Objectives: Food animals have been recognised as an important reservoir of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). This study reports the draft genome sequence of a bovine ESBL-Ec from Pakistan.
Methods: Genomic DNA from a bovine E. coli (PK-1421) was extracted and whole-genome sequencing was performed using an Illumina HiSeq 2500 platform. De novo genome assembly was performed using SPAdes v.3.9 and annotation of the assembled genome was performed using the DDBJ Fast Annotation and Submission Tool (DFAST). In silico tools from the Center for Genomic Epidemiology were used to find out for analysis of antimicrobial resistance genes, sequence type (ST), plasmid replicon type, serotype and phylogenetics.
Results: Escherichia coli strain PK-1421 showed multiple drug resistance. The draft genome was calculated at 4 869 610 bp, comprising a total of 131 contigs with a G + C content of 50.6% and 4487 protein-coding sequences. Escherichia coli PK-1412 belongs to ST58 and serotype O75:H9. A large number of antimicrobial resistance genes associated with resistance to β-lactams (blaCTX-M-15, blaTEM-1B), trimethoprim (dfrA14), aminoglycosides [aph(3')-lb, aph(6)-ld], sulfonamides (sul2), tetracycline (tetA), macrolides (mdfA) and quinolones (qnrS1) were detected. A conjugation experiment showed successful transfer of the blaCTX-M-15 gene to an E. coli J53 recipient strain. The phylogenetic tree indicated that ST58 E. coli PK-1421 was distant from other strains.
Conclusion: This is the first draft genome of an E. coli of bovine origin in Pakistan. The genome sequence presented here may be helpful to understand the genomic diversity and antimicrobial resistance potential of E. coli from large ruminants.
Keywords: Antimicrobial resistance; Cattle; ESBL; Escherichia coli; Food animals; Pakistan.
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