Dissemination and persistence of extended-spectrum cephalosporin- resistance encoding IncI1-blaCTXM-1 plasmid among Escherichia coli in pigs

This study investigated the ecology, epidemiology and plasmid characteristics of extended-spectrum cephalosporin (ESC)-resistant E. coli in healthy pigs over a period of 4 years (2013–2016) following the withdrawal of ESCs. High carriage rates of ESC-resistant E. coli were demonstrated in 2013 (86.6%) and 2014 (83.3%), compared to 2015 (22%) and 2016 (8.5%). ESC resistance identified among E. coli isolates was attributed to the carriage of an IncI1 ST-3 plasmid (pCTXM1-MU2) encoding blaCTXM-1. Genomic characterisation of selected E. coli isolates (n = 61) identified plasmid movement into multiple commensal E. coli (n = 22 STs). Major STs included ST10, ST5440, ST453, ST2514 and ST23. A subset of the isolates belong to the atypical enteropathogenic E. coli (aEPEC) pathotype that harboured multiple LEE pathogenic islands. pCTXM1-MU2 was similar (99% nt identity) to IncI1-ST3 plasmids reported from Europe, encoded resistance to aminoglycosides, sulphonamides and trimethoprim, and carried colicin Ib. pCTXM1-MU2 appears to be highly stable and readily transferable. This study demonstrates that ESC resistance may persist for a protracted period following removal of direct selection pressure, resulting in the emergence of ESC-resistance in both commensal E. coli and aEPEC isolates of potential significance to human and animal health.This study was funded by the DVM clinical research programme, University of Adelaide and Small Grant Scheme of School of Veterinary Life Sciences, Murdoch University

12Files_Platygonus_compressus_SeqData_Filtered_Collapsed.fastq

FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 12 Platygonus compressus enriched genomic libraries. See main publication for full details on data processing

3Files_Pecari_tajacu_SeqData_Filtered_Collapsed.fastq

FASTQ files containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the 3 Pecari tajacu enriched genomic libraries. See main publication for full details on data processing

Tayassu_pecari_KY987556_SeqData_Filtered_Collapsed.fastq

FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Tayassu pecari enriched genomic library. See main publication for full details on data processing

Catagonus_wagneri_KY987545_SeqData_Filtered_Collapsed.fastq

FASTQ file containing filtered, de-mulitplexed, and collapsed HiSeq (Illumina) sequencing reads corresponding to the Catagonus wagneri enriched genomic library. See main publication for full details on data processing

PartitionFinder_files

Input & output from PartitionFinder analyses

RAxML_files

RAxML files, including input alignment & partition file and final tre

Consensus sequence from sample ACAD2865

Consensus sequence generated in Geneious. Final sequence too fragmentary for upload to GenBank due to poor DNA preservation. This sequence was excluded from most analyses

BEAST_files

BEAST files, including input .xml and final maximum clade credibility tree

HTS_pipeline_scripts

Scripts for analysis of high-throughput sequencing data