Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms


Submitted: 7 July 2018
Accepted: 22 October 2018
Published: 8 February 2019
Abstract Views: 1717
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Authors

  • Frederique Pasquali Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy.
  • Federica Palma Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy.
  • Marcello Trevisani Department of Veterinary Medical Sciences, Alma Mater Studiorum – University of Bologna, Italy.
  • Antonio Parisi Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Bari, Italy.
  • Alex Lucchi Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy.
  • Alessandra De Cesare Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy.
  • Gerardo Manfreda Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Italy.

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7-loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silico
using the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.


Supporting Agencies

the work was supported by the EU founded project COMPARE (Grant Agreement N° 643476).

1.
Pasquali F, Palma F, Trevisani M, Parisi A, Lucchi A, De Cesare A, Manfreda G. Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms. Ital J Food Safety [Internet]. 2019 Feb. 8 [cited 2024 Mar. 29];7(4). Available from: https://www.pagepressjournals.org/ijfs/article/view/7673

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