title: Whole genome analysis ofYersinia ruckeriisolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection.
abstract: Yersinia ruckeriis a salmonid pathogen with widespread distribution in cool-temperate waters including Australia and New Zealand, two isolated environments with recently developed salmonid farming industries. Phylogenetic comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and China based on non-recombinant core genome SNPs revealed multiple deep-branching lineages, with a most recent common ancestor estimated at 18 500 years BP (12 355-24 757 95% HPD) and evidence of Australasian endemism. Evolution within the Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs describing the variance over 27 years. Isolates from the prevailing lineage are poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997, which is highly motile but has not been isolated since from epizootics. A non-motile phenotype has arisen independently in Tasmania compared to Europe and USA through a frameshift infliI, encoding the ATPase of the flagella cluster. We report for the first time lipopolysaccharide O-antigen serotype O2 isolates in Tasmania. This phenotype results from deletion of the O-antigen cluster and consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred independently on three occasions on three continents (Australasia, North America and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen deletion but occupy distant lineages. Despite the European and North American origins of the Australasian salmonid stocks, the lineages ofY. ruckeriin Australia and New Zealand are distinct from those of the northern hemisphere, suggesting they are pre-existing ancient strains that have emerged and evolved with the introduction of susceptible hosts following European colonization.
authors.affiliation: 1​School of Biological Sciences, The University of Queensland, Gehrmann Laboratories (60), St Lucia, Brisbane, QL 4072, Australia.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Barnes
authors.affiliation: 1​School of Biological Sciences, The University of Queensland, Gehrmann Laboratories (60), St Lucia, Brisbane, QL 4072, Australia.
authors.forename: Jerome
authors.initials: J
authors.lastname: Delamare-Deboutteville
authors.affiliation: 2​CSIRO Australian Animal Health Laboratory, Newcomb, VIC 3219, Australia.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Gudkovs
authors.affiliation: 3​Ministry for Primary Industries, Animal Health Laboratory, Wallaceville, New Zealand.
authors.forename: Cara
authors.initials: C
authors.lastname: Brosnahan
authors.affiliation: 4​Department of Primary Industries Parks Water & Environment (DPIPWE), Kings Meadows, Launceston, TAS 7249, Australia.
authors.forename: Richard
authors.initials: R
authors.lastname: Morrison
authors.affiliation: 4​Department of Primary Industries Parks Water & Environment (DPIPWE), Kings Meadows, Launceston, TAS 7249, Australia.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Carson
mesh_terms: D000818:Animals; D001208:Asia; D044362:Australasia; D002677:Chile; D005060:Europe; D005393:Fish Diseases / Q000382:microbiology*; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions / Q000235:genetics; D009656:North America; D010802:Phylogeny; D015009:Yersinia Infections / Q000382:microbiology*; D044124:Yersinia ruckeri / Q000145:classification* / Q000235:genetics*
keywords: O-antigen; Yersinia ruckeri; aquaculture; flagella; lipopolysaccharide; phylogeny