1,413
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Complete genome sequence of the emerging pathogen Cysteiniphilum spp. and comparative genomic analysis with genus Francisella: Insights into its genetic diversity and potential virulence traits

, , , , , , & show all
Article: 2214416 | Received 09 Nov 2022, Accepted 25 Apr 2023, Published online: 29 May 2023

References

  • Luo HM, Feng JH, Li LH, et al. Cysteiniphilum marinum sp. nov., isolated from coastal seawater. Antonie Van Leeuwenhoek. 2021 Jul;114(7):1079–13.
  • Liu L, Salam N, Jiao JY, et al. Cysteiniphilum litorale gen. nov., sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol. 2017 Jul;67(7):2178–2183.
  • Xiao M, Zheng ML, Salam N, et al. Facilibium subflavum gen. nov., sp. nov. and Cysteiniphilum halobium sp. nov., new members of the family Fastidiosibacteraceae isolated from coastal seawater. Int J Syst Evol Microbiol. 2019 Dec;69(12):3757–3764.
  • Xu CQ, Zhang XC, Wu Q, et al. Skin and soft tissue infection caused by Cysteiniphilum litorale in an immunocompetent patient: a case report. Indian J Med Microbiol. 2021 Oct-Dec;39(4):545–547.
  • Balloux F, van Dorp L. Q&A: what are pathogens, and what have they done to and for us? BMC Biol. 2017 Oct 19;15(1):91.
  • Diard M, Hardt WD. Evolution of bacterial virulence. FEMS Microbiol Rev. 2017 Sep 1;41(5):679–697.
  • Pechous RD, McCarthy TR, Zahrt TC. Working toward the future: insights into Francisella tularensis pathogenesis and vaccine development. Microbiol Mol Biol Rev. 2009 Dec;73(4):684–711.
  • Kumar R, Broms JE, Sjostedt A. Exploring the diversity within the Genus Francisella - an integrated pan-genome and genome-mining approach. Front Microbiol. 2020;11:1928.
  • Golicz AA, Bayer PE, Bhalla PL, et al. Pangenomics comes of age: from bacteria to plant and animal applications. Trends Genet. 2020 Feb;36(2):132–145.
  • Schwengers O, Jelonek L, Dieckmann MA, et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11). DOI:10.1099/mgen.0.000685.
  • Cantalapiedra CP, Hernandez-Plaza A, Letunic I, et al. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol. 2021 Dec 9;38(12):5825–5829. DOI:10.1093/molbev/msab293
  • Meier-Kolthoff JP, Goker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019 May 16;10(1):2182.
  • Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics. 2005 Feb 15;21(4):537–539.
  • Richter M, Rossello-Mora R, Oliver Glockner F, et al. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics. 2016 Mar 15;32(6):929–931. DOI:10.1093/bioinformatics/btv681
  • Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, et al. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res. 2022 Jan 7;50(D1):D801–807. DOI:10.1093/nar/gkab902
  • Parks DH, Imelfort M, Skennerton CT, et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043–1055.
  • Gautreau G, Bazin A, Gachet M, et al. PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol. 2020 Mar;16(3):e1007732.
  • Bazin A, Gautreau G, Medigue C, et al. panRGP: a pangenome-based method to predict genomic islands and explore their diversity. Bioinformatics. 2020 Dec 30;36(Suppl_2):i651–658. DOI:10.1093/bioinformatics/btaa792
  • Garber AI, Armbruster CR, Lee SE, et al. SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs. BMC Genomics. 2022 Mar 12;23(1):202. DOI:10.1186/s12864-022-08382-2
  • Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016 Jul 8;44(W1):W16–21. DOI:10.1093/nar/gkw387
  • Xie Z, Tang H. Isescan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics. 2017 Nov 1;33(21):3340–3347.
  • Schwengers O, Barth P, Falgenhauer L, et al. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb Genom. 2020 Oct;6(10). DOI:10.1099/mgen.0.000398.
  • Katz LS, Griswold T, Morrison SS, et al. Mashtree: a rapid comparison of whole genome sequence files. J Open Source Softw. 2019 Dec 10;4(44):1762. DOI:10.21105/joss.01762
  • Ondov BD, Treangen TJ, Melsted P, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016 Jun 20;17(1):132. DOI:10.1186/s13059-016-0997-x
  • Kim J, Na SI, Kim D, et al. UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol. 2021 Jun;59(6):609–615.
  • Letunic I, Bork P. Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021 Jul 2;49(W1):W293–296.
  • Liu B, Zheng D, Zhou S, et al. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 2022 Jan 7;50(D1):D912–917. DOI:10.1093/nar/gkab1107
  • Feldgarden M, Brover V, Gonzalez-Escalona N, et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728. DOI:10.1038/s41598-021-91456-0
  • Gilchrist CLM, Booth TJ, van Wersch B, et al. Cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters. Bioinformat Adv. 2021;1(1):vbab016.
  • Wambui J, Cernela N, Stevens MJA, et al. Whole genome sequence-based identification of clostridium estertheticum complex strains supports the need for taxonomic reclassification within the species clostridium estertheticum. Front Microbiol. 2021;12:727022.
  • Tran PN, Savka MA, Gan HM. In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus pseudomonas. Front Microbiol. 2017;8:1296.
  • McCutcheon JP, Moran NA. Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol. 2011 Nov 8;10(1):13–26.
  • Challacombe JF, Pillai S, Kuske CR. Shared features of cryptic plasmids from environmental and pathogenic Francisella species. PLoS ONE. 2017;12(8):e0183554.
  • Challacombe JF, Petersen JM, Gallegos-Graves V, et al. Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection. Appl Environ Microbiol. 2017 Feb 1;83(3). doi:10.1128/AEM.02589-16
  • Mesa V, Monot M, Ferraris L, et al. Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity. Microb Genom. 2022 May;8(5). DOI:10.1099/mgen.0.000813.
  • Treangen TJ, Rocha EP, Moran NA. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 2011 Jan 27;7(1):e1001284.
  • Niehus R, Mitri S, Fletcher AG, et al. Migration and horizontal gene transfer divide microbial genomes into multiple niches. Nat Commun. 2015 Nov 23;6:8924. doi:10.1038/ncomms9924
  • Goncalves IG, Simoes LC, Simoes M. Legionella pneumophila. Trends Microbiol. 2021 Sep;29(9):860–861.
  • Zhang G, Meredith TC, Kahne D. On the essentiality of lipopolysaccharide to Gram-negative bacteria. Curr Opin Microbiol. 2013 Dec;16(6):779–785.
  • Montminy SW, Khan N, McGrath S, et al. Virulence factors of Yersinia pestis are overcome by a strong lipopolysaccharide response. Nat Immunol. 2006 Oct;7(10):1066–1073.
  • Needham BD, Trent MS. Fortifying the barrier: the impact of lipid a remodelling on bacterial pathogenesis. Nat Rev Microbiol. 2013 Jul;11(7):467–481.
  • Clemens DL, Lee BY, Horwitz MA. The Francisella type VI secretion system. Front Cell Infect Microbiol. 2018;8:121.
  • Broms JE, Sjostedt A, Lavander M. The role of the Francisellatularensis pathogenicity island in type vi secretion, intracellular survival, and modulation of host cell signaling. Front Microbiol. 2010;1:136.
  • Brodmann M, Dreier RF, Broz P, et al. Francisella requires dynamic type VI secretion system and ClpB to deliver effectors for phagosomal escape. Nat Commun. 2017 Jun 16;8:15853. doi:10.1038/ncomms15853