Adaptation of multilocus sequencing for studying variation within a major clone: Evolutionary relationships of Salmonella enterica serovar typhimurium

Genetics

Volumn 172, Issue 2, 2006, Pages 743-750

  Hu, Honghua ^a   Lan, Ruiting ^b   Reeves, Peter R ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BACTERIOPHAGE; BACTERIUM ISOLATE; COMPARATIVE STUDY; COMPUTER MODEL; CONTROLLED STUDY; GENE MUTATION; GENE SEQUENCE; GENETIC IDENTIFICATION; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR MODEL; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; SALMONELLA ENTERICA; SALMONELLA ENTERITIDIS; SALMONELLA GALLINARUM; SALMONELLA PARATYPHI; SALMONELLA TYPHI; SALMONELLA TYPHIMURIUM; SEROTYPE; SPECIES DISTRIBUTION;

CLONE CELLS; DNA MUTATIONAL ANALYSIS; DNA, INTERGENIC; EVOLUTION, MOLECULAR; GENETIC MARKERS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMONELLA TYPHIMURIUM; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); ENTERITIDIS; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR GALLINARUM; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; SALMONELLA ENTERITIDIS; SALMONELLA PARATYPHI; SALMONELLA TYPHI; SALMONELLA TYPHIMURIUM;

EID: 33644751750     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.046466     Document Type: Article

References (28)

1. ALLAND, D., T. S. WHITTAM, M. B. MURRAY, M. D. CAVE, M. H. HAZBON et al., 2003 Modeling bacterial evolution with comparative-genome-based marker systems: application to mycobacterium tuberculosis evolution and pathogenesis. J. Bacteriol. 185: 3392-3399.
2. ANDERSON, E. S., L. R. WARD, M. J. SAXE and J. D. DE SA, 1977 Bacteriophage typing designations of Salmonella typhimurium. J. Hyg. 78: 297-300.
3. BÄUMLER, A. J., R.M. TSOLIS, T. A. FICHT and L. G. ADAMS, 1998 Evolution of host adaptation in Salmonella enterica. Infect. Immun. 66: 4579-4587.
4. BISERCIC, M., J. Y. FEUTRIER and P. R. REEVES, 1991 Nucleotide sequence of the gnd gene from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus. J. Bacteriol. 173: 3894-3900.
5. CASJENS, S., D. A. WINN-STAPLEY, E. B. GILCREASE, R. MORONA, C. KUHLEWEIN et al., 2004 The chromosome of shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J. Mol. Biol. 339: 379-394.
6. DENG, W., S.-R. LIOU, G. PLUNKETT, III, G. F. MAYHEW, D. J. ROSE et al., 2003 Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185: 2330-2337.
7. FAKHR, M. K., L. K. NOLAN and C. M. LOGUE, 2005 Multilocus sequencing typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium. J. Clin. Microbiol. 43: 2215-2219.
8. FEIL, E. J., J. E. COOPER, H. GRUNDMANN, D. A. ROBINSON, M. C. ENRIGHT et al., 2003 How clonal is Staphylococcus aureus? J. Bacteriol. 185: 3307-3316.
9. GLYNN, M. K., C. BOPP, W. DEWITT, P. DABNEY, M. MOKHTAR et al., 1998 Emergence of multidrug-resistant Salmonella enterica serotype typhimurium DT104 infections in the United States. N. Engl. J. Med. 338: 1333-1338.
10. GORDON, D., C. ABAJIAN and P. GREEN, 1998 CONSED - A graphical tool for sequence finishing. Genome Res. 8: 195-202.
11. GUTACKER, M. M., J. C. SMOOT, C. A. L. MIGLIACCIO, S. M. RICKLEFS, S. HUA et al., 2002 Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 162: 1533-1543.
12. HU, H., R. LAN and P. R. REEVES, 2002 Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar Typhimurium reveals phage-type specific markers and potential for microarray typing. J. Clin. Microbiol. 40: 3406-3415.
13. KOTETISHVILI, M., O. C. STINE, A. KREGER, J. G. J. MORRIS AND A. SULAKVELIDZE, 2002 Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J. Clin. Microbiol. 40: 1626-1635.
14. LAM, S., and J. R. ROTH, 1983 IS200: a Salmonella-specific insertion sequence. Cell 34: 951-960.
15. LOW, J. C., M. ANGUS, G. HOPKINS, D. MUNRO and S. C. RANKIN, 1997 Antimicrobial resistance of Salmonella enterica typhimurium DT104 isolates and investigation of strains with transferable apramycin resistance. Epidemiol. Infect. 118: 97-103.
16. MCCLELLAND, M., K. E. SANDERSON, J. SPIETH, S. W. CLIFTON, P. LATREILLE et al., 2001 Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852-856.
17. MMOLAWA, P. T., R. WILLMORE, C. J. THOMAS and M. W. HEUZENROEDER, 2002 Temperate phages in Salmonella enterica serovar Typhimurium: implications for epidemiology. Int. J. Med. Microbiol. 291: 633-644.
18. PARKHILL, J., G. DOUGAN, K. D. JAMES, N. R. THOMSON, D. PICKARD et al., 2001 Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413: 848-852.
19. POWLING, J. (Editor), 1997a National Enteric Pathogens Surveillance Scheme: Human Annual Report 1996. Microbiological Diagnostic Unit, The University of Melbourne, Victoria, Australia.
20. POWLING, J. (Editor), 1997b National Enteric Pathogens Surveillance Scheme: Non-Human Annual Report 1996. Microbiological Diagnostic Unit, The University of Melbourne, Victoria, Australia.
21. RABSCH, W., H. L. ANDREWS, R. A. KINGSLEY, R. PRAGER, H. TSCHAPE et al., 2002 Salmonella enterica serotype Typhimurium and its host-adapted variants. Infect. Immun. 70: 2249-2255.
22. READ, T. D., S. L. SALZBERG, M. POP, M. SHUMWAY, L. UMAYAM et al., 2002 Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296: 2028-2033.
23. REEVES, P. R., L. FARNELL and R. LAN, 1994 MULTICOMP: a program for preparing sequence data for phylogenetic analysis. Comput. Appl. Biosci. 10: 281-284.
24. STADEN, R., 1994 Staden: searching for restriction sites. Methods Mol. Biol. 25: 79-85.
25. SWOFFORD, D. L., 1998 PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods). Sinauer Associates, Sunderland, MA.
26. THAMPAPILLAI, G., R. LAN and P. R. REEVES, 1994 Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11: 813-828.
27. THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON, 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specifc gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
28. VOS, P., R. HOGERS, M. BLEEKER, M. REIJANS, T. VAN DE LEE et al., 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23: 4407-4414.