AUTHOR=Gulla Snorre , Colquhoun Duncan J. , Olsen Anne Berit , Spilsberg Bjørn , Lagesen Karin , Åkesson Caroline P. , Strøm Sverri , Manji Farah , Birkbeck Thomas H. , Nilsen Hanne K. 

TITLE=Phylogeography and host specificity of Pasteurellaceae pathogenic to sea-farmed fish in the north-east Atlantic

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1236290

DOI=10.3389/fmicb.2023.1236290

ISSN=1664-302X

ABSTRACT=<p>The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (<italic>Salmo salar</italic>) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (<italic>Cyclopterus lumpus</italic>) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as <italic>bona fide</italic> members of the <italic>Pasteurellaceae</italic> family, with phylogenetic reconstruction dividing them into two distinct branches sharing &lt;88% average nucleotide identity. These branches therefore constitute two separate species, namely <italic>Pasteurella skyensis</italic> and the as-yet invalidly named “<italic>Pasteurella atlantica</italic>”. Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved “<italic>P. atlantica</italic> gv. <italic>cyclopteri</italic>” (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by “<italic>P. atlantica</italic> gv. <italic>salmonicida</italic>” (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving <italic>P. skyensis</italic> (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to <italic>P. skyensis</italic> and “<italic>P. atlantica</italic>” from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and <italic>Phocoenobacter uteri</italic> associated with harbor porpoise (<italic>Phocoena phocoena</italic>), and their relatively distant relationship with other members of the genus <italic>Pasteurella</italic>, suggests that both <italic>P. skyensis</italic> and “<italic>P. atlantica</italic>” should be moved to the genus <italic>Phocoenobacter</italic>.</p>