Regression-based ranking of pathogen strains with respect to their contribution to natural epidemics

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Soubeyrand, Samuel ^a   Tollenaere, Charlotte ^b,c   Haon Lasportes, Emilie ^a   Laine, Anna Liisa ^b  

^a INRA   (France)

^b UNIVERSITY OF HELSINKI   (Finland)

^c Campus International de Baillarguet   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DISEASE COURSE; EPIDEMIOLOGICAL DATA; EPIDEMIOLOGICAL MONITORING; FUNGAL STRAIN; FUNGAL VIRULENCE; GENETIC DATABASE; GENETIC VARIABILITY; NONHUMAN; PLANTAGO LANCEOLATA; PODOSPHAERA; PODOSPHAERA PLANTAGINIS; POWDERY MILDEW; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; TAXONOMIC RANK;

ALGORITHMS; ASCOMYCOTA; COMPUTER SIMULATION; GENETIC VARIATION; GENOTYPE; HOST-PATHOGEN INTERACTIONS; PLANT DISEASES; PLANT LEAVES; PLANTAGO; POLYMORPHISM, SINGLE NUCLEOTIDE; REGRESSION ANALYSIS; SPECIES SPECIFICITY; TIME FACTORS;

EID: 84900344056     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086591     Document Type: Article

References (36)

1. Anderson RM, May RM (1991) Infectious diseases of humans: dynamics and control. Oxford: Oxford University Press.
2. Gilligan CA (2002) An epidemiological framework for disease management. Advances in botanical research 38: 1-64.
3. Shaw MW (2002) Epidemic modelling and disease forecasting. In: Waller JM, Lenn'e JM, Waller SJ, editors, Plant Pathologists' Pocketbook. Wallingford: CABI Publishing, 252-265.
4. Gibson GJ, Gilligan CA, Kleczkowski A (1999) Predicting variability in biological control of a plantpathogen system using stochastic models. Proceedings of the Royal Society of London Series B: Biological Sciences 266: 1743-1753. (Pubitemid 29433455)
5. Pullan RL, Sturrock HJW, Soares Magalhães RJ, Clements ACA, Brooker SJ (2012) Spatial parasite ecology and epidemiology: a review of methods and applications. Parasitology 139: 1870-1887.
6. Morens DM, Folkers GK, Fauci AS (2004) The challenge of emerging and re-emerging infectious diseases. Nature 430: 242-249. (Pubitemid 38902437)
7. Ostfeld RS, Glass GE, Keesing F (2005) Spatial epidemiology: an emerging (or re-emerging) discipline. Trends in Ecology & Evolution 20: 328-336. (Pubitemid 40772080)
8. Tack AJM, Thrall PH, Barrett LG, Burdon JJ, Laine AL (2012) Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: causes and consequences. Journal of Evolutionary Biology 25: 1918-1936.
9. Criscione CD, Poulin R, Blouin MS (2005) Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Molecular ecology 14: 2247-2257. (Pubitemid 40886028)
10. Giraud T, Enjalbert J, Fournier E, Delmotte F, Dutech C (2008) Population genetics of fungal diseases of plants. Parasite 15: 449-454.
11. Qi W, Kaser M, Roltgen K, Yeboah-Manu D, Pluschke G (2009) Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing. PLoS pathogens 5: e1000580.
12. Frenkel O, Portillo I, Brewer MT, Peros JP, Cadle-Davidson L, et al. (2012) Development of microsatellite markers from the transcriptome of Erysiphe necator for analysing population structure in North America and Europe. Plant Pathology 61: 106-119.
13. Cui Y, Yu C, Yan Y, Li D, Li Y, et al. (2013) Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proceedings of the National Academy of Sciences 110: 577-582.
14. Archie EA, Luikart G, Ezenwa VO (2009) Infecting epidemiology with genetics: a new frontier in disease ecology. Trends in Ecology & Evolution 24: 21-30.
15. Thrall PH, Burdon JJ, Bever JD (2002) Local adaptation in the Linum marginale-Melampsora lini host-pathogen interaction. Evolution 56: 1340-1351. (Pubitemid 34881588)
16. Luijckx P, Ben-Ami F, Mouton L, Du Pasquier L, Ebert D (2011) Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions. Ecology letters 14: 125-131.
17. Laine AL (2007) Pathogen fitness components and genotypes differ in their sensitivity to nutrient and temperature variation in a wild plant-pathogen association. Journal of evolutionary biology 20: 2371-2378.
18. Wolinska J, King KC (2009) Environment can alter selection in host-parasite interactions. Trends in parasitology 25: 236-244.
19. Tollenaere C, Susi H, Nokso-Koivisto J, Koskinen P, Tack A, et al. (2012) SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection. PLoS One 7: e52492.
20. Laine AL, Hanski I (2006) Large-scale spatial dynamics of specialist plant pathogen. Journal of Ecology 94: 217-226.
21. Soubeyrand S, Laine AL, Hanski I, Penttinen A (2009) Spatio-temporal structure of host-pathogen interactions in a metapopulation. The American Naturalist 174: 308-320.
22. Ovaskainen O, Laine AL (2006) Inferring evolutionary signals form ecological data in a plantpathogen metapopulation. Ecology 87: 880-891.
23. Ruppert D,Wand MP, Carroll RJ (2003) Semiparametric Regression. Cambridge University Press.
24. Silverman BW (1986) Density Estimation for Statistics and Data Analysis. London: Chapman and Hall.
25. Manly BFJ (1997) Randomization, Bootstrap and Monte Carlo Methods in Biology, 2nd Ed. London: Chapman & Hall.
26. Miller RG Jr (1981) Simultaneous Statistical Inference. New York: Springer-Verlag.
27. Carroll RJ, Ruppert D, Stefanski LA, Crainiceanu CM (2006) Measurement error in nonlinear vmodels: a modern perspective, volume 105. Chapman & Hall/CRC.
28. Soubeyrand S, Chadoeuf J, Sache I, Lannou C (2006) Residual-based specification of the randome effects distribution for cluster data. Statistical Methodology 3: 464-482. (Pubitemid 44419506)
29. Soubeyrand S, Chadoeuf J (2007) Residual-based specification of a hidden random field included in a hierarchical spatial model. Computational Statistics and Data Analysis 51: 6404-6422. (Pubitemid 47161040)
30. Bruns E, Carson M, May G (2012) Pathogen and host genotype differently affect pathogen fitness through their effects on different life-history stages. BMC Evolutionary Biology 12: 135.
31. Grech K, Watt K, Read AF (2006) Host-parasite interactions for virulence and resistance in a malaria model system. Journal of Evolutionary Biology 19: 1620-1630.
32. Pariaud B, Ravigné V, Halkett F, Goyeau H, Carlier J, et al. (2009) Aggressiveness and its role in the adaptation of plant pathogens. Plant Pathology 58: 409-424.
33. Salvaudon L, Héraudet V, Shykoff JA (2005) Parasite-host fitness trade-offs change with parasite identity: Genotype-specific interactions in a plant-pathogen system. Evolution 59: 2518-2524. (Pubitemid 43069934)
34. Smith I (2003) Mycobacterium tuberculosis pathogenesis and molecular determinants of virulence. Clinical microbiology reviews 16: 463-496.
35. Vale PF, Little TJ (2009) Measuring parasite fitness under genetic and thermal variation. Heredity 103: 102-109.
36. Vojvodic S, Jensen AB, Markussen B, Eilenberg J, Boomsma JJ (2011) Genetic variation in virulence among chalkbrood strains infecting honeybees. PloS one 6: e25035.