Analysis of Bottlenecks in Experimental Models of Infection

1. Reece JB (2014) Campbell biology. Tenth edition. Boston: Pearson.

2. Levin BR (1981) Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99: 1–23. 7042453

3. Levin BR, Perrot V, Walker N (2000) Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics 154: 985–997. 10757748

4. Grenfell BT, Pybus OG, Gog JR, Wood JLN, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327–332. 14726583

5. Kouyos RD, Althaus CL, Bonhoeffer S (2006) Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol 14: 507–511. 17049239

6. Kouyos RD, Silander OK, Bonhoeffer S (2007) Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol Evol 22: 308–315. 17337087

7. Ebert D (1998) Experimental evolution of parasites. Science 282: 1432–1435. 9822369

8. Yuste E, Sánchez-Palomino S, Casado C, Domingo E, López-Galíndez C (1999) Drastic fitness loss in human immunodeficiency virus type 1 upon serial bottleneck events. J Virol 73: 2745–2751. 10074121

9. Shaw GM, Hunter E (2012) HIV transmission. Cold Spring Harb Perspect Med 2.

10. Angelichio MJ, Spector J, Waldor MK, Camilli A (1999) Vibrio cholerae intestinal population dynamics in the suckling mouse model of infection. Infect Immun 67: 3733–3739. 10417131

11. Edwards CTT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, et al. (2006) Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol Biol 6: 28. 16556318

12. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, et al. (2004) Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303: 2019–2022. doi: 10.1126/science.1093137 15044802

13. Wang GP, Sherrill-Mix SA, Chang K- M, Quince C, Bushman FD (2010) Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol 84: 6218–6228. doi: 10.1128/JVI.02271-09 20375170

14. Moxon ER, Murphy PA (1978) Haemophilus influenzae bacteremia and meningitis resulting from survival of a single organism. Proc Natl Acad Sci U S A 75: 1534–1536. 306628

15. Barnes PD, Bergman MA, Mecsas J, Isberg RR (2006) Yersinia pseudotuberculosis disseminates directly from a replicating bacterial pool in the intestine. J Exp Med 203: 1591–1601. 16754724

16. Pfeiffer JK, Kirkegaard K (2006) Bottleneck-mediated quasispecies restriction during spread of an RNA virus from inoculation site to brain. Proc Natl Acad Sci U S A 103: 5520–5525. 16567621

17. Grant AJ, Restif O, McKinley TJ, Sheppard M, Maskell DJ, et al. (2008) Modelling within-host spatiotemporal dynamics of invasive bacterial disease. PLoS Biol 6: e74. doi: 10.1371/journal.pbio.0060074 18399718

18. Monsion B, Froissart R, Michalakis Y, Blanc S (2008) Large bottleneck size in Cauliflower Mosaic Virus populations during host plant colonization. PLoS Pathog 4: e1000174. doi: 10.1371/journal.ppat.1000174 18846207

19. Schwartz DJ, Chen SL, Hultgren SJ, Seed PC (2011) Population dynamics and niche distribution of uropathogenic Escherichia coli during acute and chronic urinary tract infection. Infect Immun 79: 4250–4259. doi: 10.1128/IAI.05339-11 21807904

20. Fu Y, Waldor MK, Mekalanos JJ (2013) Tn-Seq analysis of Vibrio cholerae intestinal colonization reveals a role for T6SS-mediated antibacterial activity in the host. Cell Host Microbe 14: 652–663. doi: 10.1016/j.chom.2013.11.001 24331463

21. Kaiser P, Slack E, Grant AJ, Hardt W- D, Regoes RR (2013) Lymph Node Colonization Dynamics after Oral Salmonella Typhimurium Infection in Mice. PLoS Pathog 9: e1003532.

22. Li Y, Thompson CM, Trzciński K, Lipsitch M (2013) Within-host selection is limited by an effective population of Streptococcus pneumoniae during nasopharyngeal colonization. Infect Immun 81: 4534–4543. doi: 10.1128/IAI.00527-13 24082074

23. Troy EB, Lin T, Gao L, Lazinski DW, Camilli A, et al. (2013) Understanding barriers to Borrelia burgdorferi dissemination during infection using massively parallel sequencing. Infect Immun 81: 2347–2357. doi: 10.1128/IAI.00266-13 23608706

24. Lam LH, Monack DM (2014) Intraspecies Competition for Niches in the Distal Gut Dictate Transmission during Persistent Salmonella Infection. PLoS Pathog 10: e1004527. doi: 10.1371/journal.ppat.1004527 25474319

25. Lim CH, Voedisch S, Wahl B, Rouf SF, Geffers R, et al. (2014) Independent bottlenecks characterize colonization of systemic compartments and gut lymphoid tissue by salmonella. PLoS Pathog 10: e1004270. doi: 10.1371/journal.ppat.1004270 25079958

26. Varble A, Albrecht RA, Backes S, Crumiller M, Bouvier NM, et al. (2014) Influenza a virus transmission bottlenecks are defined by infection route and recipient host. Cell Host Microbe 16: 691–700. doi: 10.1016/j.chom.2014.09.020 25456074

27. Abel S, Abel Zur Wiesch P, Chang H-H, Davis BM, Lipsitch M, et al. (2015) Sequence tag-based analysis of microbial population dynamics. Nat Methods 12: 223–226. doi: 10.1038/nmeth.3253 25599549

28. Wright S (1938) Size of population and breeding structure in relation to evolution. Science 87: 430–431.

29. Krimbas CB, Tsakas S (1971) The Genetics of Dacus oleae. V. Changes of Esterase Polymorphism in a Natural Population Following Insecticide Control-Selection or Drift? Evolution 25: 454–460.

30. De Kievit TR, Iglewski BH (2000) Bacterial Quorum Sensing in Pathogenic Relationships. Infect Immun 68: 4839–4849. 10948095

31. Parsek MR, Greenberg EP (2000) Acyl-homoserine lactone quorum sensing in Gram-negative bacteria: A signaling mechanism involved in associations with higher organisms. Proc Natl Acad Sci 97: 8789–8793. 10922036

32. Pritchard JR, Chao MC, Abel S, Davis BM, Baranowski C, et al. (2014) ARTIST: High-Resolution Genome-Wide Assessment of Fitness Using Transposon-Insertion Sequencing. PLoS Genet 10: e1004782. doi: 10.1371/journal.pgen.1004782 25375795

33. Worby CJ, Lipsitch M, Hanage WP (2014) Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput Biol 10: e1003549. doi: 10.1371/journal.pcbi.1003549 24675511