1887

Abstract

A bacterial strain isolated from a food processing drainage system in Costa Rica fulfilled the criteria as belonging to the genus , but could not be assigned to any of the known species. Phylogenetic analysis based on the 16S rRNA gene revealed highest sequence similarity with the type strain of (98.7 %). Phylogenetic analysis based on core genomes placed the novel taxon within the , and clade (). Whole-genome sequence analyses based on the average nucleotide identity (ANI<80 %) indicated that this isolate belonged to a novel species. Results of pairwise amino acid identity (AAI>70 %) and percentage of conserved proteins (POCP>68 %) with currently known species, as well as of biochemical characterization, confirmed that the strain constituted a novel species within the genus . The name sp. nov. is proposed for the novel species, and is represented by the type strain CLIP 2016/00682 (=CIP 111400=DSM 105474).

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2018-03-01
2024-12-10
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References

  1. Orsi RH, Wiedmann M. Characteristics and distribution of Listeria spp., including Listeria species newly described since 2009. Appl Microbiol Biotechnol 2016; 100:5273–5287 [View Article][PubMed]
    [Google Scholar]
  2. Chiara M, Caruso M, D'Erchia AM, Manzari C, Fraccalvieri R et al. Comparative genomics of Listeria sensu lato: genus-wide differences in evolutionary dynamics and the progressive gain of complex, potentially pathogenicity-related traits through lateral gene transfer. Genome Biol Evol 2015; 7:2154–2172 [View Article][PubMed]
    [Google Scholar]
  3. den Bakker HC, Manuel CS, Fortes ED, Wiedmann M, Nightingale KK. Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch. Int J Syst Evol Microbiol 2013; 63:3257–3268 [View Article][PubMed]
    [Google Scholar]
  4. den Bakker HC, Warchocki S, Wright EM, Allred AF, Ahlstrom C et al. Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments. Int J Syst Evol Microbiol 2014; 64:1882–1889 [View Article][PubMed]
    [Google Scholar]
  5. McLauchlin J, Reese CED. Genus I. Listeria Piere 1940a 383AL. In Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey's Mnual of Systematic Bacteriology New York, NY: Springer; 2009 pp. 244–257
    [Google Scholar]
  6. Pirie JH. The genus Listerella pirie. Science 1940; 91:383 [View Article][PubMed]
    [Google Scholar]
  7. Seeliger HP. Nonpathogenic Listeriae: L. innocua sp. n. Zentralbl Bakteriol Mikrobiol Hyg A 1981; 249:487–493
    [Google Scholar]
  8. Rocourt J, Grimont PAD. Listeria welshimeri sp. nov. and Listeria seeligeri sp. nov. Int J Syst Bacteriol 1983; 33:866–869 [View Article]
    [Google Scholar]
  9. Seeliger HPR, Rocourt J, Schrettenbrunner A, Grimont PAD, Jones D. Listeria ivanovii sp. nov. Int J Syst Bacteriol 1984; 34:336–337 [View Article]
    [Google Scholar]
  10. Graves LM, Helsel LO, Steigerwalt AG, Morey RE, Daneshvar MI et al. Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest. Int J Syst Evol Microbiol 2010; 60:1280–1288 [View Article][PubMed]
    [Google Scholar]
  11. Larsen HE, Seeliger HPR. (editors) A mannitol fermenting Listeria: Listeria grayi sp. n. Proceedings of the Third International Symposium on Listeriosis 1994 Bilthoven, the Netherlands: 1966
    [Google Scholar]
  12. Rocourt J, Boerlin P, Grimont F, Jacquet C, Piffaretti JC. Assignment of Listeria grayi and Listeria murrayi to a single species, Listeria grayi, with a revised description of Listeria grayi. Int J Syst Bacteriol 1992; 42:171–174 [View Article][PubMed]
    [Google Scholar]
  13. Leclercq A, Clermont D, Bizet C, Grimont PA, Le Flèche-Matéos A et al. Listeria rocourtiae sp. nov. Int J Syst Evol Microbiol 2010; 60:2210–2214 [View Article][PubMed]
    [Google Scholar]
  14. Bertsch D, Rau J, Eugster MR, Haug MC, Lawson PA et al. Listeria fleischmannii sp. nov., isolated from cheese. Int J Syst Evol Microbiol 2013; 63:526–532 [View Article][PubMed]
    [Google Scholar]
  15. Lang Halter E, Neuhaus K, Scherer S. Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond. Int J Syst Evol Microbiol 2013; 63:641–647 [View Article][PubMed]
    [Google Scholar]
  16. Weller D, Andrus A, Wiedmann M, den Bakker HC. Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA. Int J Syst Evol Microbiol 2015; 65:286–292 [View Article][PubMed]
    [Google Scholar]
  17. Allerberger F, Wagner M. Listeriosis: a resurgent foodborne infection. Clin Microbiol Infect 2010; 16:16–23 [View Article][PubMed]
    [Google Scholar]
  18. Guillet C, Join-Lambert O, Le Monnier A, Leclercq A, Mechaï F et al. Human listeriosis caused by Listeria ivanovii. Emerg Infect Dis 2010; 16:136–138 [View Article][PubMed]
    [Google Scholar]
  19. Leclercq A, Charlier C, Lecuit M. Global burden of listeriosis: the tip of the iceberg. Lancet Infect Dis 2014; 14:1027–1028 [View Article][PubMed]
    [Google Scholar]
  20. Hitchins AD, Jinneman K, Chen Y. Detection of Listeria monocytogenes in foods and environmental samples, and enumeration of Listeria monocytogenes in foods. In US Food and Drug Administration. (editor) Bacteriological Analytical Manual MD:: Silver Spring; 2016
    [Google Scholar]
  21. Cocolin L, Rantsiou K, Iacumin L, Cantoni C, Comi G. Direct identification in food samples of Listeria spp. and Listeria monocytogenes by molecular methods. Appl Environ Microbiol 2002; 68:6273–6282 [View Article][PubMed]
    [Google Scholar]
  22. Thouvenot P, Vales G, Bracq-Dieye H, Tessaud-Rita N, Maury MM et al. MALDI-TOF mass spectrometry-based identification of Listeria species in surveillance: a prospective study. J Microbiol Methods 2018; 144:29–32 [View Article][PubMed]
    [Google Scholar]
  23. Moura A, Tourdjman M, Leclercq A, Hamelin E, Laurent E et al. Real-time whole-genome sequencing for surveillance of Listeria monocytogenes, France. Emerg Infect Dis 2017; 23:1462–1470 [View Article][PubMed]
    [Google Scholar]
  24. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  25. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  26. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
    [Google Scholar]
  27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  28. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
    [Google Scholar]
  29. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  30. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  31. Rodriguez-R L, Konstantinidis K. The enveomics collection : a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Prepr 2016; 4:e1900v1
    [Google Scholar]
  32. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
    [Google Scholar]
  33. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  34. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  35. Doumith M, Buchrieser C, Glaser P, Jacquet C, Martin P. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol 2004; 42:3819–3822 [View Article][PubMed]
    [Google Scholar]
  36. Hughes RB, Smith AC. Capsule stain protocol. Laboratory Protocols Washington, DC: American Society for Microbiology; 2013
    [Google Scholar]
  37. Cepeda JA, Millar M, Sheridan EA, Warwick S, Raftery M et al. Listeriosis due to infection with a catalase-negative strain of Listeria monocytogenes. J Clin Microbiol 2006; 44:1917–1918 [View Article][PubMed]
    [Google Scholar]
  38. Swartz MA, Welch DF, Narayanan RP, Greenfield RA. Catalase-negative Listeria monocytogenes causing meningitis in an adult. Clinical and laboratory features. Am J Clin Pathol 1991; 96:130–133 [View Article][PubMed]
    [Google Scholar]
  39. Maury MM, Tsai YH, Charlier C, Touchon M, Chenal-Francisque V et al. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat Genet 2016; 48:308–313 [View Article][PubMed]
    [Google Scholar]
  40. Vázquez-Boland JA, Kuhn M, Berche P, Chakraborty T, Domínguez-Bernal G et al. Listeria pathogenesis and molecular virulence determinants. Clin Microbiol Rev 2001; 14:584–640 [View Article][PubMed]
    [Google Scholar]
  41. Bille J, Catimel B, Bannerman E, Jacquet C, Yersin MN et al. API Listeria, a new and promising one-day system to identify Listeria isolates. Appl Environ Microbiol 1992; 58:1857–1860[PubMed]
    [Google Scholar]
  42. European Committee on Antimicrobial Susceptibility Testing (EUCAST) Breakpoint tables for interpretation of MICs and zone diameters, Version 7.1. In EUCAST. (editor) The European Committee on Antimicrobial Susceptibility Testing 2017
    [Google Scholar]
  43. Société Française de Microbiologie 2015; Recommandations 2015 du Comité de l'antibiogramme de la Société Française de Microbiologie. Available from www.sfm-microbiologie.org/UserFiles/files/casfm/CASFMV2_030915.pdf
  44. Troxler R, von Graevenitz A, Funke G, Wiedemann B, Stock I. Natural antibiotic susceptibility of Listeria species: L. grayi, L. innocua, L. ivanovii, L. monocytogenes, L. seeligeri and L. welshimeri strains. Clin Microbiol Infect 2000; 6:525–535 [View Article][PubMed]
    [Google Scholar]
  45. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  46. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001; 18:691–699 [View Article][PubMed]
    [Google Scholar]
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