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SUMMARY:Detection of outbreaks using epidemiological and genetic data: cas
 e-study of Campylobacter infections in England - Laura Guzman (University 
 of Warwick)
DTSTART:20230705T110000Z
DTEND:20230705T120000Z
UID:TALK202939@talks.cam.ac.uk
CONTACT:Dr Ciara Dangerfield
DESCRIPTION:Health authorities consider the identification and investigati
 on of outbreaks a top priority. Timely detection of infectious disease out
 breaks enables effective interventions to prevent further transmission. Th
 e whole-genome sequencing of pathogens provides a promising source of info
 rmation that can enhance outbreak detection methods. However\, incorporati
 ng the complex and rich nature of genomics data into Bayesian models poses
  a challenge. We propose a new statistical method that leverages spatiotem
 poral and genetic data to detect outbreaks and demonstrate its use in anal
 ysing Campylobacter infections reported in two regions in England.\nIn our
  approach\, we employ a Bayesian hierarchical model to classify reported i
 nfections as either sporadic or outbreak cases. We integrate a Gaussian pr
 ocess into the model to capture similarities in genome sequences and emplo
 y Markov Chain Monte Carlo (MCMC) methods for inference. To address the ch
 allenge of Bayesian inference in a high-dimensional Gaussian process\, we 
 utilise a block sampling algorithm that enhances the MCMC performance.\nWe
  applied our method to various subsets of the Campylobacter dataset\, incl
 uding spatial-temporal\, spatial-genetic and temporal-genetic subsets. Thi
 s approach enabled us to identify potential outbreaks with different chara
 cteristics. Particularly\, by analysing temporal-genetic data\, our method
  identified cases that could potentially be linked with nationwide outbrea
 ks\, which would have gone unnoticed using only spatial-temporal methods.\
 nIntegrating both epidemiological and genetic data is vital for the detect
 ion of otherwise unnoticed outbreaks. Early identification of infectious d
 isease outbreaks plays a crucial role in enabling health institutions and 
 policymakers to promptly pinpoint the sources of the outbreak and implemen
 t effective interventions.
LOCATION:Zoom
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