RESEARCH ,SEQUENCE analysis ,DOG diseases ,ANIMAL experimentation ,RESEARCH methodology ,MEDICAL cooperation ,EVALUATION research ,STAPHYLOCOCCAL diseases ,CEPHALOSPORINS ,COMPARATIVE studies ,DOGS ,ENZYME inhibitors ,MICROBIAL sensitivity tests ,ANTIBIOTICS ,PHARMACODYNAMICS - 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. [ABSTRACT FROM AUTHOR]- Published
- 2020
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34. Implementation and evaluation of an antimicrobial stewardship programme in companion animal clinics: A stepped-wedge design intervention study.
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Hopman, Nonke E. M., Portengen, Lützen, Hulscher, Marlies E. J. L., Heederik, Dick J. J., Verheij, T. J. M., Wagenaar, Jaap A., Prins, Jan M., Bosje, Tjerk, Schipper, Louska, van Geijlswijk, Ingeborg M., and Broens, Els M.
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PETS ,VETERINARY medicine ,TIME series analysis ,CLINICS ,QUANTITATIVE research ,QUALITATIVE research - Abstract
Background: To curb increasing resistance rates, responsible antimicrobial use (AMU) is needed, both in human and veterinary medicine. In human healthcare, antimicrobial stewardship programmes (ASPs) have been implemented worldwide to improve appropriate AMU. No ASPs have been developed for and implemented in companion animal clinics yet. Objectives: The objective of the present study was to implement and evaluate the effectiveness of an ASP in 44 Dutch companion animal clinics. The objectives of the ASP were to increase awareness on AMU, to decrease total AMU whenever possible and to shift AMU towards 1
st choice antimicrobials, according to Dutch guidelines on veterinary AMU. Methods: The study was designed as a prospective, stepped-wedge, intervention study, which was performed from March 2016 until March 2018. The multifaceted intervention was developed using previous qualitative and quantitative research on current prescribing behaviour in Dutch companion animal clinics. The number of Defined Daily Doses for Animal (DDDAs) per clinic (total, 1st , 2nd and 3rd choice AMU) was used to quantify systemic AMU. Monthly AMU data were described using a mixed effect time series model with auto-regression. The effect of the ASP was modelled using a step function and a change in the (linear) time trend. Results: A statistically significant decrease of 15% (7%-22%) in total AMU, 15% (5%-24%) in 1st choice AMU and 26% (17%-34%) in 2nd choice AMU was attributed to participation in the ASP, on top of the already ongoing time trends. Use of 3rd choice AMs did not significantly decrease by participation in the ASP. The change in total AMU became more prominent over time, with a 16% (4%-26%) decrease in (linear) time trend per year. Conclusions: This study shows that, although AMU in Dutch companion animal clinics was already decreasing and changing, AMU could be further optimised by participation in an antimicrobial stewardship programme. [ABSTRACT FROM AUTHOR]- Published
- 2019
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35. Successful Host Adaptation of IncK2 Plasmids.
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Rozwandowicz, Marta, Brouwer, Michael S. M., Mughini-Gras, Lapo, Wagenaar, Jaap A., Gonzalez-Zorn, Bruno, Mevius, Dik J., and Hordijk, Joost
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PLASMIDS ,DIRECT costing ,PROTEIN expression ,ESCHERICHIA coli ,PHYSIOLOGICAL adaptation - Abstract
The IncK plasmid group can be divided into two separate lineages named IncK1 and IncK2. IncK2 is found predominantly in poultry while IncK1 was reported in various mammals, including animals and humans. The physiological basis of this distinction is not known. In this manuscript we examined fitness cost of IncK1 and IncK2 plasmids at 37 and 42°C, which resembles mammalian and chicken body temperatures, respectively. We analyzed conjugation frequency, plasmid copy number and plasmid fitness cost in direct competition. Additionally, we measured levels of σ-32 in Escherichia coli carrying either wild type or conjugation-deficient IncK plasmids. The results show that IncK2 plasmids have a higher conjugation frequency and lower copy number at 42°C compared to IncK1. While the overall fitness cost to the host bacterium of IncK2 plasmids was higher than that of IncK1, it was not affected by the temperature while the fitness cost of IncK1 was shown to increase at 42°C compared to 37°C. These differences correlate with an increased expression of σ-32, a regulator of heat-shock protein expression, in E. coli with IncK2 compared to cells containing IncK1. This effect was not seen in cells containing conjugation deficient plasmids. Therefore, it is hypothesized that the assembly of the functional T4S may lead to these increased levels of σ–32. Increased activation of CpxR at 42°C may explain why IncK2 plasmids, and not IncK1, are predominantly found in chicken isolates. [ABSTRACT FROM AUTHOR]
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- 2019
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36. Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries.
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Luiken, Roosmarijn E C, Gompel, Liese Van, Munk, Patrick, Sarrazin, Steven, Joosten, Philip, Dorado-García, Alejandro, Hansen, Rasmus Borup, Knudsen, Berith E, Bossers, Alex, Wagenaar, Jaap A, Aarestrup, Frank M, Dewulf, Jeroen, Mevius, Dik J, Heederik, Dick J J, Smit, Lidwien A M, Schmitt, Heike, consortium, EFFORT, Van Gompel, Liese, Borup Hansen, Rasmus, and EFFORT consortium
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GENE clusters ,FARMS ,LACTAMS ,TETRACYCLINES ,RECORD collecting ,PEPTIDE antibiotics ,BIOSECURITY ,TETRACYCLINE - Abstract
Objectives: To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms.Methods: In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored.Results: Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity.Conclusions: The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes. [ABSTRACT FROM AUTHOR]- Published
- 2019
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37. Dynamics of faecal shedding of ESBL- or AmpC-producing Escherichia coli on dairy farms.
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Hordijk, Joost, Fischer, Egil A J, Werven, Tine van, Sietsma, Steven, Gompel, Liese Van, Timmerman, Arjen J, Spaninks, Mirlin P, Heederik, Dick J J, Nielen, Mirjam, Wagenaar, Jaap A, Stegeman, Arjan, van Werven, Tine, and Van Gompel, Liese
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ESCHERICHIA coli ,DAIRY farms ,MOLTING ,ANTI-infective agents ,FECES ,BETA lactamases ,CATTLE microbiology ,BACTERIAL protein metabolism ,ANIMAL experimentation ,ANTIBIOTICS ,BACTERIAL proteins ,COMPARATIVE studies ,DRUG resistance in microorganisms ,GENES ,HYDROLASES ,RESEARCH methodology ,MEDICAL cooperation ,RESEARCH ,EVALUATION research ,CROSS-sectional method ,GENOTYPES ,PHARMACODYNAMICS - 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. [ABSTRACT FROM AUTHOR]- Published
- 2019
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38. The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.
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Gompel, Liese Van, Luiken, Roosmarijn E C, Sarrazin, Steven, Munk, Patrick, Knudsen, Berith E, Hansen, Rasmus B, Bossers, Alex, Aarestrup, Frank M, Dewulf, Jeroen, Wagenaar, Jaap A, Mevius, Dik J, Schmitt, Heike, Heederik, Dick J J, Dorado-García, Alejandro, Smit, Lidwien A M, Van Gompel, Liese, and EFFORT consortium
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ANTI-infective agents ,BIOSECURITY ,GENOMES ,MACROLIDE antibiotics ,ESCHERICHIA coli ,DRUG utilization statistics ,RESEARCH ,AGRICULTURE ,CROSS-sectional method ,ANIMAL experimentation ,RESEARCH methodology ,SWINE ,EVALUATION research ,MEDICAL cooperation ,FECES ,BIOINFORMATICS ,COMPARATIVE studies ,GENES ,DRUG resistance in microorganisms ,BIOTIC communities - 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. [ABSTRACT FROM AUTHOR]- Published
- 2019
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39. Occurrence and Characterization of Methicillin Resistant Staphylococcus aureus in Processed Raw Foods and Ready-to-Eat Foods in an Urban Setting of a Developing Country.
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Islam, Mohammad Aminul, Parveen, Sahana, Rahman, Mahdia, Huq, Mohsina, Nabi, Ashikun, Khan, Zahed Uddin Mahmood, Ahmed, Niyaz, and Wagenaar, Jaap A.
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METHICILLIN-resistant staphylococcus aureus ,RAW foods ,STREET food ,STAPHYLOCOCCUS aureus ,DEVELOPING countries - Abstract
Infections by methicillin-resistant Staphylococcus aureus (MRSA) are gradually increasing in the community. In this study, we investigated a total of 162 food samples including 112 ready-to-eat (RTE) foods and 40 processed raw meat and fish samples collected from retail vendors in Dhaka, Bangladesh and determined the occurrence of toxigenic S. aureus and MRSA. Around 22% of samples were positive for S. aureus , RTE foods being more positive (23%) than the processed raw meat/fish samples (18%). Among 35 S. aureus isolates, 74% were resistant to erythromycin, 49% to ciprofloxacin and around 30% to oxacillin and cefoxitin. Around 37% of isolates were resistant to ≥3 classes of antibiotics and 26% of isolates (n = 9) were identified as MRSA. Majority of the isolates were positive for enterotoxin genes (74%), followed by pvl gene (71%), toxic shock syndrome toxin (tsst) gene (17%) and exfoliative toxin genes (11%). Multi locus sequence typing (MLST) of 9 MRSA isolates identified four different types such as ST80 (n = 3), ST6 (n = 2), ST239 (n = 2) and ST361 (n = 2). spa typing of MRSA isolates revealed seven different types including t1198 (n = 2), t315 (n = 2), t037 (n = 1), t275 (n = 1), t304 (n = 1), t8731 (n = 1) and t10546 (n = 1). To our knowledge, this is the first report entailing baseline data on the occurrence of MRSA in RTE foods in Dhaka highlighting a potential public health risk to street food consumers. [ABSTRACT FROM AUTHOR]
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- 2019
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40. Quantitative and qualitative analysis of antimicrobial usage at farm and flock level on 181 broiler farms in nine European countries.
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Joosten, Philip, Sarrazin, Steven, Gompel, Liese Van, Luiken, Roosmarijn E C, Mevius, Dik J, Wagenaar, Jaap A, Heederik, Dick J J, Dewulf, Jeroen, Van Gompel, Liese, and EFFORT consortium
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DRUG resistance ,ANTI-infective agents ,BROILER chickens ,FLUOROQUINOLONES ,POULTRY farms - Abstract
Objectives: To control the emerging threat of antimicrobial resistance, international policy appeals for appropriate monitoring of antimicrobial usage (AMU) at supranational, species and farm level. The aim of this study was to quantify AMU in broilers at farm and flock level in nine European countries.Methods: Antimicrobial treatment data of one flock and purchased antimicrobials over one year were collected at 181 European broiler farms. Afterwards AMU was quantified using treatment incidence (TI) per 100 days based on Defined Daily Dose (DDDvet), Defined Course Dose (DCDvet) or Used Daily Dose (UDDvet) values. Total AMU at flock level was obtained by summing the TIDDDvet of all treatments in the sampled flock (TIDDDvetFl*).Results: The median TIDDDvetFl* was 9.0 (95% CI 5.5-10.8), meaning that broilers were treated with antimicrobials during 9% of their rearing period. TIDDDvetFl* varied considerably within and between countries. However, in every country at least one untreated flock was present. Average TIDDDvetFl* at country level ranged from 3.3 to 36.7. Polymyxins, extended-spectrum aminopenicillins and fluoroquinolones were the most used antimicrobials, accounting for 26%, 26% and 18% of total AMU, respectively. Twenty-six percent of the farms started a treatment on day 1 of production, and 49% of overall AMU was administered within the first week.Conclusions: Results show that rearing broilers without AMU is feasible. However, a huge variation in AMU in terms of amount, moment of administration and antimicrobial classes was observed. This shows that there is still ground to be covered when it comes to AMU on broiler farms. [ABSTRACT FROM AUTHOR]- Published
- 2019
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41. Quantitative and qualitative analysis of antimicrobial usage patterns in 180 selected farrow-to-finish pig farms from nine European countries based on single batch and purchase data.
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Sarrazin, Steven, Joosten, Philip, Gompel, Liese Van, Luiken, Roosmarijn E C, Mevius, Dik J, Wagenaar, Jaap A, Heederik, Dick J J, Dewulf, Jeroen, Van Gompel, Liese, and EFFORT consortium
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ANTI-infective agents ,PENICILLIN ,POLYMYXIN ,ANTIBACTERIAL agents ,DRUG administration - Abstract
Objectives: Farm-level quantification of antimicrobial usage (AMU) in pig farms.Methods: In a cross-sectional study, AMU data on group treatments administered to a single batch of fattening pigs from birth to slaughter (group treatment data) and antimicrobials purchased during 1 year (purchase data) were collected at 180 pig farms in nine European countries. AMU was quantified using treatment incidence (TI) based on defined (DDDvet) and used (UDDvet) daily doses and defined (DCDvet) and used (UCDvet) course doses.Results: The majority of antimicrobial group treatments were administered to weaners (69.5% of total TIDDDvet) followed by sucklers (22.5% of total TIDDDvet). AMU varied considerably between farms with a median TIDDDvet of 9.2 and 7.1 for a standardized rearing period of 200 days based on group treatment and purchase data, respectively. In general, UDDvet and UCDvet were higher than DDDvet and DCDvet, respectively, suggesting that either the defined doses were set too low or that group treatments were often dosed too high and/or administered for too long. Extended-spectrum penicillins (31.2%) and polymyxins (24.7%) were the active substances most often used in group treatments, with the majority administered through feed or water (82%). Higher AMU at a young age was associated with higher use in older pigs.Conclusions: Collecting farm-level AMU data of good quality is challenging and results differ based on how data are collected (group treatment data versus purchase data) and reported (defined versus used daily and course doses). [ABSTRACT FROM AUTHOR]- Published
- 2019
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42. Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis.
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Nguyen, Vinh Trung, Jamrozy, Dorota, Matamoros, Sébastien, Carrique-Mas, Juan J, Ho, Huynh Mai, Thai, Quoc Hieu, Nguyen, Thi Nhu Mai, Wagenaar, Jaap A, Thwaites, Guy, Parkhill, Julian, Schultsz, Constance, and Ngo, Thi Hoa
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ESCHERICHIA coli ,ANTI-infective agents ,GENOMICS ,POULTRY ,EPIDEMIOLOGY - Abstract
Objectives: To investigate the risk of colonization with ESBL-producing Escherichia coli (ESBL-Ec) in humans in Vietnam associated with non-intensive chicken farming.Methods: Faecal samples from 204 randomly selected farmers and their chickens, and from 306 age- and sex-matched community-based individuals who did not raise poultry were collected. Antimicrobial usage in chickens and humans was assessed by medicine cabinet surveys. WGS was employed to obtain a high-resolution genomic comparison between ESBL-Ec isolated from humans and chickens.Results: The adjusted prevalence of ESBL-Ec colonization was 20.0% (95% CI 10.8%-29.1%) and 35.2% (95% CI 30.4%-40.1%) in chicken farms and humans in Vietnam, respectively. Colonization with ESBL-Ec in humans was associated with antimicrobial usage (OR = 2.52, 95% CI = 1.08-5.87) but not with involvement in chicken farming. blaCTX-M-55 was the most common ESBL-encoding gene in strains isolated from chickens (74.4%) compared with blaCTX-M-27 in human strains (47.0%). In 3 of 204 (1.5%) of the farms, identical ESBL genes were detected in ESBL-Ec isolated from farmers and their chickens. Genomic similarity indicating recent sharing of ESBL-Ec between chickens and farmers was found in only one of these farms.Conclusions: The integration of epidemiological and genomic data in this study has demonstrated a limited contribution of non-intensive chicken farming to ESBL-Ec colonization in humans in Vietnam and further emphasizes the importance of reducing antimicrobial usage in both human and animal host reservoirs. [ABSTRACT FROM AUTHOR]- Published
- 2019
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43. Evolutionary Regression and Species-Specific Codon Usage of TLR15.
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Voogdt, Carlos G. P., Merchant, Mark E., Wagenaar, Jaap A., and van Putten, Jos P. M.
- Abstract
Toll-like receptors (TLRs) form an ancient family of innate immune receptors that detect microbial structures and activate the host immune response. Most subfamilies of TLRs (including TLR3, TLR5, and TLR7) are highly conserved among vertebrate species. In contrast, TLR15, a member of the TLR1 subfamily, appears to be unique to birds and reptiles. We investigated the functional evolution of TLR15. Phylogenetic and synteny analyses revealed putative TLR15 orthologs in bird species, several reptilian species and also in a shark species, pointing to an unprecedented date of origin of TLR15 as well as large scale reciprocal loss of this TLR in most other vertebrates. Cloning and functional analysis of TLR15 of the green anole lizard (Anolis carolinensis), salt water crocodile (Crocodylus porosus), American alligator (Alligator mississippiensis), and chicken (Gallus gallus) showed for all species TLR15 specific protease-induced activation of NF-κB, despite highly variable TLR15 protein expression levels. The variable TLR15 expression was consistent in both human and reptilian cells and could be attributed to species-specific differences in TLR15 codon usage. The species-specific codon bias was not or barely noted for more evolutionarily conserved TLRs (e.g., TLR3). Overall, our results indicate that TLR15 originates before the divergence of chondrichthyes fish and tetrapods and that TLR15 of both avian and reptilian species has a conserved function as protease activated receptor. The species-specific codon usage and large scale loss of TLR15 in most vertebrates suggest evolutionary regression of this ancient TLR. [ABSTRACT FROM AUTHOR]
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- 2018
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44. Reducing antimicrobial use in farm animals: how to support behavioral change of veterinarians and farmers.
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Speksnijder, David C. and Wagenaar, Jaap A.
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ANTI-infective agents ,VETERINARY medicine ,DOMESTIC animals ,VETERINARIANS ,FARMERS ,SOCIAL sciences - Abstract
The article focuses on reducing antimicrobial use in farm animals and how to support behavioral change of veterinarians and farmers. Topics include the use of social sciences can be of great value in understanding why veterinarians and farmers act in certain ways and how they can be motivated to change antimicrobial use practices.
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- 2018
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45. Duplicated TLR5 of zebrafish functions as a heterodimeric receptor.
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Voogdt, Carlos G. P., Wagenaar, Jaap A., and van Putten, Jos P. M.
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TOLL-like receptors ,PATHOGENIC microorganisms ,ZEBRA danio ,MEMBRANE proteins ,PSEUDOMONAS aeruginosa - Abstract
Toll-like receptor 5 (TLR5) of mammals, birds, and reptiles detects bacterial flagellin and signals as a homodimeric complex. Structural studies using truncated TLR5b of zebrafish confirm the homodimeric TLR5-flagellin interaction. Here we provide evidence that zebrafish (Danio rerio) TLR5 unexpectedly signals as a heterodimer composed of the duplicated gene products drTLR5b and drTLR5a. Flagellin-induced signaling by the zebrafish TLR5 heterodimer increased in the presence of the TLR trafficking chaperone UNC93B1. Targeted exchange of drTLR5b and drTLR5a regions revealed that TLR5 activation needs a heterodimeric configuration of the receptor ectodomain and cytoplasmic domain, consistent with ligand-induced changes in receptor conformation. Structureguided substitution of the presumed principal flagellin-binding site in human TLR5 with corresponding zebrafish TLR5 residues abrogated human TLR5 activation, indicating a species-specific TLR5-flagellin interaction. Our findings indicate that the duplicated TLR5 of zebrafish underwent subfunctionalization through concerted coevolution to form a unique heterodimeric flagellin receptor that operates fundamentally differently from TLR5 of other species. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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46. Homologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation.
- Author
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Gilbert, Maarten J., Duim, Birgitta, van der Graaf-van Bloois, Linda, Wagenaar, Jaap A., and Zomer, Aldert L.
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CAMPYLOBACTER fetus ,LINEAGE ,MICROBIAL evolution ,HOMOLOGOUS recombination ,CRISPRS - Abstract
Homologous recombination is amajor driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1-5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3%to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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47. Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the environment: a pooled analysis.
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Smid, Joost H., Dohmen, Wietske, Schmitt, Heike, Liakopoulos, Apostolos, Pacholewicz, Ewa, Heederik, Dick J. J., Dorado-García, Alejandro, de Roda Husman, Ana Maria, Havelaar, Arie H., Wagenaar, Jaap A., Hordijk, Joost, Mevius, Dik J., van Pelt, Wilfrid, Dierikx, Cindy M., van Duijkeren, Engeline, van Hoek, Angela H. A. M., Blaak, Hetty, Bonten, Marc J. M., den Bunt, Gerrita van, and de Koeijer, Aline
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BETA lactamases ,ESCHERICHIA coli DNA ,ESCHERICHIA coli growth ,ESCHERICHIA coli physiology ,BACTERIAL genetics ,ESCHERICHIA coli ,ANIMAL experimentation ,BIRDS ,INFECTIOUS disease transmission ,COMPARATIVE studies ,ESCHERICHIA coli diseases ,FOOD microbiology ,GENETICS ,HYDROLASES ,RESEARCH methodology ,MEDICAL cooperation ,MICROBIAL ecology ,POULTRY ,QUESTIONNAIRES ,RESEARCH ,SWINE ,EVALUATION research - Abstract
Background: In recent years, ESBL/AmpC-producing Escherichia coli (ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising >27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human-animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7-0.8), while similarities to livestock or food reservoirs were lower (0.3-0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.Conclusions: Our 'One Health' approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population. [ABSTRACT FROM AUTHOR]- Published
- 2018
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48. Campylobacter in Broiler Chicken and Broiler Meat in Sri Lanka: Influence of Semi-Automated vs. Wet Market Processing on Campylobacter Contamination of Broiler Neck Skin Samples.
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Kottawatta, Kottawattage S. A., Van Bergen, Marcel A. P., Abeynayake, Preeni, Wagenaar, Jaap A., Veldman, Kees T., and Kalupahana, Ruwani S.
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BROILER chickens ,CHICKEN as food ,CAMPYLOBACTER ,CAMPYLOBACTER coli ,CAMPYLOBACTER infections - Abstract
Broiler meat can become contaminated with Campylobacter of intestinal origin during processing. The present study aimed to identify the prevalence of Campylobacter in broiler flocks and meat contamination at retail shops, and determine the influence of semi-automated and wet market processing on Campylobacter contamination of neck skin samples. Samples were collected from semi-automated plants (n = 102) and wet markets (n = 25). From each batch of broilers, pooled caecal samples and neck skin samples were tested for Campylobacter. Broiler meat purchased from retail outlets (n = 37) was also tested. The prevalence of Campylobacter colonized broiler flocks was 67%. The contamination of meat at retail was 59%. Both semi-automated and wet market processing resulted to contaminate the broiler neck skins to the levels of 27.4% and 48%, respectively. When Campylobacter-free broiler flocks were processed in semi-automated facilities 15% (5/33) of neck skin samples became contaminated by the end of processing whereas 25% (2/8) became contaminated after wet market processing. Characterization of isolates revealed a higher proportion of C. coli compared to C. jejuni. Higher proportions of isolates were resistant to important antimicrobials. This study shows the importance of Campylobacter in poultry industry in Sri Lanka and the need for controlling antimicrobial resistance. [ABSTRACT FROM AUTHOR]
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- 2017
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49. Raw pet food as a risk factor for shedding of extended-spectrum beta-lactamase-producing Enterobacteriaceae in household cats.
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Baede, Valérie O., Broens, Els M., Spaninks, Mirlin P., Timmerman, Arjen J., Graveland, Haitske, Wagenaar, Jaap A., Duim, Birgitta, and Hordijk, Joost
- Subjects
BETA lactamases ,ENTEROBACTERIACEAE ,ANTI-infective agents ,HEALTH of cats ,PUBLIC health - Abstract
Background: Close contact between pets and owners provides the opportunity for transmission of antimicrobial resistant organisms like extended-spectrum beta-lactamase (ESBL)/AmpC beta-lactamase (AmpC)-producing Enterobacteriaceae, posing a risk to public health. Objectives: To investigate whether raw feed is a risk factor for household cats to shed ESBL-producing Enterobacteriaceae, a cohort study was designed. Additionally, raw and non-raw commercial pet food products were screened for the presence of ESBL-producing Enterobacteriaceae. Methods: Weekly fecal samples of 17 cats in the control group and 19 cats in the exposed group were collected for three weeks and analyzed for the presence of ESBL-producing Enterobacteriaceae. Questionnaires were obtained to determine additional risk factors. Fecal samples were cultured on MacConkey agar supplemented with 1 mg/L cefotaxime. PCR and sequence analysis was used for screening for ESBL genes in suspected isolates. Pet food samples were cultured in LB broth supplemented with 1 mg/L cefotaxime and processed as described above. Results: In the cohort study, ESBL-producing bacteria were isolated from 3 of 51 (5.9%) samples in the control group compared to 37 of 57 (89.5%) samples in the exposed group. A significant association was found between ESBL shedding and feeding raw pet food products (OR = 31.5). No other risk factors were identified in this study. ESBL-producing Enterobacteriaceae were isolated from 14 of 18 (77.8%) raw pet food products and 0 of 35 non-raw pet food products. Conclusions: This study shows a strong association between shedding of ESBL-producing bacteria in household cats and feeding raw pet food. Raw pet food was often contaminated with ESBL-producing Enterobacteriaceae. [ABSTRACT FROM AUTHOR]
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- 2017
- Full Text
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50. Effect of Simultaneous Exposure of Pigs to Streptococcus suis Serotypes 2 and 9 on Their Colonization and Transmission, and on Mortality.
- Author
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Dekker, Niels, Bouma, Annemarie, Daemen, Ineke, Vernooij, Hans, Leengoed, Leo van, Wagenaar, Jaap A., and Stegeman, Arjan
- Subjects
STREPTOCOCCACEAE ,GRAM-positive bacteria ,ELECTRON-transfer catalysis ,STREPTOCOCCUS suis ,STREPTOCOCCUS - Abstract
The distribution of Streptococcus suis serotypes isolated from clinically infected pigs differs between geographical areas, and varies over time. In several European countries, predomination of serotype 2 has changed to serotype 9. We hypothesize a relation, with one serotype affecting the other in colonization and invasion. The aim of this study was to evaluate whether simultaneous exposure of pigs to serotypes 2 and 9 affects colonization and transmission of each type, and mortality. Thirty-six caesarean-derived/colostrum-deprived piglets were randomly assigned to three groups, and there housed pair-wise. At six weeks old, one pig per pair was inoculated with either one (serotype 2 or 9; mono-group) or two serotypes simultaneously (dual-group); the other pig was contact-exposed. Tonsillar and nasal samples were collected within three weeks post inoculation. Bacterial loads in samples were quantified using multiplex real-time polymerase chain reaction (PCR). Transmission rates of the serotypes among pigs were estimated using a mathematical Susceptible-Infectious (SI) model. Bacterial loads and transmission rates did not differ significantly between serotypes. Compared to the mono-group, in the dual-group the average serotype 2 load in tonsillar samples from contact pigs was reduced on days 1 to 4 and on day 6. Simultaneous exposure to the serotypes reduced the mortality hazard 6.3 times (95% C.I.: 2.0-19.8) compared to exposure to serotype 2 only, and increased it 6.6 times (95% C.I.: 1.4-30.9) compared to exposure to serotype 9 only. This study indicates that serotype 2 load and mortality were affected in pigs exposed to these two serotypes. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
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