Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection

Abstract

Yersinia ruckeri is 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 in fliI, 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 of Y. ruckeri in 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.

Microevolution of aquaticStreptococcus agalactiaeST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment

“…agalactiae (35). The rapid fall in cost of whole genome sequencing coupled with multiplexing and rapid development of open source bioinformatics tools has permitted much deeper analysis of evolution, host adaptation and epidemiological modelling within single bacterial species (36) including those from aquatic hosts (14, 15). Bacteria such as S .…”

A pan genome reverse vaccinology approach to prevent Streptococcus agalactiae infection in farmed tilapia

“…Vaccination in aquaculture has successfully reduced the use of antibiotics while increasing production by protecting fish against pathogens (Gudding, 2014;Håstein et al, 2005;Sommerset et al, 2014). Today, many commercial vaccines against bacterial pathogens are available to aquaculture producers in several countries (Barnes et al, 2016;Håstein et al, 2005;Munang'andu, 2018). However, vaccines are not a perfect solution to all bacterial diseases and some bacterial pathogens, like Streptococcus, present challenges to effective long-term protective vaccines.…”

“…achromogenes and Yersinia ruckeri in salmonid fish (Barnes et al, 2016;Gudmundsdóttir et al, 1997;Ormsby et al, 2016) and against Streptococcus iniae in barramundi and GBS in stingrays Millard et al, 2012). Autogenous vaccines are also known as emergency vaccine, which can be used under the circumstances where fully licensed vaccines are not available, not effective or the causative agent is not covered (Hoelzer et al, 2018).…”

“…Microevolution within a bacterial species can be driven by host or environmental adaptation (Brynildsrud et al, 2014;Rosinski-Chupin et al, 2013), permitting an inference of the epidemiology of disease outbreaks and how pathogens may have transferred within and between geographic regions (Barnes et al, 2016;Brynildsrud et al, 2014;Sabat et al, 2013).…”

“…and Streptococcus spp. (Barnes et al, 2016;Håstein et al, 2005;Munang'andu, 2018). However, some bacterial fish pathogens are still hard to control by vaccination.…”