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

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

doi:10.1128/AAC.02556-20

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

Antimicrob Agents Chemother. 2023 May 1;65(5):e02556-20. doi: 10.1128/AAC.02556-20. Epub 2021 Feb 22.

Authors

Adam Valcek^{1

2}, Petra Sismova^{1

2}, Kristina Nesporova^{1

2}, Søren Overballe-Petersen³, Ibrahim Bitar^{4

5}, Ivana Jamborova¹, Arie Kant⁶, Jaroslav Hrabak^{4

5}, Jaap A Wagenaar^{6

7}, Jean-Yves Madec⁸, Peter Damborg⁹, Engeline van Duijkeren¹⁰, Christa Ewers¹¹, Joost Hordijk⁷, Henrik Hasman³, Michael S M Brouwer⁶, Monika Dolejska^{12

2}

Affiliations

¹ CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
² Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
³ Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
⁴ Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.
⁵ Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
⁶ Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands.
⁷ Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
⁸ Université de Lyon-ANSES, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France.
⁹ Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
¹⁰ Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
¹¹ Institute of Hygiene and Infectious Diseases of Animals, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
¹² CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic monika.dolejska@gmail.com.

Abstract

The relatedness of the equine-associated Escherichia coli 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 2008-2017 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 and one IncHI1/ST2 plasmids were obtained using long-read sequencing by PacBio or MinION. In the collection of 79 isolates, only 10 were phylogenetically close (<8 SNP). The majority of isolates belonged to phylogroup B1 (73/79, 92.4%) and carried bla _CTX-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) bla _CTX-M-1 genes were associated with presence of IncHI1 replicon of ST9 and 6.9% (4/58) with IncHI1 replicon of ST2 within the corresponding isolates. The operon for the utilization of short chain fructooligosaccharides (fos operon) was present in 55 (55/79, 69.6%) isolates, and all of these carried IncHI1/ST9 plasmids. The eight complete IncHI1/ST9 plasmid sequences showed the presence of bla _CTX-M-1 and the fos operon within the same molecule. Sequences of IncHI1/ST9 plasmids were highly conserved (>98% similarity) regardless of country of origin and varied only in the structure and integration site of MDR region. E. coli ST1250 and ST1250-SLV/DLV are phylogenetically-diverse strains associated with horses. A strong linkage of E. coli ST1250 with epidemic multi-drug resistance plasmid lineage IncHI1/ST9 carrying bla _CTX-M-1 and the fos operon was identified.