Sequences of antimicrobial resistant Escherichia coli and other Enterobacteriaceae isolated from retail seafood in Italy
We evaluated Escherichia coli as an indicator of antimicrobial resistance (AMR) in retail seafood, investigating its occurrence in 7 categories of raw seafood (422 samples) from retail markets in Central Italy. Overall, E. coli was cultured from 55 (13%) samples, with a higher isolation rates in bivalves (23%; Odds Ratios p =0.022) and crustaceans (20%; Odds Ratios p=0.046 %). The occurrence of Extended-ß-Lactamase (ESBL)-, AmpC- and carbapenemase- producing Enterobacteriaceae was also determined. Carbapenemase-producing Enterobacteriaceae were not isolated on MacConkey agar supplemented with ertapenem. Cefotaxime-resistant E. coli were cultured on MacConkey agar supplemented with cefotaxime  from 7 (2%) samples. These were characterised by whole genome sequencing (WGS) and antimicrobial susceptibility testing. Of these, 4 (0.9%), 2 (0.5%) and 1 (0.2%) harboured ESBL-, AmpC-, ESBL- and AmpC- producing E. coli isolatescoding genes, respectively. The highest prevalence was found in bivalves (7%; 4 of 61). Phylogroup A was the most prevalent (3 out of 7). ESBL- and ESBL-/AmpC- producing E. coli isolates were multidrug-resistant. The blaCTX-M-15 gene was prevalent (3 out of 5). The blaCYM-2 gene was present in two AmpC isolates. Noteworthy, from a sample of frozen shrimps we isolated an ESBL-producing Atlantibacter hermannii carrying a blaCTX-M-55 gene. By in silico analysis, contigs harboring ESBL- or AmpC- genes were predicted as plasmid-derived sequences. AmpC-producers other than E. coli (Citrobacter spp. and Enterobacter spp.) were isolated from 15 (3%) seafood samples.  The prevalence of cefotaxime-resistant E. coli was 1% (2 of 176), 2% (5 of 246), 2% (5 of 248) and 1% (2 of 174) in wild-caught, farm-raised, fresh and frozen seafood samples, respectively. No association was found considering farm-raised or wild-caught (OR p = 0.4773) or frozen or fresh (OR p = 0.4894) samples. This study provided supporting evidence for E. coli as a candidate indicator of AMR in retail bivalves and crustaceans. Moreover, the occurrence of ESBL-producing E. coli in seafood, particularly bivalves, carrying CTX-M-encoding genes on plasmids supports the need for ESBL surveillance in this seafood commodity.