Genomic insights into multidrug-resistant Enterobacter hormaechei isolates from seafood at retail carrying the mcr-9 gene and other resistance determinants on IncHI2 plasmids

Abstract

Objectives

We aimed to characterise the genomic features of two multidrug-resistant (MDR) isolates from retail seafood samples.

Methods

Antimicrobial susceptibility was determined by minimum inhibitory concentration (MIC) tests. Genome sequences were obtained by hybrid sequences of short and long.

Results

The two MDR (ampicillin, cefotaxime, ciprofloxacin, ceftazidime, nalidixic acid, gentamicin, tetracycline, sulfamethoxazole, cefoxitin, and trimethoprim) Enterobacter hormaechei (E. hormaechei) isolates belonged to ST114. Nineteen antibiotic resistance genes (ARGs), including 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 was present in the qseB. Virulence genes of T6SS or involved in motility were identified in both genomes. Comparison of mcr-9 plasmids allowed us to identify similar plasmids in the isolates from Italy and in the five best hits of the PLSDB database, with some regions of difference in the MDR region. A genome cluster analysis grouped our isolates into the same clade of ST114 E. hormaechei isolated from humans in Guadeloupe in 2018 and Switzerland in 2019, most of which harboured an IncHI2 replicon but not the mcr-9 gene.

Conclusions

The finding of MDR E. hormaechei in seafood, carrying the mcr-9 and other resistance determinants on IncHI2 plasmids, enhances our understanding of antimicrobial resistance (AMR) and highlights the importance of gaining more data on the occurrence and circulation of AMR and ARGs in aquatic environments, in order to better understand sources, transmission routes, and evolution of AMR mechanisms.