DOI: 10.5061/dryad.zw3r228kp
title: Genomic analysis reveals close genetic similarity between ESBL-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission

description: 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) and WGS (N = 109) from the National Center for
 Biotechnology Information (NCBI) database (accessed August 2022-July
 2023). The Bacterial and Viral Bioinformatic Resource Center (BV-BRC),
 Comparative Antibiotic Resistance Database (CARD), plasmid Multi-Locus
 Sequence Typing (pMLST), Center for Genomic Epidemiology (CGE), and
 Multi-Locus Sequence Typing (MLST) were used to analyze plasmid and whole
 genome sequences. Phylogenetic analysis was also performed on plasmid and
 whole genome sequences. Results: Of 149 plasmids collected from humans (n
 = 125) and dogs (n = 24), 110(73.8%) were class A ESBLs with blaCTX-M-14
 (32%), and blaTEM-1 (32%), predominant among the human population and
 blaCTX-M-1 (31%) and blaTEM-1 (27%) among the dog population. pMLST showed
 that IncF, IncI1, and IncN plasmids were the main groups contributing to
 dissemination of ESBLs amongst human and dog populations. Genome
 annotations revealed that plasmids carrying ESBLs harbored genes
 responsible for HGT by conjugation. Neighbor-joining cluster analysis
 showed human and dog-derived plasmids do share ESBL genes and other
 antibiotic-resistant genes(ARGs). The maximum-likelihood tree revealed a
 high predominance of ST-131 carried by E. coli serotypes O25:H4 amongst
 humans and dogs. Virulence gene identification showed that UPEC strains
 were not the only carriers of ESBL-producing bacteria. Discussion: Results
 revealed evidence of cross-species transmission of ESBLs between humans
 and dogs at plasmid and E. coli clonal levels, underscoring the need to
 increase surveillance of ARGs in the community to mitigate ESBL
 transmission in community settings.
description: # 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 name. Following the underscore if the
 basepair size of the plasmid. The last portion of the file name just
 respresents plasmid DNA. The FASTA folder contains the sequence files in
 FASTA format that you should be able to open in a text editor application
 of your choice. #### File: ESBL_Nanopore_Sequences_GenBank_Files.zip
 **Description:** CTX(Number) represents the deidentifiable sample name.
 Following the underscore if the basepair size of the plasmid. The last
 portion of the file name just represents plasmid DNA. The GenBank files
 contain the annotations of the plasmid sequences that you should be able
 to open up in a text editor application of your choice or SnapGene. ##
 Code/software SnapGene Viewer 8.0 can be used to view sequence maps with
 genes when opening the GenBank files. ## Human subjects data 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.