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

Dongsheng Yang*, Dick J.J. Heederik, Peter Scherpenisse, Liese Van Gompel, Roosmarijn E.C. Luiken, Katharina Wadepohl, Magdalena Skarżyńska, Eri Van Heijnsbergen, Inge M. Wouters, Gerdit D. Greve, Betty G.M. Jongerius-Gortemaker, Monique Tersteeg-Zijderveld, Lützen Portengen, Katharina Juraschek, Jennie Fischer, Magdalena Zajac, Dariusz Wasyl, Jaap A. Wagenaar, Dik J. Mevius, Lidwien A.M. SmitHeike Schmitt, Haitske Graveland, Philip Joosten, Steven Sarrazin, Jeroen Dewulf, Alieda Van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Julie David, Christophe Soumet, Antonio Battisti, Andrea Caprioli, Thomas Blaha, Maximiliane Brandt, Frank Aarestrup, Tine Hald, Ana Sofia Ribeiro Duarte, Andrzej Hoszowski, Agnieszka Pekala-Safinnska, Ewa Pazdzior, Hristo Daskalov, Helmut W. Saatkamp, Katharina D.C. Stark, Dick J.J. Heederik, Dik J. Mevius, Jaap A. Wagenaar, Lidwien A.M. Smit, Heike Schmitt

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)


Background: Real-Time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives: We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods: A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman's rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results: ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains ('farm to fork') was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman's ρ>0.7) between qPCR data and metagenomic data of pooled samples. Conclusions: qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-Associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.

Original languageEnglish
Pages (from-to)1883-1893
Number of pages11
JournalJournal of Antimicrobial Chemotherapy
Issue number7
Publication statusPublished - 1 Jul 2022


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