Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA

References

1. Angiuoli S. V., Gussman A., Klimke W., Cochrane G., Field D., Garrity G., Kodira C. D., Kyrpides N., Madupu R. & other authors ( 2008 ). Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. . OMICS 12, 137–141. [View Article] [PubMed]
   [Google Scholar]
2. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. & other authors ( 2012 ). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. . J Comput Biol 19, 455–477. [View Article] [PubMed]
   [Google Scholar]
3. Baranyi J., Roberts T. A., McClure P. ( 1993 ). A non-autonomous differential equation to model bacterial growth. . Food Microbiol 10, 43–59. [View Article]
   [Google Scholar]
4. Batz M. B., Doyle M. P., Morris G. Jr, Painter J., Singh R., Tauxe R. V., Taylor M. R., Lo Fo Wong D. M. Food Attribution Working Group ( 2005 ). Attributing illness to food. . Emerg Infect Dis 11, 993–999. [View Article] [PubMed]
   [Google Scholar]
5. Benedict M. N., Henriksen J. R., Metcalf W. W., Whitaker R. J., Price N. D. ( 2014 ). ITEP: an integrated toolkit for exploration of microbial pan-genomes. . BMC Genomics 15, 8. [View Article] [PubMed]
   [Google Scholar]
6. Bertsch D., Rau J., Eugster M. R., Haug M. C., Lawson P. A., Lacroix C., Meile L. ( 2013 ). Listeria fleischmannii sp. nov., isolated from cheese. . Int J Syst Evol Microbiol 63, 526–532. [View Article] [PubMed]
   [Google Scholar]
7. Bille J., Catimel B., Bannerman E., Jacquet C., Yersin M. N., Caniaux I., Monget D., Rocourt J. ( 1992 ). API Listeria, a new and promising one-day system to identify Listeria isolates. . Appl Environ Microbiol 58, 1857–1860.[PubMed]
   [Google Scholar]
8. Bolger A. M., Lohse M., Usadel B. ( 2014 ). Trimmomatic: a flexible trimmer for Illumina sequence data. . Bioinformatics 30, 2114–2120. [View Article] [PubMed]
   [Google Scholar]
9. Castresana J. ( 2000 ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. . Mol Biol Evol 17, 540–552. [View Article] [PubMed]
   [Google Scholar]
10. Chan J. Z.-M., Halachev M. R., Loman N. J., Constantinidou C., Pallen M. J. ( 2012 ). Defining bacterial species in the genomic era: insights from the genus Acinetobacter. . BMC Microbiol 12, 302. [CrossRef]
    [Google Scholar]
11. den Bakker H. C., Warchocki S., Wright E. M., Allred A. F., Ahlstrom C., Manuel C. S., Stasiewicz M. J., Burrell A., Roof S. & other authors ( 2014 ). 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 64, 1882–1889. [View Article] [PubMed]
    [Google Scholar]
12. Gillespie I. A., Mook P., Little C. L., Grant K. A., McLauchlin J. ( 2010 ). Human listeriosis in England, 2001-2007: association with neighbourhood deprivation. . Euro Surveill 15, 7–16.[PubMed]
    [Google Scholar]
13. Graves L. M., Helsel L. O., Steigerwalt A. G., Morey R. E., Daneshvar M. I., Roof S. E., Orsi R. H., Fortes E. D., Milillo S. R. & other authors ( 2010 ). Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest. . Int J Syst Evol Microbiol 60, 1280–1288. [View Article] [PubMed]
    [Google Scholar]
14. Hughes R. B., Smith A. C. ( 2013 ). Capsule Stain Protocols. Laboratory protocols. American Society for Microbiology, Washington, DC. www.microbelibrary.org. Accessed 25 August 2014..
15. Hussey M. A., Zayaitz A. ( 2013 ). Endospore Stain Protocol. Laboratory protocols. American Society for Microbiology, Washington, DC. www.microbelibrary.org. Accessed 25 August 2014..
16. Katoh K., Standley D. M. ( 2014 ). mafft: iterative refinement and additional methods. . Methods Mol Biol 1079, 131–146. [View Article] [PubMed]
    [Google Scholar]
17. Lang Halter E., Neuhaus K., Scherer S. ( 2013 ). Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond. . Int J Syst Evol Microbiol 63, 641–647. [View Article] [PubMed]
    [Google Scholar]
18. Larsen H. E., Seeliger H. P. R. ( 1966 ). A mannitol fermenting Listeria: Listeria grayi sp. n. In Proceedings of the Third International Symposium on Listeriosis 1994, pp. 35–39. Bilthoven, the Netherlands..
    [Google Scholar]
19. Leclercq A., Clermont D., Bizet C., Grimont P. A. D., Le Flèche-Matéos A., Roche S. M., Buchrieser C., Cadet-Daniel V., Le Monnier A. & other authors ( 2010 ). Listeria rocourtiae sp. nov.. Int J Syst Evol Microbiol 60, 2210–2214. [View Article] [PubMed]
    [Google Scholar]
20. Malley T. J. V., Stasiewicz M. J., Gröhn Y. T., Roof S., Warchocki S., Nightingale K., Wiedmann M. ( 2013 ). Implementation of statistical tools to support identification and management of persistent Listeria monocytogenes contamination in smoked fish processing plants. . J Food Prot 76, 796–811. [View Article] [PubMed]
    [Google Scholar]
21. McLauchlin J., Rees C. ( 2009 ). Genus I. Listeria Pirie 1940a 383^AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 3 ( The Firmicutes ). pp. 244–257. Edited by Vos P., Garrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K.-H., Whitman W. . New York:: Springer;.
    [Google Scholar]
22. Painter J. A., Hoekstra R. M., Ayers T., Tauxe R. V., Braden C. R., Angulo F. J., Griffin P. M. ( 2013 ). Attribution of foodborne illnesses, hospitalizations, and deaths to food commodities by using outbreak data, United States, 1998-2008. . Emerg Infect Dis 19, 407–415. [View Article] [PubMed]
    [Google Scholar]
23. Pirie J. H. ( 1940 ). The Genus Listerella Pirie. . Science 91, 383. [View Article] [PubMed]
    [Google Scholar]
24. R Core Team ( 2013 ). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3–900051–07–0. http://www.R-project.org/..
25. Richter M., Rosselló-Móra R. ( 2009 ). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106, 19126–19131. [View Article] [PubMed]
    [Google Scholar]
26. Rocourt J., Grimont P. A. D. ( 1983 ). Listeria welshimeri sp. nov. and Listeria seeligeri sp. nov.. Int J Syst Bacteriol 33, 866–869. [View Article]
    [Google Scholar]
27. Sauders B. D., Overdevest J., Fortes E., Windham K., Schukken Y., Lembo A., Wiedmann M. ( 2012 ). Diversity of Listeria species in urban and natural environments. . Appl Environ Microbiol 78, 4420–4433. [View Article] [PubMed]
    [Google Scholar]
28. Seeliger H. P. R. ( 1981 ). Apathogene Listerien: L. innocua sp. n. (Seeliger et Schoofs, 1977). . Zentralbl Bakteriol Hyg 1 Abt Orig A 249, 487–493.
    [Google Scholar]
29. Seeliger H. P. R., Rocourt J., Schrettenbrunner A., Grimont P. A. D., Jones D. ( 1984 ). Listeria ivanovii sp. nov.. Int J Syst Bacteriol 34, 336–337. [View Article]
    [Google Scholar]
30. Stamatakis A. ( 2006 ). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22, 2688–2690. [View Article] [PubMed]
    [Google Scholar]
31. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013 ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30, 2725–2729. [View Article] [PubMed]
    [Google Scholar]
32. U.S. Food and Drug Administration ( 2014 ). Bacteriological Analytical Manual. http://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm2006949.htm .
33. Vázquez-Boland J. A., Kuhn M., Berche P., Chakraborty T., Domínguez-Bernal G., Goebel W., González-Zorn B., Wehland J., Kreft J. ( 2001 ). Listeria pathogenesis and molecular virulence determinants. . Clin Microbiol Rev 14, 584–640. [View Article] [PubMed]
    [Google Scholar]