Genomic analysis reveals close genetic similarity between ESBL and other β-lactamase-producing E. coli isolates from humans and dogs, suggesting potential for inter-species transmission
Data files
Jul 28, 2025 version files 1.62 MB
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ESBL_Nanopore_Sequences_FASTA_Files.zip
567.39 KB
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ESBL_Nanopore_Sequences_GenBank_Files.zip
1.05 MB
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README.md
2.34 KB
Jul 28, 2025 version files 1.62 MB
-
ESBL_Nanopore_Sequences_FASTA_Files.zip
567.39 KB
-
ESBL_Nanopore_Sequences_GenBank_Files.zip
1.05 MB
-
README.md
2.37 KB
Abstract
Background: Extended-spectrum β-lactamase-(ESBL)-producing Enterobacteriaceae are emerging in hospital and community settings as important causes of urinary tract infections. These plasmid-mediated enzymes have been identified in human and dog hosts, with blaCTX-M variants~~ being the most prevalent ESBLs worldwide. Our objective was to identify horizontal gene transfer (HGT) events amongst human and dog-derived ESBL-producing bacteria by examining the genetic relatedness of plasmid and bacterial whole genome sequences (WGS) associated with ESBLs and other β-lactamase genes. 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.
Results: Of 149 plasmids collected from humans (n = 125) and dogs (n = 24), 111 (74.5%) carried class A ESBL genes with blaCTX-M-14 (31.6%) predominating in human-derived plasmids and blaCTX-M-1 in dog-derived plasmids (29.6%). In addition, ESBLs and other β-lactamase genes, including blaTEM-1, were also identified in both populations. pMLST showed that IncF, IncI1, and IncN plasmids were the main groups contributing to the dissemination of ESBLs amongst human and dog populations. Neighbor-joining analysis revealed clustering of human and dog-derived plasmids carrying similar ESBL genes as well as other antibiotic-resistant genes. The maximum-likelihood tree revealed a high predominance of ST131 carried by E. coli serotypes O25:H4 in humans but not dogs. Virulence gene analysis revealed that ESBL-producing bacteria were not limited to UPEC.
Conclusions: The presence of conserved ESBLs, other β-lactamase genes, and E. coli clones in both humans and dogs highlights widespread circulation of shared resistance elements. These findings support the need for broader One Health surveillance, particularly involving companion animals, to better track and mitigate ARG spread in community settings.
Dataset DOI: 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/). 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.