1887

Abstract

Recent studies have provided evidence for rapid pathogen genome diversification, some of which could potentially affect the course of disease. We have previously described such variation seen between isolates infecting the blood and cerebrospinal fluid (CSF) of a single patient during a case of bacterial meningitis. Here, we performed whole-genome sequencing of paired isolates from the blood and CSF of 869 meningitis patients to determine whether such variation frequently occurs between these two niches in cases of bacterial meningitis. Using a combination of reference-free variant calling approaches, we show that no genetic adaptation occurs in either invaded niche during bacterial meningitis for two major pathogen species, Streptococcus pneumoniae and Neisseria meningitidis. This study therefore shows that the bacteria capable of causing meningitis are already able to do this upon entering the blood, and no further sequence change is necessary to cross the blood–brain barrier. Our findings place the focus back on bacterial evolution between nasopharyngeal carriage and invasion, or diversity of the host, as likely mechanisms for determining invasiveness.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000103
2017-01-31
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/mgen/3/1/mgen000103.html?itemId=/content/journal/mgen/10.1099/mgen.0.000103&mimeType=html&fmt=ahah

References

  1. Mook-Kanamori BB, Geldhoff M, Van der Poll T, Van de Beek D. Pathogenesis and pathophysiology of pneumococcal meningitis. Clin Microbiol Rev 2011;24:557–591 [CrossRef][PubMed]
    [Google Scholar]
  2. Brouwer MC, Tunkel AR, Van de Beek D. Epidemiology, diagnosis, and antimicrobial treatment of acute bacterial meningitis. Clin Microbiol Rev 2010;23:467–492 [CrossRef][PubMed]
    [Google Scholar]
  3. Caugant DA, Høiby EA, Magnus P, Scheel O, Hoel T et al. Asymptomatic carriage of Neisseria meningitidis in a randomly sampled population. J Clin Microbiol 1994;32:323–330[PubMed]
    [Google Scholar]
  4. Hammitt LL, Bruden DL, Butler JC, Baggett HC, Hurlburt DA et al. Indirect effect of conjugate vaccine on adult carriage of Streptococcus pneumoniae: an explanation of trends in invasive pneumococcal disease. J Infect Dis 2006;193:1487–1494 [CrossRef][PubMed]
    [Google Scholar]
  5. Gerlini A, Colomba L, Furi L, Braccini T, Manso AS et al. The role of host and microbial factors in the pathogenesis of pneumococcal bacteraemia arising from a single bacterial cell bottleneck. PLoS Pathog 2014;10:e1004026 [CrossRef][PubMed]
    [Google Scholar]
  6. Weisfelt M, Van de Beek D, Spanjaard L, Reitsma JB, De Gans J. Clinical features, complications, and outcome in adults with pneumococcal meningitis: a prospective case series. Lancet Neurol 2006;5:123–129 [CrossRef][PubMed]
    [Google Scholar]
  7. Adriani KS, Brouwer MC, van de Beek D. Risk factors for community-acquired bacterial Meningitis in adults. Neth J Med 2015;73:53–60[PubMed]
    [Google Scholar]
  8. Ochman H, Elwyn S, Moran NA. Calibrating bacterial evolution. Proc Natl Acad Sci USA 1999;96:12638–12643[PubMed][CrossRef]
    [Google Scholar]
  9. Mwangi MM, Wu SW, Zhou Y, Sieradzki K, De Lencastre H et al. Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc Natl Acad Sci USA 2007;104:9451–9456 [CrossRef][PubMed]
    [Google Scholar]
  10. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 2006;103:8487–8492 [CrossRef][PubMed]
    [Google Scholar]
  11. Bryant JM, Grogono DM, Greaves D, Foweraker J, Roddick I et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 2013;381:1551–1560 [CrossRef][PubMed]
    [Google Scholar]
  12. Morelli G, Didelot X, Kusecek B, Schwarz S, Bahlawane C et al. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet 2010;6:e1001036 [CrossRef][PubMed]
    [Google Scholar]
  13. Wilson DJ, Gabriel E, Leatherbarrow AJ, Cheesbrough J, Gee S et al. Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol Biol Evol 2009;26:385–397 [CrossRef][PubMed]
    [Google Scholar]
  14. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N Engl J Med 2013;369:1195–1205 [CrossRef][PubMed]
    [Google Scholar]
  15. Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B et al. Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA 2011;108:5033–5038 [CrossRef][PubMed]
    [Google Scholar]
  16. Ehrlich GD, Ahmed A, Earl J, Hiller NL, Costerton JW et al. The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes. FEMS Immunol Med Microbiol 2010;59:269–279 [CrossRef][PubMed]
    [Google Scholar]
  17. Rau MH, Marvig RL, Ehrlich GD, Molin S, Jelsbak L. Deletion and acquisition of genomic content during early stage adaptation of Pseudomonas aeruginosa to a human host environment. Environ Microbiol 2012;14:2200–2211 [CrossRef][PubMed]
    [Google Scholar]
  18. Li J, Li JW, Feng Z, Wang J, An H et al. Epigenetic switch driven by DNA inversions dictates phase variation in Streptococcus pneumoniae. PLoS Pathog 2016;12:e1005762 [CrossRef][PubMed]
    [Google Scholar]
  19. Manso AS, Chai MH, Atack JM, Furi L, de Ste Croix M et al. A random six-phase switch regulates pneumococcal virulence via global epigenetic changes. Nat Commun 2014;5:5055 [CrossRef][PubMed]
    [Google Scholar]
  20. Marvig RL, Sommer LM, Molin S, Johansen HK. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat Genet 2015;47:57–64 [CrossRef][PubMed]
    [Google Scholar]
  21. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 2009;461:1243–1247 [CrossRef][PubMed]
    [Google Scholar]
  22. Yang L, Jelsbak L, Marvig RL, Damkiær S, Workman CT et al. Evolutionary dynamics of bacteria in a human host environment. Proc Natl Acad Sci USA 2011;108:7481–7486 [CrossRef][PubMed]
    [Google Scholar]
  23. Young BC, Golubchik T, Batty EM, Fung R, Larner-Svensson H et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci USA 2012;109:4550–4555 [CrossRef][PubMed]
    [Google Scholar]
  24. Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L et al. Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection. PLoS Genet 2013;9:e1003868 [CrossRef][PubMed]
    [Google Scholar]
  25. Omer H, Rose G, Jolley KA, Frapy E, Zahar JR et al. Genotypic and phenotypic modifications of Neisseria meningitidis after an accidental human passage. PLoS One 2011;6:e17145 [CrossRef][PubMed]
    [Google Scholar]
  26. Brueggemann AB, Griffiths DT, Meats E, Peto T, Crook DW et al. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. J Infect Dis 2003;187:1424–1432 [CrossRef][PubMed]
    [Google Scholar]
  27. Del Amo E, Selva L, De Sevilla MF, Ciruela P, Brotons P et al. Estimation of the invasive disease potential of Streptococcus pneumoniae in children by the use of direct capsular typing in clinical specimens. Eur J Clin Microbiol Infect Dis 2015;34:705–711 [CrossRef][PubMed]
    [Google Scholar]
  28. Robinson DA, Edwards KM, Waites KB, Briles DE, Crain MJ et al. Clones of Streptococcus pneumoniae isolated from nasopharyngeal carriage and invasive disease in young children in central Tennessee. J Infect Dis 2001;183:1501–1507 [CrossRef][PubMed]
    [Google Scholar]
  29. Kulohoma BW, Cornick JE, Chaguza C, Yalcin F, Harris SR et al. Comparative genomic analysis of meningitis and bacteremia causing pneumococci identifies a common core genome. Infect Immun 2015;83:4165–4173 [CrossRef][PubMed]
    [Google Scholar]
  30. Cremers AJ, Zomer AL, Gritzfeld JF, Ferwerda G, Van Hijum SA et al. The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition. Microbiome 2014;2:44 [CrossRef][PubMed]
    [Google Scholar]
  31. Habets MGJL, Rozen DE, Brockhurst MA. Variation in Streptococcus pneumoniae susceptibility to human antimicrobial peptides may mediate intraspecific competition. P Roy Soc Lond B Bio 2012;279:3803–3811 [CrossRef]
    [Google Scholar]
  32. Van de Beek D. Progress and challenges in bacterial Meningitis. Lancet 2012;380:1623–1624 [CrossRef]
    [Google Scholar]
  33. Woehrl B, Brouwer MC, Murr C, Heckenberg SG, Baas F et al. Complement component 5 contributes to poor disease outcome in humans and mice with pneumococcal meningitis. J Clin Invest 2011;121:3943–3953 [CrossRef][PubMed]
    [Google Scholar]
  34. Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O et al. Reference-free detection of isolated SNPs. Nucleic Acids Res 2014;33:1–11
    [Google Scholar]
  35. Lqbal Z, Caccamo M, Turner I, Flicek P, Mcvean G. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat Genet 2012;44:226–232 [CrossRef][PubMed]
    [Google Scholar]
  36. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. spades: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  37. Page AJ, Parkhill J, Quail MA, Hunt M, de Silva N et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom 2016;2: [CrossRef]
    [Google Scholar]
  38. Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson DA et al. Faster and more accurate sequence alignment with SNAP. arXiv 2011;1111.5572v1:
    [Google Scholar]
  39. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011;27:2987–2993 [CrossRef][PubMed]
    [Google Scholar]
  40. Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010;11:R116 [CrossRef][PubMed]
    [Google Scholar]
  41. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012;22:549–556 [CrossRef][PubMed]
    [Google Scholar]
  42. Hoskins J, Alborn WE, Arnold J, Blaszczak LC, Burgett S et al. Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 2001;183:5709–5717 [CrossRef][PubMed]
    [Google Scholar]
  43. Denapaite D, Brückner R, Nuhn M, Reichmann P, Henrich B et al. The genome of Streptococcus mitis B6–what is a commensal?. PLoS One 2010;5:e9426 [CrossRef][PubMed]
    [Google Scholar]
  44. Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D et al. Cactus: algorithms for genome multiple sequence alignment. Genome Res 2011;21:1512–1528 [CrossRef][PubMed]
    [Google Scholar]
  45. Hu X, Yuan J, Shi Y, Lu J, Liu B et al. pIRS: profile-based Illumina pair-end reads simulator. Bioinformatics 2012;28:1533–1535 [CrossRef][PubMed]
    [Google Scholar]
  46. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 2001;293:498–506 [CrossRef][PubMed]
    [Google Scholar]
  47. Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A et al. cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res 2012;40:e69 [CrossRef][PubMed]
    [Google Scholar]
  48. Croucher NJ, Walker D, Romero P, Lennard N, Paterson GK et al. Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniae Spain23F ST81. J Bacteriol 2009;191:1480–1489 [CrossRef][PubMed]
    [Google Scholar]
  49. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 2000;287:1809–1815 [CrossRef][PubMed]
    [Google Scholar]
  50. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010;26:2069–2070 [CrossRef][PubMed]
    [Google Scholar]
  51. Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res 2002;12:656–664 [CrossRef][PubMed]
    [Google Scholar]
  52. Spiegelhalter DJ, Best NG, Carlin BP, Van der Linde A. Bayesian measures of model complexity and fit.. J R Stat Soc Series B Stat Methodol 2002;64:583–639 [CrossRef]
    [Google Scholar]
  53. Moxon ER, Murphy PA. Haemophilus influenzae bacteremia and meningitis resulting from survival of a single organism. Proc Natl Acad Sci USA 1978;75:1534–1536 [CrossRef][PubMed]
    [Google Scholar]
  54. Brown PD, Davies SL, Speake T, Millar ID. Molecular mechanisms of cerebrospinal fluid production. Neuroscience 2004;129:957–970 [CrossRef][PubMed]
    [Google Scholar]
  55. La Scolea LJ, Dryja D. Quantitation of bacteria in cerebrospinal fluid and blood of children with meningitis and its diagnostic significance. J Clin Microbiol 1984;19:187–190[PubMed]
    [Google Scholar]
  56. Allegrucci M, Hu FZ, Shen K, Hayes J, Ehrlich GD et al. Phenotypic characterization of Streptococcus pneumoniae biofilm development. J Bacteriol 2006;188:2325–2335 [CrossRef][PubMed]
    [Google Scholar]
  57. Gang TB, Hanley GA, Agrawal A. C-reactive protein protects mice against pneumococcal infection via both phosphocholine-dependent and phosphocholine-independent mechanisms. Infect Immun 2015;83:1845–1852 [CrossRef][PubMed]
    [Google Scholar]
  58. Patwa Z, Wahl LM. The fixation probability of beneficial mutations. J R Soc Interface 2008;5:1279–1289 [CrossRef][PubMed]
    [Google Scholar]
  59. Brouwer MC, Heckenberg SG, De Gans J, Spanjaard L, Reitsma JB et al. Nationwide implementation of adjunctive dexamethasone therapy for pneumococcal meningitis. Neurology 2010;75:1533–1539 [CrossRef][PubMed]
    [Google Scholar]
  60. Heckenberg SG, Brouwer MC, Van der Ende A, Van de Beek D. Adjunctive dexamethasone in adults with meningococcal meningitis. Neurology 2012;79:1563–1569 [CrossRef][PubMed]
    [Google Scholar]
  61. Fransen F, Heckenberg SG, Hamstra HJ, Feller M, Boog CJ et al. Naturally occurring lipid A mutants in Neisseria meningitidis from patients with invasive meningococcal disease are associated with reduced coagulopathy. PLoS Pathog 2009;5:e1000396 [CrossRef][PubMed]
    [Google Scholar]
  62. Van der Ende A, Hopman CT, Zaat S, Essink BB, Berkhout B et al. Variable expression of class 1 outer membrane protein in Neisseria meningitidis is caused by variation in the spacing between the -10 and -35 regions of the promoter. J Bacteriol 1995;177:2475–2480[PubMed][CrossRef]
    [Google Scholar]
  63. Van der Ende A, Hopman CT, Dankert J. Multiple mechanisms of phase variation of PorA in Neisseria meningitidis. Infect Immun 2000;68:6685–6690 [CrossRef][PubMed]
    [Google Scholar]
  64. Deininger S, Figueroa-Perez I, Sigel S, Stadelmaier A, Schmidt RR et al. Use of synthetic derivatives to determine the minimal active structure of cytokine-inducing lipoteichoic acid. Clin Vaccine Immunol 2007;14:1629–1633 [CrossRef][PubMed]
    [Google Scholar]
  65. Kovács M, Halfmann A, Fedtke I, Heintz M, Peschel A et al. A functional dlt operon, encoding proteins required for incorporation of d-alanine in teichoic acids in gram-positive bacteria, confers resistance to cationic antimicrobial peptides in Streptococcus pneumoniae. J Bacteriol 2006;188:5797–5805 [CrossRef][PubMed]
    [Google Scholar]
  66. Wörmann ME, Horien CL, Bennett JS, Jolley KA, Maiden MC et al. Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences. BMC Genomics 2014;15:253 [CrossRef][PubMed]
    [Google Scholar]
  67. Russell JE, Jolley KA, Feavers IM, Maiden MC, Suker J. PorA variable regions of Neisseria meningitidis. Emerg Infect Dis 2004;10:674–678 [CrossRef][PubMed]
    [Google Scholar]
  68. Gripenland J, Netterling S, Loh E, Tiensuu T, Toledo-Arana A et al. RNAs: regulators of bacterial virulence. Nat Rev Microbiol 2010;8:857–866 [CrossRef][PubMed]
    [Google Scholar]
  69. Johansson J, Mandin P, Renzoni A, Chiaruttini C, Springer M et al. An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes. Cell 2002;110:551–561 [CrossRef][PubMed]
    [Google Scholar]
  70. Sreevatsan S, Pan X, Zhang Y, Deretic V, Musser JM. Analysis of the oxyR-ahpC region in isoniazid-resistant and -susceptible Mycobacterium tuberculosis complex organisms recovered from diseased humans and animals in diverse localities. Antimicrob Agents Chemother 1997;41:600–606[PubMed]
    [Google Scholar]
  71. Magnusson M, Tobes R, Sancho J, Pareja E. Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9. J Immunol 2007;179:31–35[PubMed][CrossRef]
    [Google Scholar]
  72. Hung MC, Christodoulides M. The biology of Neisseria adhesins. Biology 2013;2:1054–1109 [CrossRef][PubMed]
    [Google Scholar]
  73. Griffiths NJ, Hill DJ, Borodina E, Sessions RB, Devos NI et al. Meningococcal surface fibril (Msf) binds to activated vitronectin and inhibits the terminal complement pathway to increase serum resistance. Mol Microbiol 2011;82:1129–1149 [CrossRef][PubMed]
    [Google Scholar]
  74. Delany I, Grifantini R, Bartolini E, Rappuoli R, Scarlato V. Effect of Neisseria meningitidis fur mutations on global control of gene transcription. J Bacteriol 2006;188:2483–2492 [CrossRef][PubMed]
    [Google Scholar]
  75. Bucci C, Lavitola A, Salvatore P, Del Giudice L, Massardo DR et al. Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype. Mol Cell 1999;3:435–445[PubMed][CrossRef]
    [Google Scholar]
  76. Moxon ER, Rainey PB, Nowak MA, Lenski RE. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 1994;4:24–33[PubMed][CrossRef]
    [Google Scholar]
  77. Snyder LA, Butcher SA, Saunders NJ. Comparative whole-genome analyses reveal over 100 putative phase-variable genes in the pathogenic Neisseria spp. Microbiology 2001;147:2321–2332 [CrossRef][PubMed]
    [Google Scholar]
  78. Sarkari J, Pandit N, Moxon ER, Achtman M. Variable expression of the Opc outer membrane protein in Neisseria meningitidis is caused by size variation of a promoter containing poly-cytidine. Mol Microbiol 1994;13:207–217 [CrossRef][PubMed]
    [Google Scholar]
  79. Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD et al. Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun 2014;5:5471 [CrossRef][PubMed]
    [Google Scholar]
  80. Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H et al. Regional isolation drives bacterial diversification within cystic fibrosis lungs. Cell Host Microbe 2015;18:307–319 [CrossRef][PubMed]
    [Google Scholar]
  81. Paterson GK, Harrison EM, Murray GG, Welch JJ, Warland JH et al. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nat Commun 2015;6:6560 [CrossRef][PubMed]
    [Google Scholar]
  82. Shea PR, Beres SB, Flores AR, Ewbank AL, Gonzalez-Lugo JH et al. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci USA 2011;108:5039–5044 [CrossRef][PubMed]
    [Google Scholar]
  83. Das S, Lindemann C, Young BC, Muller J, Österreich B et al. Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation. Proc Natl Acad Sci USA 2016;113:E3101E3110 [CrossRef][PubMed]
    [Google Scholar]
  84. Didelot X, Walker AS, Peto TE, Crook DW, Wilson DJ. Within-host evolution of bacterial pathogens. Nat Rev Microbiol 2016;14:150–162 [CrossRef][PubMed]
    [Google Scholar]
  85. Viana D, Comos M, McAdam PR, Ward MJ, Selva L et al. A single natural nucleotide mutation alters bacterial pathogen host tropism. Nat Genet 2015;47:361–366 [CrossRef][PubMed]
    [Google Scholar]
  86. Fischer W. Phosphocholine of pneumococcal teichoic acids: role in bacterial physiology and pneumococcal infection. Res Microbiol 2000;151:421–427 [CrossRef][PubMed]
    [Google Scholar]
  87. Brouwer MC, De Gans J, Heckenberg SG, Zwinderman AH, Van der Poll T et al. Host genetic susceptibility to pneumococcal and meningococcal disease: a systematic review and meta-analysis. Lancet Infect Dis 2009;9:31–44 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000103
Loading
/content/journal/mgen/10.1099/mgen.0.000103
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error