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

Abstract

Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3′-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.

Can Improved Farm Biosecurity Reduce the Need for Antimicrobials in Food Animals? A Scoping Review

“…Furthermore, two studies indibiosecurity practices is a cost-effective strategy for reducing AMU (Table 1). On the other hand, five studies reported an uncertain or spurious association between farm biosecurity and AMU, which could be attributed to confounders such as recent outbreaks, underreporting of AMU, misclassification, or missing information on AMU and/or biosecurity [9,34,36,40,46] (Table 1). Small pig farms resisted colistin and fluoroquinolones, while medium-sized farms showed resistance to streptomycin.…”

“…Furthermore, two studies indicated that coaching and awareness among farmers could lead to reduced AMU, while a single economic assessment study concluded that implementing biosecurity practices is a cost-effective strategy for reducing AMU (Table 1). On the other hand, five studies reported an uncertain or spurious association between farm biosecurity and AMU, which could be attributed to confounders such as recent outbreaks, underreporting of AMU, misclassification, or missing information on AMU and/or biosecurity [9,34,36,40,46] (Table 1).…”

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

“…The sampling procedures have been partially described before. 5,6,13,[15][16][17][18][19][20][21][22][23] Faecal samples were taken from farm animals [pigs, 5,13,23 broilers, 6,23 veal calves, 15 turkeys, 16 fish (intestines were collected)], companion animals (cats, dogs) 17 and wild boars. Carcass samples were taken from pigs 13 and broilers at slaughterhouses.…”

“…Before DNA extraction, animal faecal samples were stored at 4°C, transported to the laboratory within 24 h and stored at −80°C. [4][5][6]15,16,23 Exposed EDC cloths were put into a small resealable bag with sterile tweezers and frozen at −80°C. 19,20 Carcass, meat and glove samples were collected in a stomacher bag (INTERSCIENCE, 400 mL, UK), transported and stored at 4°C, followed by further preparations.…”

Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data—Part II, Application

“…In Canada, for example, the use of ceftiofur, a 3rd generation cephalosporin (3GC's) for the prevention of neonatal infections in poultry has been associated with the emergence of ceftriaxone-resistant (CRO-R) Salmonella Heidelberg in people [1]. In recent years, numerous studies [2][3][4][5][6][7][8][9][10][11] have demonstrated linkages between AMU in food producing animals and AMR in select bacterial species. Linkages between AMU in livestock and AMR have also been reported in the European Union's (EU) joint interagency antimicrobial consumption and resistance analysis (JIACRA) report [12].…”