AUTHOR=Yao Mianzhi , Zhu Qianhui , Zou Jin , Shenkutie Abebe Mekuria , Hu Songnian , Qu Jiuxin , He Zilong , Leung Polly H. M. 

TITLE=Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring blaCTX-M-15-Encoding IncFIA-FIB Plasmid, blaCTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.845045

DOI=10.3389/fmicb.2022.845045

ISSN=1664-302X

ABSTRACT=<p><italic>Escherichia coli</italic> sequence type 405 is an emerging antibiotic-resistant clonal group associated with the global dissemination of extended-spectrum β-lactamase-producing <italic>E. coli</italic>. In this study, we report the genome assembly and characterization of a uropathogenic <italic>E. coli</italic> ST405 strain, SZESBLEC201, based on long and short reads obtained from the Nanopore and Illumina sequencing platforms, respectively. Whole-genome sequencing revealed that SZESBLEC201 harbors a 5,020,403 bp chromosome and three plasmids, namely, pSZESBLEC201-1, pSZESBLEC201-2, and pSZESBLEC201-3. pSZESBLEC201-1 (111,621 bp) belongs to the IncFIA-FIB type and harbors <italic>bla</italic><sub>CTX-M-15</sub>. However, this plasmid does not harbor conjugative transfer-associated genes, rendering pSZESBLEC201-1 unable to be conjugatively transferred. pSZESBLEC201-2 (95,138 bp) is a phage-like plasmid that shows a strong genome synteny with <italic>Escherichia</italic> phage P1 but with the absence of mobile genetic elements and some regulatory genes. pSZESBLEC201-3 (92,865 bp) belongs to the IncI1 type and carries <italic>bla</italic><sub>CTX-M-24</sub>. In contrast to pSZESBLEC201-1, pSZESBLEC201-3 retains its full active conjugation machinery and can be transferred <italic>via</italic> conjugation. The genetic features of the genome show that the SZESBLEC201 has a unique virulence pattern compared with genetically similar strains found in the same country (China). The plasmid backbones exhibit a high degree of similarity to those of geographically distant isolates, highlighting the global spread of <italic>bla</italic><sub>CTX-M</sub> genes and the genome plasticity of this clonal group. The coexistence of two <italic>bla</italic><sub>CTX-M</sub> variants in the same strain increases the risk of the emergence of new <italic>bla</italic><sub>CTX-M</sub> variants. Further studies on phage-like plasmids are necessary to provide insights into their biological activities and clinical significance.</p>