Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms

Alice Roedel; Szilvia Vincze; Michaela Projahn; Uwe Roesler; Caroline Robé; Jens Andre Hammerl; Matthias Noll; Sascha Al Dahouk; Ralf Dieckmann

doi:10.3390/microorganisms9030651

Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms

Microorganisms. 2021 Mar 21;9(3):651. doi: 10.3390/microorganisms9030651.

Authors

Alice Roedel¹, Szilvia Vincze¹, Michaela Projahn¹, Uwe Roesler², Caroline Robé², Jens Andre Hammerl¹, Matthias Noll³, Sascha Al Dahouk¹, Ralf Dieckmann¹

Affiliations

¹ German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
² Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Robert-von-Ostertag Str. 7-13, 14163 Berlin, Germany.
³ Institute for Bioanalysis, University of Applied Sciences and Arts, Friedrich-Streib-Str. 2, 96450 Coburg, Germany.

Abstract

Biocides are frequently applied as disinfectants in animal husbandry to prevent the transmission of drug-resistant bacteria and to control zoonotic diseases. Concerns have been raised, that their use may contribute to the selection and persistence of antimicrobial-resistant bacteria. Especially, extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli have become a global health threat. In our study, 29 ESBL-/AmpC-producing and 64 NON-ESBL-/AmpC-producing E.coli isolates from three German broiler fattening farms collected in 2016 following regular cleaning and disinfection were phylogenetically characterized by whole genome sequencing, analyzed for phylogenetic distribution of virulence-associated genes, and screened for determinants of and associations between biocide tolerance and antibiotic resistance. Of the 30 known and two unknown sequence types detected, ST117 and ST297 were the most common genotypes. These STs are recognized worldwide as pandemic lineages causing disease in humans and poultry. Virulence determinants associated with extraintestinal pathogenic E.coli showed variable phylogenetic distribution patterns. Isolates with reduced biocide susceptibility were rarely found on the tested farms. Nine isolates displayed elevated MICs and/or MBCs of formaldehyde, chlorocresol, peroxyacetic acid, or benzalkonium chloride. Antibiotic resistance to ampicillin, trimethoprim, and sulfamethoxazole was most prevalent. The majority of ESBL-/AmpC-producing isolates carried bla_CTX-M (55%) or bla_CMY-2 (24%) genes. Phenotypic biocide tolerance and antibiotic resistance were not interlinked. However, biocide and metal resistance determinants were found on mobile genetic elements together with antibiotic resistance genes raising concerns that biocides used in the food industry may lead to selection pressure for strains carrying acquired resistance determinants to different antimicrobials.

Keywords: Escherichia coli; antibiotic resistance; biocide determinants; biocide tolerance; food safety; virulence.