Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment: a pooled analysis

Alejandro Dorado-Garcia, J.H. Smid, Wilfrid Van Pelt, M.J.M. Bonten, A.C. Fluit, Gerrita van den Bunt, J.A. Wagenaar, J. Hordijk, C.M. Dierikx, K.T. Veldman, A.A. de Koeijer, W. Dohmen, H. Schmitt, A. Liakopoulos, Ewa Pacholewicz, T.J.G.M. Lam, Annet Velthuis, A. Heuvelink, Maaike Gonggrijp, E. van Duijkeren & 6 others A.H.A.M. van Hoek, A.N. de Roda Husman, H. Blaak, A.H. Havelaar, D.J. Mevius, D.J.J. Heederik

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24 Citations (Scopus)

Abstract

Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.
Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.
Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).
Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.
Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.
Original languageEnglish
Pages (from-to)339-347
JournalJournal of Antimicrobial Chemotherapy
Volume73
Issue number2
DOIs
Publication statusPublished - 1 Feb 2018

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Replicon
Escherichia coli
Food
Plasmids
Genes
Livestock
Principal Component Analysis
Population
Sewage
Agriculture
Netherlands
Birds
Swine
Water

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Dorado-Garcia, A., Smid, J. H., Van Pelt, W., Bonten, M. J. M., Fluit, A. C., van den Bunt, G., ... Heederik, D. J. J. (2018). Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment: a pooled analysis. Journal of Antimicrobial Chemotherapy, 73(2), 339-347. https://doi.org/10.1093/jac/dkx397
Dorado-Garcia, Alejandro ; Smid, J.H. ; Van Pelt, Wilfrid ; Bonten, M.J.M. ; Fluit, A.C. ; van den Bunt, Gerrita ; Wagenaar, J.A. ; Hordijk, J. ; Dierikx, C.M. ; Veldman, K.T. ; de Koeijer, A.A. ; Dohmen, W. ; Schmitt, H. ; Liakopoulos, A. ; Pacholewicz, Ewa ; Lam, T.J.G.M. ; Velthuis, Annet ; Heuvelink, A. ; Gonggrijp, Maaike ; van Duijkeren, E. ; van Hoek, A.H.A.M. ; de Roda Husman, A.N. ; Blaak, H. ; Havelaar, A.H. ; Mevius, D.J. ; Heederik, D.J.J. / Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment : a pooled analysis. In: Journal of Antimicrobial Chemotherapy. 2018 ; Vol. 73, No. 2. pp. 339-347.
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title = "Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment: a pooled analysis",
abstract = "Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.",
author = "Alejandro Dorado-Garcia and J.H. Smid and {Van Pelt}, Wilfrid and M.J.M. Bonten and A.C. Fluit and {van den Bunt}, Gerrita and J.A. Wagenaar and J. Hordijk and C.M. Dierikx and K.T. Veldman and {de Koeijer}, A.A. and W. Dohmen and H. Schmitt and A. Liakopoulos and Ewa Pacholewicz and T.J.G.M. Lam and Annet Velthuis and A. Heuvelink and Maaike Gonggrijp and {van Duijkeren}, E. and {van Hoek}, A.H.A.M. and {de Roda Husman}, A.N. and H. Blaak and A.H. Havelaar and D.J. Mevius and D.J.J. Heederik",
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Dorado-Garcia, A, Smid, JH, Van Pelt, W, Bonten, MJM, Fluit, AC, van den Bunt, G, Wagenaar, JA, Hordijk, J, Dierikx, CM, Veldman, KT, de Koeijer, AA, Dohmen, W, Schmitt, H, Liakopoulos, A, Pacholewicz, E, Lam, TJGM, Velthuis, A, Heuvelink, A, Gonggrijp, M, van Duijkeren, E, van Hoek, AHAM, de Roda Husman, AN, Blaak, H, Havelaar, AH, Mevius, DJ & Heederik, DJJ 2018, 'Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment: a pooled analysis' Journal of Antimicrobial Chemotherapy, vol. 73, no. 2, pp. 339-347. https://doi.org/10.1093/jac/dkx397

Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment : a pooled analysis. / Dorado-Garcia, Alejandro; Smid, J.H.; Van Pelt, Wilfrid; Bonten, M.J.M.; Fluit, A.C.; van den Bunt, Gerrita; Wagenaar, J.A.; Hordijk, J.; Dierikx, C.M.; Veldman, K.T.; de Koeijer, A.A.; Dohmen, W.; Schmitt, H.; Liakopoulos, A.; Pacholewicz, Ewa; Lam, T.J.G.M.; Velthuis, Annet; Heuvelink, A.; Gonggrijp, Maaike; van Duijkeren, E.; van Hoek, A.H.A.M.; de Roda Husman, A.N.; Blaak, H.; Havelaar, A.H.; Mevius, D.J.; Heederik, D.J.J.

In: Journal of Antimicrobial Chemotherapy, Vol. 73, No. 2, 01.02.2018, p. 339-347.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Molecular relatedness of ESBL/AmpC-producing Escherichia coli from humans, animals, food and the enviroment

T2 - a pooled analysis

AU - Dorado-Garcia, Alejandro

AU - Smid, J.H.

AU - Van Pelt, Wilfrid

AU - Bonten, M.J.M.

AU - Fluit, A.C.

AU - van den Bunt, Gerrita

AU - Wagenaar, J.A.

AU - Hordijk, J.

AU - Dierikx, C.M.

AU - Veldman, K.T.

AU - de Koeijer, A.A.

AU - Dohmen, W.

AU - Schmitt, H.

AU - Liakopoulos, A.

AU - Pacholewicz, Ewa

AU - Lam, T.J.G.M.

AU - Velthuis, Annet

AU - Heuvelink, A.

AU - Gonggrijp, Maaike

AU - van Duijkeren, E.

AU - van Hoek, A.H.A.M.

AU - de Roda Husman, A.N.

AU - Blaak, H.

AU - Havelaar, A.H.

AU - Mevius, D.J.

AU - Heederik, D.J.J.

PY - 2018/2/1

Y1 - 2018/2/1

N2 - Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.

AB - Background: In recent years, ESBL/AmpC-producing Escherichia coli ESBL/AmpC-EC) have been isolated with increasing frequency from animals, food, environmental sources and humans. With incomplete and scattered evidence, the contribution to the human carriage burden from these reservoirs remains unclear.Objectives: To quantify molecular similarities between different reservoirs as a first step towards risk attribution.Methods: Pooled data on ESBL/AmpC-EC isolates were recovered from 35 studies in the Netherlands comprising.27 000 samples, mostly obtained between 2005 and 2015. Frequency distributions of ESBL/AmpC genes from 5808 isolates and replicons of ESBL/AmpC-carrying plasmids from 812 isolates were compared across 22 reservoirs through proportional similarity indices (PSIs) and principal component analyses (PCAs).Results: Predominant ESBL/AmpC genes were identified in each reservoir. PCAs and PSIs revealed close human–animal ESBL/AmpC gene similarity between human farming communities and their animals (broilers and pigs) (PSIs from 0.8 to 0.9). Isolates from people in the general population had higher similarities to those from human clinical settings, surface and sewage water and wild birds (0.7–0.8), while similarities to livestock or food reservoirs were lower (0.3–0.6). Based on rarefaction curves, people in the general population had more diversity in ESBL/AmpC genes and plasmid replicon types than those in other reservoirs.Conclusions: Our ‘One Health’ approach provides an integrated evaluation of the molecular relatedness of ESBL/AmpC-EC from numerous sources. The analysis showed distinguishable ESBL/AmpC-EC transmission cycles in different hosts and failed to demonstrate a close epidemiological linkage of ESBL/AmpC genes and plasmid replicon types between livestock farms and people in the general population.

U2 - 10.1093/jac/dkx397

DO - 10.1093/jac/dkx397

M3 - Article

VL - 73

SP - 339

EP - 347

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

IS - 2

ER -