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      Phenotypic and Genetic Characterization of Flavobacterium psychrophilum Recovered from Diseased Salmonids in China

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          ABSTRACT

          Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, causes great economic losses in salmonid aquaculture worldwide. Recent molecular studies have uncovered important epidemiological and ecological aspects of this pathogen; however, such data are lacking for F. psychrophilum populations affecting aquaculture in China. Herein, F. psychrophilum phenotype, genotype, and virulence were characterized for isolates recovered from epizootics in multiple salmonid aquaculture facilities across China. Thirty-one F. psychrophilum isolates, originating from four provinces and three host fish species, were predominantly homogeneous biochemically but represented 5 sequence types (STs) according to multilocus sequence typing (MLST) that belonged to clonal complex CC-ST10 or 3 newly recognized singleton STs. PCR-based serotyping classified 19 and 12 F. psychrophilum isolates into molecular serotypes 1 and 0, respectively, showing an obvious relationship with host species. Antimicrobial susceptibility analysis via broth microdilution revealed reduced susceptibility to enrofloxacin, flumequine, and oxolinic acid, moderate susceptibility to gentamicin, erythromycin, and florfenicol, and variable susceptibility to ampicillin and oxytetracycline. In vivo challenge experiments confirmed the ability of two representative Chinese F. psychrophilum isolates to induce typical signs of BCWD and mortality in 1-year-old rainbow trout ( Oncorhynchus mykiss). Findings collectively demonstrate (i) that BCWD outbreaks in China studied thus far are caused by F. psychrophilum lineages that are common on other continents (e.g., CC-ST10) and others that have not been reported elsewhere (e.g., ST355, ST356, ST357), (ii) that F. psychrophilum molecular serotypes distinguish isolates from different host fish species, even within STs, and (iii) reduced F. psychrophilum antimicrobial susceptibility against compounds used for BCWD control in China.

          IMPORTANCE Flavobacterium psychrophilum causes substantial economic losses in salmonid aquaculture worldwide. Although this bacterium is also believed to be a disease source in China, published reports of its presence do not yet exist. Herein, F. psychrophilum was linked to multiple disease outbreaks in several salmonid aquaculture facilities within four Chinese provinces, and polyphasic characterization revealed that most isolates were genetically distinct from strains recovered on other continents. Analyses further revealed the predominating molecular serotypes, antimicrobial susceptibility profiles, and pathogenic potential of two representative recovered isolates. Collectively, the results presented here provide important data on the epidemiology and disease ecology of F. psychrophilum in China and pave the way for targeted prevention and control methods to be pursued in the future.

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          ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

          After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
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            Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

            The recent advent of DNA sequencing technologies facilitates the use of genome sequencing data that provide means for more informative and precise classification and identification of members of the Bacteria and Archaea. Because the current species definition is based on the comparison of genome sequences between type and other strains in a given species, building a genome database with correct taxonomic information is of paramount need to enhance our efforts in exploring prokaryotic diversity and discovering novel species as well as for routine identifications. Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea, which is represented by quality-controlled 16S rRNA gene and genome sequences. Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. As a result, the database is made of 61 700 species/phylotypes, including 13 132 with validly published names, and 62 362 whole-genome assemblies that were identified taxonomically at the genus, species and subspecies levels. Genomic properties, such as genome size and DNA G+C content, and the occurrence in human microbiome data were calculated for each genus or higher taxa. This united database of taxonomy, 16S rRNA gene and genome sequences, with accompanying bioinformatics tools, should accelerate genome-based classification and identification of members of the Bacteria and Archaea. The database and related search tools are available at www.ezbiocloud.net/.
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              Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

              The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.  Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes.  Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications.  The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation.  Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes.  There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question.  In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Spectr
                Microbiol Spectr
                spectrum
                Microbiology Spectrum
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2165-0497
                15 September 2021
                Sep-Oct 2021
                15 September 2021
                : 9
                : 2
                : e00330-21
                Affiliations
                [a ] Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
                [b ] Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
                [c ] College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
                [d ] Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State Universitygrid.17088.36, , East Lansing, Michigan, USA
                [e ] Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State Universitygrid.17088.36, , East Lansing, Michigan, USA
                [f ] Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
                University of Minnesota
                Author notes

                Citation Li S, Chai J, Knupp C, Nicolas P, Wang D, Cao Y, Deng F, Chen F, Lu T, Loch TP. 2021. Phenotypic and genetic characterization of Flavobacterium psychrophilum recovered from diseased salmonids in China. Microbiol Spectr 9:e00330-21. https://doi.org/10.1128/Spectrum.00330-21.

                Author information
                https://orcid.org/0000-0003-1682-7830
                https://orcid.org/0000-0002-6985-2477
                Article
                00330-21 spectrum.00330-21
                10.1128/Spectrum.00330-21
                8557942
                34523994
                04f1f3d1-4c1b-41da-9574-0832b200940c
                Copyright © 2021 Li et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 19 August 2021
                : 19 August 2021
                Page count
                supplementary-material: 1, Figures: 5, Tables: 4, Equations: 0, References: 64, Pages: 14, Words: 8995
                Funding
                Funded by: Central Public-interest Scientific Institution Basal Research Fund, Heilongjiang River Fisheries Research Institute;
                Award ID: HSY201902Q
                Award Recipient :
                Funded by: USDA Agriculture and Food Research Initiative;
                Award ID: 2016-67015-24891
                Award Recipient :
                Funded by: USDA | National Institute of Food and Agriculture (NIFA), FundRef https://doi.org/10.13039/100005825;
                Award ID: 2016-70007-25756
                Award Recipient :
                Funded by: MOA | CAFS | Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (Central Public-interest Scientific Institution Basal Research Fund, CAFS), FundRef https://doi.org/10.13039/501100012428;
                Award ID: 2019GH08
                Award Recipient :
                Categories
                Research Article
                epidemiology, Epidemiology
                Custom metadata
                September/October 2021

                bacterial coldwater disease,flavobacterium psychrophilum,mlst,genetic diversity,serotype,antimicrobial susceptibility,virulence

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