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Rozwandowicz M, Kant A, Wagenaar J, Mevius D, Hordijk J, Brouwer M. Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids. Open Res Eur 2023; 3:53. [PMID: 38106640 PMCID: PMC10724649 DOI: 10.12688/openreseurope.15121.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/23/2023] [Indexed: 12/19/2023]
Abstract
Antimicrobial resistance is a persistent challenge in human and veterinary medicine, which is often encoded on plasmids which are transmissible between bacterial cells. Incompatibility is the inability of two plasmids to be stably maintained in one cell which is caused by the presence of identical or closely related shared determinants between two plasmids originating from partition or replication mechanisms. For I-complex plasmids in Enterobacteriacae, replication- based incompatibility is caused by the small antisense RNA stem-loop structure called RNAI. The I-complex plasmid group IncK consists of two compatible subgroups, IncK1 and IncK2, for which the RNAI differs only by five nucleotides. In this study we focussed on the interaction of the IncK1 and IncK2 RNAI structures by constructing minireplicons containing the replication region of IncK1 or IncK2 plasmids coupled with a kanamycin resistance marker. Using minireplicons excludes involvement of incompatibility mechanisms other than RNAI. Additionally, we performed single nucleotide mutagenesis targeting the five nucleotides that differ between the IncK1 and IncK2 RNAI sequences of these minireplicons. The obtained results show that a single nucleotide change in the RNAI structure is responsible for the compatible phenotype of IncK1 with IncK2 plasmids. Only nucleotides in the RNAI top loop and interior loop have an effect on minireplicon incompatibility with wild type plasmids, while mutations in the stem of the RNAI structure had no significant effect on incompatibility. Understanding the molecular basis of incompatibility is relevant for future in silico predictions of plasmid incompatibility.
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Affiliation(s)
- Marta Rozwandowicz
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Arie Kant
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Jaap Wagenaar
- Utrecht University, Utrecht, 3584 CS, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
| | - Joost Hordijk
- National Institute for Public Health and the Environment, Bilthoven, 3721 MA, The Netherlands
| | - Michael Brouwer
- Wageningen Bioveterinary Research, Lelystd, 8221 RA, The Netherlands
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2
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Macedo G, Olesen AK, Maccario L, Hernandez Leal L, v. d. Maas P, Heederik D, Mevius D, Sørensen SJ, Schmitt H. Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms. Environ Sci Technol 2022; 56:11398-11408. [PMID: 35896060 PMCID: PMC9387108 DOI: 10.1021/acs.est.2c02686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10-5 and 10-4 transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.
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Affiliation(s)
- Gonçalo Macedo
- Department
of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Asmus K. Olesen
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Lorrie Maccario
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Lucia Hernandez Leal
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Peter v. d. Maas
- Van
Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, The Netherlands
| | - Dick Heederik
- Institute
for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Dik Mevius
- Department
of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
- Department
of Bacteriology and Epidemiology, Wageningen
Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands
| | - Søren J. Sørensen
- Department
of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Heike Schmitt
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
- Institute
for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
- Centre
for Infectious Disease Control, National
Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
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3
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Hesp A, van Schaik G, Wiegel J, Heuvelink A, Mevius D, Veldman K. Antimicrobial resistance monitoring in commensal and clinical Escherichia coli from broiler chickens: differences and similarities. Prev Vet Med 2022; 204:105663. [DOI: 10.1016/j.prevetmed.2022.105663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022]
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Sanders P, Mevius D, Veldman K, van Geijlswijk I, Wagenaar JA, Bonten M, Heederik D. Comparison of different antimicrobial use indicators and antimicrobial resistance data in food-producing animals. JAC Antimicrob Resist 2022; 3:dlab172. [PMID: 35224492 PMCID: PMC8569442 DOI: 10.1093/jacamr/dlab172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
Objectives To explore the effects of using different indicators to quantify antimicrobial usage (AMU) in livestock and compare outcomes with antimicrobial resistance (AMR) data. Methods Three indicators were used to quantify AMU, two indicators in which the denominator varied: defined daily doses per average mass of the animals present per year (DDD/AY) and defined daily doses per population correction unit (DDD/PCU) and one in which the numerator varied: milligrams of active ingredient per PCU (mg/PCU). AMU was compared with antimicrobial resistance data from the national monitoring programme from 2013 to 2018 with the proportion of Escherichia coli isolates fully susceptible to a predefined panel of antimicrobials for the broiler, dairy cattle and pig farming livestock sectors in the Netherlands. Results The ranking of livestock sectors differs between sectors when using different indicators to express AMU. Dairy cattle rank lowest when expressing AMU in DDD/AY, followed by pigs and broilers corresponding to the rankings of the sectors for AMR. When changing the denominator to PCU, the ranking in AMU is reversed: use ranks highest in dairy cattle and lowest broilers. Conclusions Using different denominators in AMU indicators has a major impact on measured use. This might result in misinterpretation of effects of interventions on AMU and the associations of AMU with AMR across animal sectors. From an epidemiological perspective, indicators that take into account time at risk of exposure to antimicrobials are to be preferred and reflect the AMR risk most accurately.
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Affiliation(s)
- Pim Sanders
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands
| | - Dik Mevius
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands
| | - Kees Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Inge van Geijlswijk
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,Pharmacy Department, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marc Bonten
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Heederik
- The Netherlands Veterinary Medicines Institute (SDa), Utrecht, The Netherlands.,Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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5
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Pallares-Vega R, Macedo G, Brouwer MSM, Hernandez Leal L, van der Maas P, van Loosdrecht MCM, Weissbrodt DG, Heederik D, Mevius D, Schmitt H. Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains. Front Microbiol 2021; 12:656250. [PMID: 34349732 PMCID: PMC8326584 DOI: 10.3389/fmicb.2021.656250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmid-mediated dissemination of antibiotic resistance among fecal Enterobacteriaceae in natural ecosystems may contribute to the persistence of antibiotic resistance genes in anthropogenically impacted environments. Plasmid transfer frequencies measured under laboratory conditions might lead to overestimation of plasmid transfer potential in natural ecosystems. This study assessed differences in the conjugative transfer of an IncP-1 (pKJK5) plasmid to three natural Escherichia coli strains carrying extended-spectrum beta-lactamases, by filter mating. Matings were performed under optimal laboratory conditions (rich LB medium and 37°C) and environmentally relevant temperatures (25, 15 and 9°C) or nutrient regimes mimicking environmental conditions and limitations (synthetic wastewater and soil extract). Under optimal nutrient conditions and temperature, two recipients yielded high transfer frequencies (5 × 10-1) while the conjugation frequency of the third strain was 1000-fold lower. Decreasing mating temperatures to psychrophilic ranges led to lower transfer frequencies, albeit all three strains conjugated under all the tested temperatures. Low nutritive media caused significant decreases in transconjugants (-3 logs for synthetic wastewater; -6 logs for soil extract), where only one of the strains was able to produce detectable transconjugants. Collectively, this study highlights that despite less-than-optimal conditions, fecal organisms may transfer plasmids in the environment, but the transfer of pKJK5 between microorganisms is limited mainly by low nutrient conditions.
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Affiliation(s)
- Rebeca Pallares-Vega
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Lucia Hernandez Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Leeuwarden, Netherlands
| | | | - David G. Weissbrodt
- Department Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
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6
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Cardozo MV, Liakopoulos A, Brouwer M, Kant A, Pizauro LJL, Borzi MM, Mevius D, de Ávila FA. Occurrence and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacterales Recovered From Chicken, Chicken Meat, and Human Infections in Sao Paulo State, Brazil. Front Microbiol 2021; 12:628738. [PMID: 34239503 PMCID: PMC8259509 DOI: 10.3389/fmicb.2021.628738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
This study aimed to investigate the phylogenetic diversity and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae from chicken, chicken meat, and human clinical isolates in Sao Paolo, Brazil, and characterize their respective ESBL-encoding plasmids. Three hundred samples from chicken cloaca, chicken meat, and clinical isolates were phenotypically and genotypically assessed for ESBL resistance. Isolates were identified by MALDI TOF-MS and further characterized by MLST analysis and phylogenetic grouping. ESBL genes were characterized and their location was determined by I-Ceu-I-PFGE and Southern blot, conjugation, transformation, and PCR-based replicon typing experiments. Thirty-seven ESBL-producing isolates (28 E. coli and 9 K. pneumoniae) that were positive for the bla CTX-M-1 or bla CTX-M-2 gene groups were obtained. Two isolates were negative in the transformation assay, and the chromosomal location of the genes was deduced by Southern blot. The bla CTX-M genes identified were carried on plasmid replicon-types X1, HI2, N, FII-variants, I1 and R. The E. coli isolates belonged to nine sequence types, while the K. pneumoniae isolates belonged to four sequence types. The E. coli isolates belonged to phylotype classification groups A, B1, D, and F. This study demonstrated that isolates from cloacal swabs, chicken meat, and human feces had genetic diversity, with a high frequency of bla CTX-M-15 among chickens, chicken meat, and human feces. Thus, this reinforces the hypothesis that chickens, as well as their by-products, could be an important source of transmission for ESBL-producing pathogens to humans in South America.
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Affiliation(s)
- Marita Vedovelli Cardozo
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Michael Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Lucas José Luduvério Pizauro
- Department of Tecnology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Mariana Monezi Borzi
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Fernando Antonio de Ávila
- Department of Veterinary Pathology, Faculty of Agricultural and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil
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7
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van den Bunt G, Fluit AC, Spaninks MP, Timmerman AJ, Geurts Y, Kant A, Scharringa J, Mevius D, Wagenaar JA, Bonten MJM, van Pelt W, Hordijk J. Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household. J Antimicrob Chemother 2021; 75:342-350. [PMID: 31711228 PMCID: PMC6966097 DOI: 10.1093/jac/dkz462] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/06/2019] [Accepted: 10/10/2019] [Indexed: 11/21/2022] Open
Abstract
Background ESBL-producing Enterobacteriaceae (ESBL-E) are observed in many reservoirs. Pets might play an important role in the dissemination of ESBL-E to humans since they live closely together. Objectives To identify prevalence, risk factors, molecular characteristics, persistence and acquisition of ESBL-E in dogs and cats, and co-carriage in human–pet pairs belonging to the same household. Methods In a nationwide study, one person per household was randomly invited to complete a questionnaire and to submit a faecal sample. Dog and cat owners were invited to also submit a faecal sample from their pet. Repeated sampling after 1 and 6 months was performed in a subset. ESBL-E were obtained through selective culture and characterized by WGS. Logistic regression analyses and random forest models were performed to identify risk factors. Results The prevalence of ESBL-E carriage in these cohorts was 3.8% (95% CI: 2.7%–5.4%) for human participants (n=550), 10.7% (95% CI: 8.3%–13.7%) for dogs (n=555) and 1.4% (95% CI: 0.5%–3.8%) for cats (n=285). Among animals, blaCTX-M-1 was most abundant, followed by blaCTX-M-15. In dogs, persistence of carriage was 57.1% at 1 month and 42.9% at 6 months. Eating raw meat [OR: 8.8, 95% CI: 4.7–16.4; population attributable risk (PAR): 46.5%, 95% CI: 41.3%–49.3%] and dry food (OR: 0.2, 95% CI: 0.1–0.5; PAR: 56.5%, 95% CI: 33.2%–66.6%) were predictors for ESBL-E carriage in dogs. Human–dog co-carriage was demonstrated in five households. Human–cat co-carriage was not observed. Conclusions ESBL-E prevalence was higher in dogs than in humans and lowest in cats. The main risk factor for ESBL-E carriage was eating raw meat. Co-carriage in dogs and household members was uncommon.
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Affiliation(s)
- G van den Bunt
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - M P Spaninks
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - A J Timmerman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Y Geurts
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - A Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Scharringa
- Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - D Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - M J M Bonten
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Medical Microbiology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - W van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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8
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Hesp A, Veldman K, Brouwer MSM, Wagenaar JA, Mevius D, van Schaik G. Latent class analysis to assess whole-genome sequencing versus broth microdilution for monitoring antimicrobial resistance in livestock. Prev Vet Med 2021; 193:105406. [PMID: 34147959 DOI: 10.1016/j.prevetmed.2021.105406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) monitoring in animals is performed in commensal Escherichia coli, and other microorganisms relevant for human or veterinary health. Due to advances in the field and major reductions in cost, it is expected that whole-genome sequencing (WGS)-based antimicrobial susceptibility testing (AST) will (partly) replace culture-based AST. So far, no studies have been performed without using culture-based AST as the gold standard. Our aim was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility testing of commensal E. coli by WGS-based AST versus culture-based AST as this test does not assume a gold standard. OpenBUGS was used to model two independent tests in three animal populations (N = 150, 50 bacterial isolates per population): veal calves, pigs, and broilers. This resulted in the first estimation of sensitivity and specificity of WGS-based AST versus culture-based AST to detect AMR without a gold standard. Both methods had high sensitivity (>0.92, lowest limit probability interval: 0.76) and specificity was generally high for both methods for all antimicrobial classes except for aminoglycosides and macrolides. We compared WGS results for different length and identity settings (%) of gene alignment and found few differences between the 60/90, 90/90 and 95/95 settings. We recommend to further investigate sensitivity and specificity of WGS-based AST by means of latent class analysis, especially for low-prevalent resistance.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Kees Veldman
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Bacteriology, Host Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Gerdien van Schaik
- Royal GD, Deventer, the Netherlands; Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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9
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Macedo G, van Veelen HPJ, Hernandez-Leal L, van der Maas P, Heederik D, Mevius D, Bossers A, Schmitt H. Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application. Sci Total Environ 2021; 770:145399. [PMID: 33736375 DOI: 10.1016/j.scitotenv.2021.145399] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 05/26/2023]
Abstract
Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.
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Affiliation(s)
- Gonçalo Macedo
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands.
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Lucia Hernandez-Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, the Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584, CM, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Alex Bossers
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584, CM, Utrecht, the Netherlands; Department of Infection Biology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Heike Schmitt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
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10
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Hesp A, ter Braak C, van der Goot J, Veldman K, van Schaik G, Mevius D. Antimicrobial resistance clusters in commensal Escherichia coli from livestock. Zoonoses Public Health 2021; 68:194-202. [PMID: 33455079 PMCID: PMC8048968 DOI: 10.1111/zph.12805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/19/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022]
Abstract
To combat antimicrobial resistance (AMR), policymakers need an overview of evolution and trends of AMR in relevant animal reservoirs, and livestock is monitored by susceptibility testing of sentinel organisms such as commensal E. coli. Such monitoring data are often vast and complex and generates a need for outcome indicators that summarize AMR for multiple antimicrobial classes. Model-based clustering is a data-driven approach that can help to objectively summarize AMR in animal reservoirs. In this study, a model-based cluster analysis was carried out on a dataset of minimum inhibitory concentrations (MIC), recoded to binary variables, for 10 antimicrobials of commensal E. coli isolates (N = 12,986) derived from four animal species (broilers, pigs, veal calves and dairy cows) in Dutch AMR monitoring, 2007-2018. This analysis revealed four clusters in commensal E. coli in livestock containing 201 unique resistance combinations. The prevalence of these combinations and clusters differs between animal species. Our results indicate that to monitor different animal populations, more than one indicator for multidrug resistance seems necessary. We show how these clusters summarize multidrug resistance and have potential as monitoring outcome indicators to benchmark and prioritize AMR problems in livestock.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
- Department of Infectious Diseases and ImmunologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Cajo ter Braak
- BiometrisWageningen University & ResearchWageningenThe Netherlands
| | - Jeanet van der Goot
- Department of Diagnostics and Crisis OrganisationWageningen Bioveterinary ResearchLelystadThe Netherlands
| | - Kees Veldman
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
| | - Gerdien van Schaik
- Royal GDDeventerThe Netherlands
- Department of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Dik Mevius
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
- Department of Infectious Diseases and ImmunologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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11
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Macedo G, Hernandez-Leal L, van der Maas P, Heederik D, Mevius D, Schmitt H. The impact of manure and soil texture on antimicrobial resistance gene levels in farmlands and adjacent ditches. Sci Total Environ 2020; 737:139563. [PMID: 32512295 DOI: 10.1016/j.scitotenv.2020.139563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 05/26/2023]
Abstract
Manure application can spread antimicrobial resistance (AMR) from manure to soil and surface water. This study evaluated the role of the soil texture on the dynamics of antimicrobial resistance genes (ARGs) in soils and surrounding surface waters. Six dairy farms with distinct soil textures (clay, sand, and peat) were sampled at different time points after the application of manure, and three representative ARGs sul1, erm(B), and tet(W) were quantified with qPCR. Manuring initially increased levels of erm(B) by 1.5 ± 0.5 log copies/kg of soil and tet(W) by 0.8 ± 0.4 log copies/kg across soil textures, after which levels gradually declined. In surface waters from clay environments, regardless of the ARG, the gene levels initially increased by 2.6 ± 1.6 log copies/L, after which levels gradually declined. The gene decay in soils was strongly dependent on the type of ARG (erm(B) < tet(W) < sul1; half-lives of 7, 11, and 75 days, respectively), while in water, the decay was primarily dependent on the soil texture adjacent to the sampled surface water (clay < peat < sand; half-lives of 2, 6, and 10 days, respectively). Finally, recovery of ARG levels was predicted after 29-42 days. The results thus showed that there was not a complete restoration of ARGs in soils between rounds of manure application. In conclusion, this study demonstrates that rather than showing similar dynamics of decay, factors such as the type of ARG and soil texture drive the ARG persistence in the environment.
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Affiliation(s)
- Gonçalo Macedo
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands.
| | - Lucia Hernandez-Leal
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands
| | - Peter van der Maas
- Van Hall Larenstein, University of Applied Sciences, Agora 1, 8901 BV Leeuwarden, the Netherlands
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands
| | - Heike Schmitt
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
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12
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Brouwer MSM, Goodman RN, Kant A, Mevius D, Newire E, Roberts AP, Veldman KT. Mobile colistin resistance gene mcr-1 detected on an IncI1 plasmid in Escherichia coli from meat. J Glob Antimicrob Resist 2020; 23:145-148. [PMID: 32889139 DOI: 10.1016/j.jgar.2020.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/20/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Mobile colistin resistance (mcr) genes encoded on conjugative plasmids, although described only relatively recently, have been reported globally both in humans and livestock. The genes are often associated with the insertion sequence ISApl1 that can transpose the genes to novel genetic locations. Since its first report, multiple variants of mcr have been discovered in a variety of genetic locations in Escherichia coli, in plasmids and integrated into the chromosome. METHODS Using hybrid assembly of short-read and long-read whole-genome sequencing data, the presence ofmcr-1 was confirmed on an IncI1 plasmid in E. coli. In vitro conjugation assays were performed to determine the potential to transfer between strains. Genetic comparison with previously reported IncI1 plasmids was performed. RESULTS The genomic sequence identified thatmcr-1 is present on a complete IncI1 plasmid. Comparison with previously reported extended-spectrum β-lactamase (ESBL)-encoding plasmids from E. coli in the Netherlands from the same time period indicated a distinct lineage for this plasmid. CONCLUSIONS The observation ofmcr-1 on an IncI1 plasmid confirms that the genetic region of this gene is actively transposed between genetic locations. This active transposition has consequences for the study of the epidemiology of mcr in populations.
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Affiliation(s)
| | | | - Arie Kant
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Enas Newire
- Institute of Systems, Molecular & Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
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13
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Hesp A, Veldman K, van der Goot J, Mevius D, van Schaik G. Monitoring antimicrobial resistance trends in commensal Escherichia coli from livestock, the Netherlands, 1998 to 2016. ACTA ACUST UNITED AC 2020; 24. [PMID: 31241037 PMCID: PMC6593905 DOI: 10.2807/1560-7917.es.2019.24.25.1800438] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BackgroundMonitoring of antimicrobial resistance (AMR) in animals is essential for public health surveillance. To enhance interpretation of monitoring data, evaluation and optimisation of AMR trend analysis is needed.AimsTo quantify and evaluate trends in AMR in commensal Escherichia coli, using data from the Dutch national AMR monitoring programme in livestock (1998-2016).MethodsFaecal samples were collected at slaughter from broilers, pigs and veal calves. Minimum inhibitory concentration values were obtained by broth microdilution for E. coli for 15 antimicrobials of eight antimicrobial classes. A Poisson regression model was applied to resistant isolate counts, with explanatory variables representing time before and after 2009 (reference year); for veal calves, sampling changed from 2012 represented by an extra explanatory variable.ResultsResistant counts increased significantly from 1998-2009 in broilers and pigs, except for tetracyclines and sulfamethoxazole in broilers and chloramphenicol and aminoglycosides in pigs. Since 2009, resistant counts decreased for all antimicrobials in broilers and for all but the phenicols in pigs. In veal calves, for most antimicrobials no significant decrease in resistant counts could be determined for 2009-16, except for sulfamethoxazole and nalidixic acid. Within animal species, antimicrobial-specific trends were similar.ConclusionsUsing Dutch monitoring data from 1998-2016, this study quantified AMR trends in broilers and slaughter pigs and showed significant trend changes in the reference year 2009. We showed that monitoring in commensal E. coli is useful to quantify trends and detect trend changes in AMR. This model is applicable to similar data from other European countries.
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Affiliation(s)
- Ayla Hesp
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Kees Veldman
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.,Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Gerdien van Schaik
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.,GD Animal Health, Deventer, the Netherlands
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14
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Griffioen K, Cornelissen J, Heuvelink A, Adusei D, Mevius D, Jan van der Wal F. Development and evaluation of 4 loop-mediated isothermal amplification assays to detect mastitis-causing bacteria in bovine milk samples. J Dairy Sci 2020; 103:8407-8420. [PMID: 32564949 DOI: 10.3168/jds.2019-18035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/06/2020] [Indexed: 12/22/2022]
Abstract
Farmers prefer fast, sensitive, and on-site tests for treatment decisions on mastitis. Due to the time to results of the currently available diagnostic tools, these are rarely used for that purpose. Genotypic tests that do not require a growth step may be suitable for on-site testing, for example loop-mediated isothermal amplification (LAMP), which has been described as a sensitive test that can be used on-site. Therefore, this study aimed to develop and evaluate LAMP assays for the detection of a subset of mastitis-causing pathogens, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus spp., in milk from cows with clinical mastitis. Furthermore, a generic nucleic acid lateral flow immunoassay (NALFIA) was evaluated as a potential on-site readout of the LAMP assays. For each assay of LAMP and NALFIA, the limit of detection and analytical specificity were determined using isolates, and the diagnostic specificity was determined using selected samples with known etiology. In addition, the diagnostic specificity of LAMP was determined using field samples with unknown etiology at testing. Bacteriological culture with identification by mass spectrometry was used as a reference method. The 4 assays had a kappa ≥0.73 with the reference method when testing the selected samples, but ≥0.47 when testing field samples. After correcting for prevalence, kappa was ≥0.80 for the E. coli, K. pneumoniae, and Staph. aureus assays. The Streptococcus spp. assay had a kappa of 0.47 (0.48 after correction) with the reference method, probably caused by the assay broadly targeting a genus instead of a particular species. The NALFIA readout was found to have kappa ≥0.81 for the E. coli, Staph. aureus, and Streptococcus spp. assays at a generic runtime, but for the K. pneumoniae assay a shorter runtime could be used. In conclusion, LAMP is a promising method for fast on-site tests for mastitis-causing pathogens if the current elaborate method for sample preparation is replaced by a simplified protocol. The NALFIA is an easy and reliable readout for on-site use, with the observation that for the current assay designs a generic runtime is not yet possible for the chosen set of pathogens. If associated with a simple and fast sample preparation protocol, the combination of LAMP and NALFIA has the potential to enable fast and reliable on-site testing of clinical mastitis milk samples.
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Affiliation(s)
- Karien Griffioen
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, PO Box 80151, 3508 TD Utrecht, the Netherlands.
| | - Jan Cornelissen
- Wageningen Bioveterinary Research, Department of Infection Biology, Wageningen UR, PO Box 65, 8200 AB Lelystad, the Netherlands
| | | | - Daniela Adusei
- Wageningen Bioveterinary Research, Department of Infection Biology, Wageningen UR, PO Box 65, 8200 AB Lelystad, the Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Department of Infection Biology, Wageningen UR, PO Box 65, 8200 AB Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80165, 3508 TD Utrecht, the Netherlands
| | - Fimme Jan van der Wal
- Wageningen Bioveterinary Research, Department of Infection Biology, Wageningen UR, PO Box 65, 8200 AB Lelystad, the Netherlands
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15
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Dame-Korevaar A, Fischer EAJ, van der Goot J, Velkers F, Ceccarelli D, Mevius D, Stegeman A. Early life supply of competitive exclusion products reduces colonization of extended spectrum beta-lactamase-producing Escherichia coli in broilers. Poult Sci 2020; 99:4052-4064. [PMID: 32731993 PMCID: PMC7597911 DOI: 10.1016/j.psj.2020.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022] Open
Abstract
Broilers are an important reservoir of extended spectrum beta-lactamase and AmpC beta-lactamase (ESBL/pAmpC)-producing bacteria. In previous studies, a single supply of a competitive exclusion (CE) product before challenge with a high dose of ESBL/pAmpC-producing Escherichia coli led to reduced colonization, excretion, and transmission, but could not prevent colonization. The hypothesized mechanism is competition; therefore, in this study the effect of a prolonged supply of CE products on colonization, excretion, and transmission of ESBL-producing E. coli after challenge with a low dose at day 0 or day 5 was investigated. Day-old broilers (Ross 308) (n = 220) were housed in isolators. Two CE products, containing unselected fermented intestinal bacteria (CEP) or a selection of pre- and probiotics (SYN), were supplied in drinking water from day 0 to 14. At day 0 or 5, broilers were challenged with 0.5 mL with 101 or 102 cfu/mL E. coli encoding the beta-lactamase gene blaCTX-M-1 on an IncI plasmid (CTX-M-1-E. coli). Presence and concentration of CTX-M-1-E. coli were determined using cloacal swabs (days 0–14, 16, 19, and 21) and cecal content (day 21). Cox proportional hazard model and a mixed linear regression model were used to determine the effect of the intervention on colonization and excretion (log10 cfu/g). When challenged on the day of hatch, no effect of CEP was observed. When challenged at day 5, both CEP and SYN led to a prevention of colonization with CTX-M-1-E. coli in some isolators. In the remaining isolators, we observed reduced time until colonization (hazard ratio between 3.71 × 10−3 and 3.11), excretion (up to −1.60 log10 cfu/g), and cecal content (up to −2.80 log10 cfu/g), and a 1.5 to 3-fold reduction in transmission rate. Colonization after a low-dose challenge with ESBL-producing E. coli can be prevented by CE products. However, if at least 1 bird is colonized it spreads through the whole flock. Prolonged supply of CE products, provided shortly after hatch, may be applicable as an intervention to reduce the prevalence of ESBL/pAmpC-producing bacteria in the broiler production chain.
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Affiliation(s)
- Anita Dame-Korevaar
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Egil A J Fischer
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Francisca Velkers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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16
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Joosten P, Ceccarelli D, Odent E, Sarrazin S, Graveland H, Van Gompel L, Battisti A, Caprioli A, Franco A, Wagenaar JA, Mevius D, Dewulf J. Antimicrobial Usage and Resistance in Companion Animals: A Cross-Sectional Study in Three European Countries. Antibiotics (Basel) 2020; 9:E87. [PMID: 32079072 PMCID: PMC7175148 DOI: 10.3390/antibiotics9020087] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022] Open
Abstract
Companion animals have been described as potential reservoirs of antimicrobial resistance (AMR), however data remain scarce. Therefore, the objectives were to describe antimicrobial usage (AMU) in dogs and cats in three European countries (Belgium, Italy, and The Netherlands) and to investigate phenotypic AMR. A questionnaire and one fecal sample per animal (n = 303) were collected over one year and AMU was quantified using treatment incidence (TI). Phenotypic resistance profiles of 282 Escherichia coli isolates were determined. Nineteen percent of the animals received at least one antimicrobial treatment six months preceding sampling. On average, cats and dogs were treated with a standard daily dose of antimicrobials for 1.8 and 3.3 days over one year, respectively. The most frequently used antimicrobial was amoxicillin-clavulanate (27%). Broad-spectrum antimicrobials and critically important antimicrobials for human medicine represented 83% and 71% of the total number of treatments, respectively. Resistance of E. coli to at least one antimicrobial agent was found in 27% of the isolates. The most common resistance was to ampicillin (18%). Thirteen percent was identified as multidrug resistant isolates. No association between AMU and AMR was found in the investigated samples. The issue to address, regarding AMU in companion animal, lies within the quality of use, not the quantity. Especially from a One-Health perspective, companion animals might be a source of transmission of resistance genes and/or resistant bacteria to humans.
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Affiliation(s)
- Philip Joosten
- Veterinary Epidemiology Unit, Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (E.O.); (S.S.); (J.D.)
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (D.C.); (J.A.W.); (D.M.)
| | - Evelien Odent
- Veterinary Epidemiology Unit, Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (E.O.); (S.S.); (J.D.)
| | - Steven Sarrazin
- Veterinary Epidemiology Unit, Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (E.O.); (S.S.); (J.D.)
| | - Haitske Graveland
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands;
| | - Antonio Battisti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Via Appia Nuova, 1411, 00178 Rome, Italy; (A.B.); (A.F.)
| | - Andrea Caprioli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Via Appia Nuova, 1411, 00178 Rome, Italy; (A.B.); (A.F.)
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Via Appia Nuova, 1411, 00178 Rome, Italy; (A.B.); (A.F.)
| | - Jaap A. Wagenaar
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (D.C.); (J.A.W.); (D.M.)
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (D.C.); (J.A.W.); (D.M.)
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Department of Obstetrics, Reproduction and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (E.O.); (S.S.); (J.D.)
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17
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Dame-Korevaar A, Fischer EAJ, van der Goot J, Stegeman A, Mevius D. Transmission routes of ESBL/pAmpC producing bacteria in the broiler production pyramid, a literature review. Prev Vet Med 2018; 162:136-150. [PMID: 30621893 DOI: 10.1016/j.prevetmed.2018.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
Plasmid mediated Extended Spectrum Beta-Lactamase and AmpC Beta-Lactamase (ESBL/pAmpC) producing bacteria are resistant to beta-lactam antimicrobials and are widespread in humans, the environment and animals. Animals, especially broilers, are an important reservoir of ESBL/pAmpC producing bacteria. To control ESBL/pAmpC prevalence in broilers, transmission within the entire broiler production pyramid should be considered. This study, including 103 articles originating from two electronic databases, searched for evidence for possible routes of transmission of ESBL/pAmpC producing bacteria in the broiler production pyramid. Possible routes of transmission were categorised as 1) vertical between generations, 2) at hatcheries, 3) horizontal on farm, and 4) horizontal between farms and via the environment of farms. This review presents indications for transmission of ESBL/pAmpC producing bacteria for each of these routes. However, the lack of quantitative results in the literature did not allow an estimation of the relative contribution or magnitude of the different routes. Future research should be specifically targeted towards such information as it is crucial to guide reduction strategies for the spread of ESBL/pAmpC producing bacteria in the broiler production chain.
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Affiliation(s)
- Anita Dame-Korevaar
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands.
| | - Egil A J Fischer
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, the Netherlands; Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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18
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Liakopoulos A, van der Goot J, Bossers A, Betts J, Brouwer MSM, Kant A, Smith H, Ceccarelli D, Mevius D. Genomic and functional characterisation of IncX3 plasmids encoding bla SHV-12 in Escherichia coli from human and animal origin. Sci Rep 2018; 8:7674. [PMID: 29769695 PMCID: PMC5955891 DOI: 10.1038/s41598-018-26073-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 05/03/2018] [Indexed: 01/09/2023] Open
Abstract
The blaSHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding blaSHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in blaSHV-12 in animal-related Escherichia coli isolates. Four representative blaSHV-12-encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their blaSHV-12-flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands. .,Institute of Biology, University of Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| | - Jeanet van der Goot
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Jonathan Betts
- Department of Bacteriology, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Michael S M Brouwer
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Hilde Smith
- Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Leekitcharoenphon P, Garcia‐Graells C, Botteldoorn N, Dierick K, Kempf I, Olkkola S, Rossi M, Nykäsenoja S, Malorny B, Stingl K, Battisti A, Franco A, Mossong J, Veldman K, Mevius D, Wasyl D, Wieczorek K, Osek J, Clemente L, Lacatus A, Nicorescu I, García MA, Escobar CDF, Ferrer MD, Ugarte‐Ruiz M, Anjum MF, Teale C, Ågren J, Hendriksen RS, Aarestrup FM. Comparative genomics of quinolone‐resistant and susceptible Campylobacter jejuni of poultry origin from major poultry producing European countries (GENCAMP). ACTA ACUST UNITED AC 2018. [DOI: 10.2903/sp.efsa.2018.en-1398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pimlapas Leekitcharoenphon
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | | | - Nadine Botteldoorn
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | - Katelijne Dierick
- Institut Scientifique Santé Publique (WIV‐ISP) Faculty of Veterinary University of Zaragoza
| | | | - Satu Olkkola
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Mirko Rossi
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | - Suvi Nykäsenoja
- Microbiology Research Unit Finnish Food Safety Authority Evira Finland
| | | | - Kerstin Stingl
- NRL for the Analysis and Testing of Zoonoses (Salmonella)
| | - Antonio Battisti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana Italy
| | | | - Kees Veldman
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | - Dik Mevius
- Central Veterinary Institute (CVI) part of Wageningen UR The Netherlands
| | | | | | - Jacek Osek
- National Veterinary Research Institute Poland
| | - Lurdes Clemente
- INIAV ‐ National Institute for Agrarian and Veterinary Research Microbiology and Mycology Laboratory Portugal
| | - Angela Lacatus
- Institute for Hygiene and Veterinary Public Health Romania
| | | | | | | | | | - María Ugarte‐Ruiz
- VISAVET Health Surveillance Centre Universidad Complutense Madrid Spain
| | | | | | | | - Rene S. Hendriksen
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
| | - Frank M. Aarestrup
- National Food Institute Technical University of Denmark WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics European Union Reference Laboratory for Antimicrobial Resistance Denmark
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Köck R, Daniels-Haardt I, Becker K, Mellmann A, Friedrich AW, Mevius D, Schwarz S, Jurke A. Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review. Clin Microbiol Infect 2018; 24:1241-1250. [PMID: 29654871 DOI: 10.1016/j.cmi.2018.04.004] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/30/2018] [Accepted: 04/04/2018] [Indexed: 01/05/2023]
Abstract
OBJECTIVES The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans. METHODS We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities. RESULTS We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33-67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2-26% in Africa, and 1-15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16-19%. CONCLUSIONS The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.
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Affiliation(s)
- R Köck
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany; University Hospital Münster, University of Münster, Institute for Hygiene, Münster, Germany; Institute of Hospital Hygiene Oldenburg, Oldenburg, Germany.
| | - I Daniels-Haardt
- NRW Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
| | - K Becker
- University Hospital Münster, University of Münster, Institute of Medical Microbiology, Münster, Germany
| | - A Mellmann
- University Hospital Münster, University of Münster, Institute for Hygiene, Münster, Germany
| | - A W Friedrich
- Department for Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - D Mevius
- Wageningen Bioveterinary Research, Department of Bacteriology and Epidemiology, Lelystad, The Netherlands; Faculty of Veterinary Medicine, Department of Infectious Diseases & Immunology, Utrecht University, Utrecht, The Netherlands
| | - S Schwarz
- Freie Universität Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
| | - A Jurke
- NRW Centre for Health, Section Infectious Disease Epidemiology, Bochum, Germany
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Toutain PL, Bousquet-Mélou A, Damborg P, Ferran AA, Mevius D, Pelligand L, Veldman KT, Lees P. En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach. Front Microbiol 2017; 8:2344. [PMID: 29326661 PMCID: PMC5736858 DOI: 10.3389/fmicb.2017.02344] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/15/2017] [Indexed: 01/05/2023] Open
Abstract
VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs) for antimicrobial drugs (AMDs) used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve challenges for the determination of specific CBPs for animal species, drug substances and disease conditions. VetCAST will adopt EUCAST approaches: the initial step will be data assessment; then procedures for decisions on the CBP; and finally the release of recommendations for CBP implementation. The principal challenges anticipated by VetCAST are those associated with the differing modalities of AMD administration, including mass medication, specific long-acting product formulations or local administration. Specific challenges comprise mastitis treatment in dairy cattle, the range of species and within species breed considerations and several other variable factors not relevant to human medicine. Each CBP will be based on consideration of: (i) an epidemiological cut-off value (ECOFF) - the highest MIC that defines the upper end of the wild-type MIC distribution; (ii) a PK/PD breakpoint obtained from pre-clinical pharmacokinetic data [this PK/PD break-point is the highest possible MIC for which a given percentage of animals in the target population achieves a critical value for the selected PK/PD index (fAUC/MIC or fT > MIC)] and (iii) when possible, a clinical cut-off, that is the relationship between MIC and clinical cure. For the latter, VetCAST acknowledges the paucity of such data in veterinary medicine. When a CBP cannot be established, VetCAST will recommend use of ECOFF as surrogate. For decision steps, VetCAST will follow EUCAST procedures involving transparency, consensus and independence. VetCAST will ensure freely available dissemination of information, concerning standards, guidelines, ECOFF, PK/PD breakpoints, CBPs and other relevant information for AST implementation. Finally, after establishing a CBP, VetCAST will promulgate expert comments and/or recommendations associated with CBPs to facilitate their sound implementation in a clinical setting.
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Affiliation(s)
- Pierre-Louis Toutain
- UMR 1331 Toxalim, INRA, ENVT, Toulouse, France
- The Royal Veterinary College, University of London, London, United Kingdom
| | | | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Ludovic Pelligand
- The Royal Veterinary College, University of London, London, United Kingdom
| | - Kees T. Veldman
- National Reference Laboratory on Antimicrobial Resistance in Animals, Lelystad, Netherlands
| | - Peter Lees
- The Royal Veterinary College, University of London, London, United Kingdom
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22
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Dame-Korevaar A, Fischer EA, Stegeman A, Mevius D, van Essen-Zandbergen A, Velkers F, van der Goot J. Dynamics of CMY-2 producing E. coli in a broiler parent flock. Vet Microbiol 2017; 203:211-214. [DOI: 10.1016/j.vetmic.2017.03.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 01/27/2023]
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Dohmen W, Dorado-García A, Bonten MJM, Wagenaar JA, Mevius D, Heederik DJJ. Risk factors for ESBL-producing Escherichia coli on pig farms: A longitudinal study in the context of reduced use of antimicrobials. PLoS One 2017; 12:e0174094. [PMID: 28323856 PMCID: PMC5360262 DOI: 10.1371/journal.pone.0174094] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/04/2017] [Indexed: 11/19/2022] Open
Abstract
The presence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) in food animals is a public health concern. This study aimed to determine prevalence of ESBL-E. coli on pig farms and to assess the effect of reducing veterinary antimicrobial use (AMU) and farm management practices on ESBL-E. coli occurrence on pig farms. During 2011–2013, 36 Dutch conventional pig farms participated in a longitudinal study (4 sampling times in 18 months). Rectal swabs were taken from 60 pigs per farm and pooled per 6 pigs within the same age category. Presence of ESBL-E. coli was determined by selective plating and ESBL genes were characterized by microarray, PCR and gene sequencing. An extensive questionnaire on farm characteristics and AMU as Defined Daily Dosages per Animal Year (DDDA/Y) was available for the 6-month periods before each sampling moment. Associations between the presence of ESBL-E. coli-positive pigs and farm management practices were modelled with logistic regression. The number of farms with ESBL-E. coli carrying pigs decreased from 16 to 10 and the prevalence of ESBL-E. coli-positive pooled pig samples halved from 27% to 13%. Overall, the most detected ESBL genes were blaCTX-M-1, blaTEM-52 and blaCTX-M-14. The presence of ESBL-E. coli carrying pigs was not related to total AMU, but it was strongly determined by the presence or absence of cephalosporin use at the farm (OR = 46.4, p = 0.006). Other farm management factors, related with improved biosecurity, were also plausibly related to lower probabilities for ESBL-E. coli-positive farms (e.g. presence of a hygiene lock, pest control delivered by a professional). In conclusion, ESBL-E. coli prevalence decreased in pigs during 2011 and 2013 in the Netherlands. On pig farms, the use of cephalosporins was associated with the presence of ESBL-E. coli carrying pigs.
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Affiliation(s)
- Wietske Dohmen
- Department of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
- * E-mail: (WD); (ADG)
| | - Alejandro Dorado-García
- Department of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- * E-mail: (WD); (ADG)
| | - Marc J. M. Bonten
- Department of Medical Microbiology, University Medical Centre, Utrecht, the Netherlands
- Julius Centre for Health Sciences and Primary Care, University Medical Centre, Utrecht, the Netherlands
| | - Jaap A. Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, the Netherlands
| | - Dik Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, the Netherlands
| | - Dick J. J. Heederik
- Department of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
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Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2016; 23:2-22. [PMID: 27890457 DOI: 10.1016/j.cmi.2016.11.012] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
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Affiliation(s)
- M J Ellington
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - O Ekelund
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - F M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - R Canton
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - C Giske
- Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - H Grundman
- University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Hasman
- Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark
| | - M T G Holden
- School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - J Iredell
- Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia
| | - G Kahlmeter
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - A MacGowan
- Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - D Mevius
- Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - M Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - T Naas
- French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France
| | - T Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - J-M Rolain
- PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
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Liakopoulos A, Mevius D, Ceccarelli D. A Review of SHV Extended-Spectrum β-Lactamases: Neglected Yet Ubiquitous. Front Microbiol 2016; 7:1374. [PMID: 27656166 PMCID: PMC5011133 DOI: 10.3389/fmicb.2016.01374] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 12/29/2022] Open
Abstract
β-lactamases are the primary cause of resistance to β-lactams among members of the family Enterobacteriaceae. SHV enzymes have emerged in Enterobacteriaceae causing infections in health care in the last decades of the Twentieth century, and they are now observed in isolates in different epidemiological settings both in human, animal and the environment. Likely originated from a chromosomal penicillinase of Klebsiella pneumoniae, SHV β-lactamases currently encompass a large number of allelic variants including extended-spectrum β-lactamases (ESBL), non-ESBL and several not classified variants. SHV enzymes have evolved from a narrow- to an extended-spectrum of hydrolyzing activity, including monobactams and carbapenems, as a result of amino acid changes that altered the configuration around the active site of the β -lactamases. SHV-ESBLs are usually encoded by self-transmissible plasmids that frequently carry resistance genes to other drug classes and have become widespread throughout the world in several Enterobacteriaceae, emphasizing their clinical significance.
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Affiliation(s)
- Apostolos Liakopoulos
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
| | - Dik Mevius
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen URLelystad, Netherlands; Faculty of Veterinary Medicine, Utrecht UniversityUtrecht, Netherlands
| | - Daniela Ceccarelli
- Department of Bacteriology and Epidemiology, Central Veterinary Institute of Wageningen UR Lelystad, Netherlands
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Veldman K, van Essen-Zandbergen A, Rapallini M, Wit B, Heymans R, van Pelt W, Mevius D. Location of colistin resistance genemcr-1in Enterobacteriaceae from livestock and meat: Table 1. J Antimicrob Chemother 2016; 71:2340-2. [DOI: 10.1093/jac/dkw181] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Oikonomou O, Liakopoulos A, Phee LM, Betts J, Mevius D, Wareham DW. Providencia stuartii Isolates from Greece: Co-Carriage of Cephalosporin (blaSHV-5, blaVEB-1), Carbapenem (blaVIM-1), and Aminoglycoside (rmtB) Resistance Determinants by a Multidrug-Resistant Outbreak Clone. Microb Drug Resist 2016; 22:379-86. [PMID: 27380549 DOI: 10.1089/mdr.2015.0215] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Providencia stuartii has emerged as an important nosocomial pathogen. We describe an outbreak due to a multidrug-resistant strain over a 4-month period in a critical care unit in Athens. Molecular typing revealed each of the isolates to be clonally related with coresistance to cephalosporins, carbapenems, aminoglycosides, and quinolones. Each isolate contained a 220-kb multi-replicon (IncA/C and IncR) conjugative plasmid encoding TEM-1, SHV-5, VEB-1, and VIM-1 β-lactamases and the 16S rDNA methylase RmtB. Antimicrobial therapy was unsuccessful in 3 of 6 cases, and resistance was readily transmissible to susceptible strains of Escherichia coli by transformation and conjugation. This highlights the clinical importance of P. stuartii and its ability to disseminate critical resistance determinants to other bacterial pathogens.
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Affiliation(s)
- Olga Oikonomou
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Apostolos Liakopoulos
- 2 Department of Bacteriology and TSEs, Central Veterinary Institute, Wageningen University , Lelystad, the Netherlands
| | - Lynette M Phee
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Jonathan Betts
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Dik Mevius
- 2 Department of Bacteriology and TSEs, Central Veterinary Institute, Wageningen University , Lelystad, the Netherlands
| | - David W Wareham
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
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Day MJ, Rodríguez I, van Essen-Zandbergen A, Dierikx C, Kadlec K, Schink AK, Wu G, Chattaway MA, DoNascimento V, Wain J, Helmuth R, Guerra B, Schwarz S, Threlfall J, Woodward MJ, Coldham N, Mevius D, Woodford N. Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK. J Antimicrob Chemother 2016; 71:1178-82. [PMID: 26803720 DOI: 10.1093/jac/dkv485] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/17/2015] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES This study aimed to compare ESBL-producing Escherichia coli causing infections in humans with infecting or commensal isolates from animals and isolates from food of animal origin in terms of the strain types, the ESBL gene present and the plasmids that carry the respective ESBL genes. METHODS A collection of 353 ESBL-positive E. coli isolates from the UK, the Netherlands and Germany were studied by MLST and ESBL genes were identified. Characterization of ESBL gene-carrying plasmids was performed using PCR-based replicon typing. Moreover, IncI1-Iγ and IncN plasmids were characterized by plasmid MLST. RESULTS The ESBL-producing E. coli represented 158 different STs with ST131, ST10 and ST88 being the most common. Overall, blaCTX-M-1 was the most frequently detected ESBL gene, followed by blaCTX-M-15, which was the most common ESBL gene in the human isolates. The most common plasmid replicon type overall was IncI1-Iγ followed by multiple IncF replicons. CONCLUSIONS ESBL genes were present in a wide variety of E. coli STs. IncI1-Iγ plasmids that carried the blaCTX-M-1 gene were widely disseminated amongst STs in isolates from animals and humans, whereas other plasmids and STs appeared to be more restricted to isolates from specific hosts.
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Affiliation(s)
| | - Irene Rodríguez
- Federal Institute for Risk Assessment (BfR), Berlin, Germany University Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - Cindy Dierikx
- Central Veterinary Institute (CVI) of Wageningen UR, Lelystad, The Netherlands
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Anne-Kathrin Schink
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Guanghui Wu
- Animal and Plant Health Agency (APHA, Weybridge), Addlestone, UK
| | | | | | - John Wain
- University of East Anglia, Norwich, UK
| | - Reiner Helmuth
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Beatriz Guerra
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | | | | | - Nick Coldham
- Animal and Plant Health Agency (APHA, Weybridge), Addlestone, UK
| | - Dik Mevius
- Central Veterinary Institute (CVI) of Wageningen UR, Lelystad, The Netherlands Utrecht University, Utrecht, The Netherlands
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Koningstein M, Leenen MA, Mughini-Gras L, Scholts RMC, van Huisstede-Vlaanderen KW, Enserink R, Zuidema R, Kooistra-Smid MAMD, Veldman K, Mevius D, van Pelt W. Prevalence and Risk Factors for Colonization With Extended-Spectrum Cephalosporin-Resistant Escherichia coli in Children Attending Daycare Centers: A Cohort Study in the Netherlands. J Pediatric Infect Dis Soc 2015; 4:e93-9. [PMID: 26407274 DOI: 10.1093/jpids/piv042] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 06/24/2015] [Indexed: 11/14/2022]
Abstract
BACKGROUND The purpose of this study was to determine the prevalence and risk factors for colonization with extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli in daycare center (DCC)-attending children. METHODS This is a prospective cohort study including 44 DCCs in the Netherlands, combining DCC characteristics and monthly collected stool samples from their attendees, and was performed in 2010-2012. During a 22-month study period, 852 stool samples were collected and screened for ESC-R E coli. Risk factors were studied using logistic regression analysis. RESULTS In DCC-attending children (<4 years old), the overall prevalence of ESC-R E coli was 4.5%, and it was 8% in <1-year-old attendees. Among the 38 children carrying ESC-R E coli, the most common types were blaCMY-2 (26%), blaCTX-M-1 (16%), and chromosomal AmpC type 3 promoter mutants (13%). Extended-spectrum cephalosporin-resistant E coli was less common in DCCs where stricter hygiene protocols were enforced, eg, not allowing ill children to enter the DCC (odds ratio [OR], 0.34; 95% confidence interval [CI], 0.14-0.84), performing extra checks on handwashing of ill children (OR, 0.42; 95% CI, 0.20-0.87), and reporting suspected outbreaks to local health authorities (OR, 0.27; 95% CI, 0.11-0.69). CONCLUSIONS The distribution of ESC-R E coli types in DCCs differs from that of the general population. Extended-spectrum cephalosporin-resistant E coli carriage in DCC-attending children is associated with the hygiene policies enforced in the DCC. Although our results are not conclusive enough to change current DCC practice beyond ensuring compliance with standing policies, they generated hypotheses and defined the degree of ESC resistance among DCC attendees, which may influence empiric antibiotic therapy choices, and tracked the increasing trend in ESC resistance.
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Affiliation(s)
- Maike Koningstein
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, the Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Margriet A Leenen
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, the Netherlands Faculty of Medicine, Utrecht University, the Netherlands
| | - Lapo Mughini-Gras
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands Department of Infectious Diseases and Immunology, Utrecht University, Faculty of Veterinary Medicine, the Netherlands
| | - Rianne M C Scholts
- Certe - Laboratory for Infectious Diseases, Department of Research and Development, Groningen, the Netherlands
| | | | - Remko Enserink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Rody Zuidema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirjam A M D Kooistra-Smid
- Certe - Laboratory for Infectious Diseases, Department of Research and Development, Groningen, the Netherlands Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Kees Veldman
- Department of Bacteriology and TSEs, Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands
| | - Dik Mevius
- Department of Bacteriology and TSEs, Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands Department of Infectious Diseases and Immunology, Utrecht University, Faculty of Veterinary Medicine, the Netherlands
| | - Wilfrid van Pelt
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Chattaway MA, Jenkins C, Ciesielczuk H, Day M, DoNascimento V, Day M, Rodríguez I, van Essen-Zandbergen A, Schink AK, Wu G, Threlfall J, Woodward MJ, Coldham N, Kadlec K, Schwarz S, Dierikx C, Guerra B, Helmuth R, Mevius D, Woodford N, Wain J. Evidence of evolving extraintestinal enteroaggregative Escherichia coli ST38 clone. Emerg Infect Dis 2015; 20:1935-7. [PMID: 25340736 PMCID: PMC4214294 DOI: 10.3201/eid2011.131845] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Bonten MJM, Mevius D. Less Evidence for an Important Role of Food-Producing Animals as Source of Antibiotic Resistance in Humans. Clin Infect Dis 2015; 60:1867. [DOI: 10.1093/cid/civ275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rodríguez I, Thomas K, Van Essen A, Schink AK, Day M, Chattaway M, Wu G, Mevius D, Helmuth R, Guerra B. Chromosomal location of blaCTX-M genes in clinical isolates of Escherichia coli from Germany, The Netherlands and the UK. Int J Antimicrob Agents 2014; 43:553-7. [PMID: 24816185 DOI: 10.1016/j.ijantimicag.2014.02.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 11/16/2022]
Abstract
This study aimed to detect and characterise clinical Escherichia coli isolates suspected of carrying chromosomally encoded CTX-M enzymes. Escherichia coli (n=356) obtained in Germany, The Netherlands and the UK (2005-2009) and resistant to third-generation cephalosporins were analysed for the presence of ESBL-/AmpC-encoding genes within the European SAFEFOODERA-ESBL project. β-Lactamases and their association with IS26 and ISEcp1 were investigated by PCR. Isolates were typed by phylogenetic grouping, MLST and PFGE. Plasmids were visualised by S1 nuclease PFGE, and the location of blaCTX-M genes was determined by Southern hybridisation of XbaI-, S1- and I-CeuI-digested DNA. ESBL enzymes could not be located on plasmids in 17/356 isolates (4.8%). These 17 isolates, from different countries and years, were ascribed to phylogenetic groups D (9), B2 (6) and B1 (2), and to seven sequence types, with ST38 being the most frequent (7 phylogroup D isolates). Eleven isolates produced CTX-M-15. blaCTX-M-15 genes were associated with ISEcp1. The remaining isolates expressed the CTX-M group 9 β-lactamases CTX-M-14 (4), CTX-M-9 (1) and CTX-M-51 (1). blaCTX-M probes hybridised with I-CeuI- and/or XbaI-digested DNA, but not with S1-digested DNA, corroborating their chromosomal location. To summarise, only 4.8% of a large collection of ESBL-producing E. coli isolates harboured chromosomal blaCTX-M genes. These isolates were of human origin and belonged predominantly to ST38 and ST131, which possibly indicates the role of these sequence types in this phenomenon. However, heterogeneity among isolates was found, suggesting that their spread is not only due to the dispersion of successful E. coli clones.
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Affiliation(s)
- I Rodríguez
- Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany.
| | - K Thomas
- Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - A Van Essen
- Central Veterinary Institute (CVI) of Wageningen UR, Department of Bacteriology and TSEs, P.O. Box 65, 8200 AB Lelystad, The Netherlands
| | - A-K Schink
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - M Day
- Public Health England (PHE), 61 Colindale Avenue, London NW9 5EQ, UK
| | - M Chattaway
- Public Health England (PHE), 61 Colindale Avenue, London NW9 5EQ, UK
| | - G Wu
- Animal Health and Veterinary Laboratories Agency (AHVLA), Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - D Mevius
- Central Veterinary Institute (CVI) of Wageningen UR, Department of Bacteriology and TSEs, P.O. Box 65, 8200 AB Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, 3584 CL Utrecht, The Netherlands
| | - R Helmuth
- Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - B Guerra
- Federal Institute for Risk Assessment (BfR), Department for Biological Safety, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
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García P, Hopkins KL, García V, Beutlich J, Mendoza MC, Threlfall J, Mevius D, Helmuth R, Rodicio MR, Guerra B. Diversity of plasmids encoding virulence and resistance functions in Salmonella enterica subsp. enterica serovar Typhimurium monophasic variant 4,[5],12:i:- strains circulating in Europe. PLoS One 2014; 9:e89635. [PMID: 24586926 PMCID: PMC3935914 DOI: 10.1371/journal.pone.0089635] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 01/22/2014] [Indexed: 11/19/2022] Open
Abstract
Plasmids encoding resistance and virulence properties in multidrug resistant (MDR) Salmonella enterica (S.) serovar Typhimurium monophasic variant 4,[5],12:i:- isolates recovered from pigs and humans (2006-2008) in Europe were characterised. The isolates were selected based on the detection by PCR-amplification of S. Typhimurium virulence plasmid pSLT genes and were analysed by multi-locus sequence typing (MLST). The resistance genes present in the isolates and the association of these genes with integrons, transposons and insertion sequences were characterised by PCR-sequencing, and their plasmid location was determined by alkaline lysis and by S1-nuclease pulsed-field gel electrophoresis (PFGE) Southern-blot hybridisation. Plasmids were further analysed by replicon typing, plasmid MLST and conjugation experiments. The 10 S. 4,[5],12,i:- selected isolates belonged to ST19. Each isolate carried a large plasmid in which MDR with pSLT-associated virulence genes were located. After analysis, eight different plasmids of three incompatibility groups (IncA/C, IncR and IncF) were detected. Two IncA/C plasmids represented novel variants within the plasmid family of the S. 4,[5],12:i:- Spanish clone, and carried an empty class 1 integron with a conventional qacEΔ1-sul1 3′ conserved segment or an In-sul3 type III with estX-psp-aadA2-cmlA1-aadA1-qacH variable region linked to tnpA440-sul3, part of Tn2, Tn21 and Tn1721 transposons, and ISCR2. Four newly described IncR plasmids contained the resistance genes within In-sul3 type I (dfrA12-orfF-aadA2-cmlA1-aadA1-qacH/tnpA440-sul3) and part of Tn10 [tet(B)]. Two pSLT-derivatives with FIIs-ST1+FIB-ST17 replicons carried cmlA1-[aadA1-aadA2]-sul3-dfrA12 and blaTEM-1 genes linked to an In-sul3 type I integron and to Tn2, respectively. In conclusion, three emerging European clones of S. 4,[5],12:i:- harboured MDR plasmids encoding additional virulence functions that could contribute significantly to their evolutionary success.
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Affiliation(s)
- Patricia García
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Asturias, Spain
| | - Katie L. Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England (PHE), London, United Kingdom
| | - Vanesa García
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Asturias, Spain
| | - Janine Beutlich
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - M. Carmen Mendoza
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Asturias, Spain
| | - John Threlfall
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England (PHE), London, United Kingdom
| | - Dik Mevius
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI), Lelystad, The Netherlands
| | - Reiner Helmuth
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - M. Rosario Rodicio
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Asturias, Spain
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
- * E-mail:
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Veldman K, Heuvelink A, De Leure PT, Mevius D. [Quality control for antibiotic sensitivity testing in 2013]. Tijdschr Diergeneeskd 2014; 139:36-39. [PMID: 24909035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Beutlich J, Rodicio MR, Mendoza MC, García P, Kirchner M, Luzzi I, Mevius D, Threlfall J, Helmuth R, Guerra, on behalf of the Med-Vet-Ne B. Salmonella entericaserovarTyphimurium Virulence-Resistance Plasmids Derived from the pSLT Carrying Nonconventional Class 1 Integrons withdfrA12Gene in Their Variable Region andsul3in the 3′ Conserved Segment. Microb Drug Resist 2013; 19:437-45. [DOI: 10.1089/mdr.2012.0226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Janine Beutlich
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - M. Rosario Rodicio
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Spain
| | - M. Carmen Mendoza
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Spain
| | - Patricia García
- Department of Functional Biology, Area of Microbiology, University of Oviedo, Oviedo, Spain
| | - Miranda Kirchner
- Animal Health and Veterinary Laboratories Agency (AHVLA), Department of Bacteriology, Addlestone, United Kingdom
| | - Ida Luzzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanita (ISS), Rome, Italy
| | - Dik Mevius
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen UR, Lelystad, The Netherlands
| | - John Threlfall
- Health Protection Agency (HPA), Centre for Infections, London, United Kingdom
| | - Reiner Helmuth
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
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Wendlandt S, Kadlec K, Feßler AT, Mevius D, van Essen-Zandbergen A, Hengeveld PD, Bosch T, Schouls L, Schwarz S, van Duijkeren E. Transmission of methicillin-resistant Staphylococcus aureus isolates on broiler farms. Vet Microbiol 2013; 167:632-7. [DOI: 10.1016/j.vetmic.2013.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/10/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
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Wu G, Day MJ, Mafura MT, Nunez-Garcia J, Fenner JJ, Sharma M, van Essen-Zandbergen A, Rodríguez I, Dierikx C, Kadlec K, Schink AK, Wain J, Helmuth R, Guerra B, Schwarz S, Threlfall J, Woodward MJ, Woodford N, Coldham N, Mevius D. Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany. PLoS One 2013; 8:e75392. [PMID: 24086522 PMCID: PMC3784421 DOI: 10.1371/journal.pone.0075392] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/12/2013] [Indexed: 11/26/2022] Open
Abstract
The putative virulence and antimicrobial resistance gene contents of extended spectrum β-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring blaCTX-M-group-1 dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both blaCTX-M-group-1 and blaOXA-1-like genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6’)-Ib, catB3, blaOXA-1-like and blaCTX-M-group-1. forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans.
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Affiliation(s)
- Guanghui Wu
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
- * E-mail:
| | | | - Muriel T. Mafura
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Javier Nunez-Garcia
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Jackie J. Fenner
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Meenaxi Sharma
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Alieda van Essen-Zandbergen
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
| | - Irene Rodríguez
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Cindy Dierikx
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Anne-Kathrin Schink
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - John Wain
- Public Health England, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Reiner Helmuth
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Beatriz Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | | | - Martin J. Woodward
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | | | - Nick Coldham
- Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), Addlestone, United Kingdom
| | - Dik Mevius
- Department of Bacteriology and TSEs, Central Veterinary Institute (CVI) of Wageningen, Lelystad, the Netherlands
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van de Vijver LPL, Tulinski P, Bondt N, Mevius D, Verwer C. Prevalence and Molecular Characteristics of Methicillin-ResistantStaphylococcus aureus(MRSA) in Organic Pig Herds in The Netherlands. Zoonoses Public Health 2013; 61:338-45. [DOI: 10.1111/zph.12076] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
| | - P. Tulinski
- Faculty of Veterinary Medicine; Department of Infectious Diseases and Immunology; Utrecht University; Utrecht The Netherlands
| | - N. Bondt
- LEI; Agricultural Economics Research Institute of Wageningen University and Research Centre; The Hague The Netherlands
| | - D. Mevius
- Faculty of Veterinary Medicine; Department of Infectious Diseases and Immunology; Utrecht University; Utrecht The Netherlands
- Central Veterinary Institute of Wageningen University and Research Centre; Lelystad The Netherlands
| | - C. Verwer
- Department of Animal and Environment; Louis Bolk Institute; Driebergen The Netherlands
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Hordijk J, Schoormans A, Kwakernaak M, Duim B, Broens E, Dierikx C, Mevius D, Wagenaar JA. High prevalence of fecal carriage of extended spectrum β-lactamase/AmpC-producing Enterobacteriaceae in cats and dogs. Front Microbiol 2013; 4:242. [PMID: 23966992 PMCID: PMC3745002 DOI: 10.3389/fmicb.2013.00242] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/01/2013] [Indexed: 11/16/2022] Open
Abstract
Extended-spectrum-β-lactamase (ESBL)/AmpC producing Enterobacteriaceae have been reported worldwide amongst isolates obtained from humans, food-producing animals, companion animals, and environmental sources. However, data on prevalence of fecal carriage of ESBL/AmpC producing Enterobacteriaceae in healthy companion animals is limited. This pilot study describes the prevalence of ESBL/AmpC encoding genes in healthy cats and dogs, and cats and dogs with diarrhea. Twenty fecal samples of each group were cultured on MacConkey agar supplemented with 1 mg/L cefotaxime and in LB-enrichment broth supplemented with 1 mg/L cefotaxime, which was subsequently inoculated on MacConkey agar supplemented with 1 mg/L cefotaxime. ESBL/AmpC genes were identified using the Check-Points CT103 micro array kit and subsequently by sequencing analysis. Chromosomal ampC promoter mutations were detected by PCR and sequencing analysis. From the healthy and diarrheic dogs, respectively 45 and 55% were positive for Escherichia coli with reduced susceptibility for cefotaxime. From the healthy and diarrheic cats, the estimated prevalence was respectively 0 and 25%. One diarrheic cat was positive for both reduced susceptible E.coli and Proteus mirabilis. The ESBL/AmpC genes found in this study were mainly blaCTX-M-1, but also blaCTX-M-14, blaCTX-M-15, blaTEM-52-StPaul, blaSHV-12, and blaCMY-2 were detected. This pilot study showed that the prevalence of ESBL/AmpC producing Enterobacteriaceae in healthy and diarrheic dogs, and diarrheic cats was relatively high. Furthermore, the genes found were similar to those found in isolates of both human and food-producing animal origin. However, since the size of this study was relatively small, extrapolation of the data to the general population of cats and dogs should be done with great care.
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Affiliation(s)
- Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University Utrecht, Netherlands
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Hordijk J, Wagenaar JA, Kant A, van Essen-Zandbergen A, Dierikx C, Veldman K, Wit B, Mevius D. Cross-sectional study on prevalence and molecular characteristics of plasmid mediated ESBL/AmpC-producing Escherichia coli isolated from veal calves at slaughter. PLoS One 2013; 8:e65681. [PMID: 23724148 PMCID: PMC3665799 DOI: 10.1371/journal.pone.0065681] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/25/2013] [Indexed: 11/18/2022] Open
Abstract
Objectives The presence of ESBL/AmpC-producing E. coli in cattle has been reported previously, however information on veal calves is limited. This study describes the prevalence and molecular characteristics of E. coli with non-wild type susceptibility to cefotaxime in veal calves at slaughter. Methods Faecal samples from 100 herds, 10 individual animals per herd, were screened for E. coli with non-wild type susceptibility for cefotaxime. Molecular characterization of ESBL/AmpC genes and plasmids was performed on one isolate per herd by microarray, PCR and sequence analysis. Results 66% of the herds were positive for E. coli with non-wild type susceptibility for cefotaxime. Within-herd prevalence varied from zero to 90%. 83% of E. coli producing ESBL/AmpC carried blaCTX-M genes, of which blaCTX-M-1, blaCTX-M-14 and blaCTX-M-15 were most prevalent. The dominant plasmids were IncI1 and IncF-type plasmids. Conclusions A relatively high prevalence of various blaCTX-M producing E. coli was found in veal calves at slaughter. The genes were mainly located on IncI1 and IncF plasmids.
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Affiliation(s)
- Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Hordijk J, Wagenaar JA, van de Giessen A, Dierikx C, van Essen-Zandbergen A, Veldman K, Kant A, Mevius D. Increasing prevalence and diversity of ESBL/AmpC-type β-lactamase genes in Escherichia coli isolated from veal calves from 1997 to 2010. J Antimicrob Chemother 2013; 68:1970-3. [PMID: 23657803 DOI: 10.1093/jac/dkt132] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Several studies on faecal carriage of extended-spectrum β-lactamase (ESBL)/AmpC-producing Escherichia coli have been performed in cattle, but little is known about faecal carriage in veal calves. This study describes the prevalence and molecular characteristics of ESBL/AmpC genes in E. coli isolated from faecal samples of veal calves from 1997 to 2010. METHODS Pooled faecal samples were inoculated using selective enrichment broth and subsequently selective MacConkey agar. All isolates with reduced susceptibility to cefotaxime were screened by PCR and sequencing analysis for the presence of ESBL/AmpC genes. RESULTS The prevalence of E. coli with reduced susceptibility to cefotaxime showed a discontinuous increasing trend, ranging from 4% in 1998 and 1999 to 39% in 2010. Promoter mutations of the chromosomal ampC gene were present in all years. In 2000, ESBL genes blaCTX-M-1, blaTEM-52 and blaTEM-20 were first observed. Before 2005 the majority of E. coli with reduced susceptibility to cefotaxime harboured ampC promoter mutations. From 2005 onwards the majority harboured blaCTX-M genes, of which blaCTX-M-1 was the most abundant, followed by blaCTX-M-14 and blaCTX-M-15. The diversity of blaCTX-M genes gradually increased from one variant in 2000 to six variants in 2010. The prevalence of blaTEM-52 was relatively low, but it was detected from 2000 onwards. blaCMY and blaSHV were found sporadically. CONCLUSIONS The prevalence and molecular diversity of genes encoding cefotaxime resistance in E. coli isolated from veal calves over a 14 year period showed an increasing trend. From 2005 onwards, blaCTX-M genes were most abundant, especially blaCTX-M-1.
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Affiliation(s)
- Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80.165, 3508 TD Utrecht, The Netherlands.
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Heuvelink AE, Mevius D. [Quality control hypersensitivity tests]. Tijdschr Diergeneeskd 2013; 138:247. [PMID: 23638562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Liebana E, Carattoli A, Coque TM, Hasman H, Magiorakos AP, Mevius D, Peixe L, Poirel L, Schuepbach-Regula G, Torneke K, Torren-Edo J, Torres C, Threlfall J. Public health risks of enterobacterial isolates producing extended-spectrum β-lactamases or AmpC β-lactamases in food and food-producing animals: an EU perspective of epidemiology, analytical methods, risk factors, and control options. Clin Infect Dis 2012; 56:1030-7. [PMID: 23243183 DOI: 10.1093/cid/cis1043] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The blaESBL and blaAmpC genes in Enterobacteriaceae are spread by plasmid-mediated integrons, insertion sequences, and transposons, some of which are homologous in bacteria from food animals, foods, and humans. These genes have been frequently identified in Escherichia coli and Salmonella from food animals, the most common being blaCTX-M-1, blaCTX-M-14, and blaCMY-2. Identification of risk factors for their occurrence in food animals is complex. In addition to generic antimicrobial use, cephalosporin usage is an important risk factor for selection and spread of these genes. Extensive international trade of animals is a further risk factor. There are no data on the effectiveness of individual control options in reducing public health risks. A highly effective option would be to stop or restrict cephalosporin usage in food animals. Decreasing total antimicrobial use is also of high priority. Implementation of measures to limit strain dissemination (increasing farm biosecurity, controls in animal trade, and other general postharvest controls) are also important.
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Affiliation(s)
- Ernesto Liebana
- Scientific Unit on Biological Hazards, European Food Safety Authority, Parma, Italy.
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Abstract
This study was performed to determine a sampling strategy to quantify the prevalence of antimicrobial resistance on veal calf farms, based on the variation in antimicrobial resistance within and between calves on five farms. Faecal samples from 50 healthy calves (10 calves/farm) were collected. From each individual sample and one pooled faecal sample per farm, 90 selected Escherichia coli isolates were tested for their resistance against 25 mg/L amoxicillin, 25 mg/L tetracycline, 0.5 mg/L cefotaxime, 0.125 mg/L ciprofloxacin and 8/152 mg/L trimethoprim/sulfamethoxazole (tmp/s) by replica plating. From each faecal sample another 10 selected E. coli isolates were tested for their resistance by broth microdilution as a reference. Logistic regression analysis was performed to compare the odds of testing an isolate resistant between both test methods (replica plating vs. broth microdilution) and to evaluate the effect of pooling faecal samples. Bootstrap analysis was used to investigate the precision of the estimated prevalence of resistance to each antimicrobial obtained by several simulated sampling strategies. Replica plating showed similar odds of E. coli isolates tested resistant compared to broth microdilution, except for ciprofloxacin (OR 0.29, p≤0.05). Pooled samples showed in general lower odds of an isolate being resistant compared to individual samples, although these differences were not significant. Bootstrap analysis showed that within each antimicrobial the various compositions of a pooled sample provided consistent estimates for the mean proportion of resistant isolates. Sampling strategies should be based on the variation in resistance among isolates within faecal samples and between faecal samples, which may vary by antimicrobial. In our study, the optimal sampling strategy from the perspective of precision of the estimated levels of resistance and practicality consists of a pooled faecal sample from 20 individual animals, of which 90 isolates are tested for their susceptibility by replica plating.
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Affiliation(s)
- Angela B Bosman
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Dierikx C, van der Goot J, Fabri T, van Essen-Zandbergen A, Smith H, Mevius D. Extended-spectrum- -lactamase- and AmpC- -lactamase-producing Escherichia coli in Dutch broilers and broiler farmers. J Antimicrob Chemother 2012; 68:60-7. [DOI: 10.1093/jac/dks349] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Koene M, Mevius D, Wagenaar J, Harmanus C, Hensgens M, Meetsma A, Putirulan F, van Bergen M, Kuijper E. Clostridium difficile in Dutch animals: their presence, characteristics and similarities with human isolates. Clin Microbiol Infect 2012; 18:778-84. [DOI: 10.1111/j.1469-0691.2011.03651.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Hordijk J, Veldman K, Dierikx C, van Essen-Zandbergen A, Wagenaar JA, Mevius D. Prevalence and characteristics of quinolone resistance in Escherichia coli in veal calves. Vet Microbiol 2011; 156:136-42. [PMID: 22041448 DOI: 10.1016/j.vetmic.2011.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
Quinolone resistance is studied and reported increasingly in isolates from humans, food-producing animals and companion animals. Resistance can be caused by chromosomal mutations in topoisomerase genes, plasmid-mediated resistance genes, and active transport through efflux pumps. Cross sectional data on quinolone resistance mechanisms in non-pathogenic bacteria from healthy veal calves is limited. The purpose of this study was to determine the prevalence and characteristics of quinolone resistance mechanisms in Escherichia coli isolates from veal calves, after more than 20 years of quinolone usage in veal calves. MIC values were determined for all isolates collected as part of a national surveillance program on antimicrobial resistance in commensal bacteria in food-producing animals in The Netherlands. From the strains collected from veal calves in 2007 (n=175) all isolates with ciprofloxacin MIC ≥ 0.125 mg/L (n=25) were selected for this study, and screened for the presence of known quinolone resistance determinants. In this selection only chromosomal mutations in the topoisomerase type II and IV genes were detected. The number of mutations found per isolate correlated with an increasing ciprofloxacin MIC. No plasmid-mediated quinolone resistance genes were found. The contribution of efflux pumps varied from no contribution to a 16-fold increase in susceptibility. No correlation was found with the presence of resistance genes of other antimicrobial classes, even though all quinolone non-wild type isolates were resistant to 3 or more classes of antibiotics other than quinolones. Over twenty years of quinolone usage in veal calves in The Netherlands did not result in a widespread occurrence of plasmid-mediated quinolone resistance, limiting the transmission of quinolone resistance to clonal distribution.
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Affiliation(s)
- Joost Hordijk
- Utrecht University, Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, PO Box 80.165, 3508 TD Utrecht, The Netherlands.
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Veldman K, van Essen-Zandbergen A, Kant A, Mevius D. Characterization of qnr-positive Escherichia coli isolates from food-producing animals in the Netherlands. J Antimicrob Chemother 2011; 67:239-40. [PMID: 21969333 DOI: 10.1093/jac/dkr424] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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van Hoek AHAM, Mevius D, Guerra B, Mullany P, Roberts AP, Aarts HJM. Acquired antibiotic resistance genes: an overview. Front Microbiol 2011; 2:203. [PMID: 22046172 PMCID: PMC3202223 DOI: 10.3389/fmicb.2011.00203] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/08/2011] [Indexed: 01/18/2023] Open
Abstract
In this review an overview is given on antibiotic resistance (AR) mechanisms with special attentions to the AR genes described so far preceded by a short introduction on the discovery and mode of action of the different classes of antibiotics. As this review is only dealing with acquired resistance, attention is also paid to mobile genetic elements such as plasmids, transposons, and integrons, which are associated with AR genes, and involved in the dispersal of antimicrobial determinants between different bacteria.
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Affiliation(s)
- Angela H. A. M. van Hoek
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
| | - Dik Mevius
- Central Veterinary Institute of Wageningen URLelystad, Netherlands
- Department of Infectious Diseases and Immunology, Utrecht UniversityUtrecht, Netherlands
| | - Beatriz Guerra
- National Salmonella Reference Laboratory, Federal Institute for Risk AssessmentBerlin, Germany
| | - Peter Mullany
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Adam Paul Roberts
- Department of Microbial Diseases, University College London Eastman Dental Institute, University College LondonLondon, UK
| | - Henk J. M. Aarts
- Laboratory for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute of Public Health and the EnvironmentUtrecht, Netherlands
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