Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and blaNDM-5 on IncFIA/IncFIB/IncFII/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne blaCMY-2 from Egypt

Abstract

The accelerated dispersion of multidrug-resistant (MDR) Escherichia coli due to the production of extended-spectrum β-lactamases (ESBLs) or AmpC enzymes has been noted in Egypt, presenting a serious treatment challenge. In this study, we investigate the prevalence of ESBLs and AmpC enzymes among 48 E. coli isolates collected from patients with urinary tract infections admitted to a teaching hospital in Alexandria. Phenotypic and genotypic methods of detection are conducted. Isolates producing both enzymes are tested for the mobilization of their genes by a broth mating experiment. Whole genome sequencing (WGS) is performed for isolate EC13655. The results indicate that 80% of the isolates are MDR, among which 52% and 13% were ESBL and AmpC producers, respectively. Conjugation experiments fail to show the mobilization of blaCMY-2 in EC13655, which was chosen for WGS. In silico analysis reveals that the isolate belongs to a ST410-H24Rx high-risk clone. It coharbors the ESBL-encoding genes blaCTX-M-15, blaTEM-1, and blaOXA-1 on an IncFIA/IncFIB/IncFII/IncQ1 multireplicon plasmid. The chromosomal location of blaCMY-2 is detected with a flanking upstream copy of ISEcp1. This chromosomal integration of blaCMY-2 establishes the stable maintenance of the gene and thus, necessitates an imperative local surveillance to reduce further spread of such strains in different clinical settings.

A clinical KPC-producing Klebsiella michiganensis strain carrying IncFII/IncFIA (HI1)/IncFIB (K) multiple replicon plasmid

“…The IncFII/IncFIA(HI1)/IncFIB(K)-type plasmid has rarely been reported globally. Two bla NDM-5 -carrying plasmids with IncFIA/IncFIB/IncFII/IncQ1 replicons have been found in previous studies ( Hirabayashi et al, 2021 ; Mohamed et al, 2022 ). Meanwhile, some researchers discovered multiple resistance genes in an IncFII/IncFIA(HI1)/IncFIB(K) multiple replicon plasmid in E. coli ( Hayashi et al, 2020 ; Marchetti et al, 2020 ; Simner et al, 2022 ).…”

“…The IncFII/IncFIA(HI1)/IncFIB(K)-type plasmid has rarely been reported globally. Two bla NDM-5 -carrying plasmids with IncFIA/IncFIB/IncFII/IncQ1 replicons have been found in previous studies (Hirabayashi et al, 2021;Mohamed et al, 2022). Meanwhile, some researchers discovered multiple Phylogenetic tree of 22 Klebsiella michiganensis strains carrying bla KPC-2 .…”

Correlation between antimicrobial resistance, biofilm formation, and virulence determinants in uropathogenic Escherichia coli from Egyptian hospital

“…In the present study, 90% of the tested UPEC isolates were MDR/XDR. Regarding other regions in Egypt, Hassuna et al found that 62% of UPEC isolated in Upper Egypt were MDR in 2020 [ 56 ], and a recent study published in 2022 by Mohamed et al reported that 80% of UPEC were MDR in Alexandria governorate, Egypt [ 57 ]. These results reflect the increasing trend of AMR in Egypt, which is strongly linked to poor patient compliance, self-medication, and the availability of antibiotics as over-the-counter medications [ 58 ].…”

Investigating Possible Interspecies Communication of Plasmids Associated with Transfer of Third-Generation Cephalosporin, Quinolone, and Colistin Resistance Between Simultaneously Isolated Escherichia Coli and Klebsiella Pneumoniae

“…All the four plasmid types were common in Enterobacteriales , especially in E. coli and K. pneumoniae isolates. For the IncFIB/FII/Q1-type plasmid, it could be harbored by E. coli isolates collected from patients with urinary tract infections ( 20 ). As for the IncFIB/FII-type plasmid, it was usually harbored by K. pneumoniae isolates, which were isolated from sputum, infected chronic wounds, or human feces ( 21 – 23 ).…”