Oral Presentation MedVetPATHOGENS 2018

Enterococcus hirae- commensal or pathogen? (#11)

Oskar E Karlsson Lindsjö 1 , Hadrien Gourlé 2 , Jenny Larsson 3
  1. Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Uppland, Sweden
  2. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Uppland, Sweden
  3. Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Uppland, Sweden

Introduction: E. hirae has been described as an emerging cause of neonatal porcine diarrhoea (NPD) but is also found in the intestinal flora of healthy piglets1. This study aimed to investigate if strains associated with NPD are genetically different from strains found in healthy piglets.
Methods: 160 E. hirae-isolates associated with NPD were obtained from 18 piglets from six herds. All 18 animals displayed intestinal colonisation with E. hirae on histopathology1. For comparison, 35 E. hirae-isolates were obtained from 18 healthy animals from six herds with no history of NPD. All animals were <1-week old. MALDI-TOF was used for species identification. E. hirae isolates were subtyped by cpn60 gene sequencing. Two isolates per sampled herd (24 in total) were subjected to whole genome sequencing (WGS) using Oxford Nanopore MinION and Illumina NextSeq technologies. Genomes were assembled using Unicycler and further analysed by the pan-genome pipeline Roary2, 3. 
Results: cpn60-sequences were determined for 158 isolates from diarrhoeic piglets and all isolates from healthy piglets. The ~500 bp cpn60-sequence in 157 out of the 158 isolates from diarrhoeic animals was identical and differed from the isolates from healthy animals. Unicycler produced 24 near-complete genomes. The pan-genome consisted of 5382 genes, with 1616 core-genes. Isolates from healthy and diarrhoeic animals formed distinct groups based on core-gene alignment. Plasmid diversity within isolates differed between strains from sick and healthy animals, with three plasmids being conserved among isolates from diarrhoeic animals. Further, all strains from the diarrhoeic piglets shared a unique combination of 11 putative virulence genes.
Conclusion: Preliminary data support a genetic difference between strains associated with NPD and strains found in healthy animals. This differentiation strengthens the link between E. hirae and NPD. Further comparative analyses of the WGS data are on-going to characterise genetic features that are specific for E. hirae associated with NPD.

  1. Larsson, J., Lindberg, R., Aspán, A., Grandon, R., Westergren, E. and Jacobson, M., 2014. Neonatal piglet diarrhoea associated with enteroadherent Enterococcus hirae. Journal of comparative pathology, 151(2-3), pp.137-147.
  2. Wick, R.R., Judd, L.M., Gorrie, C.L. and Holt, K.E., 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS computational biology, 13(6), p.e1005595.
  3. Page, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T., Fookes, M., Falush, D., Keane, J.A. and Parkhill, J., 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics, 31(22), pp.3691-3693.