Genomic analysis reveals close genetic similarity between ESBL-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission

Introduction: Extended-spectrum β-lactamase-(ESBL) producing Enterobacteriaceae are emerging in hospital and community settings as important causes of urinary tract infections. This group of plasmid-mediated enzymes has been identified primarily in human and dog hosts with blaCTX-M’s being most prevalent ESBLs worldwide. Our objective was to identify horizontal gene transfer(HGT) events amongst human and dog-derived ESBL-producing bacteria by examining genetic relatedness of plasmid and bacterial whole genome sequences(WGS) associated with ESBLs. By understanding genetic relatedness, we aimed to provide insight into transmission dynamics of ESBLs and antibiotic resistance among humans and dogs in community-acquired settings.
Methods: DNA was extracted from 16 Uropathogenic E. coli (UPEC) strains from humans to determine plasmid sequences using Nanopore Technology. Plasmid sequences acquired in Nanopore were used as references to collect ESBL-producing plasmid sequences (N = 149) an..., , # Genomic analysis reveals close genetic similarity between ESBL-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission

Dataset DOI: [10.5061/dryad.zw3r228kp](10.5061/dryad.zw3r228kp)

## Description of the data and file structure

All sequence files are extracted plasmid DNA from isolated E. coli from human patients with UTI seen at a medical center. Plasmid DNA was isolated using the Qiagen Plasmid Midi Kit manufacturer’s protocols (Qiagen, Catalogue. No. / ID: 12143) then sequenced using Oxford Nanopore Technology GridION flow to get long reads.

Long reads of these files were annotated using online genomic annotation tool RAST Server 3.35.5. and the Bacterial and Viral Bioinformatic Resource Center (BV-BRC)([https://www.bv-brc.org/](https://www.bv-brc.org/)). Plasmids were viewed using SnapGene

### Files and variables

#### File: ESBL_Nanopore_Sequences_FASTA_Files.zip

**Description:** CTX(Number) represents the deidentifiable sample ..., Patients at the medical center were recruited between 2006 and 2009 a parent study approved under ethics protocol GIRBA 2212. We used de-identified genome sequences derived from patient isolates, including individuals with urinary tract infections. No identifiable clinical information was accessed, and all sequencing data were fully anonymized prior to analysis. As such, the use of these de-identified genomic sequences is considered exempt from Institutional Review Board (IRB) review at Michigan State University.