Emergence and clonal expansion in Europe of Vibrio aestuarianus lineages pathogenic for oysters

Crassostrea gigas oysters, with 4.7 million tons harvested per year, represent a considerable food supply worldwide. Since 2001 Vibrio aestuarianus has emerged as a pathogenic bacterium causing adult oyster mortality events in France and Ireland, and its impact on oyster aquaculture has increased in Europe since its reemergence in 2012. To better understand the evolutionary mechanisms leading to the emergence and persistence over time of this pathogen, we conducted a survey with national reference laboratories (NRLs) at the European scale for mollusk diseases. We analyzed genomes of V. aestuarianus isolated from multiple countries, since 2001, with or without bivalve mortalities, and from multiple environmental compartments. Using a combination of comparative genomics and population genetics approaches, we show that two oyster pathogen lineages have almost clonally expanded in Europe, after a probable recent selective bottleneck. Low mutation and recombination rates, as well as purifying selective pressure, have preserved virulent selected genotypes. Furthermore, we identified a specific cus-cop-containing island conferring copper resistance to V. aestuarianus that could have favored the emergence of V. aestuarianus pathogenic lineages adapted to oysters. ### Competing Interest Statement The authors have declared no competing interest.