E-Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2021

Genomic analysis of Pasteurella multocida isolates associated with fowl cholera reveals potential phase variation mechanisms in the lipopolysaccharide outer core biosynthesis loci (#243)

Lida Omaleki 1 2 3 , Pat Blackall 2 , Thom Cuddihy 4 , Rhys White 1 3 , Jodi Courtice 5 , Conny Turni 2 , Brian Forde 1 3 , Scott Beatson 1 3
  1. Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
  2. Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
  3. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
  4. QFAB Bioinformatics, Research Compute Centre, The University of Queensland, St Lucia, Queensland, Australia
  5. Division of Research and Innovation, University of Southern Queensland, Toowoomba, QLD, Australia

Fowl cholera caused by Pasteurella multocida is a problem in meat chicken breeders, organic meat chickens and free-range layer chickens.  In work funded by AgriFutures and Australian Eggs, we used whole genome sequencing (WGS) and phylogenomic analysis to investigate outbreak dynamics as well as monitoring and comparing the variations in the lipopolysaccharide (LPS) outer core biosynthesis loci of the outbreak and vaccine strains. Lipopolysaccharide is one of the most important immunogenic virulence factors of P. multocida.

Comprehensive genomics and metadata analyses were performed on two sets of P. multocida isolates (73 isolates that included vaccine strains and field challenge isolates), from the two free-range layer farms that suffered repeated fowl cholera outbreaks despite the use of fowl cholera vaccines. The isolates belonged to five different sequence types (ST) with ST9 and ST20 isolates being most prevalent. The isolates carried ST-specific mutations within their LPS type L3 outer core biosynthesis loci, including frameshift mutations. As killed fowl cholera vaccines were used on both farms, the vaccine strains had to have the same LPS outer core structure to ensure protection against the field challenge. The predicted LPS structures, based on the genomic data, consistently showed that outbreaks were associated with field challenge isolates with a different LPS outer core structure to that of the vaccine strains.

Using the genomic data, two potential phase variation mechanisms in the glycosyltransferase genes of LPS outer core biosynthesis loci of some P. multocida isolates were identified.  The potential phase variation mechanisms included a tandem repeat insertion in the natC and a single base deletion in a homopolymer region of the gatG. Our results strongly suggest the need for a metagenomics approach and a genetic LPS typing scheme to ensure an appropriate vaccine strain with a matching predicted LPS structure is used.