Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis

Abstract

Sequence type 58 (ST58) phylogroup B1 Escherichia 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 multidrug-resistant E. coli ST58 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 bla, sul2 and strAB genes that confer resistance to ampicillin, sulfathiazole 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 implicated in life-threatening extraintestinal pathogenic E. coli (ExPEC) infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 strain from a patient with blood sepsis from a hospital in San Francisco. These data suggest that extraintestinal infections caused by E. coli carrying ColV-like plasmids, irrespective of their phylogroup or ST, may pose a potential threat to human health, particularly to the elderly and immunocompromised.

Clinically Relevant Extended-Spectrum β-Lactamase–Producing Escherichia coli Isolates From Food Animals in South Korea

“…Clonal populations of ST410 are present in humans, companion animals, livestock, and the environment (Falgenhauer et al, 2016) and pose a high risk of causing ExPEC outbreaks in hospitals worldwide (Roer et al, 2018). ST10, ST58, and ST117 lineages have also been detected in both humans and food animals (Manges et al, 2015;McKinnon et al, 2018). In addition, ST38 and ST101 were present in chicken and pig samples analyzed in this study, respectively, which are more related to hospital-onset than to communityonset infections in South Korea (Yoo et al, 2013;Kim et al, 2016).…”

Whole Genome Sequencing of Escherichia coli From Store-Bought Produce

“…With regard to phylogeny, the dominance of phylogroup B1 was notable. Phylogroup B1 is typically considered to be an environmental lineage, however human extra-intestinal infections, including sepsis caused by B1 E. coli such as ST58 are reported (McKinnon et al, 2018). It is difficult to compare to other studies that sample different types of produce including leafy greens and vegetables, however phylogroup B1 similarly dominated 68 samples of E. coli from farmers' market lettuce in British Columbia (Wood et al, 2015).…”

Deadly Puppy Infection Caused by an MDR Escherichia coli O39 blaCTX–M–15, blaCMY–2, blaDHA–1, and aac(6)-Ib-cr – Positive in a Breeding Kennel in Central Italy

“…Escherichia coli O39:H21 has been rarely reported globally except for some reports relating it to be isolated from animals (Constantiniu, 2002). The CC ST155 has been identified in human, animal, and environmental samples as reported elsewhere (McKinnon et al, 2018). Furthermore, most of the reports indicate plasmid mediated production of CTX-M-15 within this ST (Chen et al, 2016;Mohsin et al, 2017;Blanco et al, 2019).…”