Genomic analysis of multiple drug resistant Escherichia coli ST58 causing urosepsis.

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Journal Article
Int J Antimicrob Agents, 2018
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ST58 phylogroup B1 E. coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multiple drug resistant ST58 Escherichia coli strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing. Both ST58 strains were clonal and were characterised as serotype O8:H25 phylogroup B1 and carried a complex resistance locus/loci (CRL) that featured an atypical class 1 integron with a dfrA5 (trimethoprim resistance) gene cassette followed by only 24 bp of the 3´-CS. CRL that carry this particular integron have been described previously in E. coli from cattle, pigs and humans in Australia. The integron abuts a copy of Tn6029, an IS26-flanked composite transposon encoding blaTEM, sul2, strAB genes that confer resistance to ampicillin, sulphathiazole and streptomycin respectively. The CRL resides within a novel Tn2610-like hybrid Tn1721/Tn21 transposon on an IncF, colV plasmid (pSDJ2009-52F) of 138,553 bp that encodes virulence associated genes (VAGs) implicated in life threatening ExPEC infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 from a patient with blood sepsis from a hospital in San Francisco. Our data suggest that extraintestinal infections caused by E. coli that carry colV-like plasmids, irrespective of their phylogroup or MLST, may pose a potential threat to human health, particularly to the elderly and the immunocompromised.
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