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,Jorge Blanco,Isidro García-Meniño,Vanesa García,Azucena Mora,María De Toro,Dafne Díaz-Jiménez,Alexandra Herrera

doi:10.3389/fmicb.2020.00387

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 MOBH11/IncHI2-ST4, one MOBP3/IncX4, and one MOBF12/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.

Highlights

Escherichia coli exists as part of the commensal microbiota in the mammalian digestive tract, as well as a zoonotic pathogen responsible for intestinal and extraintestinal infections in both humans and animals (Poirel et al, 2018)
Virotypes The 11 ST131 isolates harbored between 17 and 20 virulence gene markers screened by polymerase chain reaction (PCR)
All the 11 porcine ST131 isolates exhibited a virulence profile that satisfied the avian pathogenic E. coli (APEC), uropathogenic E. coli (UPEC), and extraintestinal pathogenic E. coli clones (ExPEC) status and because of their origin were classified as APEC, UPEC, and ExPEC like isolates (Table 1 and Supplementary Table S1)

Summary

Introduction

Escherichia coli exists as part of the commensal microbiota in the mammalian digestive tract, as well as a zoonotic pathogen responsible for intestinal and extraintestinal infections in both humans and animals (Poirel et al, 2018). Even though ST131 clone is prevalent in human samples, it remains less frequent from animals and especially rare from porcine source (Reid et al, 2019). The majority of animal isolates belong to clade B (associated with fimH22), whereas in those that cause extraintestinal infections in humans predominate clade C (associated with fimH30) and especially those belonging to subclades C1-nM27, C1-M27, and C2 (H30Rx). This could be the reason of the underrepresentation of ST131 clade B isolates in the literature and sequence databases (Reid et al, 2019)

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