Genomic characterization and epidemiological insights into a blaNDM-1-harbouring Citrobacter portucalensis strain isolated from hospital wastewater in China.

OBJECTIVE

Citrobacter portucalensis is an emerging pathogen of growing clinical and environmental concern. Here, we report the genomic features of a carbapenem-resistant C. portucalensis strain carrying the blaNDM-1 gene on an IncHI2A-IncHI2-RepA plasmid, isolated from the wastewater of a tertiary hospital in China.

METHODS

Antimicrobial susceptibility testing was performed using the VITEK2 Gram-negative card and broth microdilution per CLSI guidelines. Illumina NovaSeq short reads and Nanopore MinION long reads were jointly used for sequencing, and hybrid assembly was generated with Unicycler (v0.4.7). Multilocus sequence typing, plasmid replicon typing, and ARG detection were conducted using Pathogenwatch and ABRicate (v1.0.1). Phylogenetic analysis of CRNMS3 alongside 52 publicly available C. portucalensis genomes was conducted using a core-genome single-nucleotide polymorphism-based approach.

RESULTS

The CRNMS3 genome comprises a chromosome and a 364 750 bp multidrug-resistant plasmid harbouring blaNDM-1. The strain displays broad β-lactam and carbapenem resistance and carries 12 antimicrobial resistance genes, most of which, including blaNDM-1, are plasmid-encoded. Among 52 globally identified blaNDM-1-positive C. portucalensis genomes, the majority were from China, spanning multiple sequence types, with sequence type 677 being the most prevalent. Phylogenomic analysis revealed close genomic relatedness between human and environmental isolates within some sequence type 677 strains, indicating potential ongoing transmission across ecological reservoirs.

CONCLUSIONS

In summary, we report a blaNDM-1-carrying C. portucalensis strain isolated from hospital wastewater in China and analyse the global prevalence of blaNDM-1-positive C. portucalensis, highlighting its potential for environmental dissemination and the urgent need for coordinated measures to curb blaNDM-1 spread.