Whole Genome Sequencing and Characteristics of mcr-1-Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

Saskia-Camille Flament-Simon; María de Toro; Azucena Mora; Vanesa García; Isidro García-Meniño; Dafne Díaz-Jiménez; Alexandra Herrera; Jorge Blanco

doi:10.3389/fmicb.2020.00387

Whole Genome Sequencing and Characteristics of mcr-1-Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

Front Microbiol. 2020 Mar 24:11:387. doi: 10.3389/fmicb.2020.00387. eCollection 2020.

Authors

Saskia-Camille Flament-Simon^{1

2}, María de Toro³, Azucena Mora^{1

2}, Vanesa García^{1

2}, Isidro García-Meniño^{1

2}, Dafne Díaz-Jiménez^{1

2}, Alexandra Herrera¹, Jorge Blanco^{1

2}

Affiliations

¹ Laboratorio de Referencia de E. coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain.
² Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain.
³ Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CBIR), Logroño, Spain.

Abstract

Porcine Escherichia coli ST131 isolates are scarcely documented. Here, whole genome sequencing and core genome (CG) and plasmidome analysis of seven isolates collected from diarrheic piglets and four from pork meat were performed. All of the 11 ST131 isolates belonged to serotype O25b:H4 and clade B and showed fimH22 allele or mutational derivatives. The 11 porcine isolates possessed virulence traits that classified the isolates as avian pathogenic, uropathogenic, and extraintestinal pathogenic E. coli-like (APEC-, UPEC-, and ExPEC-like) and constituted virotype D. The CG was performed for all porcine isolates in addition to 73 ST131 reference isolates from different origins. Within clade B, the CG showed nine subclusters, allowing us to describe five new subclades (B6, B6-like, B7, B8, and B9). There was an association between subclade B6, PST43, virotype D2, and food origin, whereas subclade B7 included PST9 isolates with virotype D5 from diarrheic piglets (p = 0.007). The distance between human and porcine isolates from subclades B6 and B7 had an average of 20 and 15 SNP/Mb, respectively. [F2:A-:B1]-IncF, ColE1-like, and IncX plasmids were the most prevalent. Besides, IncF plasmids harbored a ColV region frequent among APEC isolates. Antimicrobial resistance genes conferring resistance to penicillin, tetracycline, quinolones, and colistin were the most common. The mcr-1.1 gene was detected in 5 of 11 porcine isolates, integrated into the chromosome of one isolate and into plasmids in the remainder isolates (two MOB _H ₁₁/IncHI2-ST4, one MOB _P ₃/IncX4, and one MOB _F ₁₂/IncF [F2:A-:B1] supposedly cointegrated with an IncHI2). The surrounding environments of the mcr-1 cassette showed variability. However, there were conserved structures within the same plasmid family. In conclusion, CG analysis defined five new subclades. The ST131 porcine isolates belonged to new subclades B6 and B7. Moreover, porcine and clinical human isolates were strongly related. The 11 porcine ST131 isolates harbored a wide variety of plasmids, virulence, and resistance genes. Furthermore, epidemic plasmids IncX4 and IncHI2 are responsible for the acquisition of mcr-1.1 gene. We hypothesize that the APEC-IncF plasmid acquired the mcr-1.1 gene via cointegrating an IncHI2 plasmid, which is worrying due to combination of virulence and resistance attributes in a single mobile genetic element.

Keywords: Escherichia coli; ST131; colistin; core genome; mcr-1.1; plasmidome; swine.