Shewanella khirikhana sp. nov. – a shrimp pathogen isolated from a cultivation pond exhibiting early mortality syndrome

Summary Early mortality syndrome (EMS) in cultivated shrimp is of complex aetiology. One of the causes is acute hepatopancreatic necrosis disease (AHPND) caused by unique Vibrio isolates that carry two Pir vp toxin genes, but other causes of EMS remain mostly unexplained. Here, we describe the discovery of a Shewanella isolate TH2012 T from an EMS/AHPND outbreak pond and demonstrate its virulence for shrimp (the mean lethal concentration of 10 5 colony‐forming units per millilitre by immersion challenge) accompanied by distinctive histopathology, particularly of the ventral nerve cord and lymphoid organ but also including the digestive tract. On the basis of its complete genome sequence, multilocus phylogenetic trees, digital DNA–DNA hybridization analysis and differential phenotypic characteristics, we propose that Shewanella isolate TH2012 T represents a novel species, separated sufficiently from the type strains S. litorisediminis and S. amazonensis to justify naming it Shewanella khirikhana sp. nov. Analysis of the TH2012 T genome revealed no homologues of the Pir vp toxin genes but revealed a number of other potential virulence factors. It constitutes the first Shewanella isolate reported to be pathogenic to shrimp.