Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies.

Ainsley Beaton,Sylvie Chevalier,Edward Cunningham-Oakes,Alison Macfadyen,Vera Van Noort,Martin Welch,Cédric Lood,Chloe Dalzell,Alberto Faccenda,Alexander Kutschera,Jordan Murray,Nathan Smits,Rob Lavigne,João Botelho,Talal Sabhan Salih ,R P.m Thomson ,Alex J Mullins ,Maarten G K Ghequire ,Stephen K Dolan ,Martha L Redway ,Stuart Daniel Woodcock ,Ana C Da Silva ,Walid E.l Bestawy ,Pierre Cornélis ,Shannon R Coleman ,Brian A Smith ,Steven A Higgins ,Nicholas P Tucker

doi:10.1093/femsle/fny069

Abstract

Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.

Highlights

In September 2017, the biannual conference on the biology of Pseudomonas was held in Liverpool, UK
Whole-genome sequencing has become ubiquitous in microbiology and access to the technology is widespread
Our phylogenetic analyses show that P. baetica is closely related to P. koreensis in the P. fluorescens group

Summary

Introduction

In September 2017, the biannual conference on the biology of Pseudomonas was held in Liverpool, UK. In order to contribute to addressing this imbalance, the genome of P. baetica, a recently described member of the genus, was sequenced for the Pseudomonas 2017 genomics forum. Pseudomonas baetica strain a390 is one of five Gram-negative organisms that were isolated from a fish disease outbreak in an aquaculture facility in Huelva, Spain, in 2006 (Lopez et al 2012). A disadvantage to aquaculture systems is that the unusually high population density of the farmed fish leads to an elevated risk of infectious disease outbreaks. For this reason, antibiotics such as oxytetracycline (OT) are routinely used as growth promoters in aquaculture fish food pellets (Leal et al 2017). Other members of the Pseudomonadaceae are well known to cause disease in aquaculture scenarios, most notably P. anguilliseptica is a pathogen of both farmed and wild eels (Joh et al 2013)

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