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Chapter 8 : Evolutionary and Population Biology of

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Abstract:

Bacteria exist within populations, whether it is the population of pneumococci in the nasopharynx of an individual child or the isolates circulating within a local community, within a country, or globally. Multilocus enzyme electrophoresis (MLEE) is such a technique, and it has provided key insights into the population biology of many bacterial pathogens. The relationships among major lineages could be explored using a tree constructed from the concatenated sequences of all seven MLST loci. Pneumococcal clones diversify relatively rapidly, due mainly to the substantial impact of homologous recombination, presumably mediated by genetic transformation, which results in small segments of the chromosome of a recipient pneumococcus being replaced with the corresponding region from a distinct strain. Multiply antibiotic-resistant isolates of cannot have existed prior to the introduction of antibiotics into medicine and are probably less than 30 years old, yet considerable variation in the allelic profiles of the major resistant clones is observed. The carried population is thus of primary interest to the population biologist, and disease isolates need to be considered in the context of carriage. Antibiotic resistance might be expected to have arisen in those clones that were commonly carried in the nasopharynges of children. Serotypes that are rarely encountered in developed countries appear to cause a substantial amount of disease in some developing countries.

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8

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Acute Otitis Media
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Multilocus Sequence Typing
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Figures

Image of FIGURE 1
FIGURE 1

Emergence of a clonal complex. (A) A pneumococcal isolate increases in frequency in the population (shown by the increasing size of the circle) and starts to diversify. Initially the isolates appear uniform by MLST (ST1), but diversification results in variants (ST2 to ST10) that have a different allele at one of the seven MLST loci (SLVs); one of these SLVs (ST10) has diversified further to form a DLV (ST11). (B) The isolates resulting from the diversification of ST1 are shown as an eBURST diagram. The founder of the clonal complex identified by eBURST is placed centrally with radial links to its derived SLVs. The SLV that diversified to form a DLV is also linked.

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8
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Image of FIGURE 2
FIGURE 2

Relatedness among isolates of the Spain-1 (ST81) clonal complex. The tree was constructed from the matrix of pairwise differences between the allelic profiles of isolates in the pneumococcal MLST database that shared alleles at four or more loci with ST81. The pneumococcal MLST database was analyzed by eBURST, and the clonal complex including ST81 was displayed as an eBURST diagram. The areas of the circles representing the individual STs (except for ST81, ST numbers are not shown) indicate the prevalence of each ST in the current database. The isolate on the tree indicated by an arrow is a DLV of ST81. eBURST is conservative, and DLVs of the founding genotype for which the linking SLV is not represented in the input data are not shown ( ). For this reason the DLV of ST81 is not shown in the eBURST diagram. The serotypes of the isolates of ST81 in the MLST database are shown on the tree (the number of isolates of each serotype is shown in parentheses), as are the serotypes of its SLVs on the eBURST diagram. Except for ST81, ST numbers are not shown on the tree or eBURST diagram.

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8
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Image of FIGURE 3
FIGURE 3

Relatedness of the alleles at MLST loci. A neighbor-joining tree was constructed from the sequences of the alleles at five of the MLST loci (http://spneumoniae.mlst.net). Only those alleles present in serotypeable pneumococci were included, as these almost certainly are authentic pneumococci. The alleles at one of these housekeeping loci () are all very similar in sequence, as are the great majority of alleles at , and (and and [data not shown]), but a few alleles of the latter loci are about 5% diverged from the typical pneumococcal alleles. The rare divergent alleles have presumably been introduced by interspecies recombination from very closely related streptococcal isolates. The large number of more highly divergent alleles (typically 10% divergent), which occur in penicillin-resistant isolates, are also the result of interspecies recombination, which in this case is driven by its close genetic linkage to the penicillin-binding protein 2b gene (see text). The scale bar corresponds to a genetic distance of 0.01 (1%).

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8
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Image of FIGURE 4
FIGURE 4

Genetic diversity of isolates of serotype 19F. The allelic profiles of all isolates of serotype 19F were extracted from the MLST database, and a dendrogram was constructed based on the pairwise differences in the profiles. The two most prevalent serotype 19F clones in the database are labeled; one of these corresponds to ST81, the Spain-1 clone, as serotype 19F variants of this clone are now prevalent.

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8
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Image of FIGURE 5
FIGURE 5

Serotype changes within a penicillin-susceptible clonal complex. The clonal complex was identified within the MLST database and was displayed using eBURST; the serotypes of isolates of each ST were obtained from the pneumococcal MLST database.

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8
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References

/content/book/10.1128/9781555816537.chap8
1. Adrian, P. V,, and K. P. Klugman. 1997. Mutations in the dihydrofolate reductase gene of trimethoprim-resistant isolates of Streptococcus pneumoniae. Antimicrob. Agents Chemother. 41:24062413.
2. Austrian, R. 1986. Some aspects of the pneumococcal carrier state. J. Antimicrob. Chemother. 18(Suppl. A):3545.
3. Brito, D. A.,, M. Ramirez,, and H. de Lencastre. 2003. Serotyping Streptococcus pneumoniae by multiplex PCR. J. Clin. Microbiol. 41:23782384.
4. Brueggemann, A. B.,, D. T. Griffiths,, E. Meats,, T. Peto,, D. W. Crook,, and B. G. Spratt. 2003. Clonal relationships between invasive and carriage Streptococcus pneumoniae, and serotype- and clone-specific differences in invasive disease potential. J. Infect. Dis. 187:14241432.
5. Brueggemann, A. B.,, and B. G. Spratt. 2003. Geographic distribution and clonal diversity of Streptococcus pneumoniae serotype 1 isolates. J. Clin. Microbiol., 41:386392.
6. Coffey, T. J.,, C. G. Dowson,, M. Daniels,, and B. G. Spratt. 1995. Genetics and molecular biology of β-lactam-resistant pneumococci. Microb. Drug Resist. 1:2530.
7. Coffey, T. J.,, M. C. Enright,, M. Daniels,, J. K. Morona,, R. Morona,, W. Hryniewicz,, J. C. Paton,, and B. G. Spratt. 1998. Recombinational exchanges at the capsular polysaccharide biosynthetic locus lead to frequent serotype changes among natural isolates of Streptococcus pneumoniae. Mol. Microbiol. 27:7383.
8. Coffey, T. J.,, M. Daniels,, M. C. Enright,, and B. G. Spratt. 1999. Serotype 14 variants of the Spanish penicillin-resistant serotype 9V clone of Streptococcus pneumoniae arose by large recombinational replacements of the cpsA-pbp1a region. Microbiology 145:20232031.
9. Dagan, R.,, N. Givon-Lavi,, O. Zamir,, M. Sikuler-Cohen,, L. Guy,, J. Janco,, P. Yagupsky,, and D. Fraser. 2002. Reduction of nasopharyngeal carriage of Streptococcus pneumoniae after administration of a 9-valent pneumococcal conjugate vaccine to toddlers attending day care centers. J. Infect. Dis. 185:927936.
10. de Lencastre, H.,, and A. Tomasz. 2002. From ecological reservoir to disease: the nasopharynx, day-care centres and drug-resistant clones of Streptococcus pneumoniae. J. Antimicrob. Chemother. 50(Suppl. S2):7581.
11. DeMaria, A.,, K. Browne,, S. L. Berk,, E. J. Sherwood,, and W. McCabe. 1980. An outbreak of type 1 pneumococcal pneumonia in a men’s shelter. JAMA 244:14461449.
12. Dicuonzo, G.,, G. Gherardi,, R. E. Gertz,, F. D’Ambrosio,, A. Goglio,, G. Lorino,, S. Recchia,, A. Pantosti,, and B. Beall. 2002. Genotypes of invasive pneumococcal isolates recently recovered from Italian patients. J. Clin. Microbiol. 40:36603665.
13. Enright, M. C.,, and B. G. Spratt. 1998. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144:30493060.
14. Enright, M. C.,, A. Fenoll,, D. Griffiths,, and B. G. Spratt. 1999. The three major Spanish clones of penicillin-resistant Streptococcus pneumoniae are the most common clones recovered from recent cases of meningitis in Spain. J. Clin. Microbiol. 37:32103216.
15. Enright, M. C.,, and B. G. Spratt. 1999. Extensive variation in the ddl gene of penicillin-resistant Streptococcus pneumoniae results from a hitch-hiking effect driven by the penicillin-binding protein 2b gene. Mol. Biol. Evol. 16:16871695.
16. Feil, E. J.,, J. Maynard Smith,, M. C. Enright,, and B. G. Spratt. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:14391450.
17. Feil, E. J.,, E. C. Holmes,, D. E. Bessen,, M.-S. Chan,, N. P. J. Day,, M. C. Enright,, R. Goldstein,, D. W. Hood,, A. Kalia,, C. E. Moore,, J. Zhou,, and B. G. Spratt. 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98:182187.
17a.. Feil, E. J.,, B. C. Li,, D. M. Aanensen,, W. P. Hanage,, and B. G. Spratt. 2004. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186:15181530.
18. Gertz, R. E.,, M. C. McEllistrem,, D. J. Boxrud,, Z. Li.,, V. Sakota,, T. A. Thompson,, R. R. Facklam,, J. M. Besser,, L. H. Harrison,, C. G. Whitney,, and B. Beall. 2003. Clonal distribution of invasive pneumococcal isolates from children and selected adults in the United States prior to 7-valent conjugate vaccine introduction. J. Clin. Microbiol. 41:41944216.
19. Greenwood, B. 1999. The epidemiology of pneumococcal infection in children in the developing world. Philos. Trans. R. Soc. Lond. B 354:777785.
20. Hakenbeck, R.,, N. Balmelle,, B. Weber,, C. Gardès,, W. Keck,, and A. de Saizieu. 2001. Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69:24772486.
21. Hanage, W. P.,, K. Auranen,, R. Syrjänen,, E. Herva,, P. H. Mäkelä,, T. Kilpi,, and B. G. Spratt. 2004. Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infect. Immun. 72:7681.
22. Hausdorff, W. P.,, J. Bryant,, P. R. Paradiso,, and G. R. Siber. 2000. Which pneumococcal serogroups cause the most invasive disease: implications for conjugate vaccine formulation and use, part I. Clin. Infect. Dis. 30:100121.
23. Henriques Normark, B.,, M. Kalin,, Å. Örtqvist,, T. Åkerlund,, B. Olsson Liljequist,, J. Hedlund,, S. B. Svenson,, J. Zhou,, B. G. Spratt,, S. Normark,, and G. Källenius. 2001. Dynamics of penicillin-susceptible clones in invasive pneumococcal disease. J. Infect. Dis. 184:861869.
24. Huebner, R. E.,, R. Dagan,, N. Porath,, A. D. Wasas,, and K. P. Klugman. 2000. Lack of utility of serotyping multiple colonies for detection of simultaneous nasopharyngeal carriage of different pneumococcal serotypes. Pediatr. Infect. Dis. J. 19:10171020.
25. Jebaraj, R.,, T. Cherian,, P. Raghupathy,, K. N. Brahmadathan,, M. K. Lalitha,, K. Thomas,, and M. C. Steinhoff. 1999. Nasopharyngeal colonization of infants in southern India with Streptococcus pneumoniae. Epidemiol. Infect. 123:383388.
26. Kadioglu, A.,, S. Taylor,, F. Iannelli,, G. Pozzi,, T. J. Mitchell,, and P. W. Andrew. 2002. Upper and lower respiratory tract infection by Streptococcus pneumoniae is affected by pneumolysin deficiency and differences in capsule type. Infect. Immun. 70:28862890.
27. Kelly, T.,, J. P. Dillard,, and J. Yother. 1994. Effect of genetic switching of capsular type on virulence of Streptococcus pneumoniae. Infect. Immun. 62:18131819.
28. Lawrence, E. R.,, D. B. Griffiths,, S. A. Martin,, R. C. George,, and L. M. C. Hall. 2003. Evaluation of semiautomated multiplex PCR assay for determination of Streptococcus pneumoniae serotypes and serogroups. J. Clin. Microbiol. 41:601607.
29. Lipsitch, M.,, and E. R. Moxon. 1997. Virulence and transmissibility of pathogens: what is the relationship? Trends Microbiol. 5:137.
30. Lipsitch, M. 1999. Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae. Emerg. Infect. Dis. 5:336345.
31. Maiden, M. C. J.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman,, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:31403145.
32. Mbelle, N.,, R. E. Huebner,, A. D. Wasas,, A. Kimura,, I. Chang,, and K. P. Klugman. 1999. Immunogenicity and impact on nasopharyngeal carriage of a nonavalent pneumococcal conjugate vaccine. J. Infect. Dis. 180:11711176.
33. McCracken, G. H. 2000. Etiology and treatment of pneumonia. Pediatr. Infect. Dis. J. 19:373377.
34. McGee, L.,, L. McDougal,, J. Zhou,, B. G. Spratt,, F. C. Tenover,, R. George,, R. Hakenbeck,, W. Hryniewicz,, J.-C. Lefévre,, A. Tomasz,, and K. P. Klugman. 2001. Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the Pneumococcal Molecular Epidemiology Network (PMEN). J. Clin. Microbiol. 39:25652571.
35. Muller-Graf, C. D.,, A. M. Whatmore,, S. J. King,, K. Trzcinski,, A. P. Pickerill,, N. Doherty,, J. Paul,, D. Griffiths,, D. Crook,, and C. G. Dowson. 1999. Population biology of Streptococcus pneumoniae isolated from oropharyngeal carriage and invasive disease. Microbiology 145:32833293.
36. Nesin, M.,, M. Ramirez,, and A. Tomasz. 1998. Capsular transformation of a multidrug-resistant Streptococcus pneumoniae in vivo. J. Infect. Dis. 177:707713.
37. Obaro, S. K.,, R. Adegbola,, W. A. Banya,, and B. M. Greenwood. 1996. Carriage of pneumococci after pneumococcal vaccination. Lancet 348:271272.
38. Obaro, S.,, and R. J. Adegbola. 2002. The pneumococcus: carriage, disease and conjugate vaccines. Med. Microbiol. 51:98104.
39. Porat, N.,, R. Trefler,, and R. Dagan. 2001. Persistence of two invasive Streptococcus pneumoniae clones of serotypes 1 and 5 in comparison to that of multiple clones of serotypes 6B and 23F among children in southern Israel. J. Clin. Microbiol. 39:18271832.
40. Ramirez, M.,, and A. Tomasz. 1999. Acquisition of new capsular genes among clinical isolates of antibiotic-resistant Streptococcus pneumoniae. Microb. Drug Resist. 5:241246.
41. Robinson, D. A,, K. M. Edwards,, K. B. Waites,, D. E. Briles,, M. J. Crain,, and S. K. Hollingshead. 2001. Clones of Streptococcus pneumoniae isolated from nasopharyngeal carriage and invasive disease in young children in central Tennessee. J. Infect. Dis. 183:15011507.
42. Sa-Leao, R.,, S. E. Vilhelmsson,, H. de Lencastre,, K. G. Kristinsson,, and A. Tomasz. 2002. Diversity of penicillin-nonsusceptible Streptococcus pneumoniae circulating in Iceland after the introduction of the penicillin-resistant clone Spain6B-2. J. Infect. Dis. 186:966975.
43. Selander, R. K.,, D. A. Caugant,, H. Ochman,, J. M. Musser,, M. N. Gilmour,, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51:873884.
44. Selander, R. K.,, J. M. Musser,, D. A. Caugant,, M. N. Gilmour,, and T. S. Whittam. 1987. Population genetics of pathogenic bacteria. Microb. Pathog. 3:17.
45. Smillie, W. G.,, G. H. Warnock,, and H. J. White. 1938. A study of a type I pneumococcus epidemic at the State Hospital at Worcester, Mass. Am. J. Public Health 28:293302.
46. Smith, T.,, D. Lehman,, J. Montgomery,, M. Grattan,, I. D. Riley,, and M. P. Alpers. 1993. Acquisition and invasiveness of different serotypes of Streptococcus pneumoniae in young children. Epidemiol. Infect. 111:2739.
47. Spratt, B. G. 1999. Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr. Opin. Microbiol. 2:312316.
48. Spratt, B. G.,, and B. M. Greenwood. 2000. Prevention of pneumococcal disease by vaccination: does serotype replacement matter? Lancet 356:12101211.
49. Whatmore, A. M.,, A. Efstratiou,, A. P. Pickerill,, K. Broughton,, G. Woodard,, D. Sturgeon,, R. George,, and C. G. Dowson. 2000. Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of “atypical” pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes. Infect. Immun. 68:13741382.
50. Zhou, J.,, M. C. Enright,, and B. G. Spratt. 2000. Identification of the major Spanish clones of penicillin-resistant pneumococci via the Internet using multilocus sequence typing. J. Clin. Microbiol. 38:977986.

Tables

Generic image for table
TABLE 1

Major clones of the serotypes most commonly associated with invasive disease

Citation: Spratt B, Hanage W, Brueggemann A. 2004. Evolutionary and Population Biology of , p 117-135. In Tuomanen E, Mitchell T, Morrison D, Spratt B (ed), The Pneumococcus. ASM Press, Washington, DC. doi: 10.1128/9781555816537.ch8

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