Genomic analysis reveals close genetic similarity between ESBL-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
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README.md
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Abstract
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.
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.