publication . Conference object . Article . Other literature type . 2014

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

Xavier Didelot; Jennifer L. Gardy; Caroline Colijn;
Open Access
  • Published: 08 Apr 2014 Journal: Molecular Biology and Evolution (issn: 1537-1719, Copyright policy)
Abstract
Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered—how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesian approach to reconstruct densely sampled outbreaks from genomic data while considering within-host diversity. We infer a time-labeled phylogeny using Bayesian evolutionary analysis by sampling trees (BEAST), and then infer a transmission network via a Monte Carlo Markov chain. We find that under a realistic model of within-host evolution, reconstructions of simulated ...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Methods, Genomics, Bayes' theorem, Bayesian probability, Markov chain, Markov chain Monte Carlo, symbols.namesake, symbols, Computational biology, Communicable disease transmission, Bayesian inference, Population, education.field_of_study, education, Biology
58 references, page 1 of 4

Alizon, S, Luciani, F, Regoes, RR. Epidemiological and clinical consequences of within-host evolution. Trends Microbiol.. 2011; 19 (1): 24-32 [OpenAIRE] [PubMed]

Allen, L, Brauer, F, van den Driessche, P, Wu, J. An introduction to stochastic epidemic models. Mathematical epidemiology. 2008

Barabási, A-L, Oltvai, ZN. understanding the cell’s functional organization. Nat Rev Genet.. 2004; 5 (2): 101-113 [OpenAIRE] [PubMed]

Bergstrom, CT, McElhany, P, Real, LA. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proc Natl Acad Sci U S A.. 1999; 96 (9): 5095-6100 [OpenAIRE] [PubMed]

Boeras, DI, Hraber, PT, Hurlston, M, Evans-Strickfaden, T, Bhattacharya, T, Giorgi, EE, Mulenga, J, Karita, E, Korber, BT, Allen, S. Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci U S A.. 2011; 108 (46): E1156-E1163 [OpenAIRE] [PubMed]

Bouckaert, RR. DensiTree: making sense of sets of phylogenetic trees. Bioinformatics. 2010; 26 (10): 1372-1373 [OpenAIRE] [PubMed]

Cottam, EM, Thébaud, G, Wadsworth, J, Gloster, J, Mansley, L, Paton, DJ, King, DP, Haydon, DT. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc R Soc B Biol Sci.. 2008; 275: 887-895 [OpenAIRE]

Cottam, EM, Wadsworth, J, Shaw, AE, Rowlands, RJ, Goatley, L, Maan, S, Maan, NS, Mertens, PPC, Ebert, K, Li, Y. Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007. PLoS Pathog.. 2008; 4 (4): e1000050 [OpenAIRE] [PubMed]

Didelot, X. Genomic analysis to improve the management of outbreaks of bacterial infection. Expert Rev Anti Infect Ther.. 2013; 11 (4): 335-337 [OpenAIRE] [PubMed]

Didelot, X, Bowden, R, Wilson, DJ, Peto, TEA, Crook, DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet.. 2012; 13: 601-612 [OpenAIRE] [PubMed]

Didelot, X, Eyre, DW, Cule, M, Ip, CLC, Ansari, MA, Griffiths, D, Vaughan, A, Connor, LO, Golubchik, T, Elizabeth, M. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol.. 2012; 13: R118 [OpenAIRE] [PubMed]

Didelot, X, Falush, D. Inference of bacterial microevolution using multilocus sequence data. Genetics. 2007; 175 (3): 1251-1266 [OpenAIRE] [PubMed]

Didelot, X, Nell, S, Yang, I, Woltemate, S, van der Merwe, S, Suerbaum, S. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc Natl Acad Sci U S A.. 2013; 110 (34): 13880-13885 [OpenAIRE] [PubMed]

Drummond, AJ, Nicholls, GK, Rodrigo, AG, Solomon, W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002; 161 (July): 1307-1320 [OpenAIRE] [PubMed]

Drummond, AJ, Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol.. 2007; 7: 214 [OpenAIRE] [PubMed]

58 references, page 1 of 4
Abstract
Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered—how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesian approach to reconstruct densely sampled outbreaks from genomic data while considering within-host diversity. We infer a time-labeled phylogeny using Bayesian evolutionary analysis by sampling trees (BEAST), and then infer a transmission network via a Monte Carlo Markov chain. We find that under a realistic model of within-host evolution, reconstructions of simulated ...
Subjects
free text keywords: Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Methods, Genomics, Bayes' theorem, Bayesian probability, Markov chain, Markov chain Monte Carlo, symbols.namesake, symbols, Computational biology, Communicable disease transmission, Bayesian inference, Population, education.field_of_study, education, Biology
58 references, page 1 of 4

Alizon, S, Luciani, F, Regoes, RR. Epidemiological and clinical consequences of within-host evolution. Trends Microbiol.. 2011; 19 (1): 24-32 [OpenAIRE] [PubMed]

Allen, L, Brauer, F, van den Driessche, P, Wu, J. An introduction to stochastic epidemic models. Mathematical epidemiology. 2008

Barabási, A-L, Oltvai, ZN. understanding the cell’s functional organization. Nat Rev Genet.. 2004; 5 (2): 101-113 [OpenAIRE] [PubMed]

Bergstrom, CT, McElhany, P, Real, LA. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proc Natl Acad Sci U S A.. 1999; 96 (9): 5095-6100 [OpenAIRE] [PubMed]

Boeras, DI, Hraber, PT, Hurlston, M, Evans-Strickfaden, T, Bhattacharya, T, Giorgi, EE, Mulenga, J, Karita, E, Korber, BT, Allen, S. Role of donor genital tract HIV-1 diversity in the transmission bottleneck. Proc Natl Acad Sci U S A.. 2011; 108 (46): E1156-E1163 [OpenAIRE] [PubMed]

Bouckaert, RR. DensiTree: making sense of sets of phylogenetic trees. Bioinformatics. 2010; 26 (10): 1372-1373 [OpenAIRE] [PubMed]

Cottam, EM, Thébaud, G, Wadsworth, J, Gloster, J, Mansley, L, Paton, DJ, King, DP, Haydon, DT. Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proc R Soc B Biol Sci.. 2008; 275: 887-895 [OpenAIRE]

Cottam, EM, Wadsworth, J, Shaw, AE, Rowlands, RJ, Goatley, L, Maan, S, Maan, NS, Mertens, PPC, Ebert, K, Li, Y. Transmission pathways of foot-and-mouth disease virus in the United Kingdom in 2007. PLoS Pathog.. 2008; 4 (4): e1000050 [OpenAIRE] [PubMed]

Didelot, X. Genomic analysis to improve the management of outbreaks of bacterial infection. Expert Rev Anti Infect Ther.. 2013; 11 (4): 335-337 [OpenAIRE] [PubMed]

Didelot, X, Bowden, R, Wilson, DJ, Peto, TEA, Crook, DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet.. 2012; 13: 601-612 [OpenAIRE] [PubMed]

Didelot, X, Eyre, DW, Cule, M, Ip, CLC, Ansari, MA, Griffiths, D, Vaughan, A, Connor, LO, Golubchik, T, Elizabeth, M. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol.. 2012; 13: R118 [OpenAIRE] [PubMed]

Didelot, X, Falush, D. Inference of bacterial microevolution using multilocus sequence data. Genetics. 2007; 175 (3): 1251-1266 [OpenAIRE] [PubMed]

Didelot, X, Nell, S, Yang, I, Woltemate, S, van der Merwe, S, Suerbaum, S. Genomic evolution and transmission of Helicobacter pylori in two South African families. Proc Natl Acad Sci U S A.. 2013; 110 (34): 13880-13885 [OpenAIRE] [PubMed]

Drummond, AJ, Nicholls, GK, Rodrigo, AG, Solomon, W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002; 161 (July): 1307-1320 [OpenAIRE] [PubMed]

Drummond, AJ, Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol.. 2007; 7: 214 [OpenAIRE] [PubMed]

58 references, page 1 of 4
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