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

Mianzhi Yao; Qianhui Zhu; Jin Zou; Abebe Mekuria Shenkutie; Songnian Hu; Jiuxin Qu; Zilong He; Polly H M Leung

doi:10.3389/fmicb.2022.845045

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

Front Microbiol. 2022 Apr 11:13:845045. doi: 10.3389/fmicb.2022.845045. eCollection 2022.

Authors

Mianzhi Yao¹, Qianhui Zhu^{2

3}, Jin Zou⁴, Abebe Mekuria Shenkutie^{1

5}, Songnian Hu^{2

3}, Jiuxin Qu⁴, Zilong He^{6

7}, Polly H M Leung¹

Affiliations

¹ Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China.
² State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
³ College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
⁴ Department of Clinical Laboratory, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, National Clinical Research Center for Infectious Diseases, Shenzhen, China.
⁵ Department of Microbiology, Immunology, and Parasitology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.
⁶ Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China.
⁷ School of Engineering Medicine, Beihang University, Beijing, China.

Abstract

Escherichia coli sequence type 405 is an emerging antibiotic-resistant clonal group associated with the global dissemination of extended-spectrum β-lactamase-producing E. coli. In this study, we report the genome assembly and characterization of a uropathogenic E. coli 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 bla _CTX-M-15. 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 Escherichia 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 bla _CTX-M-24. In contrast to pSZESBLEC201-1, pSZESBLEC201-3 retains its full active conjugation machinery and can be transferred via 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 bla _CTX-M genes and the genome plasticity of this clonal group. The coexistence of two bla _CTX-M variants in the same strain increases the risk of the emergence of new bla _CTX-M variants. Further studies on phage-like plasmids are necessary to provide insights into their biological activities and clinical significance.

Keywords: blaCTX-M; comparative genomics; mobile genetic elements; plasmids; uropathogenic Escherichia coli.