Identification and genomic characterization of Enterobacter kobei ST56 co-carrying mcr-9, blaNDM-1, and blaCTX−M-3 resistance genes

Objectives

This study reports the complete genome sequence of Enterobacter kobei (E. kobei) L5089hy of ST56 isolated from China, carrying mcr-9, bla_NDM-1, and bla_CTX−M-3. It aims to investigate its molecular characteristics and antibiotic resistance mechanisms.

Methods

The E. kobei strain was isolated from the faecal sample of an in-patient in a hospital in Hangzhou, China. Whole-genome sequencing was performed using Oxford Nanopore technology, and the genome was assembled with Unicycler version 0.4.7. The strain was identified by 16S rRNA sequencing. The genome sequence was uploaded to ResFinder version 4.1 to identify antimicrobial resistance genes (ARGs). Multilocus sequence typing (MLST) was used to determine the sequence type of the strain. Genome annotation and plasmid type identification were carried out with the aid of the Proksee and PlasmidFinder databases. An antimicrobial susceptibility test (AST) was conducted on the strain. Circular mapping of multiple plasmid comparisons was drawn by BLAST Ring Image.

Results

E. kobei L5089hy consists of 1 chromosome and 5 plasmids. The mcr-9 gene is located on the chromosome, bla_NDM-1 is on the IncFII(Yp) plasmid, and bla_CTX−M-3 is present on both the chromosome and the IncN2 plasmid. The MLST typing result shows that L5089hy is of the ST56 type. AST indicates that the strain is resistant to a variety of antibiotics. However, despite carrying the mcr-9 gene, it is sensitive to colistin (minimum inhibitory concentration = 1 μg/mL).

Conclusions

This study emphasizes the necessity for monitoring E. kobei© 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.