Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 70, Issue 11

sp. nov., isolated from a water trough and the faeces of healthy sheep Free

Abstract

In the context of a study on the occurrence of species in an animal farm environment in Valencia, Spain, six -like isolates could not be assigned to any known species. Phylogenetic analysis based on the 16S rRNA gene and on 231 core genes grouped these isolates in a monophyletic clade within the genus , with highest similarity to . Whole-genome sequence analyses based on DNA–DNA hybridization, the average nucleotide and the pairwise amino acid identities against all currently known species confirmed that these isolates constituted a new taxon within the genus . Phenotypically, these isolates differed from other species mainly by the production of acid from inositol, the absence of acidification in presence of methyl α--glucoside, and the absence of α-mannosidase and nitrate reductase activities. The name sp. nov. is proposed for this novel species, and the type strain is CLIP 2019/00642 (=CIP 111799=DSM 110544).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AAI , ANI , isDDH , new taxa , POCP and whole genome sequencing
Funding
This study was supported by the:
  • Ministerio de Ciencia, Innovación y Universidades (Award PID2019-110764RA-I00)
    • Principle Award Recipient: Juan J. Quereda
  • Generalitat Valenciana (Award GV/2018/A/183)
    • Principle Award Recipient: Juan J. Quereda
  • Santé Publique France
    • Principle Award Recipient: Not Applicable
  • Inserm
    • Principle Award Recipient: Not Applicable
  • Institut Pasteur
    • Principle Award Recipient: Not Applicable
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004494
2020-10-05
2025-04-30
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5868.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004494&mimeType=html&fmt=ahah

References

  1. 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]
  2. McLauchlin J, Reese CED et al. Genus Listeria. In Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York, NY: Springer; 2009 pp 244–257
     [Google Scholar]
  3. 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]
  4. Pirie JH. The genus Listerella Pirie. Science 1940; 91:383 [View Article][PubMed]
     [Google Scholar]
  5. Seeliger HP. Nonpathogenic listeriae: L. innocua sp. n. (Seeliger et Schoofs, 1977) (author's transl). Zentralbl Bakteriol Mikrobiol Hyg A 1981; 249:487–493[PubMed]
     [Google Scholar]
  6. 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]
  7. 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]
  8. 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]
  9. Larsen HE, SHP R. A mannitol fermenting Listeria: Listeria grayi sp. n. Proceedings of the Third International Symposium on Listeriosis 1994 Bilthoven: The Netherlands; 1966
     [Google Scholar]
  10. 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]
  11. Leclercq A, Clermont D, Bizet C, Grimont PA, Le Flèche-Matéos A et al. Listeriarocourtiae sp. nov. Int J Syst Evol Microbiol 2010; 60:2210–2214 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
     [Google Scholar]
  15. 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]
  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. Núñez-Montero K, Leclercq A, Moura A, Vales G, Peraza J et al. Listeria costaricensis sp. nov. Int J Syst Evol Microbiol 2018; 68:844–850 [View Article][PubMed]
     [Google Scholar]
  18. Doijad SP, Poharkar KV, Kale SB, Kerkar S, Kalorey DR et al. Listeria goaensis sp. nov. Int J Syst Evol Microbiol 2018; 68:3285–3291 [View Article][PubMed]
     [Google Scholar]
  19. Leclercq A, Moura A, Vales G, Tessaud-Rita N, Aguilhon C et al. Listeria thailandensis sp. nov. Int J Syst Evol Microbiol 2019; 69:74–81 [View Article][PubMed]
     [Google Scholar]
  20. Allerberger F, Wagner M. Listeriosis: a resurgent foodborne infection. Clin Microbiol Infect 2010; 16:16–23 [View Article][PubMed]
     [Google Scholar]
  21. Union E. Directive 2010/63/EU of the European Parliament and of the Council of 22 September 2010 on the protection of animals used for scientific purposes. Official Journal of the European Union 201033–79
     [Google Scholar]
  22. Leclercq A. Atypical colonial morphology and low recoveries of Listeria monocytogenes strains on Oxford, PALCAM, Rapid'L.mono and ALOA solid media. J Microbiol Methods 2004; 57:251–258 [View Article][PubMed]
     [Google Scholar]
  23. Barre L, Angelidis AS, Boussaid D, Brasseur ED, Manso E et al. Applicability of the EN ISO 11290-1 standard method for Listeria monocytogenes detection in presence of new Listeria species. Int J Food Microbiol 2016; 238:281–287 [View Article][PubMed]
     [Google Scholar]
  24. 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 2017; 144:29-32 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
     [Google Scholar]
  27. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  28. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article][PubMed]
     [Google Scholar]
  29. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article][PubMed]
     [Google Scholar]
  30. 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 2017; 68:461–466 [View Article]
     [Google Scholar]
  31. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  32. Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom 2018; 4: [View Article][PubMed]
     [Google Scholar]
  33. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 2014; 15:524 [View Article][PubMed]
     [Google Scholar]
  34. 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]
  35. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  36. 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]
  37. 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]
  38. 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]
  39. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  40. Erko S, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol today 2006; 8:6–9
     [Google Scholar]
  41. Kim M, 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]
  42. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  43. 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]
  44. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  45. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
     [Google Scholar]
  46. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  47. 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]
  48. 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]
  49. Hitchins A, Jinneman K, Chen Y. Detection of Listeria monocytogenes in foods and environmental samples and enumeration of Listeria monocytogenes in foods. Bacteriological Analytical Manual Washington, DC: Food and Drug Administration; 2017
     [Google Scholar]
  50. Hussey MA, Zayaitz A. Endospore stain protocol. In American Society of Microbiology editor Laboratory Protocols Washington, DC: 2013
     [Google Scholar]
  51. Breakwell DP, Moyes RB, Reynolds J. Differential staining of bacteria: capsule stain. Curr Protoc Microbiol 2009; Appendix 3:Appendix 3I [View Article][PubMed]
     [Google Scholar]
  52. Seeliger HPR, Höhne K. Serotyping of Listeria monocytogenes and related species. Methods Microbiol 1979; 13:31–49
     [Google Scholar]
  53. 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]
  54. Leclercq A, Chenal-Francisque V, Dieye H, Cantinelli T, Drali R et al. Characterization of the novel Listeria monocytogenes PCR serogrouping profile IVb-v1. Int J Food Microbiol 2011; 147:74–77 [View Article][PubMed]
     [Google Scholar]
  55. Moura A, Criscuolo A, Pouseele H, Maury MM, Leclercq A et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat Microbiol 2016; 2:16185 [View Article][PubMed]
     [Google Scholar]
  56. Christie K, Atkins NE, Munch-Petersen E. A note on a lytic phenomenon shown by group B streptococci. Aust J Exp Biol Med 1944; 22:197–200 [View Article]
     [Google Scholar]
  57. 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]
  58. 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]
  59. In Andrews W, Wang H, Jacobson A, Hammack T. BAM Chapter 5: Salmonella. Food and Drug Administration Bacteriological Analytical Manual; 2020
     [Google Scholar]
  60. 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 [View Article][PubMed]
     [Google Scholar]
  61. 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]
/content/journal/ijsem/10.1099/ijsem.0.004494
Loading
Listeria valentina sp. nov., isolated from a water trough and the faeces of healthy sheep
Int J Syst Evol Microbiol 70, 5868 (2020); https://doi.org/10.1099/ijsem.0.004494
/content/journal/ijsem/10.1099/ijsem.0.004494
/content/journal/ijsem/10.1099/ijsem.0.004494
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error