Faecal colonisation with Carbapenemase and ESBL/AmpC-producing Enterobacterales in Portugal and the United Kingdom: A One Health perspective on the Human-Companion animal relationship

Abstract

Background Companion animals contribute to the maintenance and dissemination of clinically-important antimicrobial-resistant pathogens. The aim of this study was to evaluate the possible sharing of ESBL/AmpC- and carbapenemase-producing Enterobacterales between animals under antibiotic treatment and their human household members.

Methods A prospective longitudinal study was performed from 2018 to 2021 in Portugal and the UK. Faecal samples from dogs and cats with skin and soft tissue or urinary tract infections, and their cohabiting humans, were inoculated on MacConkey agar plates supplemented with 1.5 µg/mL cefotaxime and 1.0 µg/mL meropenem. Bacterial species and the presence of beta- lactamase genes were confirmed by PCR. Antimicrobial susceptibility was assessed by microdilution testing with MicroScan® Neg MIC Panel Type 44 (Siemens, US) and results interpreted according to EUCAST. Isolates’ clonality was assessed by rep-PCR. WGS (Illumina NovaSeq), producing pair-end libraries (150 bp), was performed for animal/owner- derived paired strains with the same rep-PCR pattern to estimate genetic relatedness.

Results

In Portuguese households, one dog (1/43,2.3%) was colonised by a multidrug-resistant OXA- 181-producing extraintestinal pathogenic Escherichia coli. Twenty-four companion animals (55.8%, n=43) and 28 humans (35.9%, n=78) harboured ESBL/AmpC-producing Enterobacterales in at least one timepoint. In UK households, one dog (1/7,14.3%) was colonised by a multidrug-resistant E. coli co- producing NDM-5 and CTX-M-15 beta-lactamases. ESBL/AmpC-Enterobacterales were isolated from five animals (71.4%, n=7) and three humans (37.5%, n=8). In eight Portuguese households (18.6%, n=43) and two UK households (28.6%, n=7), at least one ESBL/AmpC-encoding gene was detected simultaneously in animal/owner paired strains (Figure 1). Of these, identical rep-PCR pattern was observed for animal/owner paired strains from six Portuguese (13.9%) and one UK household (14.3%). WGS SNPs analysis confirmed longitudinal sharing of E. coli strains for five Portuguese and one UK household (Figure 2). Klebsiella pneumonia and Enterobacter spp. strains were also shared within two Portuguese households (Figure 3).

Conclusions The occurrence of ESBL/AmpC- and carbapenemase-producing Enterobacterales among companion animals and their simultaneous presence in human contacts, emphasizes the importance of incorporating dogs/cats in the assessment of antimicrobial resistance circulation in non-clinical settings. These results demonstrate the importance of the household as an epidemiological unit in any efforts to mitigate the spread of antimicrobial resistance.