Multi-drug resistant Enterobacter hormaechei strains from seafood

Enterobacter hormaechei is an important opportunistic pathogen. We aimed to characterise the genomic features of two multidrug-resistant (MDR) isolates from retail seafood samples. Antimicrobial susceptibility was determined by the minimum inhibitory concentration. Genome sequences obtained by hybrid sequences of short and long reads were analysed using bioinformatics tools The two MDR (ampicillin, cefotaxime, ciprofloxacin, ceftazidime, nalidixic acid, gentamicin, tetracycline, sulfamethoxazole, cefoxitin and trimethoprim) E. hormaechei isolates belonged to ST114. Nineteen antibiotic resistance genes (ARGs), including the mcr-9, were identified in the genomes. The mcr-9 and other resistance determinants were on an IncHI2 plasmid. Sequence analysis showed mutations in genes implicated in colistin resistance, of which a non-conservative one present in the qseB. Virulence genes of T6SS or involved in motility were identified in both genomes. Comparison of mcr-9 plasmids allowed to identify similar plasmids in the strains isolated in Italy and in the 5 best hits of the PLSDB database, with some regions of difference in the MDR regionA genome cluster analysis grouped our strains into the same clade of ST114 human strains, most of which harboured an IncHI2 replicon but not the mcr-9 gene. The finding of MDR E. hormaechei strains in seafood, carrying the mcr-9 and other resistance determinants on IncHI2 plasmids, enhances our understanding of AMR and highlights the importance to gain more data on occurrence and circulation of AMR and ARGs in aquatic environments, in order to better understand sources, transmission routes and evolution of AMR mechanisms.