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

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  • Adam Valcek
  • Petra Sismova
  • Kristina Nesporova
  • Søren Overballe-Petersen
  • Ibrahim Bitar
  • Ivana Jamborova
  • Arie Kant
  • Jaroslav Hrabak
  • Jaap A. Wagenaar
  • Jean Yves Madec
  • Damborg, Peter Panduro
  • Engeline Van Duijkeren
  • Christa Ewers
  • Joost Hordijk
  • Henrik Hasman
  • Michael S.M. Brouwer
  • Monika Dolejska

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.

OriginalsprogEngelsk
Artikelnummere02556-20
TidsskriftAntimicrobial Agents and Chemotherapy
Vol/bind65
Udgave nummer5
ISSN0066-4804
DOI
StatusUdgivet - 2021

Bibliografisk note

Funding Information:
The study was funded mainly by the Czech Science Foundation (award 18-23532S to M.D.). P.S. received funds from the Internal Grant Agency of the University of Veterinary and Pharmaceutical Sciences Brno (award 204/2020/FVHE). J.H., I.B., and PacBio sequencing were funded by the Charles University Research Fund PROGRES (project Q39), by National Sustainability Program I (NPU I) grant LO1503, and by project CZ.02.1.01/0.0/0.0/16_019/0000787, “Fighting Infectious Diseases,” provided by the Ministry of Education, Youth, and Sports of the Czech Republic. Isolates from the Czech Republic were collected and partially characterized within the project funded by the Internal Grant Agency of the University of Veterinary and Pharmaceutical Sciences Brno (grant 116/2015/FVL). MinION sequencing was funded by Horizon 2020 (award 773830), OH-EJP-H2020-JRP-AMR-2-ARDIG, and internal funding from Utrecht University. We have no potential conflicts of interest to declare.

Publisher Copyright:
© 2021 American Society for Microbiology. All rights reserved.

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