Reconstructing transmission trees for communicable diseases using densely sampled genetic data

Annals of Applied Statistics

Volumn 10, Issue 1, 2016, Pages 395-417

  Worby, Colin J ^a,b   O’Neill, Philip D ^a   Kypraios, Theodore ^a   Robotham, Julie V ^c   De Angelis, Daniela ^c,d   Cartwright, Edward J P ^e   Peacock, Sharon J ^f   Cooper, Ben S ^g,h  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c PUBLIC HEALTH ENGLAND   (United Kingdom)

^d MRC BIOSTATISTICS UNIT   (United Kingdom)

^e IPSWICH HOSPITAL NHS TRUST   (United Kingdom)

^f UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h MAHIDOL UNIVERSITY   (Thailand)

Author keywords

Bayesian inference; Epidemics; Infectious disease; Outbreak investigation; Transmission routes

Indexed keywords

EID: 84975127301     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/15-AOAS898     Document Type: Article

References (33)

1. ALBRICH, W. C. and HARBARTH, S. (2008). Health-care workers: Source, vector, or victim of MRSA? Lancet, Infect. Dis. 8 289-301.
2. BRYANT, J. M., SCHÜRCH, A. C., VAN DEUTEKOM, H., HARRIS, S. R., DE BEER, J. L., DE JAGER, V., KREMER, K., VAN HIJUM, S. A. F. T., SIEZEN, R. J., BORGDORFF, M., BENTLEY, S. D., PARKHILL, J. and VAN SOOLINGEN, D. (2013). Inferring patient to patient transmission of mycobacterium tuberculosis from whole genome sequencing data. BMC Infect. Dis. 13 1-12.
3. COOPER, B. S.,MEDLEY, G. F. and SCOTT, G. M. (1999). Preliminary analysis of the transmission dynamics of nosocomial infections: Stochastic and management effects. J. Hosp. Infect. 43 131-147.
4. COTTAM, E. M., THÉBAUD, G., WADSWORTH, J., GLOSTER, J., MANSLEY, L., PATON, D. J., KING, D. P. and HAYDON, D. T. (2008). Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus. Proceedings of the Royal Society (Series B) 275 887-895.
5. GARDY, J. L., JOHNSTON, J. C., HO SUI, S. J., COOK, V. J., SHAH, L., BRODKIN, E., REMPEL, S.,MOORE, R., ZHAO, Y.,HOLT, R.,VARHOL, R.,BIROL, I., LEM, M., SHARMA, M. K., ELWOOD, K., JONES, S. J. M., BRINKMAN, F. S. L., BRUNHAM, R. C. and TANG, P. (2011). Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. New England Journal of Medicine 364 730-739.
6. HARRIS, S. R., FEIL, E. J., HOLDEN, M. T. G., QUAIL, M. A., NICKERSON, E. K., CHANTRATITA, N., GARDETE, S., TAVARES, A., DAY, N., LINDSAY, J. A., EDGEWORTH, J. D., DE LENCASTRE, H., PARKHILL, J., PEACOCK, S. J. and BENTLEY, S. D. (2010). Evolution of MRSA during hospital transmission and intercontinental spread. Science 327 469-474.
7. HARRIS, S. R., CARTWRIGHT, E. J. P., TÖRÖK, M. E., HOLDEN, M. T. G., BROWN, N. M., OGILVY-STUART, A. L., ELLINGTON, M. J., QUAIL, M. A., BENTLEY, S. D., PARKHILL, J. and PEACOCK, S. J. (2013). Whole-genome sequencing for analysis of an outbreak of meticillinresistant Staphyloccus aureus: A descriptive study. Lancet, Infect. Dis. 13 130-136.
8. JOMBART, T., EGGO, R. M., DODD, P. J. and BALLOUX, F. (2011). Reconstructing disease outbreaks from genetic data: A graph approach. Heredity (Edinb) 106 383-390.
9. JOMBART, T., CORI, A., DIDELOT, X., CAUCHEMEZ, S., FRASER, C. and FERGUSON, N. (2014). Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Comput. Biol. 10 e1003457.
10. KÖSER, C. U., HOLDEN, M. T. G., ELLINGTON, M. J., CARTWRIGHT, E. J. P., BROWN, N. M., OGILVY-STUART, A. L., YANG HSU, L., CHEWAPREECHA, C., CROUCHER, N. J., HARRIS, S. R., SANDERS, M., ENRIGHT, M. C., DOUGAN, G., BENTLEY, S. D., PARKHILL, J., FRASER, L. J., BETLEY, J. R., SCHULZ-TRIEGLAFF, O. B., SMITH, G. P. and PEACOCK, S. J. (2012). Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. New England Journal of Medicine 366 2267-2275.
11. KRZANOWSKI, W. J. and HAND, D. J. (2009). ROC Curves for Continuous Data. Monographs on Statistics and Applied Probability 111. CRC Press, Boca Raton, FL. MR2522628
12. KYPRAIOS, T., O'NEILL, P. D., HUANG, S. S., RIFAS-SHIMAN, S. L. and COOPER, B. (2010). Assessing the role of undetected colonisation and isolation precautions in reducing methicillinresistant Staphyloccus aureus transmission in intensive care units. BMC Infect. Dis. 10.
13. MOLLENTZE, N.,NEL, L. H., TOWNSEND, S., LE ROUX, K.,HAMPSON, K.,HAYDON, D. T. and SOUBEYRAND, S. (2014). A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data. Proceedings of the Royal Society (Series B) 281 1782.
14. MORELLI, M. J., THÉBAUD, G., CHADOEUF, J., KING, D. P., HAYDON, D. T. and SOUBEYRAND, S. (2012). A Bayesian inference framework to reconstruct transmission trees using epidemiological and genetic data. PLoS Comput. Biol. 8 e1002768, 14. MR3007333
15. NUMMINEN, E., CHEWAPREECHA, C., SIRÉN, J., TURNER, C., TURNER, P., BENTLEY, S. D. and CORANDER, J. (2014). Two-phase importance sampling for inference about transmission trees. J. R. Soc. Interface 281 20141324.
16. O'NEILL, P. and ROBERTS, G. (1999). Bayesian inference for partially observed stochastic epidemics. J. Roy. Statist. Soc. Ser. A 162 121-129.
17. PERRY, J. D., DAVIES, A., BUTTERWORTH, L. A., HOPLEY, A. L. J., NICHOLSON, A. and GOULD, F. K. (2004). Development and evaluation of a chromogenic agar medium for methicillin-resistant staphylococcus aureus. J. Clin. Microbiol. 42 4519-4523.
18. PITTET, D., ALLEGRANZI, B., STORR, J., NEJAD, S. B., DZIEKAN, G., LEOTSAKOS, A. and DONALDSON, L. (2008). Infection control as a major World Health Organization priority for developing countries. J. Hosp. Infect. 68 285-292.
19. PYBUS, O. G. and RAMBAUT, A. (2009). Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10 540-550.
20. PYBUS, O. G., CHARLESTON, M. A., GUPTA, S., RAMBAUT, A., HOLMES, E. C. and HARVEY, P. H. (2001). The epidemic behavior of the hepatitis C virus. Science 292 2323-2325.
21. RASMUSSEN, D. A., RATMANN, O. and KOELLE, K. (2011). Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comput. Biol. 7 e1002136, 11. MR2845064
22. ROMERO-SEVERSON, E., SKAR, H., BULLA, I., ALBERT, J. and LEITNER, T. (2014). Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol. Biol. Evol. 31 2472-2482.
23. SNITKIN, E. S., ZELAZNY, A. M., THOMAS, P. J., STOCK, F., NISC COMPARATIVE SEQUENCING PROGRAM GROUP, HENDERSON, D. K., PALMORE, T. N. and SEGRE, J. A. (2012). Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Science Translational Medicine 4 148ra116.
24. TANNER, M. A. andWONG, W. H. (1987). The calculation of posterior distributions by data augmentation. J. Amer. Statist. Assoc. 82 528-550. With discussion and with a reply by the authors. MR0898357
25. VOLZ, E. M., POND, S. L. K., WARD, M. J., BROWN, A. J. L. and FROST, S. D. W. (2009). Phylodynamics of infectious disease epidemics. Genetics 183 1421-1430.
26. WATTERSON, G. A. (1975). On the number of segregating sites in genetical models without recombination. Theoret. Population Biology 7 256-276. MR0366430
27. WORBY, C. J., LIPSITCH, M. and HANAGE, W. P. (2014). Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput. Biol. 10 e1003549.
28. WORBY, C. J. and READ, T. D. (2015). "seedy" (simulation of evolution and epidemiological dynamics): An R package to follow within-host mutation in pathogens. PLOS One 10 e0129745.
29. WORBY, C. J., JEYARATNAM, D., ROBOTHAM, J. V., KYPRAIOS, T., O'NEILL, P. D., ANGELIS, D. D., FRENCH, G. and COOPER, B. S. (2013). Estimating the effectiveness of isolation and decolonization measures in reducing transmission of methicillin-resistant Staphylococcus aureus in hospital general wards. Am. J. Epidemiol. 177 1306-1313.
30. WORBY, C. J., CHANG, H. H., HANAGE, W. P. and LIPSITCH, M. (2014). The distribution of pairwise genetic distances: A tool for investigating disease transmission. Genetics 198 1395-1404.
31. WORBY, C. J., O'NEILL, P. D., KYPRAIOS, T., ROBOTHAM, J. V., DE ANGELIS, D., CARTWRIGHT E. J. P., PEACOCK, S. J. and COOPER, B. S. (2016). Supplement to "Reconstructing transmission trees for communicable diseases using densely sampled genetic data." DOI:10.1214/15-AOAS898SUPPA, DOI:10.1214/15-AOAS898SUPPB.
32. YPMA, R. J. F., VAN BALLEGOOIJEN, W. M. and WALLINGA, J. (2013). Relating phylogenetic trees to transmission trees of infectious disease outbreaks. Genetics 195 1055-1062.
33. YPMA, R. J. F., BATAILLE, A. M. A., STEGEMAN, A., KOCH, G.,WALLINGA, J. and VAN BALLEGOOIJEN, W. M. (2012). Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data. Proceedings of the Royal Society (Series B) 279 444-450.