Genomic characteristics of a carbapenem-resistant NDM-1-producing Aeromonas caviae isolate from extraintestinal infection.

Abstract

Objective: This study aims to clarify the drug resistance characteristics and genomic background of bile-derived NDM-1-producing Aeromonas caviae (A. caviae) isolate from extraintestinal infection, providing a theoretical basis for the prevention and control of clinical infections.

Methods: A bile-derived LHL25108073-A. caviae isolate (NCBI accession number: JBSUSV000000000) was chosen as the study focus. Through flight mass spectrometry, VITEK-2 drug susceptibility phenotype validation, and whole-genome sequencing, multi-point sequence typing (MLST), VFDB database, CARD database, PlasmidFinder 2.1 software, whole-genome alignment, plasmid synteny analysis, and plasmid conjugation assay were applied for an integrative analysis.

Results: This isolate was identified to be ST2281, a sequence type rarely reported across clinical, environmental, and agricultural sources, with a genome size of 4,885,524 bp and a GC content of 61.27%, carrying one chromosome (4,687,937 bp) and one drug-resistant plasmid (197,587 bp). A total of 58 high-confidence virulence genes were detected, covering common flagella, polar flagella, lateral flagella, type IV pili, Msh pili, type VI/II secretion system (T6SS/T2SS), heme-uptake systems, Endotoxins, and hemolysin, forming multiple pathogenic mechanisms. Among 14 drug resistance genes, the carbapenem-resistant NDM-1 gene was highly consistent with the genotype, only sensitive to a few drugs such as amikacin and aztreonam, based on the results of drug susceptibility tests. The drug-resistant plasmid could not autonomously conjugate and transfer due to the loss of the oriT site and was untypable by conventional plasmid typing. This plasmid shared 99-100% homology in the resistance core regions with two NDM-1-carrying A. caviae plasmids, pK433-NDM (OK287926) from sputum in Taizhou, Zhejiang, and pFAHZZU2447_NDM (CP100393) from bile in Zhengzhou, with identical bla _NDM-1 sequences. Genetic background analysis based on the genomes of 157 A. caviae isolates from China and neighboring regions identified that ST313 was the dominant sequence type (ST), which accounted for the largest proportion among in Chinese isolates.

Conclusion: This study characterizes the molecular profiles of an extraintestinal, bile-derived NDM-1-producing A. caviae isolate belonging to ST2281, validates its abundant reservoir of virulence genes and comprehensive multi-drug resistance mechanisms, and further reveals the potential risk of NDM-1 dissemination via alternative horizontal gene transfer pathways, such as transformation and transduction. Genomic evolutionary analysis reveals that although the ST2281 isolate identified in this study shares certain phylogenetic relatedness with the prevalent ST313 lineage in China at the housekeeping gene level, whole-genome SNP-based phylogenetic analysis confirms a substantial genetic distance between them. ST2281 represents an independent and rare genetic lineage with limited global prevalence, which warrants heightened vigilance against its concealed transmission and potential clinical infection risks. Collectively, these results offer crucial genomic evidence for molecular tracing, targeted clinical antimicrobial therapy, and epidemiological containment of carbapenem resistant A. caviae.