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

Abstract

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

Recent Trends of Antibiotic Resistance in Staphylococcus aureus Causing Clinical Mastitis in Dairy Herds in Abruzzo and Molise Regions, Italy

“…The qPCR technique was introduced in this study for some of the AR genes for which only end point PCR tests were available because they are more rapid, specific and sensitive. The design of new tests for genes for which qPCR tests were already described [ 17 , 18 , 19 ] was decided to ensure specificity for S. aureus after the BLASTn alignment of sequences available for the species in the public domain database. Oligonucleotides were designed to match all gene variants retrieved.…”

The Use of Antibiotics and Antimicrobial Resistance in Veterinary Medicine, a Complex Phenomenon: A Narrative Review

“…Furthermore, the abundance of ARGs in the feces of people working in pig/broiler farms has often been linked to livestock AMR, potentially due to exposure to animal feces and dust in farms. This suggests that antibiotic residues in farm dust may also impact the gut microbiota by selecting for resistance [ 40 ]. The food chain (milk, eggs, and especially meat) represents one of the most important sources of ARB and ARG transmission between animals and humans [ 41 ].…”

City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics

“…S4A). Amongst the list of ARG city-core, genes sul2 and tetW were selected based on their importance and worldwide distribution [10,14] for sideby-side comparison by digital PCR and metagenomics (Fig. 1).…”

“…Then, from the list of detected ARGs in all samples (core ARGs), we subsequently selected the genes sul2 and tetW to be closely monitored by digital PCR and metagenomics. These genes confer resistance to sulfonamide and tetracycline antibiotics respectively, and are commonly detected in sewage and associated with the 'farm to fork' [14]. In addition, the sul2 gene is highly mobilized by plasmids [15], and for instance, tetW gene was ranked among the top 15 ARGs most frequently found in 79 wastewater samples analyzed from 60 different countries and 5 continents [10].…”