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3. The European livestock resistome

Author

IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., Dep Population Health Sciences, Infectious Diseases and Immunology - KLIF, IRAS – One Health Microbial, Munk, Patrick, Yang, Dongsheng, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Duarte, Ana Sofia Ribeiro, Clausen, Philip T L C, Brinch, Christian, Van Gompel, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A, Schmitt, Heike, Heederik, Dick J J, Mevius, Dik J, Smit, Lidwien A M, Bossers, Alex, Aarestrup, Frank M, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., Dep Population Health Sciences, Infectious Diseases and Immunology - KLIF, IRAS – One Health Microbial, Munk, Patrick, Yang, Dongsheng, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Duarte, Ana Sofia Ribeiro, Clausen, Philip T L C, Brinch, Christian, Van Gompel, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A, Schmitt, Heike, Heederik, Dick J J, Mevius, Dik J, Smit, Lidwien A M, Bossers, Alex, and Aarestrup, Frank M

Published
2024

4. The European livestock resistome

Author

Munk, Patrick, Yang, Dongsheng, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Duarte, Ana Sofia Ribeiro, Clausen, Philip T. L. C., Brinch, Christian, Van Gompel, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A., Schmitt, Heike, Heederik, Dick J. J., Mevius, Dik J., Smit, Lidwien A. M., Bosser, Alex, Aarestrup, Frank M., Munk, Patrick, Yang, Dongsheng, Röder, Timo, Maier, Leonie, Petersen, Thomas Nordahl, Duarte, Ana Sofia Ribeiro, Clausen, Philip T. L. C., Brinch, Christian, Van Gompel, Liese, Luiken, Roosmarijn, Wagenaar, Jaap A., Schmitt, Heike, Heederik, Dick J. J., Mevius, Dik J., Smit, Lidwien A. M., Bosser, Alex, and Aarestrup, Frank M.

Abstract

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal

Published
2024

6. Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study

Author

Van Gompel, Liese, Luiken, Roosmarijn E.C., Hansen, Rasmus B., Munk, Patrick, Bouwknegt, Martijn, Heres, Lourens, Greve, Gerdit D., Scherpenisse, Peter, Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique H.G., García-Cobos, Silvia, Dohmen, Wietske, Dorado-García, Alejandro, Wagenaar, Jaap A., Urlings, Bert A.P., Aarestrup, Frank M., Mevius, Dik J., Heederik, Dick J.J., Schmitt, Heike, Bossers, Alex, and Smit, Lidwien A.M.

Published
2020
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7. Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Author

Castellanos, L. Ricardo, Bloois, Linda van der Graaf-van, Donado-Godoy, Pilar, Veldman, Kees, Duarte, Francisco, Acuna, Maria T., Jarquin, Claudia, Weill, Francois-Xavier, Mevius, Dik J., Wagenaar, Jaap A., Hordijk, Joost, and Zomer, Aldert L.

Subjects
Genomics, Drug resistance in microorganisms, Genomes, Poultry industry, Phylogeny, Salmonella, Health
Abstract

The d-Tartrate fermenting, nonparatyphoidal variant of Salmonella enterica serovar Paratyphi B, contemporarily known as variant Java, was first reported in 1935 by De Moor (1). From then until recently, Salmonella [...]

Published
2020
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11. Longitudinal Study of Dynamic Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Pigs and Humans Living and/or Working on Pig Farms

Author

IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., Faculteit Diergeneeskunde, Dohmen, Wietske, Liakopoulos, Apostolos, Bonten, Marc J M, Mevius, Dik J, Heederik, Dick J J, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., Faculteit Diergeneeskunde, Dohmen, Wietske, Liakopoulos, Apostolos, Bonten, Marc J M, Mevius, Dik J, and Heederik, Dick J J

Published
2023

12. Understanding the genetic basis of the incompatibility of IncK1 and IncK2 plasmids

Author

Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Rozwandowicz, Marta, Kant, Arie, Wagenaar, Jaap, Mevius, Dik, Hordijk, Joost, Brouwer, Michael, Klinische infectiologie en microb. lab., Infectious Diseases and Immunology - KLIF, Rozwandowicz, Marta, Kant, Arie, Wagenaar, Jaap, Mevius, Dik, Hordijk, Joost, and Brouwer, Michael

Published
2023

13. Longitudinal Study of Dynamic Epidemiology of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Pigs and Humans Living and/or Working on Pig Farms

Author

Dohmen, Wietske, Liakopoulos, Apostolos, Bonten, Marc J.M., Mevius, Dik J., Heederik, Dick J.J., Dohmen, Wietske, Liakopoulos, Apostolos, Bonten, Marc J.M., Mevius, Dik J., and Heederik, Dick J.J.

Abstract

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales have been increasingly isolated from pigs, highlighting their potential for transmission to humans living and/or working within pig farms. As longitudinal data on the prevalence and the molecular characteristics of such isolates from the high-risk farming population remain scarce, we performed a long-term study on 39 Dutch pig farms. Fecal samples from pigs, farmers, family members, and employees were collected during four sampling occasions with a 6-month period. The presence of ESBL-producing Enterobacterales and their molecular characteristics (ESBL gene, plasmid, and sequence types) were determined by standard methods. Data on personal and farm characteristics were collected using questionnaires. ESBL-producing Escherichia coli was present in pigs at least once for 18 of 39 farms and in 17 of 146 farmers, family members, and/or employees. Among these 417 E. coli isolates, blaCTX-M-1 was the most frequently observed ESBL gene in pigs (n = 261) and humans (n = 25). Despite the great variety in plasmid (sub)types and E. coli sequence types (STs), we observed genetic similarity between human- and pig-derived isolates in (i) ESBL gene, plasmid (sub)type, and ST, suggesting potential clonal transmission in seven farms, and (ii) only ESBL gene and plasmid (sub) type, highlighting the possibility of horizontal transfer in four farms. Five pig farmers carried ESBL producers repeatedly, of whom two carried an identical combination of gene, plasmid (sub)type, and ST over time. Human ESBL carriage was associated with both presence of ESBL producers in pigs and average number of hours working on the pig farm per week, while prolonged human carriage was observed only incidentally. IMPORTANCE Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli represents a public health hazard due to reduced therapeutic options for the treatment of infections. Although direct contact with pigs is considered a ris

Published
2023

14. Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by through Manure Amendment in Soil Microcosms

Author

Macedo, Gonçalo, Olesen, Asmus K, Maccario, Lorrie, Hernandez Leal, Lucia, V D Maas, Peter, Heederik, Dick, Mevius, Dik, Sørensen, Søren J, and Schmitt, Heike

Subjects
soil microbiome, cattle manure, antibiotic resistance gene, lateral gene transfer, mating
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.

Published
2023

17. Extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg strains, the Netherlands

Author

Liakopoulos, Apostolos, Geurts, Yvon, Dierikx, Cindy M., Brouwer, Michael S.M., Kant, Arie, Wit, Ben, Heymans, Raymond, van Pelt, Wilfrid, and Mevius, Dik J.

Subjects
Moxalactam -- Health aspects, Drug resistance in microorganisms -- Health aspects, Salmonella food poisoning -- Health aspects, Infection -- Health aspects, Cephalosporins -- Health aspects, Cephaloridine -- Health aspects, Salmonella -- Health aspects, Health
Abstract

Salmonella enterica serovar Heidelberg is among the most prevalent causes of human salmonellosis in the United States and Canada but has been reported infrequently in Europe (1-3). Although most nontyphoidal [...]

Published
2016
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20. Public Health Risks of Enterobacterial Isolates Producing Extended-Spectrum ß-Lactamases or AmpC ß-Lactamases in Food and Food-Producing Animals: An EU Perspective of Epidemiology, Analytical Methods, Risk Factors, and Control Options

Author

Liebana, Ernesto, Carattoli, Alessandra, Coque, Teresa M., Hasman, Henrik, Magiorakos, Anna-Pelagia, Mevius, Dik, Peixe, Luisa, Poirel, Laurent, Schuepbach-Regula, Gertraud, Torneke, Karolina, Torren-Edo, Jordi, Torres, Carmen, and Threlfall, John

Published
2013
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21. Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Author

Luiken, Roosmarijn Ec, Heederik, Dick Jj, Scherpenisse, Peter, Van Gompel, Liese, van Heijnsbergen, Eri, Greve, Gerdit D, Jongerius-Gortemaker, Betty Gm, Tersteeg-Zijderveld, Monique Hg, Fischer, Jennie, Juraschek, Katharina, Skarżyńska, Magdalena, Zając, Magdalena, Wasyl, Dariusz, EFFORT Group, Wagenaar, Jaap A, Smit, Lidwien Am, Wouters, Inge M, Mevius, Dik J, Schmitt, Heike, Klinische infectiologie en microb. lab., dIRAS RA-I&I I&I, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, and dI&I I&I-4

Subjects
Pig, Livestock, Risk factors, Environmental Science(all), Dust, Environment, Antimicrobial resistance, Biochemistry, Poultry, One health
Abstract

Livestock feces with antimicrobial resistant bacteria reaches the farm floor, manure pit, farm land and wider environment by run off and aerosolization. Little research has been done on the role of dust in the spread of antimicrobial resistance (AMR) in farms. Concentrations and potential determinants of antimicrobial resistance genes (ARGs) in farm dust are at present not known. Therefore in this study absolute ARG levels, representing the levels people and animals might be exposed to, and relative abundances of ARGs, representing the levels in the bacterial population, were quantified in airborne farm dust using qPCR. Four ARGs were determined in 947 freshly settled farm dust samples, captured with electrostatic dustfall collectors (EDCs), from 174 poultry (broiler) and 159 pig farms across nine European countries. By using linear mixed modeling, associations with fecal ARG levels, antimicrobial use (AMU) and farm and animal related parameters were determined. Results show similar relative abundances in farm dust as in feces and a significant positive association (ranging between 0.21 and 0.82) between the two reservoirs. AMU in pigs was positively associated with ARG abundances in dust from the same stable. Higher biosecurity standards were associated with lower relative ARG abundances in poultry and higher relative ARG abundances in pigs. Lower absolute ARG levels in dust were driven by, among others, summer season and certain bedding materials for poultry, and lower animal density and summer season for pigs. This study indicates different pathways that contribute to shaping the dust resistome in livestock farms, related to dust generation, or affecting the bacterial microbiome. Farm dust is a large reservoir of ARGs from which transmission to bacteria in other reservoirs can possibly occur. The identified determinants of ARG abundances in farm dust can guide future research and potentially farm management policy.

Published
2022

22. Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Author

Klinische infectiologie en microb. lab., dIRAS RA-I&I I&I, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, dI&I I&I-4, Luiken, Roosmarijn Ec, Heederik, Dick Jj, Scherpenisse, Peter, Van Gompel, Liese, van Heijnsbergen, Eri, Greve, Gerdit D, Jongerius-Gortemaker, Betty Gm, Tersteeg-Zijderveld, Monique Hg, Fischer, Jennie, Juraschek, Katharina, Skarżyńska, Magdalena, Zając, Magdalena, Wasyl, Dariusz, EFFORT Group, Wagenaar, Jaap A, Smit, Lidwien Am, Wouters, Inge M, Mevius, Dik J, Schmitt, Heike, Klinische infectiologie en microb. lab., dIRAS RA-I&I I&I, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, dI&I I&I-4, Luiken, Roosmarijn Ec, Heederik, Dick Jj, Scherpenisse, Peter, Van Gompel, Liese, van Heijnsbergen, Eri, Greve, Gerdit D, Jongerius-Gortemaker, Betty Gm, Tersteeg-Zijderveld, Monique Hg, Fischer, Jennie, Juraschek, Katharina, Skarżyńska, Magdalena, Zając, Magdalena, Wasyl, Dariusz, EFFORT Group, Wagenaar, Jaap A, Smit, Lidwien Am, Wouters, Inge M, Mevius, Dik J, and Schmitt, Heike

Published
2022

23. Risk factors for the abundance of antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) in pig and broiler faeces in nine European countries

Author

IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, Yang, Dongsheng, Heederik, Dick J J, Mevius, Dik J, Scherpenisse, Peter, Luiken, Roosmarijn E C, Van Gompel, Liese, Skarżyńska, Magdalena, Wadepohl, Katharina, Chauvin, Claire, Van Heijnsbergen, Eri, Wouters, Inge M, Greve, Gerdit D, Jongerius-Gortemaker, Betty G M, Tersteeg-Zijderveld, Monique, Zając, Magdalena, Wasyl, Dariusz, Juraschek, Katharina, Fischer, Jennie, Wagenaar, Jaap A, Smit, Lidwien A M, Schmitt, Heike, IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, Yang, Dongsheng, Heederik, Dick J J, Mevius, Dik J, Scherpenisse, Peter, Luiken, Roosmarijn E C, Van Gompel, Liese, Skarżyńska, Magdalena, Wadepohl, Katharina, Chauvin, Claire, Van Heijnsbergen, Eri, Wouters, Inge M, Greve, Gerdit D, Jongerius-Gortemaker, Betty G M, Tersteeg-Zijderveld, Monique, Zając, Magdalena, Wasyl, Dariusz, Juraschek, Katharina, Fischer, Jennie, Wagenaar, Jaap A, Smit, Lidwien A M, and Schmitt, Heike

Published
2022

24. Antimicrobial resistance monitoring in commensal and clinical Escherichia coli from broiler chickens: Differences and similarities

Author

FAH Evidence based Veterinary Medicine, dFAH AVR, Klinische infectiologie en microb. lab., dI&I I&I-4, Hesp, Ayla, van Schaik, Gerdien, Wiegel, Jeanine, Heuvelink, Annet, Mevius, Dik, Veldman, Kees, FAH Evidence based Veterinary Medicine, dFAH AVR, Klinische infectiologie en microb. lab., dI&I I&I-4, Hesp, Ayla, van Schaik, Gerdien, Wiegel, Jeanine, Heuvelink, Annet, Mevius, Dik, and Veldman, Kees

Published
2022

25. Antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe

Author

IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, Klinische infectiologie en microb. lab., LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, dI&I I&I-4, Yang, Dongsheng, Heederik, Dick J J, Scherpenisse, Peter, Van Gompel, Liese, Luiken, Roosmarijn E C, Wadepohl, Katharina, Skarżyńska, Magdalena, Van Heijnsbergen, Eri, Wouters, Inge M, Greve, Gerdit D, Jongerius-Gortemaker, Betty G M, Tersteeg-Zijderveld, Monique, Portengen, Lützen, Juraschek, Katharina, Fischer, Jennie, Zając, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A, Mevius, Dik J, Smit, Lidwien A M, Schmitt, Heike, IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, Klinische infectiologie en microb. lab., LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, dI&I I&I-4, Yang, Dongsheng, Heederik, Dick J J, Scherpenisse, Peter, Van Gompel, Liese, Luiken, Roosmarijn E C, Wadepohl, Katharina, Skarżyńska, Magdalena, Van Heijnsbergen, Eri, Wouters, Inge M, Greve, Gerdit D, Jongerius-Gortemaker, Betty G M, Tersteeg-Zijderveld, Monique, Portengen, Lützen, Juraschek, Katharina, Fischer, Jennie, Zając, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A, Mevius, Dik J, Smit, Lidwien A M, and Schmitt, Heike

Published
2022

26. Resisting disinfectants

Author

van Dijk, Harrie, Verbrugh, Henri, Abee, Tjakko, Andriessen, Jan Willem, ter Kuile, Benno, Mevius, Dik, Montforts, Mark, van Schaik, Willem, Schmitt, Heike, Smidt, Hauke, Veening, Jan-Willem, Voss, Andreas, van Dijk, Harrie, Verbrugh, Henri, Abee, Tjakko, Andriessen, Jan Willem, ter Kuile, Benno, Mevius, Dik, Montforts, Mark, van Schaik, Willem, Schmitt, Heike, Smidt, Hauke, Veening, Jan-Willem, and Voss, Andreas

Abstract

Although often overlooked, the use of disinfectants can lead to antimicrobial resistance and this may exacerbate resistance to antibiotics. Here, we explain why all antimicrobial agents, including disinfectants, should be used prudently in a way that is guided by evidence.

Published
2022

27. Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

Author

Macedo, Goncalo, Olesen, Asmus K., Maccario, Lorrie, Leal, Lucia Hernandez, v. d. Maas, Peter, Heederik, Dick, Mevius, Dik, Sørensen, Søren J., Schmitt, Heike, Macedo, Goncalo, Olesen, Asmus K., Maccario, Lorrie, Leal, Lucia Hernandez, v. d. Maas, Peter, Heederik, Dick, Mevius, Dik, Sørensen, Søren J., and Schmitt, Heike

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.

Published
2022

28. Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Author

Luiken, Roosmarijn E.C., Heederik, Dick J.J., Scherpenisse, Peter, Van Gompel, Liese, van Heijnsbergen, Eri, Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique H.G., Fischer, Jennie, Juraschek, Katharina, Skarżyńska, Magdalena, Zając, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A., Smit, Lidwien A.M., Wouters, Inge M., Mevius, Dik J., Schmitt, Heike, Luiken, Roosmarijn E.C., Heederik, Dick J.J., Scherpenisse, Peter, Van Gompel, Liese, van Heijnsbergen, Eri, Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique H.G., Fischer, Jennie, Juraschek, Katharina, Skarżyńska, Magdalena, Zając, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A., Smit, Lidwien A.M., Wouters, Inge M., Mevius, Dik J., and Schmitt, Heike

Abstract

Livestock feces with antimicrobial resistant bacteria reaches the farm floor, manure pit, farm land and wider environment by run off and aerosolization. Little research has been done on the role of dust in the spread of antimicrobial resistance (AMR) in farms. Concentrations and potential determinants of antimicrobial resistance genes (ARGs) in farm dust are at present not known. Therefore in this study absolute ARG levels, representing the levels people and animals might be exposed to, and relative abundances of ARGs, representing the levels in the bacterial population, were quantified in airborne farm dust using qPCR. Four ARGs were determined in 947 freshly settled farm dust samples, captured with electrostatic dustfall collectors (EDCs), from 174 poultry (broiler) and 159 pig farms across nine European countries. By using linear mixed modeling, associations with fecal ARG levels, antimicrobial use (AMU) and farm and animal related parameters were determined. Results show similar relative abundances in farm dust as in feces and a significant positive association (ranging between 0.21 and 0.82) between the two reservoirs. AMU in pigs was positively associated with ARG abundances in dust from the same stable. Higher biosecurity standards were associated with lower relative ARG abundances in poultry and higher relative ARG abundances in pigs. Lower absolute ARG levels in dust were driven by, among others, summer season and certain bedding materials for poultry, and lower animal density and summer season for pigs. This study indicates different pathways that contribute to shaping the dust resistome in livestock farms, related to dust generation, or affecting the bacterial microbiome. Farm dust is a large reservoir of ARGs from which transmission to bacteria in other reservoirs can possibly occur. The identified determinants of ARG abundances in farm dust can guide future research and potentially farm management policy.

Published
2022

29. Risk factors for the abundance of antimicrobial resistance genes aph(3′)-III, erm(B), sul2 and tet(W) in pig and broiler faeces in nine European countries

Author

Yang, Dongsheng, Heederik, Dick J.J., Mevius, Dik J., Scherpenisse, Peter, Luiken, Roosmarijn E.C., Van Gompel, Liese, Skarżyńska, Magdalena, Wadepohl, Katharina, Chauvin, Claire, Van Heijnsbergen, Eri, Wouters, Inge M., Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique, ZajCrossed D Sign c, Magdalena, Wasyl, Dariusz, Juraschek, Katharina, Fischer, Jennie, Wagenaar, Jaap A., Smit, Lidwien A.M., Schmitt, Heike, Yang, Dongsheng, Heederik, Dick J.J., Mevius, Dik J., Scherpenisse, Peter, Luiken, Roosmarijn E.C., Van Gompel, Liese, Skarżyńska, Magdalena, Wadepohl, Katharina, Chauvin, Claire, Van Heijnsbergen, Eri, Wouters, Inge M., Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique, ZajCrossed D Sign c, Magdalena, Wasyl, Dariusz, Juraschek, Katharina, Fischer, Jennie, Wagenaar, Jaap A., Smit, Lidwien A.M., and Schmitt, Heike

Abstract

Objectives: The occurrence and zoonotic potential of antimicrobial resistance (AMR) in pigs and broilers has been studied intensively in past decades. Here, we describe AMR levels of European pig and broiler farms and determine the potential risk factors. Methods: We collected faeces from 181 pig farms and 181 broiler farms in nine European countries. Real-time quantitative PCR (qPCR) was used to quantify the relative abundance of four antimicrobial resistance genes (ARGs) [aph(3′)-III, erm(B), sul2 and tet(W)] in these faeces samples. Information on antimicrobial use (AMU) and other farm characteristics was collected through a questionnaire. A mixed model using country and farm as random effects was performed to evaluate the relationship of AMR with AMU and other farm characteristics. The correlation between individual qPCR data and previously published pooled metagenomic data was evaluated. Variance component analysis was conducted to assess the variance contribution of all factors. Results: The highest abundance of ARG was for tet(W) in pig faeces and erm(B) in broiler faeces. In addition to the significant positive association between corresponding ARG and AMU levels, we also found on-farm biosecurity measures were associated with relative ARG abundance in both pigs and broilers. Between-country and between-farm variation can partially be explained by AMU. Different ARG targets may have different sample size requirements to represent the overall farm level precisely. Conclusions: qPCR is an efficient tool for targeted assessment of AMR in livestock-related samples. The AMR variation between samples was mainly contributed to by between-country, between-farm and within-farm differences, and then by on-farm AMU.

Published
2022

31. Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Author

Luiken, Roosmarijn EC., primary, Heederik, Dick JJ., additional, Scherpenisse, Peter, additional, Van Gompel, Liese, additional, van Heijnsbergen, Eri, additional, Greve, Gerdit D., additional, Jongerius-Gortemaker, Betty GM., additional, Tersteeg-Zijderveld, Monique HG., additional, Fischer, Jennie, additional, Juraschek, Katharina, additional, Skarżyńska, Magdalena, additional, Zając, Magdalena, additional, Wasyl, Dariusz, additional, Wagenaar, Jaap A., additional, Smit, Lidwien AM., additional, Wouters, Inge M., additional, Mevius, Dik J., additional, and Schmitt, Heike, additional

Published
2022
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32. Antimicrobial resistance genes aph(3′)-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe

Author

Yang, Dongsheng, primary, Heederik, Dick J J, additional, Scherpenisse, Peter, additional, Van Gompel, Liese, additional, Luiken, Roosmarijn E C, additional, Wadepohl, Katharina, additional, Skarżyńska, Magdalena, additional, Van Heijnsbergen, Eri, additional, Wouters, Inge M, additional, Greve, Gerdit D, additional, Jongerius-Gortemaker, Betty G M, additional, Tersteeg-Zijderveld, Monique, additional, Portengen, Lützen, additional, Juraschek, Katharina, additional, Fischer, Jennie, additional, Zając, Magdalena, additional, Wasyl, Dariusz, additional, Wagenaar, Jaap A, additional, Mevius, Dik J, additional, Smit, Lidwien A M, additional, and Schmitt, Heike, additional

Published
2022
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33. Genomic evolution of antimicrobial resistance in Escherichia coli

Author

Leekitcharoenphon, Pimlapas, Johansson, Markus Hans Kristofer, Munk, Patrick, Malorny, Burkhard, Skarzynska, Magdalena, Wadepohl, Katharina, Moyano, Gabriel, Hesp, Ayla, Veldman, Kees T., Bossers, Alex, Graveland, Haitske, van Essen, Alieda, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Hald, Tine, Daskalov, Hristo, Saatkamp, Helmut W., Staerk, Katharina D. C., Luiken, Roosmarijn E. C., Van Gompel, Liese, Hansen, Rasmus Borup, Dewulf, Jeroen, Duarte, Ana Sofia Ribeiro, Zajac, Magdalena, Wasyl, Dariusz, Sanders, Pascal, Gonzalez-Zorn, Bruno, Brouwer, Michael S. M., Wagenaar, Jaap A., Heederik, Dick J. J., Mevius, Dik, Aarestrup, Frank M., EFFORT Consortium, for the, Technical University of Denmark [Lyngby] (DTU), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I RA, and Faculteit Diergeneeskunde

Subjects
0301 basic medicine, Genomic alteration, antibiotic resistance, Swine, Epidemiology, résistance aux antibiotiques, veterinary drug, medicine.disease_cause, Genome, Poultry, Feces, animal, évolution, bacteria, Escherichia coli Infections, Phylogeny, médicament humainélevage, 2. Zero hunger, Genetics, human drug, bactérie, Multidisciplinary, Virulence, Bacteriologie, transmission, Genomics, Bacteriology, Host Pathogen Interaction & Diagnostics, Text, Anti-Bacterial Agents, Europe, Medicine, médicament, médicament vétérinaire, Bioinformatica & Diermodellen, Science, 030106 microbiology, Microbial Sensitivity Tests, GENETIC-STRUCTURE, Biology, Article, Evolution, Molecular, 03 medical and health sciences, Antibiotic resistance, résistance aux antimicrobiens, Drug Resistance, Bacterial, Bio-informatics & Animal models, medicine, Escherichia coli, Animals, Life Science, Epidemiology, Bio-informatics & Animal models, ddc:610, Veterinary Sciences, antimicrobial resistance, microbiologie, General, genome, Host Pathogen Interaction & Diagnostics, Epidemiologie, Whole genome sequencing, génome, microbiology, Bacteriology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, livestock, Red Meat, 030104 developmental biology, Metagenomics, Genetic marker, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Molecular evolution, Cattle, POULTRY, Mobile genetic elements, humain, Genome, Bacterial
Abstract

The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

Published
2021

34. Zinc resistance of Staphylococcus aureus of animal origin is strongly associated with methicillin resistance

Author

Cavaco, Lina M., Hasman, Henrik, Aarestrup, Frank M., Members of MRSA-CG, Wagenaar, Jaap A., Graveland, Haitske, Veldman, Kees, Mevius, Dik, Fetsch, Alexandra, Tenhagen, Bernd-Alois, Concepcion Porrero, M., Dominguez, Lucas, Granier, Sophie A., Jouy, Eric, Butaye, Patrick, Kaszanyitzky, Eva, Dán, Adam, Zmudzki, Jacek, Battisti, Antonio, Franco, Alessia, Schwarz, Stefan, Gutierrez, Montserrat, Weese, J. Scott, Cui, Shengui, and Pomba, Constança

Published
2011
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35. Salmonella subtypes with increased MICs for azithromycin in travelers returned to the Netherlands

Author

Hassing, Robert-Jan, Goessens, Wil H.F., van Pelt, Wilfrid, Mevius, Dik J., Stricker, Bruno H., Molhoek, Nicky, Verbon, Annelies, and van Genderen, Perry J.J.

Subjects
Travelers -- Health aspects, Azithromycin -- Usage -- Health aspects, Typhoid fever -- Diagnosis -- Demographic aspects -- Drug therapy -- Patient outcomes, Salmonella -- Research -- Demographic aspects, Health
Abstract

Enteric fever caused by Salmonella enterica serotypes Typhi and Paratyphi A, B, and C is mainly a disease of the developing world, and it is occasionally diagnosed as an imported [...]

Published
2014
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37. Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK

Author

Day, Michaela J., Rodríguez, Irene, van Essen-Zandbergen, Alieda, Dierikx, Cindy, Kadlec, Kristina, Schink, Anne-Kathrin, Wu, Guanghui, Chattaway, Marie A., DoNascimento, Vivienne, Wain, John, Helmuth, Reiner, Guerra, Beatriz, Schwarz, Stefan, Threlfall, John, Woodward, Martin J., Coldham, Nick, Mevius, Dik, and Woodford, Neil

Published
2016
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40. Temperature and nutrient limitations decrease transfer of conjugative IncP-1 plasmid pKJK5 to wild Escherichia coli strains

Author

Pallares-Vega, Rebeca, Macedo, Gonçalo, Brouwer, Michael S M, Hernandez Leal, Lucia, van der Maas, Peter, van Loosdrecht, Mark C M, Weissbrodt, David G, Heederik, Dick, Mevius, Dik, Schmitt, Heike, Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, and dIRAS RA-I&I I&I

Subjects
Microbiology (medical), Epidemiology, Bioinformatica & Diermodellen, Microorganism, medicine.disease_cause, Microbiology, 03 medical and health sciences, Antibiotic resistance, Plasmid, Bodem, Bio-informatics & Animal models, Afvalwater, medicine, soil extract agar, Epidemiology, Bio-informatics & Animal models, AMR, antimicrobial resistance, Food science, Psychrophile, Escherichia coli, Original Research, 030304 developmental biology, Host Pathogen Interaction & Diagnostics, Epidemiologie, 0303 health sciences, Strain (chemistry), biology, 030306 microbiology, Chemistry, Bacteriologie, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, biology.organism_classification, Enterobacteriaceae, Host Pathogen Interactie & Diagnostiek, QR1-502, environmental conditions, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Horizontal gene transfer, horizontal gene transfer, Resistentie, synthetic wastewater
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.

Published
2021

42. Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E. C., Smit, Lidwien A. M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., and EFFORT Group

Published
2018
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44. Quantitative and qualitative analysis of antimicrobial usage patterns in 180 selected farrow-to-finish pig farms from nine European countries based on single batch and purchase data

Author

Sarrazin, Steven, Joosten, Philip, van Gompel, Liese, Wagenaar, Jaap, Graveland, H, Heederik, Dick, Schmitt, H, Luiken, Roosmarijn, Gompel, L Van, Mevius, Dik, van Essen, A, Gonzalez-Zorn, B, Moyano, G, Sanders, Pascal, Chauvin, C., David, J, Battisti, A, Caprioli, A, Dewulf, Jeroen, Blaha, T, Wadepohl, K, Brandt, M, Aarestrup, F, Hald, T., Duarte, S., Wasyl, D, Krasucka, D, Biernacki, B, Szumiło, J, Daskalov, H, Saatkamp, H, Stärk, K, One Health Microbieel, dIRAS RA-I&I I&I, LS Klinisch Onderzoek Wagenaar, Dep IRAS, dIRAS RA-I&I RA, dI&I I&I-4, Environmental and Occupational Health Group, Wageningen University and Research [Wageningen] (WUR), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Obstetrics, Reproduction and Herd Health, Universiteit Gent = Ghent University (UGENT), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Laboratoire de psychologie sociale et de psychologie cognitive (LAPSCO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Universiteit Gent = Ghent University [Belgium] (UGENT), Technical University of Denmark [Lyngby] (DTU), and Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Subjects
0301 basic medicine, pig, antibiotic resistance, analysis, Swine, Epidemiology, animal diseases, analyse, veterinary drug, antimicrobiens, antibiotiques, Toxicology, 0302 clinical medicine, Anti-Infective Agents, antibiotic, porcs, Pharmacology (medical), Veterinary drug, Public Health Surveillance, 030212 general & internal medicine, résistance, Practice Patterns, Physicians', Qualitative Research, 2. Zero hunger, Swine Diseases, Incidence (epidemiology), Antimicrobial, Europe, Infectious Diseases, medicine.drug, Microbiology (medical), médicament vétérinaire, Farms, Bioinformatica & Diermodellen, 030106 microbiology, Coronacrisis-Taverne, Drug Prescriptions, 03 medical and health sciences, Qualitative analysis, Bio-informatics & Animal models, Enrofloxacin, medicine, Life Science, Animals, Epidemiology, Bio-informatics & Animal models, antimicrobial resistance, Pig farms, Pharmacology, Epidemiologie, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, business.industry, antimicrobial use, Group treatment, Young age, cochons, Epidemiologie, Bioinformatica & Diermodellen, business
Abstract

Objectives: Farm-level quantification of antimicrobial usage (AMU) in pig farms. Methods: In a cross-sectional study, AMU data on group treatments administered to a single batch of fattening pigs from birth to slaughter (group treatment data) and antimicrobials purchased during 1 year (purchase data) were collected at 180 pig farms in nine European countries. AMU was quantified using treatment incidence (TI) based on defined (DDDvet) and used (UDDvet) daily doses and defined (DCDvet) and used (UCDvet) course doses. Results: The majority of antimicrobial group treatments were administered to weaners (69.5% of total TIDDDvet) followed by sucklers (22.5% of total TIDDDvet). AMU varied considerably between farms with a median TIDDDvet of 9.2 and 7.1 for a standardized rearing period of 200 days based on group treatment and purchase data, respectively. In general, UDDvet and UCDvet were higher than DDDvet and DCDvet, respectively, suggesting that either the defined doses were set too low or that group treatments were often dosed too high and/or administered for too long. Extended-spectrum penicillins (31.2%) and polymyxins (24.7%) were the active substances most often used in group treatments, with the majority administered through feed or water (82%). Higher AMU at a young age was associated with higher use in older pigs. Conclusions: Collecting farm-level AMU data of good quality is challenging and results differ based on how data are collected (group treatment data versus purchase data) and reported (defined versus used daily and course doses).

Published
2019

46. Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries

Author

Horie, Mayu, primary, Yang, Dongsheng, additional, Joosten, Philip, additional, Munk, Patrick, additional, Wadepohl, Katharina, additional, Chauvin, Claire, additional, Moyano, Gabriel, additional, Skarżyńska, Magdalena, additional, Dewulf, Jeroen, additional, Aarestrup, Frank M., additional, Blaha, Thomas, additional, Sanders, Pascal, additional, Gonzalez-Zorn, Bruno, additional, Wasyl, Dariusz, additional, Wagenaar, Jaap A., additional, Heederik, Dick, additional, Mevius, Dik, additional, Schmitt, Heike, additional, Smit, Lidwien A. M., additional, and Van Gompel, Liese, additional

Published
2021
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47. Occurrence and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacterales Recovered From Chicken, Chicken Meat, and Human Infections in Sao Paulo State, Brazil

Author

Cardozo, Marita Vedovelli, primary, Liakopoulos, Apostolos, additional, Brouwer, Michael, additional, Kant, Arie, additional, Pizauro, Lucas José Luduvério, additional, Borzi, Mariana Monezi, additional, Mevius, Dik, additional, and de Ávila, Fernando Antonio, additional

Published
2021
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48. Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application

Author

Macedo, Gonçalo, van Veelen, H Pieter J, Hernandez-Leal, Lucia, van der Maas, Peter, Heederik, Dick, Mevius, Dik, Bossers, Alex, Schmitt, Heike, Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, and dIRAS RA-I&I I&I

Subjects
010504 meteorology & atmospheric sciences, Epidemiology, Slurry, 010501 environmental sciences, 01 natural sciences, Soil, Bodem, RNA, Ribosomal, 16S, AMR, Waste Management and Disposal, Soil Microbiology, Microbiota, Bacteriologie, Drug Resistance, Microbial, Bacteriology, Host Pathogen Interaction & Diagnostics, Pollution, Anti-Bacterial Agents, Gene pool, Landbouwgronden, Environmental Engineering, Farms, Bioinformatica & Diermodellen, Field, Biology, Dairy, Dierlijke mest, Bio-informatics & Animal models, Environmental Chemistry, Animals, Epidemiology, Bio-informatics & Animal models, Microbiome, 0105 earth and related environmental sciences, Land application, Host Pathogen Interaction & Diagnostics, Epidemiologie, Bacteriome, Bacteriology, 16S ribosomal RNA, Manure, Host Pathogen Interactie & Diagnostiek, Bacteriën, Resistome, Agronomy, Metagenomics, Genes, Bacterial, Epidemiologie, Bioinformatica & Diermodellen, Soil water, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Cattle
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.

Published
2021

49. Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains

Author

Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, Pallares-Vega, Rebeca, Macedo, Gonçalo, Brouwer, Michael S M, Hernandez Leal, Lucia, van der Maas, Peter, van Loosdrecht, Mark C M, Weissbrodt, David G, Heederik, Dick, Mevius, Dik, Schmitt, Heike, Sub Research support office, Faculteit Diergeneeskunde, IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I RA, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I I&I, Pallares-Vega, Rebeca, Macedo, Gonçalo, Brouwer, Michael S M, Hernandez Leal, Lucia, van der Maas, Peter, van Loosdrecht, Mark C M, Weissbrodt, David G, Heederik, Dick, Mevius, Dik, and Schmitt, Heike

Published
2021

50. Genomic evolution of antimicrobial resistance in Escherichia coli

Author

IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I RA, Faculteit Diergeneeskunde, Leekitcharoenphon, Pimlapas, Johansson, Markus Hans Kristofer, Munk, Patrick, Malorny, Burkhard, Skarżyńska, Magdalena, Wadepohl, Katharina, Moyano, Gabriel, Hesp, Ayla, Veldman, Kees T, Bossers, Alex, Zając, Magdalena, Wasyl, Dariusz, Gonzalez-Zorn, Bruno, Sanders, Pascal, Brouwer, Michael S M, Wagenaar, Jaap A, Heederik, Dick J J, Mevius, Dik, EFFORT consortium, Aarestrup, Frank M, IRAS OH Epidemiology Microbial Agents, Klinische infectiologie en microb. lab., dI&I I&I-4, dIRAS RA-I&I RA, Faculteit Diergeneeskunde, Leekitcharoenphon, Pimlapas, Johansson, Markus Hans Kristofer, Munk, Patrick, Malorny, Burkhard, Skarżyńska, Magdalena, Wadepohl, Katharina, Moyano, Gabriel, Hesp, Ayla, Veldman, Kees T, Bossers, Alex, Zając, Magdalena, Wasyl, Dariusz, Gonzalez-Zorn, Bruno, Sanders, Pascal, Brouwer, Michael S M, Wagenaar, Jaap A, Heederik, Dick J J, Mevius, Dik, EFFORT consortium, and Aarestrup, Frank M

Published
2021

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