Annals of Clinical Microbiology and Antimicrobials (Apr 2024)

Whole-genome sequencing of clinical isolates of Citrobacter Europaeus in China carrying bla OXA−48 and bla NDM−1

  • Jie Ma,
  • Ranran Xu,
  • Wanxiang Li,
  • Mi Liu,
  • Xiaomei Ding

DOI
https://doi.org/10.1186/s12941-024-00699-y
Journal volume & issue
Vol. 23, no. 1
pp. 1 – 9

Abstract

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Abstract Objective To analyze the clinical infection characteristics and genetic environments of resistance genes in carbapenem-resistant Citrobacter europaeus using whole-genome sequencing. Methods The susceptibility of two clinical isolates of C. europaeus (WF0003 and WF1643) to 24 antimicrobial agents was assessed using the BD Phoenix™ M50 System and Kirby-Bauer (K-B) disk-diffusion method. Whole-genome sequencing was performed on the Illumina and Nanopore platforms, and ABRicate software was used to predict resistance and virulence genes of carbapenem-resistant C. europaeus. The characteristics of plasmids carrying carbapenem-resistance genes and their genetic environments were analyzed. Single nucleotide polymorphisms were used to construct a phylogenetic tree to analyze the homology of these two C. europaeus strains with ten strains of C. europaeus in the NCBI database. Results The two strains of carbapenem-resistant C. europaeus are resistant to various antimicrobial agents, particularly carbapenems and β-lactams. WF0003 carries bla NDM− 1, which is located on an IncX3 plasmid that has high homology to the pNDM-HN380 plasmid. bla NDM− 1 is located on a truncated Tn125. It differs from Tn125 by the insertion of IS5 in the upstream ISAba125 and the deletion of the downstream ISAba125, which is replaced by IS26. WF1643 carries bla OXA− 48 in a Tn1999 transposon on the IncL/M plasmid, carrying only that single drug resistance gene. Homology analysis of these two strains of C. europaeus with ten C. europaeus strains in the NCBI database revealed that the 12 strains can be classified into three clades, with both WF0003 and WF1643 in the B clade. Conclusion To the best of our knowledge, this is the first study to report an IncX3 plasmid carrying bla NDM− 1 in C. europaeus in China. C. europaeus strains harboring carbapenem-resistance genes are concerning in relation to the spread of antimicrobial resistance, and the presence of carbapenem-resistance genes in C. europaeus should be continuously monitored.

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