Inherent colistin resistance in genogroups of the Enterobacter cloacae complex: epidemiological, genetic and biochemical analysis from the BSAC Resistance Surveillance Programme.

BACKGROUND: Polymyxins have re-entered use against problem Gram-negative bacteria. Resistance rates are uncertain, with estimates confounded by selective testing. METHODS: The BSAC Resistance Surveillance Programme has routinely tested colistin since 2010; we reviewed data up to 2017 for relevant Enterobacterales (n = 10 914). Unexpectedly frequent resistance was seen among the Enterobacter cloacae complex isolates (n = 1749); for these, we investigated relationships to species, genome, carbon source utilization and LPS structure. RESULTS: Annual colistin resistance rates among E. cloacae complex isolates were 4.4%-20%, with a rising trend among bloodstream organisms; in contrast, annual rates for Escherichia coli and Klebsiella spp. (including K. aerogenes) generally remained <2%. WGS split the E. cloacae complex isolates into seven genogroup clusters, designated A-G. Among isolates assigned to genogroups A-D, 47/50 sequenced were colistin resistant, and many of those belonging to genogroups A-C identified as E. asburiae. Isolates belonging to genogroups E-G consistently identified as E. cloacae and were rarely (only 3/45 representatives sequenced) colistin resistant. Genogroups F and G, the predominant colistin-susceptible clusters, were metabolically distinct from other clusters, notably regarding utilization or not of l-fucose, formic acid, d-serine, adonitol, myo-inositol, l-lyxose and polysorbates. LPS from resistant organisms grown without colistin pressure lacked substitutions with 4-amino-arabinose or ethanolamine but was more structurally complex, with more molecular species present. CONCLUSIONS: Colistin resistance is frequent in the E. cloacae complex and increasing among bloodstream isolates. It is associated with: (i) particular genomic and metabolic clusters; (ii) identification as E. asburiae; and (iii) with more complex LPS architectures.

Antimicrobial susceptibility of enterococci recovered from healthy cattle, pigs and chickens in nine EU countries (EASSA Study) to critically important antibiotics.

The European Antimicrobial Susceptibility Surveillance in Animals (EASSA) program collects zoonotic and commensal bacteria from food-producing animals at slaughter and tracks their susceptibility to medically important antibiotics. Results of commensal enterococci species (2013-2014) are presented here. Intestinal content from cattle, pigs and chickens were randomly sampled (5-6 countries/host; ≥4 abattoirs/country; 1 sample/animal/farm) for isolation of enterococci, MICs of 9 antibiotics were assessed by CLSI agar dilution in a central laboratory. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation. In total 960 Enterococcus faecium and 779 Enterococcus faecalis strains were recovered. Seven porcine E. faecium/faecalis strains of Spanish origin were resistant to linezolid. One avian E. faecalis and one porcine E. faecium strain were non-wild type (MICs 8 mg/L) to daptomycin. Clinical vancomycin resistance was absent; 2 poultry E. faecium and 1 bovine E. faecalis strains were non-wild type, all with MICs of 8 mg/L. None of the strains tested were clinically resistant to tigecycline. Little clinical resistance to ampicillin or gentamicin was observed. Clinical resistance of E. faecium to quinupristin/dalfopristin was slightly higher (2.2-12.0%) but 61.9-83.2% of the strains were classified as non-wild type. Very high percentages resistance to tetracycline (67.4-78.3%) and to erythromycin (27.1-57.0%) were noted for both E. faecium and E. faecalis in pigs and chickens compared to cattle (5.2-30.4 and 9.0-10.4%, respectively). Similar non-wild type results were observed for E. hirae (n = 557), E. durans (n = 218) and E. casseliflavus (n = 55) including percentage non-wild type for daptomycin, linezolid, tigecycline being absent and for vancomycin low. For these species percentage non-wild type to erythromycin was lower as compared to E. faecalis/faecium. This pan-EU survey shows high variability in antibiotic susceptibility of commensal enterococci from healthy food animals. Clinical resistance to critically important antibiotics for human medicine was absent or low, except for erythromycin.