Global phylogenetic analysis and emergence of carbapenem-resistant Escherichia fergusonii carrying bla NDM-5 in clinic

Abstract

Background: Escherichia fergusonii, a newly recognized Enterobacterale member, has gained attention due to the bla _NDM-5 resistance gene found in animals. However, to date, no clinical isolates carrying this gene have been reported.

Methods: A carbapenem-resistant clinical isolate of E. fergusonii was obtained from a tertiary hospital in Zhejiang Province, China. Antimicrobial susceptibility testing, filter mating, whole-genome sequencing (WGS), plasmid stability, and fitness analysis were performed. Global phylogenetic relationships of E. fergusonii were analyzed using publicly available databases.

Results: E. fergusonii isolate EF21023765 exhibited resistance to most antibiotics, except tigecycline, colistin, and amikacin. WGS revealed bla _NDM-5 located on an IncX3 plasmid pEF-2-NDM with a genetic environment (Tn3-IS3000-IS5-bla _NDM-5-ble _MBL-trpF-dsbD-IS26-ISKox3), closely related to the previously reported plasmid pEC463-NDM5, a carbapenem resistance plasmid identified from a blood sample of Escherichia coli collected in 2016 at the same Chinese hospital. This finding demonstrates the 5-year persistence of related IncX3 plasmids across distinct Escherichia species, specifically from E. coli to E. fergusonii. The plasmid pEF-2-NDM demonstrated a relatively stable state in the plasmid stability experiment. Growth rate analysis revealed a significant fitness cost associated with the bla _NDM-5-carrying IncX3 plasmid, as evidenced by a 6 % higher growth rate in E. coli J53 compared to the transconjugant strain J53/pEF-2-NDM (1.00 ± 0.02 vs 0.94 ± 0.02). Phylogenetic analysis revealed significant genetic diversity in E. fergusonii, predominantly found in the UK, China, and the US, with livestock and avian as the primary hosts. In addition, ST12029 was the most prevalent sequence type.

Conclusion: To our knowledge, this is the first report of an IncX3 type plasmid carrying bla _NDM-5 from a clinical E. fergusonii isolate. Our findings not only reveal the cross-species transmission capability of E. fergusonii, but also underscore its potential as an emerging pathogen, highlighting the need for enhanced surveillance to monitor the spread of bla _NDM-5-producing isolates.

Keywords: Escherichia fergusonii; IncX3; Multi-drug resistant; NDM-5.

Fig. 1

Characterization of the plasmid pEF-2-NDM with closely related plasmids. (A) Structural depiction of plasmid pEF-2-NDM (CP137857), serving as a reference for alignment with pKW2‐1-NDM5 (CP102890)), pEC463-NDM5 (MG545911), and pNDM5_020031 (CP033399). (B) Schematic comparison of structural features of pEF-2-NDM(CP137857) with those of pKW2‐1-NDM5 (CP102890), pEC463-NDM5 (MG545911), and pNDM5_020031 (CP033399). Homologous regions are highlighted with dark gray shading and squares. Arrows denote open reading frames and their transcription directions: red for genes encoding antibiotic resistance, blue for transposons and integron-related genes, green for genes involved in replication, and other genes are represented by light-gray arrows. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Growth profiles of the recipient strain E. coli J53 and transconjugant E. coli J53/pEF-2-NDM across three measures: (A) Relative growth rate. (B) Growth curve. (C) Area under the growth curve. The graphed data reflect the average of three experiments, with the error bars representing the standard deviation. The significance of differences is indicated by **** for P < 0.0001, ** for P < 0.05 as assessed by t-tests.

Fig. 3

A phylogenetic tree of the 244 E. fergusonii strains was obtained from this study and from the NCBI database.

Fig. 4

Global distribution of 244 E. fergusonii strains collected in this study and the NCBI database.