Horsing around: Escherichia coli ST1250 of equine origin harboring epidemic IncHI1/ST9 plasmid with bla CTX-M-1and an operon for short-chain fructooligosaccharide metabolism

Abstract

The relatedness of the equine-associated Escherichia coli strain ST1250 and its single- and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coli ST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing. An additional 25 draft genome assemblies of E. coli ST1250 and ST1250- SLV/DLV were obtained from the public databases. The isolates were compared for genomic features, virulence genes, clade structure, and plasmid content. The complete nucleotide sequences of eight IncHI1/ST9 plasmids and one IncHI1/ST2 plasmid were obtained using long-read sequencing by PacBio or MinION. In the collection of 79 isolates, only 10 were phylogenetically close (,8 single nucleotide polymorphisms [SNP]). The majority of isolates belonged to phylogroup B1 (73/79 [92.4%]) and carried blaCTX-M-1(58/79 [73.4%]). The plasmid content of the isolates was dominated by IncHI1 of ST9 (56/62 [90.3%]) and ST2 (6/62 [9.7%]), while 84.5% (49/58) of the blaCTX-M-1genes were associated with the presence of the IncHI1 replicon of ST9 and 6.9% (4/58) with the IncHI1 replicon of ST2 within the corresponding isolates. The operon for the utilization of short-chain fructooligosaccharides (the fos operon) was present in 55 of 79 (69.6%) isolates, and all of these carried IncHI1/ST9 plasmids. The eight complete IncHI1/ST9 plasmid sequences showed the presence of blaCTX-M-1and the fos operon within the same molecule. Sequences of IncHI1/ST9 plasmids were highly conserved (.98% similarity) regardless of country of origin and differed only in the structure and integration site of the multidrug resistance (MDR) region. E. coli ST1250 and ST1250-SLV/DLV are phylogenetically diverse strains associated with horses. A strong linkage of E. coli ST1250 with the epidemic multidrug resistance plasmid lineage IncHI1/ST9 carrying blaCTX-M-1and the fos operon was identified.