What is a pathogen? Toward a process view of host-parasite interactions

References

• Keen EC. Paradigms of pathogenesis: targeting the mobile genetic elements of disease. Front Cell Infect Microbiol 2012; 2:1-3. p.1; http://dx.doi.org/10.3389/fcimb.2012.00161
   Web of Science ®Google Scholar
• Grmek MD. Western Medical Thought from Antiquity to Middle Ages. Cambridge: Harvard University Press 1999.
   Google Scholar
• Whitbeck C. Causation in medicine. The disease entity model. Philos Sci 1977; 44:619-37, p. 622; http://dx.doi.org/10.1086/288771
   Web of Science ®Google Scholar
• Temkin O. The Double Face of Janus. Essays in the History of Medicine. Johns Hopkins University Press 1977.
   Google Scholar
• Engelhardt Jr. HT Concepts of health and disease, In: Caplan AH, Engelhardt Jr HT, McCartney JJ, editors. Concepts of Health and Disease: Interdisciplinary Perspectives. Reading, MA: Addison-Wesley, 1981.
   Google Scholar
• Koch R. On the investigation of pathogenic organisms, In: Cheyne WW (ed.), Recent Essays by Various Authors on Bacteria in Relation to Disease. London, UK: New Sydenham Society; 1886; [1881], pp. 3-64, p.3.
   Google Scholar
• Zinsser H. Infection and Resistance. New York: The MacMillan Company; 1914.
   Google Scholar
• Falkow S. Commentary: ‘I never met a microbe I didn't like’. Nat Med 2008; 14(10):27-31; PMID:18841148; http://dx.doi.org/10.1038/nm1008-1053
   PubMedGoogle Scholar
• Casadevall A. Opinion. The future of biological warfare. Microb Biotech 2012; 5(5):584-7, p. 585; http://dx.doi.org/10.1111/j.1751-7915.2012.00340.x
   PubMedGoogle Scholar
• Van Baalen M, Jansen VAA. Dangerous liaisons: the ecology of private interests and common good. Oikos 2001; 95:211-24; http://dx.doi.org/10.1034/j.1600-0706.2001.950203.x
   Web of Science ®Google Scholar
• Canguilhem G. Idéologie et rationalité dans l’histoire des sciences de la vie. Paris: Vrin, 1977, p. 112.
   Google Scholar
• Gradmann C. Isolation, contamination, and pure culture: Monomorphism and polymorphism of pathogenic micro-organisms as research problem 1860-1880. Perspect Sci 2001; 9:147-72; http://dx.doi.org/10.1162/106361401317447264
   PubMedGoogle Scholar
• Mendelsohn JA. From eradication to equilibrium: How epidemics became complex after World War I. In: Lawrence C, Weisz G (eds.), Greater Than the Parts: Holism in Biomedicine, 1920-1950. New York, Oxford: Oxford University Press. 1998.
   Google Scholar
• De Kruif P. Microbe Hunters, Mariner Books, 3rd Edition. A Harvest Book, Harcourt Inc., San Diego, New York, London; 2002.
   Google Scholar
• Dubos RJ. The evolution of infectious diseases in the course of history. Can Med Assoc J 1958; 79(6):445-51.
   PubMedGoogle Scholar
• Fantini B. Les organisations internationales face à l’émergence des maladies infectieuses nouvelles. Hist Phil Life Sci 1993; 15:435-47.
   PubMed Web of Science ®Google Scholar
• Snowden F. Emerging and re-emerging diseases: an historical perspective. Immunol Rev 2008; 225:9-26; http://dx.doi.org/10.1111/j.1600-065X.2008.00677.x
   PubMed Web of Science ®Google Scholar
• Dethlefsen L, McFall-Ngai, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 2007; 449:811-8; http://dx.doi.org/10.1038/nature06245
   PubMed Web of Science ®Google Scholar
• Méthot P-O, Fantini B. (forthcoming). Medicine and ecology: historical and critical perspectives on the concept of emerging disease. In: La Vergata A, Menant G-A, Boersema JJ (eds.), Nature, Environment, and Quality of Life, Archives Internationales d’histoire des sciences, Brepols Publishers, 2014.
   Google Scholar
• Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P. Global trends in emerging infectious diseases. Nature 2008; 451(7181):990-3; http://dx.doi.org/10.1038/nature06536
   PubMed Web of Science ®Google Scholar
• Blaser MJ. Missing microbes. How the overuse of antibiotics is fuelling our modern plagues. New York: Henry Holt and Company; 2014.
   Google Scholar
• Anderson W. Natural histories of infectious disease: ecological vision in twentieth-century biomedical science. Osiris 2004; 19:39-61; http://dx.doi.org/10.1086/649393
   PubMed Web of Science ®Google Scholar
• Méthot P-O. Why do parasites harm their host? On the origin and legacy of Theobald Smith's ‘law of declining virulence’ – 1900-1980. Hist Phil Life Sci 2012; 34:561-601.
   PubMed Web of Science ®Google Scholar
• Lederberg J. Viruses and human kind: intracellular symbiosis and evolutionary competition. In: Morse, S (ed.), Emerging Viruses. New York: Oxford University Press; 1993; 3-9.
   Google Scholar
• Lederberg J. Infectious agents, hosts in constant flux. ASM News 1999; 65(1):18-22.
   Google Scholar
• Lederberg J. Infectious history. Science 2000; 288:287-93; http://dx.doi.org/10.1126/science.288.5464.287
   PubMed Web of Science ®Google Scholar
• Swerdlow JL, Johnson AD. Living with microbes, Wilson Q 2002; 42-59
   Google Scholar
• Institute of Medicine. Ending the war metaphor. The Changing Agenda for Unravelling the Host-Microbe Relationship – Workshop Summary. Washington, DC: The National Academies Press; 2006.
   Google Scholar
• Pallen MJ, Wren BW. Bacterial pathogenomics. Nature 2007; 449:835-42; PMID:17943120; http://dx.doi.org/10.1038/nature06248
   PubMed Web of Science ®Google Scholar
• National Research Council. Sequence-Based Classifications of Select Agents: A Brighter Line. Washington DC: National Academies Press; 2010; 2.
   Google Scholar
• Pirofski LA, Casadevall A. Q&A: What is a pathogen? A question that begs the point. BMC Biol 2012; 10(1):6; http://dx.doi.org/10.1186/1741-7007-10-6.
   PubMed Web of Science ®Google Scholar
• Falkow S. 1997. What is a pathogen? ASM News, 63(7):359-65.
   Google Scholar
• Pérez-Brocal V, Latorre A, Moya A. Symbionts and pathogens: what is the difference? Curr Top Microbiol Immunol 2013; 358:215-43.
   PubMed Web of Science ®Google Scholar
• Blaser MJ, Falkow S. What are the consequences of the disappearing human microbiota? Nat Rev Microbiol 2009; 7:887-94; PMID:19898491; http://dx.doi.org/10.1038/nrmicro2245
   PubMed Web of Science ®Google Scholar
• Falkow S. Is persistent bacterial infection good for your health? Cell 2006; 124:699-702; PMID:16497581; http://dx.doi.org/10.1016/j.cell.2006.02.004
   PubMed Web of Science ®Google Scholar
• Hube B. From commensal to pathogen: stage and tissue specific gene expression of Candida albicans. Curr Opin Microbiol 2004; 7:336-41; PMID:15288621; http://dx.doi.org/10.1016/j.mib.2004.06.003
   PubMed Web of Science ®Google Scholar
• Klemm P, Hancock V, Schembri M. Mellowing out: adaptation to commensalism by Escherichia coli asymptomatic bacteria strain 83972. Infect Immun 2007; 75:3688-95; PMID:17502385; http://dx.doi.org/10.1128/IAI.01730-06
   PubMedGoogle Scholar
• Armstrong D. History of opportunistic infection in the immunocompromised host. Clin Infect Dis 1993; 17:S318-21; PMID:8274594; http://dx.doi.org/10.1093/clinids/17.Supplement_2.S318
   PubMed Web of Science ®Google Scholar
• Balloy V, Huerre M, Latgé JP, Chignard M. Differences in patterns of infection and inflammation for corticosteroid treatment and chemotherapy in experimental invasive pulmonary aspergillosis. Infect Immun 2005; 73:494-503; PMID:15618189; http://dx.doi.org/10.1128/IAI.73.1.494-503.2005
   PubMed Web of Science ®Google Scholar
• Lederberg J, McCray A. ‘Ome sweet’ omics: a genealogical treasury of words. The Scientist 2001; 15:7.
   Google Scholar
• Blaser MJ, Chen Y, Reibman J. Does helicobacter pylori protect against asthma and allergy? Gut 2008; 57(5):561-7; PMID:18194986; http://dx.doi.org/10.1136/gut.2007.133462
   PubMedGoogle Scholar
• Pflughoeft KJ, Versalovic J. Human microbiome in health and disease. Annu Rev Pathol 2012; 7:99-122; PMID:21910623; http://dx.doi.org/10.1146/annurev-pathol-011811-132421
   PubMed Web of Science ®Google Scholar
• Martín R, Miquel S, Langella P, Bermúdez-Humarán LG. The role of metagenomics in under- standing the human microbiome in health and disease. Virulence 2014; 5:413-23; PMID:24429972; http://dx.doi.org/10.4161/viru.27864
   PubMed Web of Science ®Google Scholar
• Brown SP, Cornforth DM, Mideo N. Evolution of virulence in opportunistic pathogen: generalism, plasticity and control. Trends Microbiol 2012; 20:336-42; PMID:22564248; http://dx.doi.org/10.1016/j.tim.2012.04.005
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski LA. Virulence factors and the mechanisms of action: the view from a damage-response framework. J Water Health 2009; 7:2-18. p. 4; PMID:19717929; http://dx.doi.org/10.2166/wh.2009.036
   PubMed Web of Science ®Google Scholar
• Ackermann M, Stecher B, Freed NE, Songhet P, Hardt WD, Doebeli M. Self-destructive cooperation mediated by phenotypic noise. Nature 2008; 454:987-90; PMID:18719588; http://dx.doi.org/10.1038/nature07067
   PubMed Web of Science ®Google Scholar
• Mideo N, Reece SE. Plasticity in parasite phenotypes: evolutionary and ecological implications for disease. Future Microbiol 2012; 7:17-24; PMID:22191443; http://dx.doi.org/10.2217/fmb.11.134
   PubMedGoogle Scholar
• Sansonetti P. To be or not to be a pathogen: that is the mucosally relevant question. Nature 2011; 4(1):8-14; PMID:21150896; http://dx.doi.org/10.1038/mi.2010.77
   PubMedGoogle Scholar
• Schmid-Hempel P. Immune defence, parasite evasion strategies and their relevance for ‘macroscopic phenomena’ such as virulence. Phil Trans R Soc Lond B 2009; 364:85-8; PMID:18930879; http://dx.doi.org/10.1098/rstb.2008.0157
   PubMedGoogle Scholar
• Graham AL, Allen JE, Read AF. Evolutionary causes and consequences of immunpathology. Ann Rev Evol Syst 2005; 36:373-97; http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152622
   Google Scholar
• Long GH, Chan BHK, Allen JE, Read AF, Graham AL. Experimental manipulation of immune-mediated disease and its fitness costs for rodent malaria parasites. BMC Evol Biol 2008; 8:128; PMID:18447949; http://dx.doi.org/10.1186/1471-2148-8-128
   PubMedGoogle Scholar
• Cooper AM. 2009. Cell-mediated immune responses in tuberculosis. Annu Rev Immunol 27:393-422; http://dx.doi.org/10.1146/annurev.immunol.021908.132703
   PubMed Web of Science ®Google Scholar
• Moulin AM. La métaphore vaccine. Hist Philos Life Sci 1992; 14:271-97
   PubMed Web of Science ®Google Scholar
• Casadevall A, Pirofski LA. Host-pathogen interactions: basic concepts of microbial commensalism, colonization, infection, and disease. Infect Immun 2000; 68:6511-8; PMID:11083759; http://dx.doi.org/10.1128/IAI.68.12.6511-6518.2000
   PubMed Web of Science ®Google Scholar
• Flor HH. Current status of the gene-for-gene concept. Annu Rev Pythopathol 1971; 9:275-96; PMID:21599495; http://dx.doi.org/10.1146/annurev.py.09.090171.001423
   PubMedGoogle Scholar
• Paine K, Flower DR. Bacterial bioinformatics: Pathogenesis and the genome. J Mol Microbiol Biotechnol 2002; 4:357-65
   PubMed Web of Science ®Google Scholar
• Relman D. Detection and identification of previously unrecognized microbial pathogens. Emerg Infect Dis 1998; 4(3):382-9; PMID:9716951; http://dx.doi.org/10.3201/eid0403.980310
   PubMedGoogle Scholar
• Wassenaar TM, Gaastra W. Bacterial virulence: can we draw the line? Microbiol Lett 2001; 201:1-7; PMID:11445159; http://dx.doi.org/10.1111/j.1574-6968.2001.tb10724.x
   PubMed Web of Science ®Google Scholar
• Read AF. The evolution of virulence. Trends Microbiol 1994; 2(3):73-6; http://dx.doi.org/10.1016/0966-842X(94)90537-1
   PubMedGoogle Scholar
• Casadevall A, Pirofski LA. Host-pathogen interactions: the attributes of virulence. J Infect Dis 2001; 337-44; http://dx.doi.org/10.1086/322044
   PubMed Web of Science ®Google Scholar
• Stuart-Harris CH. The definition and measurement of virus virulence. In: Virus, Virulence and Pathogenicity; Ciba Symposium. London: Churchill; 1960; 3-19; PMID:24297424; http://dx.doi.org/10.1007/978-1-62703-733-4_20
   PubMedGoogle Scholar
• Gradmann C. ‘Common sense, proper training and sound reasoning’ – Koch's postulates and 20th century medicine. Michael Quart 2008; 3:217-28.
   Google Scholar
• Isenberg HD. Pathogenicity and virulence: another view. Clin Microbial Rev 1988;1:40-53.
   PubMedGoogle Scholar
• Oakes Jordan E. 1908, 11-12, quoted in Strick J. Evolution of microbiology as seen in the textbooks of Edwin O. Jordan and William H. Park. Yale J Biol Med 2000; 72:321-8.
   Google Scholar
• Strick J. Evolution of microbiology as seen in the textbooks of Edwin O. Jordan and William H. Park. Yale J Biol Med 2000; 72:321-8; PMID:11049163
   PubMedGoogle Scholar
• Falkow S. Molecular Koch's postulates applied to microbial pathogenicity. Rev Infect Dis 1988; 10:S274-6; http://dx.doi.org/10.1093/cid/10.Supplement_2.S274
   PubMedGoogle Scholar
• Brock TD. The emergence of bacterial genetics. Cold Spring Harbor Laboratory Press; 1990.
   Google Scholar
• Grote M. Hybridizing bacteria, crossing methods, cross-checking arguments: the transition from episomes to plasmids (1961-1969), Hist Phil Life Sci 2008; 30:407-30; PMID:19579711
   PubMed Web of Science ®Google Scholar
• Falkow S. Infectious Multiple Drug Resistance. Bristol: Pion Limited; 1975; 253.
   Google Scholar
• Groisman EA, Ochman H. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 1996; 87:791-4; http://dx.doi.org/10.1016/S0092-8674(00)81985-6
   PubMed Web of Science ®Google Scholar
• Hacker J, Hochhut B, Middendorf B, Schneider G, Buchrieser C, Gottschalk G, Dobrindt U. Pathogenomics of mobile genetic elements of toxigenic bacteria. Int J Med Microbiol 2004; 293:453-61. P.454; PMID:15149018; http://dx.doi.org/10.1078/1438-4221-00290
   PubMed Web of Science ®Google Scholar
• Gal-Mor O, Finlay B. Pathogenicity islands: a molecular toolbox for bacterial virulence 2006; 8(11): 1707-19. p. 1708; PMID:16939533
   PubMedGoogle Scholar
• Strauss EJ Falkow S. Microbial pathogenesis: genomics and beyond. Science 1997; 276:707-12; http://dx.doi.org/10.1126/science.276.5313.707
   PubMed Web of Science ®Google Scholar
• Hacker J, Carniel E. Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep 2001; 2:376-81. p. 377; PMID:11375927; http://dx.doi.org/10.1093/embo-reports/kve097
   PubMed Web of Science ®Google Scholar
• Hacker J, Kaper JB. Pathogenicity islands and other mobile virulence elements. Washington: ASM Press; 1999.
   Google Scholar
• Pradeu T. The Limits of the Self: Immunology and Biological Identity. New York: Oxford University Press; 2012.
   Google Scholar
• Janeway CA. Approaching the asymptote ? Evolution and revolution in immunology. Cold Spring Harb Symp Quant Biol 1989; 54:1-13; http://dx.doi.org/10.1101/SQB.1989.054.01.003
   PubMedGoogle Scholar
• Medzhitov R, Janeway C. Innate immunity. N Engl J Med 2000; 343(5):338-44; http://dx.doi.org/10.1056/NEJM200008033430506
   PubMed Web of Science ®Google Scholar
• Vance RE, Isberg RR, Portnoy DA. Patterns of pathogenesis: discrimination of pathogenic and non-pathogenic microbes by the immune system. Cell Host Microbe 2009; 6:10-21; 12; PMID:19616762; http://dx.doi.org/10.1016/j.chom.2009.06.007
   PubMed Web of Science ®Google Scholar
• Ausubel FM. Are innate immune signaling pathways in plants and animals conserved? Nature Immunol 2005; 610:973-979; http://dx.doi.org/10.1038/ni1253
   Web of Science ®Google Scholar
• Casadevall A, Pirofski LA. The damage-response framework. Nat Rev Microbiol 2003; 1:17-24; http://dx.doi.org/10.1038/nrmicro732
   PubMed Web of Science ®Google Scholar
• McCullers J. The co-pathogenesis of influenza viruses with bacteria in the lung. Nat Rev Microbiol 2014; 12:252-62; PMID:24590244; http://dx.doi.org/10.1038/nrmicro3231
   PubMed Web of Science ®Google Scholar
• Lord CC, Barnard B, Day K, Hargrove JW, McNamara JJ, Paul REL, Trenholme K, Woolhouse MEJ. Aggregation and distribution of strains in microparasites. Philos Trans R Soc B 1999; 354:799-807; PMID:10365405; http://dx.doi.org/10.1098/rstb.1999.0432
   PubMedGoogle Scholar
• Juliano JJ, Porter K, Mwapasa V, Sem R, Rogers WO, Ariey F, Wongsrichanalai C, Read A, Meshnick SR. Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing. Proc Natl Acad Sci USA 2010; 107:20138-43; PMID:21041629; http://dx.doi.org/10.1073/pnas.1007068107
   PubMed Web of Science ®Google Scholar
• Nkhoma SC, Nair S, Cheeseman IH, Rohr-Allegrini C, Singlam S, Nosten F, Anderson TJC. Close kinship within multiple-genotype malaria parasite infections. Proc Biol Sci 2012; 279:2589-98; PMID:22398165; http://dx.doi.org/10.1098/rspb.2012.0113
   PubMedGoogle Scholar
• Abu-Raddad LJ, Patnaik P, Kublin JG. Dual infection with HIV and malaria fuels the spread of both diseases in sub-Saharan Africa. Science 2006; 314:1603-6; PMID:17158329; http://dx.doi.org/10.1126/science.1132338
   PubMed Web of Science ®Google Scholar
• Kublin JG, Patnaik P, Jere CS, Miller WC, Hoffman IF, Chimbiya N, Pendame R, Taylor TE, Molyneux ME. Effect of Plasmodium falciparum malaria on concentration of HIV-1-RNA in the blood of adults in rural Malawi: a prospective cohort study. Lancet 2005; 365:233-40; PMID:15652606
   PubMed Web of Science ®Google Scholar
• Joint United Nations Programme on HIVAIDS Staff & World Health Organization Staff. AIDS epidemic update, December 2006. World Health Organization; 2006; UNAIDS06.29E
   Google Scholar
• Jamieson AM, Pasman L, Yu S, Gamradt P, Homer RJ, Decker T, Medzhitov R. Role of tissue protection in lethal respiratory viral-bacterial coinfection. Science 2013; 340:1230-4; PMID:23618765; http://dx.doi.org/10.1126/science.1233632
   PubMedGoogle Scholar
• Lewis RE, Viale P, Kontoyiannis DP. The potential impact of antifungal drug resistance mechanisms on the host immune response to candida. Virulence 2012; 3:368-76; PMID:22722245; http://dx.doi.org/10.4161/viru.20746
   PubMed Web of Science ®Google Scholar
• Tillmann HL, Heiken H, Knapik-Botor A, Heringlake S, Ockenga J, Wilber JC, Goergen B, Detmer J, McMorrow M, Stoll M, et al. Infection with GB virus C and reduced mortality among HIV-infected patients. N Engl J Med. 2001; 345:715-24; PMID:11547740; http://dx.doi.org/10.1056/NEJMoa010398
   PubMed Web of Science ®Google Scholar
• Xiang J, Wunschmann S, Diekema D, Klinzman D, Patrick K, George S, Stapleton J. Effect of coinfection with GB virus C on survival among patients with HIV infection. N Engl J Med 2001; 345:707-14; http://dx.doi.org/10.1056/NEJMoa003364
   PubMed Web of Science ®Google Scholar
• Moreira LA, Iturbe-Ormaetxe In, Jeffery JA, Lu G, Pyke AT, Hedges LM, Rocha BC, Hall-Mendelin S, Day A, Riegler M, et al. A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium. Cell 2009; 139:1268-78; PMID:20064373; http://dx.doi.org/10.1016/j.cell.2009.11.042
   PubMed Web of Science ®Google Scholar
• Vento S, Cainelli F. Can HIV-1 viral interference be used therapeutically? Lancet Infect Dis 2013; 13:9-10; http://dx.doi.org/10.1016/S1473-3099(12)70312-2
   PubMed Web of Science ®Google Scholar
• Doolan DL, Dobaño C, Baird JK. Acquired immunity to malaria. Clin Microbiol Rev 2009; 22:13-36; http://dx.doi.org/10.1128/CMR.00025-08
   PubMed Web of Science ®Google Scholar
• Dieckmann U. Adaptive dynamics of pathogen-host interactions. In: Dieckmann U, Metz JAJ, Sabelis MW, Sigmund K (eds.), Adaptive dynamics of infectious diseases: In pursuit of virulence management. Cambridge: Cambridge University Press; 2002; 39-59
   Google Scholar
• Michalakis Y, Olivieri I, Renaud F, Raymond M. Pleiotropic action of parasites: How to be good for the host. Trends Ecol Evol 1992; 7:59-63; PMID:21235952; http://dx.doi.org/10.1016/0169-5347(92)90108-N
   PubMedGoogle Scholar
• Mazumdar P. Species and Specificity: An Interpretation of the History of Immunology. Cambridge, UK: Cambridge University Press; 1995
   Google Scholar
• Creager A. Adaptation or selection? Old issues and new stakes in the postwar debates over bacterial drug resistance. Stud Hist Philos Biol Biomed Sci 2007; 38:159-90; http://dx.doi.org/10.1016/j.shpsc.2006.06.016
   PubMedGoogle Scholar
• Lederberg J. Viruses and human kind: intracellular symbiosis and evolutionary competition. In: Morse S (ed.), Emerging Viruses. New York: Oxford University Press; 1993; 3-9.
   Google Scholar
• Mendelsohn AJ. ‘Like all that lives’: biology, medicine, and bacteria in the age of Pasteur and Koch. Hist Phil Life Sci 2002; 24:3-36; PMID:12664951; http://dx.doi.org/10.1080/03919710210001714293
   PubMed Web of Science ®Google Scholar
• Levin BR, Bull JJ. Short-sighted evolution and the virulence of pathogenic microorganisms. Trends Microbiol 1994; 2:76-81; PMID:8156275; http://dx.doi.org/10.1016/0966-842X(94)90538-X
   PubMedGoogle Scholar
• Margolis E, Levin BR. Within-host evolution for the invasiveness of commensal bacteria: an experimental study of bacteremias resulting from Haemophilus influenzae nasal carriage. J Infect Dis 2007; 196:1068-75; PMID:17763330; http://dx.doi.org/10.1086/520934
   PubMedGoogle Scholar
• Kouyos RD, von Wyl V, Hinkley T, Petropoulos CJ, Haddad M, Whitcomb JM, Böni J, Yerly S, Cellerai C, Klimkait T, et al. Swiss HIV Cohort Study. Assessing predicted HIV-1 replicative capacity in a clinical setting. PLoS Pathog 2011; 7:e1002321; PMID:22072960; http://dx.doi.org/10.1371/journal.ppat.1002321
   PubMedGoogle Scholar
• Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, Di Giambenedetto S, Gras L, Günthard HF, Jacobson LP, Mullins JI, et al. Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS 2012; 26:193-205; PMID:22089381; http://dx.doi.org/10.1097/QAD.0b013e32834db418
   PubMedGoogle Scholar
• Méthot P-O. Research traditions and evolutionary explanations in medicine. Theor Med Bioeth 2011; 32:80-95; PMID:21140228; http://dx.doi.org/10.1007/s11017-010-9167-4
   PubMedGoogle Scholar
• Anderson RM, May RM. Coevolution of hosts and parasites. Parasitology 1982; 85:411-26; http://dx.doi.org/10.1017/S0031182000055360
   PubMed Web of Science ®Google Scholar
• Ewald PW. Host-parasite relations, vectors and the evolution of disease severity. Annu Rev Ecol Syst 1983; 14:465-85; http://dx.doi.org/10.1146/annurev.es.14.110183.002341
   Google Scholar
• Ebert D. Experimental evolution of parasites. Science 1998; 282:1432-5; http://dx.doi.org/10.1126/science.282.5393.1432
   PubMed Web of Science ®Google Scholar
• Atkins KE, Read AF, Savill NJ, Renz KG, Islam AF, Walkden-Brown SW, Woolhouse MEJ. Vaccination and reduced cohort duration can drive virulence evolution: Marek's disease virus and industrialised agriculture. Evolution 2013; 67:851-60; PMID:23461333; http://dx.doi.org/10.1111/j.1558-5646.2012.01803.x
   PubMedGoogle Scholar
• Dieckmann U, Metz JAJ, Sabelis MW, Sigmund K, eds. Adaptive dynamics of infectious diseases. In Pursuit of virulence management. Cambridge studies in adaptive dynamics. Cambridge, UK: Cambridge University Press; 2002.
   Google Scholar
• Read AF, Day T, Huijben S. The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proc Natl Acad Sci USA 2011; 108:10871-7; PMID:21690376; http://dx.doi.org/10.1073/pnas.1100299108
   PubMed Web of Science ®Google Scholar
• Weir L, Mykhalovski E. Global Public Health Vigilance. Creating a World on Alert. London: Routledge; 2010.
   Google Scholar
• Méthot P-O. Understanding pathogens in the era of next generation sequencing. J Infect Dev Ctries 2012; 6(9):689-91
   PubMedGoogle Scholar
• Méthot P-O. Science and science policy: regulating ‘select agent’ in the age of synthetic biology. Perspect Sci 2014; 23(3)
   Google Scholar
• Swiatczak B, Rescigno M, Cohen IR. Systemic features of immune recognition in the gut. Microb Infect 2011; 13:983-91; PMID:21782966; http://dx.doi.org/10.1016/j.micinf.2011.06.011
   PubMed Web of Science ®Google Scholar
• Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, Lopez-Galindez C et al. A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. eLife 2013; 2:e01123; PMID:24171102; http://dx.doi.org/10.7554/eLife.01123
   PubMedGoogle Scholar
• Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science 2014; 343:1243727; PMID:24653038; http://dx.doi.org/10.1126/science.1243727
   PubMedGoogle Scholar
• Dupré J. Processes of Life. Essays in the philosophy of biology. Oxford: Oxford University Press; 2012
   Google Scholar