10.5061/DRYAD.8D2F6
Numminen, Elina
University of Helsinki
Chewapreecha, Claire
Wellcome Trust
Sirén, Jukka
University of Helsinki
Turner, Claudia
Mahidol University
Turner, Paul
Mahidol University
Bentley, Stephen D.
Wellcome Trust
Corander, Jukka
University of Helsinki
Siren, J.
University of Helsinki
Data from: Two-phase importance sampling for inference about transmission trees
Dryad
dataset
2014
Molecular epidemiology
parsimony trees
SNP trees
Transmission tree
Streptococcus pneumoniae
2014-08-29T17:21:37Z
2014-08-29T17:21:37Z
en
https://doi.org/10.1098/rspb.2014.1324
20877 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
There has been growing interest in the statistics community to develop
methods for inferring transmission pathways of infectious pathogens from
molecular sequence data. For many datasets, the computational challenge
lies in the huge dimension of the missing data. Here, we introduce an
importance sampling scheme in which the transmission trees and phylogenies
of pathogens are both sampled from reasonable importance distributions,
alleviating the inference. Using this approach, arbitrary models of
transmission could be considered, contrary to many earlier proposed
methods. We illustrate the scheme by analysing transmissions of
Streptococcus pneumoniae from household to household within a refugee
camp, using data in which only a fraction of hosts is observed, but which
is still rich enough to unravel the within-household transmission dynamics
and pairs of households between whom transmission is plausible. We observe
that while probability of direct transmission is low even for the most
prominent cases of transmission, still those pairs of households are
geographically much closer to each other than expected under random
proximity.
Parsimony SNP trees for bacterial isolatesThis file contains parsimonious
SNP trees for Streptococcus Pneumoniae isolates. Trees are constructed for
serotypes NT, 23F, 23AF, 19F, 15BC, 14 and 6B, that were the most common
serotypes in the original cohort study. This study assessed pneumococcal
colonization in infants and their mothers, who lived in a refugee camp in
Northwestern Thailand. The trees contain the following information for
each isolate: MLST genotypes, household labels, mother/infant designation
and sampling dates.data from Two phase importance sampling for inference
about transmission trees.zip
Northwestern Thailand