Chromosomal rearrangements in salmonella enterica serovar typhi strains isolated from asymptomatic human carriers

mBio

Volumn 2, Issue 3, 2011, Pages

  Matthews, T David ^a   Rabsch, Wolfgang ^b   Maloy, Stanley ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b ROBERT KOCH INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GROWTH; BACTERIAL SURVIVAL; BACTERIOPHAGE TYPING; BACTERIUM CARRIER; BACTERIUM COLONY; BACTERIUM ISOLATION; CHROMOSOME REARRANGEMENT; CHROMOSOME STRUCTURE; CULTURE MEDIUM; ENVIRONMENTAL TEMPERATURE; HOST RANGE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SALMONELLA ENTERICA; SALMONELLA TYPHI; SEROTYPE; BACTERIAL CHROMOSOME; CLASSIFICATION; FEMALE; GENE REARRANGEMENT; GENETIC RECOMBINATION; GENETICS; GENOMIC INSTABILITY; HETEROZYGOTE; HUMAN; ISOLATION AND PURIFICATION; LONGITUDINAL STUDY; MICROBIOLOGY; OPERON; TYPHOID FEVER;

BACTERIA (MICROORGANISMS); SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI; SALMONELLA TYPHI;

BACTERIOPHAGE TYPING; CARRIER STATE; CHROMOSOMES, BACTERIAL; FEMALE; GENE REARRANGEMENT; GENOMIC INSTABILITY; HUMANS; LONGITUDINAL STUDIES; RECOMBINATION, GENETIC; RRNA OPERON; SALMONELLA TYPHI; TYPHOID FEVER;

EID: 84855194561     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00060-11     Document Type: Article

References (65)

1. Guibourdenche M, et al. 2010. Supplement 2003-2007 (no. 47) to the White-Kauffmann-Le Minor scheme. Res. Microbiol. 161:26-29.
2. Popoff MY, Le Minor LE. 2005. Salmonella, p 764-799. In Garrity GM, (ed), Bergey's manual of systematic bacteriology, 2nd ed. Springer Science-Business Media, Inc., New York, NY.
3. Rabsch W, et al. 2002. Salmonella enterica serotype Typhimurium and its host-adapted variants. Infect. Immun. 70:2249-2255.
4. Chiu CH, et al. 2005. The genome sequence of Salmonella enterica serovar Choleraesuis, a highly invasive and resistant zoonotic pathogen. Nucleic Acids Res. 33:1690-1698.
5. Deng W, et al. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185:2330-2337.
6. Jarvik T, Smillie C, Groisman EA, Ochman H. 2010. Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J. Bacteriol. 192:560-567.
7. Liu WQ, et al. 2009. Salmonella paratyphi C: genetic divergence from Salmonella choleraesuis and pathogenic convergence with Salmonella typhi. PLoS One 4:e4510.
8. McClelland M, et al. 2004. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nat. Genet. 36:1268-1274.
9. McClelland M, et al. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
10. Parkhill J, et al. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848-852.
11. Thomson NR, et al. 2008. Comparative genome analysis of Salmonella enteritidis PT4 and Salmonella gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res. 18:1624-1637.
12. Edwards RA, Olsen GJ, Maloy SR. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10:94-99.
13. Figueroa-Bossi N, Bossi L. 1999. Inducible prophages contribute to Salmonella virulence in mice. Mol. Microbiol. 33:167-176.
14. Figueroa-Bossi N, Coissac E, Netter P, Bossi L. 1997. Unsuspected prophage-like elements in Salmonella typhimurium. Mol. Microbiol. 25: 161-173.
15. Figueroa-Bossi N, Uzzau S, Maloriol D, Bossi L. 2001. Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol. Microbiol. 39:260-271.
16. Ho TD, Slauch JM. 2001. Characterization of grvA, an antivirulence gene on the Gifsy-2 phage in Salmonella enterica serovar Typhimurium. J. Bacteriol. 183:611-620.
17. Stanley TL, Ellermeier CD, Slauch JM. 2000. Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar Typhimurium survival in Peyer's patches. J. Bacteriol. 182:4406-4413.
18. Chain PS, et al. 2004. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. U. S. A. 101:13826-13831.
19. Chain PS, et al. 2006. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188:4453-4463.
20. Jin Q, et al. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
21. Nie H, et al. 2006. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 7:173.
22. Parkhill J, et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35:32-40.
23. Wei J, et al. 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71: 2775-2786.
24. Moran NA, McLaughlin HJ, Sorek R. 2009. The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323:379-382.
25. Lindroos H, et al. 2006. Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae. J. Bacteriol. 188: 7426-7439.
26. Matthews TD, Edwards R, Maloy S. 2010. Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars. PLoS One 5:e13503.
27. Matthews TD, Maloy S. 2010. Genome rearrangements in Salmonella, p 41-48. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of foodborne and waterborne pathogens. ASM Press, Washington, DC.
28. Petrosino JF, et al. 2006. Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J. Bacteriol. 188:6977-6985.
29. Liu GR, et al. 2002. The evolving genome of Salmonella enterica serovar Pullorum. J. Bacteriol. 184:2626-2633.
30. Wu KY, et al. 2005. The genome of Salmonella enterica serovar Gallinarum: distinct insertions/deletions and rare rearrangements. J. Bacteriol. 187:4720-4727.
31. Kothapalli S, et al. 2005. Diversity of genome structure in Salmonella enterica serovar Typhi populations. J. Bacteriol. 187:2638-2650.
32. Liu SL, Sanderson KE. 1995. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG. J. Bacteriol. 177: 6585-6592.
33. Liu SL, Sanderson KE. 1995. Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. U. S. A. 92:1018-1022.
34. Liu SL, Sanderson KE. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. U. S. A. 93:10303-10308.
35. Liu SL, Sanderson KE. 1998. Homologous recombination between rrn operons rearranges the chromosome in host-specialized species of Salmonella. FEMS Microbiol. Lett. 164:275-281.
36. Liu SL, Sanderson KE. 1995. I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J. Bacteriol. 177: 3355-3357.
37. Helm RA, Lee AG, Christman HD, Maloy S. 2003. Genomic rearrangements at rrn operons in Salmonella. Genetics 165:951-959.
38. Porwollik S, et al. 2004. DNA amplification and rearrangements in archival Salmonella enterica serovar Typhimurium LT2 cultures. J. Bacteriol. 186:1678-1682.
39. Helm RA, et al. 2004. Pigeon-associated strains of Salmonella enterica serovar Typhimurium phage type DT2 have genomic rearrangements at rRNA operons. Infect. Immun. 72:7338-7341.
40. Liu GR, et al. 2006. Genome plasticity and ori-ter rebalancing in Salmonella typhi. Mol. Biol. Evol. 23:365-371.
41. Rabsch W, Truepschuch S, Windhorst D, Gerlach R. 2011. Typing phages and prophages of Salmonella, p 25-48. In Porwollik S (ed), Salmonella: from genome to function. Caister Academic Press, Norwich, United Kingdom.
42. Craigie J, Felix A. 1947. Typing of typhoid bacilli with Vi bacteriophage; suggestions for its standardisation. Lancet i: 823-827.
43. Craigie J, Yen CE. 1938. The demonstration of types of B. typhosus by means of preparations of type II Vi-phage. Can. Public Health J. 29: 448-483.
44. Altwegg M, Hickman-Brenner FW, Farmer JJ, III. 1989. Ribosomal RNA gene restriction patterns provide increased sensitivity for typing Salmonella typhi strains. J. Infect. Dis. 160:145-149.
45. Anderson ES, Williams RE. 1956. Bacteriophage typing of enteric pathogens and staphylococci and its use in epidemiology. J. Clin. Pathol. 9:94-127.
46. Nair S, Poh CL, Lim YS, Tay L, Goh KT. 1994. Genome fingerprinting of Salmonella typhi by pulsed-field gel electrophoresis for subtyping common phage types. Epidemiol. Infect. 113:391-402.
47. Nastasi A, Mammina C, Villafrate MR. 1991. Rdna fingerprinting as a tool in epidemiological analysis of Salmonella typhi infections. Epidemiol. Infect. 107:565-576.
48. Navarro F, et al. 1996. Molecular typing of Salmonella enterica serovar Typhi. J. Clin. Microbiol. 34:2831-2834.
49. Thong KL, Cheong YM, Puthucheary S, Koh CL, Pang T. 1994. Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis. J. Clin. Microbiol. 32: 1135-1141.
50. Threlfall EJ, et al. 1994. Insertion sequence IS200 fingerprinting of Salmonella typhi: an assessment of epidemiological applicability. Epidemiol. Infect. 112:253-261.
51. Rische H, Ziesché K. 1973. Salmonella typhi, p 23-64. In Rische H (ed), Infectionskrankheiten und ihre Erreger, vol. 14. Lysotypie und andere spezielle epidemiologische Laboratoriumsmethoden. Gustav Fischer Verlag, Jena, Germany.
52. Islam A, Butler T, Ward LR. 1987. Reinfection with a different Vi-phage type of Salmonella typhi in an endemic area. J. Infect. Dis. 155:155-156.
53. Marmion DE, Naylor GR, Stewart IO. 1953. Second attacks of typhoid fever. J. Hyg. (Lond.) 51:260-267.
54. Esnault E, Valens M, Espeli O, Boccard F. 2007. Chromosome structuring limits genome plasticity in Escherichia coli. PLoS Genet. 3:e226.
55. Hill CW, Harnish BW. 1981. Inversions between ribosomal RNA genes of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 78:7069-7072.
56. Louarn J, Patte J, Louarn JM. 1982. Suppression of Escherichia coli dnaA46 mutations by integration of plasmid R100.1 derivatives: constraints imposed by the replication terminus. J. Bacteriol. 151:657-667.
57. Louarn JM, Bouché JP, Legendre F, Louarn J, Patte J. 1985. Characterization and properties of very large inversions of the E. coli chromosome along the origin-to-terminus axis. Mol. Gen. Genet. 201:467-476.
58. Matthews TD, Maloy S. 2010. Fitness effects of replichore imbalance in Salmonella enterica. J. Bacteriol. 192:6086-6088.
59. Liu GR, et al. 2003. Genomic diversification among archival strains of Salmonella enterica serovar Typhimurium LT7. J. Bacteriol. 185: 2131-2142.
60. Anderson P, Roth J. 1981. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc. Natl. Acad. Sci. U. S. A. 78:3113-3117.
61. Reams AB, Kofoid E, Savageau M, Roth JR. 2010. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 184:1077-1094.
62. Sonti RV, Roth JR. 1989. Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources. Genetics 123:19-28.
63. Echeita MA, Usera MA. 1998. Chromosomal rearrangements in Salmonella enterica serotype Typhi affecting molecular typing in outbreak investigations. J. Clin. Microbiol. 36:2123-2126.
64. Wilson K. 1994. Preparation of genomic DNA from bacteria, p 2.4.1-2.4.5. In Ausubel FM, et al. (ed), Current protocols in molecular biology, vol. 1. John Wiley & Sons, Hoboken, NJ.
65. Helm RA, Maloy S. 2001. Rapid approach to determine rrn arrangement in Salmonella serovars. Appl. Environ. Microbiol. 67:3295-3298.