Complete genome sequence and comparative analysis of antibiotic resistance plasmids in carbapenem-resistant Escherichia coli from bovine mastitis

Abstract

The present study illustrates plasmidome and resistome profile of two carbapenem-resistant Escherichia coli isolates from milk of two different cows with recurrent subclinical mastitis from semi-urban region of Kolkata, India. Both E.coli strains (IVRI KOL CP4 and CM IVRI KOL-1) were sequenced and subreads were de novo assembled. Genomeanalysis and gene prediction data revealed the presence of multi-resistance plasmids conferring resistance to β-lactams,sulphonamide, tetracycline, trimethoprim, aminoglycosides even to the last-resort drugs carbapenem in both the strains. Thestrain IVRI Kol CP4 carried 3 plasmids: a 92840 bp IncFII plasmid (CP034254) with blaTEM-1B, blaNDM-5, sul-1, dfra12,rmtB, aadA2 genes; a 50882 bp IncI plasmid (CP034255) with blaCMY-42 gene and a 28652 bp undermined replicon typeplasmid (CP034256) having blaTEM-1B, mphA and tet(A) genes. Other strain CM IVRI Kol-1 also had 3 plasmids: a146286 bp IncFIA plasmid (CP033159) with blaTEM-1B, blaNDM-5, mph(A), sul1, tet(A), dfra12, rmtB, aadA2,and TetR genes; a 62055 bp IncI plasmid (CP033160) with two copy of blaCMY-42 and a 6346 bp plasmid (CP033161) ofunknown replicon type. Additionally, two plasmids (CP034254 and CP033159) harboured dfra12-aadA2 gene cassette inthe variable region of int1 conferring resistance to trimethoprim and aminoglycoside. We compare our five plasmidsequences with publicly available data to know the evolutionary picture of how multiple drug resistant (MDR) evolutionoccurs across the plasmids from different locations. This first-ever study on the whole genome sequence of NDM-5producing E. coli from bovine milk in India highlights the role of IncF type plasmid as a common vehicle for the carriageand spread of NDM-5 gene in food animals.