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

Objectives: 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 bla_NDM-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). MLST, 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 (SNP)-based approach.

Results: The CRNMS3 genome comprises a chromosome and a 364,750 bp multidrug-resistant plasmid harboring bla_NDM-1. The strain displays broad β-lactam and carbapenem resistance and carries 12 antimicrobial resistance genes, most of which, including bla_NDM-1, are plasmid-encoded. Among 52 globally identified bla_NDM-1-positive C. portucalensis genomes, the majority were from China, spanning multiple sequence types, with ST677 being the most prevalent. Phylogenomic analysis revealed close genomic relatedness between human and environmental isolates within some ST677 strains, indicating potential ongoing transmission across ecological reservoirs.

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