Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

PLoS Genetics

Volumn 10, Issue 5, 2014, Pages

  Mostowy, Rafal ^a   Croucher, Nicholas J ^a,b,c   Hanage, William P ^b   Harris, Simon R ^c   Bentley, Stephen ^c,d   Fraser, Christophe ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIUM TRANSFORMATION; DNA FRAGMENTATION; EVOLUTIONARY ADAPTATION; EVOLUTIONARY HOMOLOGY; GENE FREQUENCY; GENE SWITCHING; GENETIC HETEROGENEITY; GENETIC TRAIT; GENETIC TRANSFORMATION; GENETIC VARIABILITY; HOMOLOGOUS RECOMBINATION; MISMATCH REPAIR; NONHUMAN; PHENOTYPIC VARIATION; POPULATION DYNAMICS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIVERSITY; STREPTOCOCCUS PNEUMONIAE; BACTERIAL GENE; BIOLOGICAL MODEL; GENETIC RECOMBINATION; GENETICS; MOLECULAR EVOLUTION;

DRUG RESISTANCE, MICROBIAL; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENETIC HETEROGENEITY; MODELS, GENETIC; RECOMBINATION, GENETIC; STREPTOCOCCUS PNEUMONIAE;

EID: 84901627197     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004300     Document Type: Article

References (30)

1. Griffith F, (1928) The Significance of Pneumococcal Types. J Hyg (Lond) 27: 113-159.
2. Coffey TJ, Dowson CG, Daniels M, Zhou J, Martin C, et al. (1991) Horizontal transfer of multiple penicillin-binding protein genes, and capsular biosynthetic genes, in natural populations of Streptococcus pneumoniae. Mol Microbiol 5: 2255-2260.
3. Smith JM, Smith NH, O'Rourke M, Spratt BG, (1993) How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384-4388.
4. Feil EJ, Smith JM, Enright MC, Spratt BG, (2000) Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154: 1439-1450.
5. Claverys JP, Lefevre JC, Sicard AM, (1980) Transformation of Streptococcus pneumoniae with S. pneumoniae-lambda phage hybrid DNA: induction of deletions. Proc Natl Acad Sci USA 77: 3534-3538.
6. Polz MF, Alm EJ, Hanage WP, (2013) Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29: 170-175.
7. Prudhomme M, Libante V, Claverys JP, (2002) Homologous recombination at the border: insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc Natl Acad Sci USA 99: 2100-2105.
8. Dowson CG, Hutchison A, Brannigan JA, George RC, Hansman D, et al. (1989) Horizontal transfer of penicillin-binding protein genes in penicillin-resistant clinical isolates of Streptococcus pneumoniae. Proc Natl Acad Sci USA 86: 8842-8846.
9. Lipsitch M, (1999) Bacterial vaccines and serotype replacement: lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae. Emerging Infect Dis 5: 336-345.
10. Spratt BG, Greenwood BM, (2000) Prevention of pneumococcal disease by vaccination: does serotype replacement matter? Lancet 356: 1210-1211.
11. Hanage WP, Fraser C, Tang J, Connor TR, Corander J, (2009) Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324: 1454-1457.
12. Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, et al. (2013) Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 45: 656-663.
13. Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD, (2012) A high-resolution view of genome-wide pneumococcal transformation. PLoS Pathog 8: e1002745.
14. Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, et al. (2010) Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog 6: e1001108.
15. Golubchik T, Brueggemann AB, Street T, Gertz RE, Spencer CC, et al. (2012) Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event. Nat Genet 44: 352-355.
16. Wyres KL, Lambertsen LM, Croucher NJ, McGee L, von Gottberg A, et al. (2012) The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success. Genome Biol 13: R103.
17. Hsieh YC, Wang JT, Lee WS, Hsueh PR, Shao PL, et al. (2006) Serotype competence and penicillin resistance in Streptococcus pneumoniae. Emerging Infect Dis 12: 1709-1714.
18. Evans BA, Rozen DE, (2013) Significant variation in transformation frequency in Streptococcus pneumoniae. ISME J 7: 791-799.
19. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, et al. (2011) Rapid pneumococcal evolution in response to clinical interventions. Science 331: 430-434.
20. Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, et al. (2013) Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet 9: e1003868.
21. Didelot X, Falush D, (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
22. Croucher NJ, Walker D, Romero P, Lennard N, Paterson GK, et al. (2009) Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81. J Bacteriol 191: 1480-1489.
23. Humbert O, Prudhomme M, Hakenbeck R, Dowson CG, Claverys JP, (1995) Homeologous recombination and mismatch repair during transformation in Streptococcus pneumoniae: saturation of the Hex mismatch repair system. Proc Natl Acad Sci USA 92: 9052-9056.
24. Majewski J, Zawadzki P, Pickerill P, Cohan FM, Dowson CG, (2000) Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J Bacteriol 182: 1016-1023.
25. Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science 327: 469-474.
26. Brochet M, Rusniok C, Couve E, Dramsi S, Poyart C, et al. (2008) Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae. Proc Natl Acad Sci USA 105: 15961-15966.
27. Attaiech L, Olivier A, Mortier-Barriere I, Soulet AL, Granadel C, et al. (2011) Role of the single-stranded DNA-binding protein SsbB in pneumococcal transformation: maintenance of a reservoir for genetic plasticity. PLoS Genet 7: e1002156.
28. Black LW, (1989) DNA packaging in dsDNA bacteriophages. Annu Rev Microbiol 43: 267-292.
29. Moscoso M, Garcia E, Lopez R, (2006) Biofilm formation by Streptococcus pneumoniae: role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion. J Bacteriol 188: 7785-7795.
30. Vos M, (2009) Why do bacteria engage in homologous recombination? Trends Microbiol 17: 226-232.