Genomic insights into a novel ST17306 Escherichia coli Isolate carrying tet(X4) from an infant with bronchopneumonia in China

Abstract

Objectives

Despite the widespread occurrence of tet(X4)-mediated tigecycline resistance in Escherichia coli from animal and environmental sources, its presence in human clinical isolates remains rare. In this study, we report the first whole-genome sequence of a E. coli isolate harboring tet(X4) and belonging to a novel sequence type, recovered from an infant in China.

Methods

The complete genome of E. coli Q65 was sequenced using a combination of Illumina NovaSeq 6000 and Oxford Nanopore MinION sequencing platforms. Functional annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP), and genomic features were further analyzed with a range of bioinformatics tools.

Results

The genome of E. coli strain Q65 is 5 442 192 bp in length and encodes 5089 proteins. Strain Q65 was classified as sequence type ST17306, a novel member of the ST69 clonal complex, and was assigned the serotype O17:H18. Q65 exhibited multidrug resistance, carrying 14 antimicrobial resistance genes, including tet(X4). The tet(X4) gene was located on a 192 048 bp hybrid plasmid belonging to the IncFIA(HI1)/IncHI1B(R27)/IncHI1A replicon types. A search of the NCBI database revealed similar tet(X4)-carrying hybrid plasmids present in various Enterobacteriaceae species, suggesting that such plasmids may play a key role in mediating the horizontal transfer of tet(X4).

Conclusion

This study presents the first complete genome sequence of a tet(X4)-positive, multidrug-resistant E. coli strain belonging to the novel sequence type ST17306, isolated from a Chinese infant with bronchopneumonia. Continuous global surveillance of the dissemination of tet(X4)-harboring strains is crucial to monitor and control the potential public health threat.