Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding

Friedman, 2016, The negative impact of antibiotic resistance, Clin. Microbiol. Infect., 22, 416, 10.1016/j.cmi.2015.12.002 Woolhouse, 2015, Antimicrobial resistance in humans, livestock and the wider environment, Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci., 370, 20140083, 10.1098/rstb.2014.0083 Adler, 2016, The continuing plague of extended-spectrum β-lactamase-producing Enterobacteriaceae infections, Infect. Dis. Clin. N. Am., 30, 347, 10.1016/j.idc.2016.02.003 Findlay, 2020, Molecular epidemiology of Escherichia coli producing CTX-M and pAmpC β-lactamases from dairy farms identifies a dominant plasmid encoding CTX-M-32 but no evidence for transmission to humans in the same geographical region, Appl. Environ. Microbiol., 87, 10.1128/AEM.01842-20 Day, 2016, Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK, J. Antimicrob. Chemother., 71, 1178, 10.1093/jac/dkv485 Ludden, 2019, One health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock, mBio, 10, 10.1128/mBio.02693-18 Alzayn, 2020, Characterization of AmpC-hyperproducing Escherichia coli from humans and dairy farms collected in parallel in the same geographical region, J. Antimicrob. Chemother., 75, 2471, 10.1093/jac/dkaa207 Mounsey, 2021, Limited phylogenetic overlap between fluoroquinolone-resistant Escherichia coli isolated on dairy farms and those causing bacteriuria in humans living in the same geographical region, J. Antimicrob. Chemother., 76, 3144, 10.1093/jac/dkab310 Toombs-Ruane, 2020, Carriage of extended-spectrum beta-lactamase-and AmpC beta-lactamase-producing Escherichia coli from humans and pets in the same households, Appl. Environ. Microbiol., 86, 10.1128/AEM.01613-20 Kidsley, 2020, Companion animals are spillover hosts of the multidrug-resistant human extraintestinal Escherichia coli pandemic clones ST131 and ST1193, Front. Microbiol., 11, 1968, 10.3389/fmicb.2020.01968 Hong, 2020, Molecular characterization of fecal extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli from healthy companion animals and cohabiting humans in South Korea, Front. Microbiol., 11, 674, 10.3389/fmicb.2020.00674 Hong, 2019, Clonal spread of extended-spectrum cephalosporin-resistant Enterobacteriaceae between companion animals and humans in South Korea, Front. Microbiol., 10, 1371, 10.3389/fmicb.2019.01371 Amos, 2014, Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment, J. Antimicrob. Chemother., 69, 1785, 10.1093/jac/dku079 Leonard, 2018, Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey), Environ. Int., 114, 326, 10.1016/j.envint.2017.11.003 Schmidt, 2018, The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets, PLoS One, 13, 10.1371/journal.pone.0201279 Gibson, 2011, Risk factors for dogs becoming rectal carriers of multidrug-resistant Escherichia coli during hospitalization, Epidemiol. Infect., 139, 1511, 10.1017/S0950268810002785 Ogeer-Gyles, 2006, Development of antimicrobial drug resistance in rectal Escherichia coli isolates from dogs hospitalized in an intensive care unit, J. Am. Vet. Med. Assoc., 229, 694, 10.2460/javma.229.5.694 Schmidt, 2018, Routine antibiotic therapy in dogs increases the detection of antimicrobial-resistant faecal Escherichia coli, J. Antimicrob. Chemother., 73, 3305 Wedley, 2017, Carriage of antimicrobial resistant Escherichia coli in dogs: prevalence, associated risk factors and molecular characteristics, Vet. Microbiol., 199, 23, 10.1016/j.vetmic.2016.11.017 Leite-Martins, 2014, Prevalence of antimicrobial resistance in enteric Escherichia coli from domestic pets and assessment of associated risk markers using a generalized linear mixed model, Prev. Vet. Med., 117, 28, 10.1016/j.prevetmed.2014.09.008 Schmidt, 2015, Antimicrobial resistance risk factors and characterisation of faecal E. coli isolated from healthy Labrador retrievers in the United Kingdom, Prev. Vet. Med., 119, 31, 10.1016/j.prevetmed.2015.01.013 Day, 2016, Vaccination Guidelines Group (VGG) of the World Small Animal Veterinary Association (WSAVA). WSAVA guidelines for the vaccination of dogs and cats, J. Small Anim. Pract., 57, E1, 10.1111/jsap.2_12431 Murray, 2021, ‘Generation Pup’ - protocol for a longitudinal study of dog behaviour and health, BMC Vet. Res., 17, 1, 10.1186/s12917-020-02730-8 EUCAST Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol., 19, 455, 10.1089/cmb.2012.0021 Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 Zankari, 2012, Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 67, 2640, 10.1093/jac/dks261 Wirth, 2006, Sex and virulence in Escherichia coli: an evolutionary perspective, Mol. Microbiol., 60, 1136, 10.1111/j.1365-2958.2006.05172.x Grüning, 2018, Bioconda: sustainable and comprehensive software distribution for the life sciences, Nat. Methods, 15, 475, 10.1038/s41592-018-0046-7 Connor, 2016, CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community, Microb. Genom., 2 Stamatakis, 2005, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, 21, 456, 10.1093/bioinformatics/bti191 Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446 Argimón, 2016, Microreact: visualizing and sharing data for genomic epidemiology and phylogeography, Microb. Genom., 2 Wan Nur Ismah, 2018, Prediction of fluoroquinolone susceptibility directly from whole-genome sequence data by using liquid chromatography-tandem mass spectrometry to identify mutant genotypes, Antimicrob. Agents Chemother., 62, 10.1128/AAC.01814-17 Abreu-Salinas, 2020, High prevalence and diversity of cephalosporin-resistant Enterobacteriaceae including extraintestinal pathogenic E. coli CC648 lineage in rural and urban dogs in Northwest Spain, Antibiotics (Basel), 9, 468, 10.3390/antibiotics9080468 Courtice, 2021, Characterization of antimicrobial-resistant Escherichia coli causing urinary tract infections in dogs: passive surveillance in Saskatchewan, Canada 2014 to 2018, J. Vet. Intern. Med., 35, 1389, 10.1111/jvim.16103 Chen, 2020, Antibiotic-resistant Escherichia coli and sequence type 131 in fecal colonization in dogs in Taiwan, Microorganisms, 8, 1439, 10.3390/microorganisms8091439 Tchesnokova, 2019, Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci, Proc. Natl. Acad. Sci. U. S. A., 116, 14740, 10.1073/pnas.1903002116 Pightling, 2018, Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations, Front. Microbiol., 9, 1482, 10.3389/fmicb.2018.01482