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Probabilistic models in infectious disease epidemiology and risk analysis of food production chains

Researchers: Kari Auranen, Jukka Ranta, Mervi Eerola, Elja Arjas

The work of the group is focused on dynamical modelling of the spread of infection and pathogenic contamination in human and animal populations. Common features of the methodology include data augmentation, latent variables, hidden Markov models, and extensive use of Markov chain Monte Carlo simulation in Bayesian hierarchical modelling. The work is mostly joint research with the Department of Vaccines in the National Public Health Institute (KTL) and the Department of Risk Assessment in the National Veterinary and Food Research Institute (EELA).

A major part of the collaboration with KTL has dealt with bacterial infections. Their dynamics is characterised by transmission via subclinical (asymptomatic) infections, temporary immunity against re-infection and relatively rare clinical (observed) diseases. Specific applications include development of Bayesian estimation methods for point process models of transmission of recurrent infections: spread of Haemophilus influenzae type b (Hib) bacteria in a family environment, transmission of Streptococcus pneumoniae (Pnc) within families, and studies on the time course from Pnc infection until disease, modified by immunological responses, as well as the time course of a single outbreak of meningococcal epidemics in a military garrison.

Auranen is currently leading one of the workpackages in an EU funded research project (Pnc Euro, www.ktl.fi/pnceuro/ ). Specific aims in the project include development and applications of data analysis in multilevel transmission models, studies of Pnc transmission using stochastic simulation models, and assessment of underlying Pnc disease rates in surveillance systems with non-perfect sensitivity and specificity. In addition, Auranen is involved in the analysis of data from two major pneumoccocal vaccine trials run by KTL: FinOM (acute otitis media in Finnish children) and ARIVAC (pneumonia in Filipino children).

In addition to meningococcal outbreaks, Ranta has previously modelled the spatial distribution of childhood diabetes incidence and the detection probability of poliovirus in an environmental sampling scheme. His current work concentrates on risk analysis of health hazards in animal and food production. Specifically, the spread of salmonella contamination in a production chain from farm to fork has been modelled both for broiler meat and beef meat. The models combine expert knowledge with data about hierarchically structured production processes. In addition to modelling the current situation, a special interest is in modelling the effect of interventions under different possible scenarios by means of predictive distributions. Occasionally, Ranta has taken part in jointly organized short courses by giving lectures on probabilistic models for risk assessment.

Eerola has recently studied possibilities to use expert opinions and Bayesian information processing in the risk assessment of food production chains where typically very little, or no measured data at all, is available. Eerola has also been developing multilevel models to evaluate protective immunity of vaccines by the aid of animal models instead of large scale population trials.


Auranen K., Ranta J., Takala A.K. and Arjas E. (1996) A statistical model of transmission of Hib in a family. Statistics in Medicine 15: 2235-2252.

Ranta J., Pitkäniemi J., Karvonen M., Virtala E., Rusanen J., Colpaert A., Naukkarinen A. and the DiMe study group (1996) Detection of overall space-time clustering in a non-uniformly distributed population. Statistics in Medicine 15: 2561-2572.

Ranta J., Mäkelä P.H., Takala A.K., and Arjas E. (1999) Predicting the course of meningococcal disease outbreaks in closed subpopulations. Epidemiology and Infection 123: 359-371.

Auranen K., Eichner M., Käyhty H., Takala A.K. and Arjas E. (1999) A hierarchical Bayesian model to predict the duration of immunity against Hib. Biometrics 55: 1306-1313.

Eerola, M., Mannila, H., Salmenkivi, M.: Frailty factors and time-dependent hazards in modelling ear infections by BASSIST. In: Proceedings of 13th Symposium of Computational Statistics in Bristol (R. Payne and P. Green, eds.), Physica-Verlag: Heidelberg, 287-292, 1998.

Auranen K. (2000) Backcalculating the age-specific incidence rate of recurrent subclinical Haemophilus influenzae type b infection. Statistics in Medicine 19: 281-296.

Auranen K. (1999) On Bayesian modelling of recurrent infections. Ph.D. thesis. University of Helsinki. Rolf Nevanlinna Institute Reasearch Reports A26. Yliopistopaino, Helsinki. ISBN 952-9528-52-3. ISSN 0787-8338.

Ranta J. and Penttinen A. (2000) Probabilistic small area risk assessment using GIS-based data: a case study on Finnish childhood diabetes. Statistics in Medicine 19: 2345-2359.

Auranen K., Arjas E., Leino T., and Takala A. K. (2000) Transmission of pneumococcal carriage in families: a latent Markov process model for binary data. JASA 95: 1044-1053.

Ranta J., Rytkönen M., Karvonen M. Näkökulmia paikkatietoa hyödyntävään alueelliseen terveystutkimukseen ja tilastollisiin menetelmiin. (A few aspects on spatially referenced data, health geographics and statistical methods) Sosiaalilääketieteellinen aikakauslehti (Journal of Social Medicine) 1999; 36: 285-293.

O'Neill, P., Balding, D., Becker, N., Eerola, M., Mollison, D.: Analyses of Infectious Disease Data from Household Outbreaks by Markov Chain Monte Carlo Methods. Journal of the Royal Statistical Society (2000), C 49: 517-542.

Edwards, J, van der Heijden, O., Eerola, M., Gay, N. (2000) Modelling Rubella in Europe. Epidemiology and Infection 125: 617-634.

Leino, T. and Auranen, K. and Jokinen, J. and Leinonen, M and Tervonen P. and Takala, A.K. (2001) Pneumococcal carriage in children during their first two years: important role of family exposure. Pediatric Infectious Disease Journal, ISSN 0891-3668.20: 1022-1027.

Leino, T and Auranen, K. (2002) Voidaanko rokotuspäätösten seurauksia väestöstä ennustaa?,Duodecim 118: 57-61.

Puumalainen, T. and Zeta-Capeding, M. R. and Käyhty, H. and Lucero, M. G. and Auranen, K. and Leroy, O. and Nohynek, H. (2001) Antibody response to an elevenvalent pneumococcal conjugate vaccine in Filipino infants", The Pediatric Infectious Disease Journal, accepted for publication.

Mäkelä, P. H. and Käyhty, H. and Leino, T. and Auranen, K and Peltola, H. and Lindholm, N and Eskola, J. (2001) Long term persistence of immunity after conjugate vaccines, analysed with Hib vaccine as the mode, submitted.

Leino, T., Auranen, K., Mäkelä, P. H., Käyhty, H. and Takala, A. K. Dynamics of natural immunity caused by subclinical infections; a case study on Haemophilus influenzae type b (Hib)', to appear in Epidemiology and Infection.

Ranta, J. and Hovi, T and Arjas, E. (2001) Poliovirus surveillance by examining sewage water specimens; studies on detection probability using simulation models. Risk Analysis 21: 1087-1096.

Rytkönen, M and Ranta, J and Tuomilehto, J and Karvonen, M. (2001) Bayesian analysis of geographical variation in the incidence of type I diabetes in Finland", Diabetologia 44 (Suppl. 3): B 37--B 44.

Kokki, E and Ranta, J. and Penttinen, A. and Pukkala, E. and Pekkanen, J. (2001) Small area estimation of incidence of cancer around a known source of exposure with fine resolution data. Occupational & Environmental Medicine 58 No. 5: 315-320.

Ranta, J. (2001) On probabilistic models for surveillance and prediction of disease incidence with latent processes: case studies on meningococcal outbreaks, childhood diabetes and poliomyelitis. Ph.D. thesis. University of Helsinki. Rolf Nevanlinna Institute Reasearch Reports A34. Yliopistopaino, Helsinki. ISBN 952-9528-61-2 (nid.), 952-9528-62-0 ( PDF). ISSN 0787-8338.

Ranta, J. and Maijala, R. (2001) A probabilistic transmission model of salmonella in the primary broiler production chain. Risk Analysis, accepted for publication.

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