In view of the intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15 extended-spectrum β-lactamase (ESBL) in human clinical settings it would be of great interest to explore its existence in animals to unravel a possible reservoir function and the origin and transmission of this group of multiresistant strains. A total of 177 clinical phenotypically ESBL-producing E. coli isolates, mainly obtained from companion animals with urinary tract infections, wound infections and diarrhoea, were collected in a veterinary diagnostic laboratory covering a European-wide service area. They were screened for molecular subtype O25b and multilocus sequence type 131. O25b-ST131 isolates were subsequently tested for ESBL types, and phenotypic and genotypic resistance determinants. Further characterization of the strains was performed by PFGE and virulence gene typing. Ten (5.6%) of 177 phenotypically ESBL-producing E. coli isolates, nine strains from dogs and one strain from a horse, were allocated to the B2-O25b-ST131 lineage. Nine of these isolates harboured a CTX-M-15-type β-lactamase enzyme while one strain possessed an SHV-12-type ESBL. Macrorestriction analysis revealed a cluster formation of six of the animal CTX-M-15-type ESBL-producing strains from five different European countries together with a human control strain constituting a group of clonally related strains at a similarity value of 87.0%. Our findings demonstrate that the group of clonally related human B2-O25:H4-ST131 CTX-M-15-type ESBL-producing E. coli strains is present in companion animals from various European countries. This highlights the possibility of inter-species transmission of these multiresistant strains from human to animal and vice versa.

Since the first description of a plasmid-mediated colistin resistance gene (mcr-1) in November 2015 multiple reports of mcr-1 positive isolates indicate a worldwide spread of this newly discovered resistance gene in Enterobacteriaceae. Although the occurrence of mcr-1 positive isolates of livestock, food, environment and human origin is well documented only few systematic studies on the prevalence of mcr-1 are available yet. Here, comprehensive data on the prevalence of mcr-1 in German livestock and food isolates are presented. Over 10.600 E. coli isolates from the national monitoring on zoonotic agents from the years 2010–2015 were screened for phenotypic colistin resistance (MIC value >2 mg/l). Of those, 505 resistant isolates were screened with a newly developed TaqMan-based real-time PCR for the presence of the mcr-1 gene. In total 402 isolates (79.8% of colistin resistant isolates) harboured the mcr-1 gene. The prevalence was depending on the food production chain. The highest prevalence was detected in the turkey food chain (10.7%), followed by broilers (5.6%). A low prevalence was determined in pigs, veal calves and laying hens. The mcr-1 was not detected in beef cattle, beef and dairy products in all years investigated. In conclusion, TaqMan based real-time PCR provides a fast and accurate tool for detection of mcr-1 gene. The overall detection rate of 3.8% for mcr-1 among all E. coli isolates tested is due to high prevalence of mcr-1 in poultry production chains. More epidemiological studies of other European countries are urgently needed to assess German prevalence data.

To discern the relevance of ST648 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli as a putative new group of multiresistant and extraintestinal pathogenic strains in animals, its frequency, ESBL types, antimicrobial resistance patterns and virulence gene (VG) profiles should be determined and compared with ST131 strains from the same collection of strains. ESBL-producing E. coli isolates (n = 1152), consecutively sampled from predominantly dogs, cats and horses between 2008 and 2011, were assigned to a phylogenetic group by PCR. Partial multilocus sequence typing was performed for group D and B2 strains and strains presumed to be D-ST648 and B2-ST131 were fully typed. ESBL genes and extraintestinal pathogenic E. coli (ExPEC)-like VGs were characterized by PCR and sequence analysis and antimicrobial resistance was determined by broth dilution. Clonal analysis was done by PFGE. Forty (3.5%) ESBL-producing E. coli were determined as D-ST648, whereas B2-ST131 isolates occurred less frequently (2.8%). Although the predominant ESBL type in both groups was CTX-M-15 (72.5% versus 46.9%), ST648 strains from companion animals and horses displayed a lower variety of ESBL types (CTX-M-1, -3, -14, -15 and -61 versus CTX-M-1,-2,-14,-15,-27 and -55 and SHV-12). In contrast to ST131 strains, a higher proportion of ST648 strains showed resistance to most non-β-lactam antibiotics. Overall, VGs were less abundant in ST648 strains, although some strains had VG profiles comparable to those of ST131 strains. ExPEC-associated serotype O1:H6 was predominant (46.8%) among the ST648 strains. Some PFGE clusters comprised ST648 isolates from pets, horses and wild birds and humans included from previous studies. Our findings demonstrate that certain subgroups of E. coli D-ST648-CTX-M may represent a novel genotype that combines multiresistance, extraintestinal virulence and zoonotic potential.

The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and in vivo experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals.

The purpose of this longitudinal study was to describe the occurrence of antibiotic resistance in faecal Escherichia coli isolated from pigs between birth and slaughter and its association with antibiotic treatment. Four objectives were addressed: comparison of antibiotic resistance in isolates from a) treated vs. non-treated pigs, b) follow-up vs. initial samples of treated and non-treated pigs, c) pigs receiving treatments via different administration routes and d) sows and their piglets. Each comparison addressed the following antibiotic groups used for treatment: beta-lactams, tetracyclines, polymyxins and macrolides, and the susceptibility of E. coli isolates to the respective agents: ampicillin, tetracycline, colistin and azithromycin. Between 2014 and 2016, 406 focal animals from 29 commercial breeding herds were followed from birth to the end of the relevant fattening periods. All antibiotic treatments in these pigs were documented. Faecal samples were collected from the focal pigs once while suckling, once after weaning and three times during fattening, and from their dams once around farrowing. Escherichia coli isolated from these samples was tested for antibiotic susceptibility. In total, 264 animals from 19 breeding herds were treated with an antibiotic at least once during their lifetime. Beta-lactams, tetracyclines and colistin were used most frequently. Piglets were treated individually by injection (n = 108 treatments) or via drench (9); weaners via feed (192) or water (56) and fatteners via feed (30) or injection (15). Resistance to ampicillin and tetracycline in E. coli was already common prior to antibiotic treatment. Resistance proportions were higher for beta-lactam-, tetracycline-, colistin- and macrolide-treated pigs compared to untreated pigs at different sampling periods (p < 0.05; Fisher's exact test). In the logistic analysis, the difference was confirmed for beta-lactam-treated vs. untreated pigs. In E. coli from macrolide-untreated pigs, resistance to azithromycin was more frequent compared to pre-treatment values. Route of application did not affect rates of antibiotic resistance in the logistic analysis even though Fisher's exact test indicated associations for beta-lactams (feed/water vs. injection), tetracyclines (feed/water vs. non-treatment) and macrolides (tulathromycin-injection vs. tylosin in feed). Piglets were more likely to carry an E. coli resistant to ampicillin or azithromycin if their dams did so as well. Our results suggest further research on resistance effects by administration routes is required. Reducing antibiotic resistance in sows might lead to a lower level of beta-lactam or macrolide-resistant E. coli among their progeny. To preserve treatment options for bacterial infections, antibiotic use should be restricted to necessary cases.