Population genomics: diversity and virulence in the Neisseria

Current Opinion in Microbiology

Volumn 11, Issue 5, 2008, Pages 467-471

  Maiden, Martin CJ ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIAL VIRULENCE; GENE STRUCTURE; GENETIC VARIABILITY; HORIZONTAL GENE TRANSFER; MICROBIAL DIVERSITY; NEISSERIA; NEISSERIA GONORRHOEAE; NEISSERIA LACTAMICA; NEISSERIA MENINGITIDIS; NONHUMAN; PHENOTYPIC VARIATION; POPULATION STRUCTURE; REVIEW; SPECIES DIFFERENCE;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; HUMANS; NEISSERIA GONORRHOEAE; NEISSERIA LACTAMICA; NEISSERIA MENINGITIDIS; RECOMBINATION, GENETIC; VIRULENCE FACTORS;

BACTERIA (MICROORGANISMS); NEISSERIA; NEISSERIA GONORRHOEAE; NEISSERIA LACTAMICA; NEISSERIA MENINGITIDIS;

EID: 55049083674     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2008.09.002     Document Type: Review

References (52)

1. Medini D., Serruto D., Parkhill J., Relman D.A., Donati C., Moxon R., Falkow S., and Rappuoli R. Microbiology in the post-genomic era. Nat Rev Microbiol 6 (2008) 419-430. An excellent up-to-date review of post-genomic microbiology, covering both technological and conceptual aspects of this new science.
2. DeLong E.F. Microbial population genomics and ecology: the road ahead. Environ Microbiol 6 (2004) 875-878
3. Schoen C., Joseph B., Claus H., Vogel U., and Frosch M. Living in a changing environment: Insights into host adaptation in Neisseria meningitidis from comparative genomics. Int J Med Microbiol 297 (2007) 601-613
4. Tettelin H., Saunders N.J., Heidelberg J., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287 (2000) 1809-1815
5. Parkhill J., Achtman M., James K.D., Bentley S.D., Churcher C., Klee S.R., Morelli G., Basham D., Brown D., Chillingworth T., et al. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404 (2000) 502-506
6. Bentley S.D., Vernikos G.S., Snyder L.A., Churcher C., Arrowsmith C., Chillingworth T., Cronin A., Davis P.H., Holroyd N.E., Jagels K., et al. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C Strain FAM18. PLoS Genet 3 (2007) e23
7. Peng J., Yang L., Yang F., Yang J., Yan Y., Nie H., Zhang X., Xiong Z., Jiang Y., Cheng F., et al. Characterization of ST-4821 complex, a unique Neisseria meningitidis clone. Genomics 91 (2008) 78-87
8. Schoen C., Blom J., Claus H., Schramm-Gluck A., Brandt P., Muller T., Goesmann A., Joseph B., Konietzny S., Kurzai O., et al. Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitides. Proc Natl Acad Sci U S A 105 (2008) 3473-3478. The first whole genome comparison of meningococci isolated from disease and asymptomatic carriage, providing insights into the relationships of these bacteria and the nature and extent of the meningococcal pan genome. The study includes both full and partially assembled genome sequences.
9. Caugant D.A. Genetics and evolution of Neisseria meningitidis: importance for the epidemiology of meningococcal disease. Infect Genet Evol (2008). An informative up-to-date review of the epidemiology of meningococcal disease, with reference to the population genetics of this diverse organism.
10. Yazdankhah S.P., Kriz P., Tzanakaki G., Kremastinou J., Kalmusova J., Musilek M., Alvestad T., Jolley K.A., Wilson D.J., McCarthy N.D., et al. Distribution of serogroups and genotypes among disease-associated and carried isolates of Neisseria meningitidis from the Czech Republic, Greece, and Norway. J Clin Microbiol 42 (2004) 5146-5153
11. Tinsley C.R., and Nassif X. Analysis of the genetic differences between Neisseria meningitidis and Neisseria gonorrhoeae: two closely related bacteria expressing two different pathogenicities. Proc Natl Acad Sci U S A 93 (1996) 11109-11114
12. Bart A., Dankert J., and van der Ende A. Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone. FEMS Microbiol Lett 188 (2000) 111-114
13. Maiden M.C. Multilocus sequence typing of bacteria. Annu Rev Microbiol 60 (2006) 561-588
14. Brehony C., Jolley K.A., and Maiden M.C. Multilocus sequence typing for global surveillance of meningococcal disease. FEMS Microbiol Rev 31 (2007) 15-26
15. Maiden M.C., Ibarz-Pavon A.B., Urwin R., Gray S.J., Andrews N.J., Clarke S.C., Walker A.M., Evans M.R., Kroll J.S., Neal K.R., et al. Impact of meningococcal serogroup C conjugate vaccines on carriage and herd immunity. J Infect Dis (2008). Describing one of the largest MLST studies conducted to date; this paper shows how the population structure of carried meningococci was changed by the introduction of a serogroup C polysaccharide vaccine. The high efficacy of the vaccine was a consequence of herd immunity, made especially effective by the association of a hyperinvasive genotype with the vaccine antigen.
16. Grifantini R., Bartolini E., Muzzi A., Draghi M., Frigimelica E., Berger J., Ratti G., Petracca R., Galli G., Agnusdei M., et al. Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 20 (2002) 914-921
17. Stabler R.A., Marsden G.L., Witney A.A., Li Y., Bentley S.D., Tang C.M., and Hinds J. Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiology 151 (2005) 2907-2922
18. Hotopp J.C., Grifantini R., Kumar N., Tzeng Y.L., Fouts D., Frigimelica E., Draghi M., Giuliani M.M., Rappuoli R., Stephens D.S., et al. Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes. Microbiology 152 (2006) 3733-3749
19. Snyder L.A., and Saunders N.J. The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as 'virulence genes'. BMC Genomics 7 (2006) 128. A microarray-based study that shows that most genes, including candidate 'virulence' genes are shared between the meningococcus and Neisseria lactamica. This demonstrates the genetic homogeneity of these two species, not withstanding their phenotypic difference in host age preference and proclivity to cause disease.
20. Claus H., Vogel U., Swiderek H., Frosch M., and Schoen C. Microarray analyses of meningococcal genome composition and gene regulation: a review of the recent literature. FEMS Microbiol Rev 31 (2007) 43-51
21. Peng J., Zhang X., Shao Z., Yang L., and Jin Q. Characterization of a new Neisseria meningitidis serogroup C clone from China. Scand J Infect Dis 40 (2008) 63-66
22. Swiderek H., Claus H., Frosch M., and Vogel U. Evaluation of custom-made DNA microarrays for multilocus sequence typing of Neisseria meningitidis. Int J Med Microbiol 295 (2005) 39-45
23. Hanage W.P., Fraser C., and Spratt B.G. Fuzzy species among recombinogenic bacteria. BMC Biol 3 (2005) 6
24. Sheppard S.K., McCarthy N.D., Falush D., and Maiden M.C. Convergence of Campylobacter species: implications for bacterial evolution. Science 320 (2008) 237-239. This study of MLST data from Campylobacter shows how ecological factors can influence speciation events in the bacteria, with species emerging as a consequence of limitations in gene flow but converging or despeciating if these barriers are removed.
25. Taha M.K., Vazquez J.A., Hong E., Bennett D.E., Bertrand S., Bukovski S., Cafferkey M.T., Carion F., Christensen J.J., Diggle M., et al. Target gene sequencing to characterize the penicillin G susceptibility of Neisseria meningitidis. Antimicrob Agents Chemother 51 (2007) 2784-2792
26. Zhu P., van der Ende A., Falush D., Brieske N., Morelli G., Linz B., Popovic T., Schuurman I.G., Adegbola R.A., Zurth K., et al. Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc Natl Acad Sci U S A 98 (2001) 5234-5239
27. Bennett J.S., Jolley K.A., Sparling P.F., Saunders N.J., Hart C.A., Feavers I.M., and Maiden M.C. Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from MLST. BMC Biol 5 (2007) 35
28. Fraser C., Hanage W.P., and Spratt B.G. Recombination and the nature of bacterial speciation. Science 315 (2007) 476-480. A valuable account of bacterial speciation and the effect of recombination in establishing species boundaries.
29. Koeppel A., Perry E.B., Sikorski J., Krizanc D., Warner A., Ward D.M., Rooney A.P., Brambilla E., Connor N., Ratcliff R.M., et al. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Nat Acad Sci U S A 105 (2008) 2504-2509
30. Ahmed N., Dobrindt U., Hacker J., and Hasnain S.E. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol 6 (2008) 387-394
31. Snyder L.A., Jarvis S.A., and Saunders N.J. Complete and variant forms of the 'gonococcal genetic island' in Neisseria meningitidis. Microbiology 151 (2005) 4005-4013
32. Davidsen T., Rodland E.A., Lagesen K., Seeberg E., Rognes T., and Tonjum T. Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res 32 (2004) 1050-1058
33. Treangen T.J., Ambur O.H., Tonjum T., and Rocha E.P. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 9 (2008) R60. An intriguing study of the distribution of DNA uptake sequences in Neisseria genomes, with the provocative conclusion that recombination acts to stabilise genomes to evolutionary change.
34. Hanage W.P., Fraser C., and Spratt B.G. The impact of homologous recombination on the generation of diversity in bacteria. J Theor Biol 239 (2006) 210-219
35. Davidsen T., and Tonjum T. Meningococcal genome dynamics. Nat Rev Microbiol 4 (2006) 11-22
36. Claus H., Friedrich A., Frosch M., and Vogel U. Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis. J Bacteriol 182 (2000) 1296-1303
37. Claus H., Maiden M.C., Wilson D.J., McCarthy N.D., Jolley K.A., Urwin R., Hessler F., Frosch M., and Vogel U. Genetic analysis of meningococci carried by children and young adults. J Infect Dis 191 (2005) 1263-1271
38. Jolley K.A., Kalmusova J., Feil E.J., Gupta S., Musilek M., Kriz P., and Maiden M.C. Carried meningococci in the Czech Republic: a diverse recombining population. J Clin Microbiol 40 (2002) 3549-3550
39. Jolley K.A., Wilson D.J., Kriz P., McVean G., and Maiden M.C. The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol Biol Evol 22 (2005) 562-569
40. Caugant D.A., Frøholm L.O., Bovre K., Holten E., Frasch C.E., Mocca L.F., Zollinger W.D., and Selander R.K. Intercontinental spread of a genetically distinctive complex of clones of Neisseria meningitidis causing epidemic disease. Proc Natl Acad Sci U S A 83 (1986) 4927-4931
41. Fraser C., Hanage W.P., and Spratt B.G. Neutral microepidemic evolution of bacterial pathogens. Proc Natl Acad Sci U S A 102 (2005) 1968-1973
42. Buckee CO, Jolley K, Recker M, Penman B, Kriz P, Gupta S, Maiden MC: Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis. Proc Natl Acad Sci U S A, in press.
43. Urwin R., Russell J.E., Thompson E.A., Holmes E.C., Feavers I.M., and Maiden M.C. Distribution of surface protein variants among hyperinvasive meningococci: implications for vaccine design. Infect Immun 72 (2004) 5955-5962
44. Harrison L.H., Jolley K.A., Shutt K.A., Marsh J.W., O'Leary M., Sanza L.T., and Maiden M.C. Antigenic shift and increased incidence of meningococcal disease. J Infect Dis 193 (2006) 1266-1274
45. Callaghan M.J., Jolley K.A., and Maiden M.C. Opacity-associated adhesin repertoire in hyperinvasive Neisseria meningitidis. Infect Immun 74 (2006) 5085-5094
46. Callaghan M.J., Buckee C.O., Jolley K.A., Kriz P., Maiden M.C., and Gupta S. The effect of immune selection on the structure of the meningococcal opa protein repertoire. PLoS Pathogens 4 (2008) e1000020
47. Falush D., and Bowden R. Genome-wide association mapping in bacteria?. Trends Microbiol 14 (2006) 353-355
48. Bille E., Zahar J.R., Perrin A., Morelle S., Kriz P., Jolley K.A., Maiden M.C., Dervin C., Nassif X., and Tinsley C.R. A chromosomally integrated bacteriophage in invasive meningococci. J Exp Med 201 (2005) 1905-1913
49. Russell J.E., Urwin R., Gray S.J., Fox A.J., Feavers I.M., and Maiden M.C. Molecular epidemiology of meningococcal disease in England and Wales 1975-1995, before the introduction of serogroup C conjugate vaccines. Microbiology 154 (2008) 1170-1177
50. Pizza M., Scarlato V., Masignani V., Giuliani M.M., Arico B., Comanducci M., Jennings G.T., Baldi L., Bartolini E., Capecchi B., et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287 (2000) 1816-1820
51. Geoffroy M.C., Floquet S., Metais A., Nassif X., and Pelicic V. Large-scale analysis of the meningococcus genome by gene disruption: resistance to complement-mediated lysis. Genome Res 13 (2003) 391-398
52. Sun Y.H., Bakshi S., Chalmers R., and Tang C. Functional genomics of Neisseria meningitidis pathogenesis. Nat Med 6 (2000) 1269-1273