Gnom Cmp: A quantitative approach for comparative analysis of closely related genomes of bacterial pathogens

Genome

Volumn 54, Issue 5, 2011, Pages 402-418

  Yu, Gongxin ^a  

^a Boise State University   (United States)

Author keywords

genetic heterogeneity; genome comparative analysis; genotypes

Indexed keywords

ANTIINFECTIVE AGENT; RNA 23S; VANCOMYCIN;

ARTICLE; BACTERIAL GENOME; CLASSIFICATION; DRUG EFFECT; GENETIC HETEROGENEITY; GENETICS; GENOMICS; GENOTYPE; METHODOLOGY; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; STAPHYLOCOCCUS AUREUS;

ANTI-BACTERIAL AGENTS; BASE SEQUENCE; GENETIC HETEROGENEITY; GENOME, BACTERIAL; GENOMICS; GENOTYPE; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; RNA, RIBOSOMAL, 23S; SEQUENCE ALIGNMENT; STAPHYLOCOCCUS AUREUS; VANCOMYCIN;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS AUREUS;

EID: 79961199886     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g11-005     Document Type: Article

References (85)

1. Allen J.E. Gardner S.N. Slezak T.R. 2008. DNA signatures for detecting genetic engineering in bacteria. Genome Biol. 9 (3): R56. 10.1186/gb-2008-9-3- r56 18348716 (Pubitemid 351959559)
2. Aury J.M. Cruaud C. Barbe V. Rogier O. Mangenot S. Samson G. et al. 2008. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies. BMC Genomics, 9 (1): 603. 10.1186/1471-2164-9-603 19087275
3. Bandara A.B. Sriranganathan N. Schurig G.G. Boyle S.M. 2005. Putative outer membrane autotransporter protein influences survival of Brucella suis in BALB/c mice. Vet. Microbiol. 109 (1-2): 95-104. 10.1016/j.vetmic.2005.05.012 15970403 (Pubitemid 40943350)
4. Betts J.C. Dodson P. Quan S. Lewis A.P. Thomas P.J. Duncan K. McAdam R.A. 2000. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology, 146 (12): 3205-3216. 11101678 (Pubitemid 32040820)
5. Bhavsar A.P. Erdman L.K. Schertzer J.W. Brown E.D. 2004. Teichoic acid is an essential polymer in Bacillus subtilis that is functionally distinct from teichuronic acid. J. Bacteriol. 186 (23): 7865-7873. 10.1128/JB.186.23.7865- 7873.2004 15547257 (Pubitemid 39552496)
6. Brennan M.J. Delogu G. Chen Y. Bardarov S. Kriakov J. Alavi M. Jacobs W.R. Jr. 2001. Evidence that mycobacterial PE-PGRS proteins are cell surface constituents that influence interactions with other cells. Infect. Immun. 69 (12): 7326-7333. 10.1128/IAI.69.12.7326-7333.2001 11705904 (Pubitemid 33086555)
7. Brudno M. 2008. An introduction to the Lagan alignment toolkit. Methods Mol. Biol. 395: 205-219. 10.1007/978-1-59745-514-5-13 17993676
8. Brudno M. Malde S. Poliakov A. Do C.B. Couronne O. Dubchak I. Batzoglou S. 2003. Glocal alignment: finding rearrangements during alignment. Bioinformatics, 19 (Suppl. 1): i54-i62. 10.1093/bioinformatics/btg1005 12855437 (Pubitemid 41185599)
9. Brudno M. Poliakov A. Salamov A. Cooper G.M. Sidow A. Rubin E.M. et al. 2004. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 14 (4): 685-692. 10.1101/gr.2067704 15060011 (Pubitemid 38500241)
10. Canu A. Malbruny B. Coquemont M. Davies T.A. Appelbaum P.C. Leclercq R. 2002. Diversity of ribosomal mutations conferring resistance to macrolides, clindamycin, streptogramin, and telithromycin in Streptococcus pneumoniae. Antimicrob. Agents Chemother. 46 (1): 125-131. 10.1128/AAC.46.1.125-131.2002 11751122 (Pubitemid 34031613)
11. Centers for Disease Control and Prevention. 1997. Reduced susceptibility of Staphylococcus aureus to vancomycin Japan, 1996. MMWR Morb. Mortal. Wkly. Rep. 46 (27): 624-626. 9218648
12. Charles P.G. Ward P.B. Johnson P.D. Howden B.P. Grayson M.L. 2004. Clinical features associated with bacteremia due to heterogeneous vancomycin-intermediate Staphylococcus aureus. Clin. Infect. Dis. 38 (3): 448-451. 10.1086/381093 14727222 (Pubitemid 38200128)
13. Chen F. Poppe C. Liu G.-R. Li Y.-G. Peng Y.-H. Sanderson K.E. et al. 2009. A genome map of Salmonella enterica serovar Agona: numerous insertions and deletions reflecting the evolutionary history of a human pathogen. FEMS Microbiol. Lett. 293 (2): 188-195. 10.1111/j.1574-6968.2009.01539.x 19533840
14. Cole S.T. Brosch R. Parkhill J. Garnier T. Churcher C. Harris D. et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 393 (6685): 537-544. 10.1038/31159 9634230 (Pubitemid 28319235)
15. Darling A.E. Treangen T.J. Messeguer X. Perna N.T. 2007. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods Mol. Biol. 396: 135-152. 10.1007/978-1-59745-515-2-10 18025691 (Pubitemid 350190039)
16. de Hoon M.J.L. Imoto S. Nolan J. Miyano S. 2004. Open source clustering software. Bioinformatics, 20 (9): 1453-1454. 10.1093/bioinformatics/bth078 14871861 (Pubitemid 38931415)
17. Delcher A.L. Salzberg S.L. Phillippy A.M. 2003. Using MUMmer to identify similar regions in large sequence sets. Curr. Protoc. Bioinf. 10: 3.1-3.18.
18. Delgado A. Riordan J.T. Lamichhane-Khadka R. Winnett D.C. Jimenez J. Robinson K. et al. 2007. Hetero-vancomycin-intermediate methicillin-resistant Staphylococcus aureus isolate from a medical center in Las Cruces, New Mexico. J. Clin. Microbiol. 45 (4): 1325-1329. 10.1128/JCM.02437-06 17267639 (Pubitemid 46626508)
19. Diep B.A. Gill S.R. Chang R.F. Phan T.H. Chen J.H. Davidson M.G. et al. 2006. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet, 367 (9512): 731-739. 10.1016/S0140-6736(06)68231-7 16517273 (Pubitemid 43326291)
20. Fauconnier A. Allaoui A. Campos A. Van Elsen A. Cornelis G.R. Bollen A. 1997. Flagellar flhA, flhB and flhE genes, organized in an operon, cluster upstream from the inv locus in Yersinia enterocolitica. Microbiology, 143 (11): 3461-3471. 10.1099/00221287-143-11-3461 9387224 (Pubitemid 27496925)
21. Feil E.J. Maiden M.C. Achtman M. Spratt B.G. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol. Biol. Evol. 16 (11): 1496-1502. 10555280 (Pubitemid 29510892)
22. Feil E.J. Smith J.M. Enright M.C. Spratt B.G. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics, 154 (4): 1439-1450. 10747043 (Pubitemid 30211231)
23. Fleischmann R.D. Alland D. Eisen J.A. Carpenter L. White O. Peterson J. et al. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184 (19): 5479-5490. 10.1128/JB.184.19.5479- 5490.2002 12218036 (Pubitemid 35024395)
24. Fraser J.D. Proft T. 2008. The bacterial superantigen and superantigen-like proteins. Immunol. Rev. 225 (1): 226-243. 10.1111/j.1600-065X. 2008.00681.x 18837785
25. Fretin D. Fauconnier A. Kohler S. Halling S. Leonard S. Nijskens C. et al. 2005. The sheathed flagellum of Brucella melitensis is involved in persistence in a murine model of infection. Cell. Microbiol. 7 (5): 687-698. 10.1111/j.1462-5822.2005.00502.x 15839898 (Pubitemid 40585010)
26. Fridkin S.K. 2001. Vancomycin-intermediate and-resistant Staphylococcus aureus: what the infectious disease specialist needs to know. Clin. Infect. Dis. 32 (1): 108-115. 10.1086/317542 11118389 (Pubitemid 32150955)
27. Fridkin S.K. Hageman J. McDougal L.K. Mohammed J. Jarvis W.R. Perl T.M. Tenover F.C. 2003. Epidemiological and microbiological characterization of infections caused by Staphylococcus aureus with reduced susceptibility to vancomycin, United States, 1997-2001. Clin. Infect. Dis. 36 (4): 429-439. 10.1086/346207 12567300 (Pubitemid 36241308)
28. Hajirasouliha I. Hormozdiari F. Sahinalp S.C. Birol I. 2008. Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Bioinformatics, 24 (13): i32-i40. 10.1093/bioinformatics/btn173 18586730 (Pubitemid 351911655)
29. Harris L.G. Foster S.J. Richards R.G. 2002. An introduction to Staphylococcus aureus, and techniques for identifying and quantifying S. aureus adhesins in relation to adhesion to biomaterials. Eur. Cell. Mater. 4: 39-60. [review.] 14562246 (Pubitemid 38977705)
30. Hayashi T. Makino K. Ohnishi M. Kurokawa K. Ishii K. Yokoyama K. et al. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8 (1): 11-22. 10.1093/dnares/8.1.11 11258796 (Pubitemid 33617542)
31. Herron-Olson L. Fitzgerald J.R. Musser J.M. Kapur V. 2007. Molecular correlates of host specialization in Staphylococcus aureus. PLoS ONE, 2 (10): e1120. 10.1371/journal.pone.0001120 17971880 (Pubitemid 351586837)
32. Hiramatsu K. Hanaki H. Ino T. Yabuta K. Oguri T. Tenover F.C. 1997. Methicillin-resistant Staphylococcus aureus clinical strain with reduced vancomycin susceptibility. J. Antimicrob. Chemother. 40 (1): 135-136. 10.1093/jac/40.1.135 9249217 (Pubitemid 27341646)
33. Holden M.T. Feil E.J. Lindsay J.A. Peacock S.J. Day N.P. Enright M.C. et al. 2004. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc. Natl. Acad. Sci. U.S.A. 101 (26): 9786-9791. 10.1073/pnas.0402521101 15213324 (Pubitemid 38869314)
34. Howden B.P. Johnson P.D. Ward P.B. Stinear T.P. Davies J.K. 2006. Isolates with low-level vancomycin resistance associated with persistent methicillin-resistant Staphylococcus aureus bacteremia. Antimicrob. Agents Chemother. 50 (9): 3039-3047. 10.1128/AAC.00422-06 16940100 (Pubitemid 44396410)
35. Hutchings M.I. Palmer T. Harrington D.J. Sutcliffe I.C. 2009. Lipoprotein biogenesis in Gram-positive bacteria: knowing when to hold 'em, knowing when to fold 'em. Trends Microbiol. 17 (1): 13-21. 10.1016/j.tim.2008.10.001 19059780
36. Kaessmann H. 2010. Origins, evolution, and phenotypic impact of new genes. Genome Res. 20 (10): 1313-1326. 10.1101/gr.101386.109 20651121
37. Kent W.J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12 (4): 656-664. 11932250
38. Ko J. Splitter G.A. 2003. Molecular host-pathogen interaction in brucellosis: current understanding and future approaches to vaccine development for mice and humans. Clin. Microbiol. Rev. 16 (1): 65-78. 10.1128/CMR.16.1.65- 78.2003 12525425 (Pubitemid 36114707)
39. Kuroda A. Sugimoto Y. Funahashi T. Sekiguchi J. 1992. Genetic structure, isolation and characterization of a Bacillus licheniformis cell wall hydrolase. Mol. Gen. Genet. 234 (1): 129-137. 1495475
40. Kuroda M. Ohta T. Uchiyama I. Baba T. Yuzawa H. Kobayashi I. et al. 2001. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet, 357 (9264): 1225-1240. 10.1016/S0140-6736(00)04403-2 11418146 (Pubitemid 32539050)
41. Lawrence J.G. Hendrickson H. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50 (3): 739-749. 10.1046/j.1365-2958.2003. 03778.x 14617137 (Pubitemid 37372239)
42. LeClerc J.E. Li B. Payne W.L. Cebula T.A. 1996. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science, 274 (5290): 1208-1211. 10.1126/science.274.5290.1208 8895473 (Pubitemid 26389290)
43. LeClerc J.E. Payne W.L. Kupchella E. Cebula T.A. 1998. Detection of mutator subpopulations in Salmonella typhimurium LT2 by reversion of his alleles. Mutat. Res. 400 (1-2): 89-97. 10.1016/S0027-5107(98)00069-4 9685594 (Pubitemid 28440214)
44. Lowder B.V. Guinane C.M. Ben Zakour N.L. Weinert L.A. Conway-Morris A. Cartwright R.A. et al. 2009. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc. Natl. Acad. Sci. U.S.A. 106 (46): 19545-19550. 10.1073/pnas.0909285106 19884497
45. Matic I. Radman M. Taddei F. Picard B. Doit C. Bingen E. et al. 1997. Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science, 277 (5333): 1833-1834. 10.1126/science.277.5333.1833 9324769 (Pubitemid 27449197)
46. Maynard Smith J. Smith N.H. 1998. Detecting recombination from gene trees. Mol. Biol. Evol. 15 (5): 590-599. 9580989 (Pubitemid 28194624)
47. Mostowy S. Inwald J. Gordon S. Martin C. Warren R. Kremer K. et al. 2005. Revisiting the evolution of Mycobacterium bovis. J. Bacteriol. 187 (18): 6386-6395. 10.1128/JB.187.18.6386-6395.2005 16159772 (Pubitemid 41318398)
48. Mwangi M.M. Wu S.W. Zhou Y. Sieradzki K. de Lencastre H. Richardson P. et al. 2007. Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc. Natl. Acad. Sci. U.S.A. 104 (22): 9451-9456. 10.1073/pnas.0609839104 17517606 (Pubitemid 47185800)
49. Neoh H.M. Cui L. Yuzawa H. Takeuchi F. Matsuo M. Hiramatsu K. 2008. Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob. Agents Chemother. 52 (1): 45-53. 10.1128/AAC.00534-07 17954695
50. Noble W.C. Virani Z. Cree R.G. 1992. Co-transfer of vancomycin and other resistance genes from Enterococcus faecalis NCTC 12201 to Staphylococcus aureus. FEMS Microbiol. Lett. 93 (2): 195-198. 10.1111/j.1574-6968.1992.tb05089.x 1505742
51. Nowick K. Stubbs L. 2010. Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief. Funct. Genomics, 9 (1): 65-78. 10.1093/bfgp/elp056 20081217
52. O'Brien F.G. Lim T.T. Winnett D.C. Coombs G.W. Pearson J.C. Delgado A. et al. 2005. Survey of methicillin-resistant Staphylococcus aureus strains from two hospitals in El Paso, Texas. J. Clin. Microbiol. 43 (6): 2969-2972. 10.1128/JCM.43.6.2969-2972.2005 15956434 (Pubitemid 40827989)
53. Ohta T. Hirakawa H. Morikawa K. Maruyama A. Inose Y. Yamashita A. et al. 2004. Nucleotide substitutions in Staphylococcus aureus strains, Mu50, Mu3, and N315. DNA Res. 11 (1): 51-56. 10.1093/dnares/11.1.51 15141945 (Pubitemid 40036634)
54. Oliver A. Baquero F. Blazquez J. 2002. The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants. Mol. Microbiol. 43 (6): 1641-1650. 10.1046/j.1365-2958.2002.02855.x 11952911 (Pubitemid 34595553)
55. Post F.A. Willcox P.A. Mathema B. Steyn L.M. Shean K. Ramaswamy S.V. et al. 2004. Genetic polymorphism in Mycobacterium tuberculosis isolates from patients with chronic multidrug-resistant tuberculosis. J. Infect. Dis. 190 (1): 99-106. 10.1086/421501 15195248 (Pubitemid 38858409)
56. Poulet S. Cole S.T. 1995. Characterization of the highly abundant polymorphic GC-rich-repetitive sequence (PGRS) present in Mycobacterium tuberculosis. Arch. Microbiol. 163 (2): 87-95. 10.1007/BF00381781 7710330
57. Prunier A.L. Leclercq R. 2005. Role of mutS and mutL genes in hypermutability and recombination in Staphylococcus aureus. J. Bacteriol. 187 (10): 3455-3464. 10.1128/JB.187.10.3455-3464.2005 15866932 (Pubitemid 40628701)
58. Prunier A.L. Malbruny B. Tande D. Picard B. Leclercq R. 2002. Clinical isolates of Staphylococcus aureus with ribosomal mutations conferring resistance to macrolides. Antimicrob. Agents Chemother. 46 (9): 3054-3056. 10.1128/AAC.46.9.3054-3056.2002 12183270
59. Reinhardt J.A. Baltrus D.A. Nishimura M.T. Jeck W.R. Jones C.D. Dangl J.L. 2009. De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Res. 19 (2): 294-305. 10.1101/gr.083311.108 19015323
60. Richardson A.R. Yu Z. Popovic T. Stojiljkovic I. 2002. Mutator clones of Neisseria meningitidis in epidemic serogroup A disease. Proc. Natl. Acad. Sci. U.S.A. 99 (9): 6103-6107. 10.1073/pnas.092568699 11983903 (Pubitemid 34493272)
61. Saldanha A.J. 2004. Java Treeview-extensible visualization of microarray data. Bioinformatics, 20 (17): 3246-3248. 10.1093/bioinformatics/bth349 15180930 (Pubitemid 39619217)
62. Schneewind O. Fowler A. Faull K.F. 1995. Structure of the cell wall anchor of surface proteins in Staphylococcus aureus. Science, 268 (5207): 103-106. 10.1126/science.7701329 7701329
63. Schwaber M.J. Wright S.B. Carmeli Y. Venkataraman L. DeGirolami P.C. Gramatikova A. et al. 2003. Clinical implications of varying degrees of vancomycin susceptibility in methicillin-resistant Staphylococcus aureus bacteremia. Emerg. Infect. Dis. 9 (6): 657-664. 12781004 (Pubitemid 36676360)
64. Sieradzki K. Roberts R.B. Haber S.W. Tomasz A. 1999. The development of vancomycin resistance in a patient with methicillin-resistant Staphylococcus aureus infection. N. Engl. J. Med. 340 (7): 517-523. 10.1056/NEJM199902183400704 10021472 (Pubitemid 29093287)
65. Sieradzki K. Leski T. Dick J. Borio L. Tomasz A. 2003. Evolution of a vancomycin-intermediate Staphylococcus aureus strain in vivo: multiple changes in the antibiotic resistance phenotypes of a single lineage of methicillin-resistant S. aureus under the impact of antibiotics administered for chemotherapy. J. Clin. Microbiol. 41 (4): 1687-1693. 10.1128/JCM.41.4.1687- 1693.2003 12682161 (Pubitemid 36428118)
66. Sivaraman K. Venkataraman N. Tsai J. Dewell S. Cole A.M. 2008. Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage. BMC Genomics, 9 (1): 433. 10.1186/1471-2164-9-433 18808706
67. Smania A.M. Segura I. Pezza R.J. Becerra C. Albesa I. Argarana C.E. 2004. Emergence of phenotypic variants upon mismatch repair disruption in Pseudomonas aeruginosa. Microbiology, 150 (5): 1327-1338. 10.1099/mic.0.26751-0 15133095 (Pubitemid 38744735)
68. T and comparative genomic insights into plant pathogenicity. BMC Genomics, 11 (1): 2. 10.1186/1471-2164-11-2 20047678
69. Sniegowski P.D. Gerrish P.J. Lenski R.E. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature, 387 (6634): 703-705. 10.1038/42701 9192894 (Pubitemid 27270609)
70. Sutcliffe I.C. Harrington D.J. 2002. Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes. Microbiology, 148 (7): 2065-2077. 12101295 (Pubitemid 34785291)
71. Sutcliffe I.C. Harrington D.J. 2004. Lipoproteins of Mycobacterium tuberculosis: an abundant and functionally diverse class of cell envelope components. FEMS Microbiol. Rev. 28 (5): 645-659. 10.1016/j.femsre.2004.06.002 15539077 (Pubitemid 39469923)
72. Sutcliffe I.C. Black G.W. Harrington D.J. 2008. Bioinformatic insights into the biosynthesis of the Group B carbohydrate in Streptococcus agalactiae. Microbiology, 154 (5): 1354-1363. 10.1099/mic.0.2007/014522-0 18451044
73. Tenover, F.C., and Gayne, R.P. 2000. The epidemiology of Staphylococcus infections. In Gram-Positive Pathogens. Edited by V.A. Fischetti, R.P. Novick, J.J. Ferretti, D.A. Portnoy, and J.I. Rood. American Society for Microbiology, Washington, DC.
74. Tenover F.C. Lancaster M.V. Hill B.C. Steward C.D. Stocker S.A. Hancock G.A. et al. 1998. Characterization of staphylococci with reduced susceptibilities to vancomycin and other glycopeptides. J. Clin. Microbiol. 36 (4): 1020-1027. 9542929 (Pubitemid 28146289)
75. Tenover F.C. Biddle J.W. Lancaster M.V. 2001. Increasing resistance to vancomycin and other glycopeptides in Staphylococcus aureus. Emerg. Infect. Dis. 7 (2): 327-332. 10.3201/eid0702.010237 11294734 (Pubitemid 32374355)
76. Thompson J.D. Higgins D.G. Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (22): 4673-4680. 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
77. Watson M.E. Jr Burns J.L. Smith A.L. 2004. Hypermutable Haemophilus influenzae with mutations in mutS are found in cystic fibrosis sputum. Microbiology, 150 (9): 2947-2958. 10.1099/mic.0.27230-0 15347753 (Pubitemid 39317796)
78. Weidenmaier C. Kokai-Kun J.F. Kristian S.A. Chanturiya T. Kalbacher H. Gross M. et al. 2004. Role of teichoic acids in Staphylococcus aureus nasal colonization, a major risk factor in nosocomial infections. Nat. Med. 10 (3): 243-245. 10.1038/nm991 14758355 (Pubitemid 38667612)
79. Weidenmaier C. Peschel A. Xiong Y.Q. Kristian S.A. Dietz K. Yeaman M.R. Bayer A.S. 2005. Lack of wall teichoic acids in Staphylococcus aureus leads to reduced interactions with endothelial cells and to attenuated virulence in a rabbit model of endocarditis. J. Infect. Dis. 191 (10): 1771-1777. 10.1086/429692 15838806 (Pubitemid 40656767)
80. Weidenmaier C. Kokai-Kun J.F. Kulauzovic E. Kohler T. Thumm G. Stoll H. et al. 2008. Differential roles of sortase-anchored surface proteins and wall teichoic acid in Staphylococcus aureus nasal colonization. Int. J. Med. Microbiol. 298 (5-6): 505-513. 10.1016/j.ijmm.2007.11.006 18221914
81. Wong S.S. Ng T.K. Yam W.C. Tsang D.N. Woo P.C. Fung S.K. Yuen K.Y. 2000. Bacteremia due to Staphylococcus aureus with reduced susceptibility to vancomycin. Diagn. Microbiol. Infect. Dis. 36 (4): 261-268. 10.1016/S0732- 8893(99)00141-8 10764969 (Pubitemid 30179648)
82. Yang R. Guo X. Yang J. Jiang Y. Pang B. Chen C. et al. 2009. Genomic research for important pathogenic bacteria in China. Sci. China C Life Sci. 52 (1): 50-63. 10.1007/s11427-009-0009-4 19152084
83. Yu G.X. 2009. Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution. BMC Bioinformatics, 10 (Suppl. 1): S3. 10.1186/1471-2105-10-S1-S3 19208130
84. Htr, a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing. BMC Bioinformatics, 11 (1): 508. 10.1186/1471-2105-11-508 20939910
85. Yu G.X. Snyder E.E. Boyle S.M. Crasta O.R. Czar M. Mane S.P. et al. 2007. A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case. Nucleic Acids Res. 35 (12): 3953-3962. 10.1093/nar/gkm377 17553834 (Pubitemid 47244617)