FSL J1-208, a virulent uncommon phylogenetic lineage IV Listeria monocytogenes strain with a small chromosome size and a putative virulence plasmid carrying internalin-like genes

Applied and Environmental Microbiology

Volumn 78, Issue 6, 2012, Pages 1876-1889

  den Bakker, Henk C ^a   Bowen, Barbara M ^a   Rodriguez Rivera, Lorraine D ^a   Wiedmann, Martin ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENUS; CHROMOSOME SIZE; GENE CLUSTERS; GENOME SIZES; HIGHLY-CORRELATED; INTESTINAL EPITHELIAL CELLS; INVASIVENESS; LISTERIA MONOCYTOGENES; MONOCYTOGENES; PATHOGENIC POTENTIAL; PATHOGENIC SPECIES; PHYLOGENETIC LINEAGES; PROPHAGES; PROTEIN-CODING GENES; RESISTANCE TO ANTIBIOTICS; VIRULENCE PLASMIDS;

DISEASES; DNA; HEAVY METALS; LISTERIA;

GENES;

BACTERIAL DNA; BACTERIAL PROTEIN; INTERNALIN PROTEIN, BACTERIA; VIRULENCE FACTOR;

ANTIBIOTICS; BACTERIUM; CHROMOSOME; GENOME; HEAVY METAL; PATHOGENICITY; PHYLOGENETICS; PLASMID; SAPROTROPHY; VIRULENCE;

ANIMAL; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; CHEMISTRY; DNA SEQUENCE; GENETICS; GOAT; HUMAN; ISOLATION AND PURIFICATION; LISTERIA MONOCYTOGENES; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PLASMID; VIRULENCE;

ANIMALS; BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; DNA, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; GOATS; HUMANS; LISTERIA MONOCYTOGENES; MOLECULAR SEQUENCE DATA; PLASMIDS; SEQUENCE ANALYSIS, DNA; VIRULENCE; VIRULENCE FACTORS;

BACTERIA (MICROORGANISMS); CAPRA; LISTERIA; LISTERIA MONOCYTOGENES; LISTERIA SEELIGERI; LISTERIA WELSHIMERI;

EID: 84857947717     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06969-11     Document Type: Article

References (56)

1. Abascal F, Zardoya R, Telford MJ. 2010. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Res. 38:W7-W13.
2. Aziz RK, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
3. Bannam TL, Teng WL, Bulach D, Lyras D, Rood JI. 2006. Functionalidentification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens. J. Bacteriol. 188: 4942-4951.
4. Bierne H, Sabet C, Personnic N, Cossart P. 2007. Internalins: a complex family of leucine-rich repeat-containing proteins in Listeria monocytogenes. Microbes Infect. 9:1156 -1166.
5. Braun U, Stehle C, Ehrensperger F. 2002. Clinical findings and treatment of listeriosis in 67 sheep and goats. Vet. Rec. 150:38-42.
6. Darling ACE, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394 -1403.
7. Degnan PH, Yu Y, Sisneros N, Wing RA, Moran NA. 2009. Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors. Proc. Natl. Acad. Sci. U. S. A. 106:9063-9068.
8. Deivanayagam CC, et al. 2000. Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. Structure 8:67-78.
9. De Jesus AJ, Whiting RC. 2003. Thermal inactivation, growth, and survival studies of Listeria monocytogenes strains belonging to three distinct genotypic lineages. J. Food Prot. 66:1611-1617.
10. den Bakker HC, Bundrant BN, Fortes ED, Orsi RH, Wiedmann M. 2010. A population genetics-based and phylogenetic approach to understanding the evolution of virulence in the genus Listeria. Appl. Environ. Microbiol. 76:6085- 6100.
11. den Bakker HC, et al. 2010. Comparative genomics of the bacterial genus Listeria: genome evolution is characterized by limited gene acquisition and limited gene loss. BMC Genomics 11:688.
12. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
13. Flamm RK, Hinrichs DJ, Thomashow MF. 1984. Introduction of pAM beta 1 into Listeria monocytogenes by conjugation and homology between native L. monocytogenes plasmids. Infect. Immun. 44:157-161.
14. Glaser P, et al. 2001. Comparative genomics of Listeria species. Science 294:849-852.
15. Graves LM, Swaminathan B. 2001. PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis. Int. J. Food Microbiol. 65:55- 62.
16. Gray M, et al. 2004. Listeria monocytogenes isolates from foods and humans form distinct but overlapping populations. Appl. Environ. Microbiol. 70:5833-5841.
17. Guindon S, et al. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
18. Hain T, Steinweg C, Chakraborty T. 2006. Comparative and functional genomics of Listeria spp. J. Biotechnol. 126:37-51.
19. Hain T, et al. 2006. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J. Bacteriol. 188:7405-7415.
20. Jeffers G, et al. 2001. Comparative genetic characterization of Listeria monocytogenes isolates from human and animal listeriosis cases. Microbiology 147:1095-1104.
21. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinformatics 9:286 -298.
22. Kleerebezem M, et al. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U. S. A. 100:1990 -1995.
23. Kuenne C, et al. 2010. Comparative analysis of plasmids in the genus Listeria. PLoS One 5:e12511.
24. Langille MGI, Brinkman FSL. 2009. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25:664-665.
25. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R. 2008. Prophinden der: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24:863- 865.
26. Margolles A, de los Reyes-Gavilán CG. 1998. Characterization of plasmids from Listeria monocytogenes and Listeria innocua strains isolated from short-ripened cheeses. Int. J. Food Microbiol. 39:231-236.
27. Marshall KM, Bradshaw M, Johnson EA. 2010. Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum. PLoS One 5:e11087.
28. Moran NA. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-586.
29. Newton ILG, Bordenstein SR. 2010. Correlations between bacterial ecology and mobile DNA. Curr. Microbiol. 62:198 -208.
30. Nightingale KK, Windham K, Martin KE, Yeung M, Wiedmann M. 2005. Select Listeria monocytogenes subtypes commonly found in foods carry distinct nonsense mutations in inlA, leading to expression of truncated and secreted internalin A, and are associated with a reduced invasion phenotype for human intestinal epithelial cells. Appl. Environ. Microbiol. 71:8764-8772.
31. Oliver HF, Orsi RH, Wiedmann M, Boor KJ. 2010. Listeria monocytogenes sigma B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains. Appl. Environ. Microbiol. 76:4216-4232.
32. Orsi RH, et al. 2008. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9:539.
33. Orsi RH, Bowen BM, Wiedmann M. 2010. Homopolymeric tracts represent a general regulatory mechanism in prokaryotes. BMC Genomics 11:102.
34. Piffaretti JC, et al. 1989. Genetic characterization of clones of the bacterium Listeria monocytogenes causing epidemic disease. Proc. Natl. Acad. Sci. U. S. A. 86:3818 -3822.
35. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
36. Rankin DJ, Rocha EPC, Brown SP. 2010. What traits are carried on mobile genetic elements, and why? Heredity 106:1-10.
37. Rasmussen OF, Skouboe P, Dons L, Rossen L, Olsen JE. 1995. Listeria monocytogenes exists in at least three evolutionary lines: evidence from flagellin, invasive associated protein and listeriolysin O genes. Microbiology 141:2053-2061.
38. Rice LB, Carias LL, Marshall SH, Hutton-Thomas R, Rudin S. 2007. Characterization of Tn5386, a Tn916-related mobile element. Plasmid 58:61- 67.
39. Roberts A, et al. 2006. Genetic and phenotypic characterization of Listeria monocytogenes lineage III. Microbiology 152:685- 693.
40. Rood JI, Scott VN, Duncan CL. 1978. Identification of a transferabletetracycline resistance plasmid (pCW3) from Clostridium perfringens. Plasmid 1:563-570.
41. Rutherford K, et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944 -945.
42. Sayeed S, Li J, McClane BA. 2007. Virulence plasmid diversity in Clostridium perfringens type D isolates. Infect. Immun. 75:2391-2398.
43. Schroeter J, Klaenhammer T. 2009. Genomics of lactic acid bacteria. FEMS Microbiol. Lett. 292:1- 6.
44. Snyder L, Champness W. 2007. Molecular genetics of bacteria, 3rd ed. ASM Press, Washington, DC.
45. Southern E. 2006. Southern blotting. Nat. Protoc. 1:518 -525.
46. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688 -2690.
47. Steele CL, et al. 2011. Genome sequence of lineage III Listeria monocytogenes strain HCC23. J. Bacteriol. 193:3679 -3680.
48. Steinweg C, et al. 2010. Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria. J. Bacteriol. 192:1473-1474.
49. van de Guchte M, et al. 2006. The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc. Natl. Acad. Sci. U. S. A. 103:9274 -9279.
50. Waack S, et al. 2006. Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7:142.
51. Ward T, et al. 2004. Intraspecific phylogeny and lineage group identification based on the prfA virulence gene cluster of Listeria monocytogenes. J. Bacteriol. 186:4994 -5002.
52. Ward TJ, Ducey TF, Usgaard T, Dunn KA, Bielawski JP. 2008. Multilocus genotyping assays for single nucleotide polymorphism-based subtyping of Listeria monocytogenes isolates. Appl. Environ. Microbiol. 74: 7629-7642.
53. Ward TJ, et al. 2010. Molecular and phenotypic characterization of Listeria monocytogenes from U.S. Department of Agriculture Food Safety and Inspection Service surveillance of ready-to-eat foods and processing facilities. J. Food Prot. 73:861- 869.
54. Wesley IV. 1999. Listeriosis in animals, p. 39-73. In Ryser ET, Marth EH (ed), Listeria, listeriosis and food safety, 2nd ed. Marcel Dekker, Inc., New York, NY.
55. Wiedmann M, et al. 1999. Molecular investigation of a listeriosis outbreak in goats caused by an unusual strain of Listeria monocytogenes. J. Am. Vet. Med. Assoc. 215:369 -371.
56. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821- 829.