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ESS, effective sample size; R, Pearson correlation between date of isolation and maximum likelihood tree branch length.
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However, this observation is consistent with studies from chronic infections [ 28] and explains the complex relationship between phylogeny and date of isolation.
We did not perform this analysis for the whole S. Typhimurium data set as there was no relationship between branch lengths and date of isolation across the rest of the tree.
Patient information such as age, sex, clinical presentation, isolated site and date of isolation are given in Table 1.
No relationship was evident between their original environment, geographical location or date of isolation and the clustering pattern.
To test for temporal signal in the phylogeny, we assessed the correlation between root-to-tip distance and the date of isolation (day, month, year) in Path-O-Gen (v1.4).
A date of isolation was available for 197 of the isolates.
This conclusion is supported by the number of isolates recovered from HIV-positive patients (n=177), the age distribution, which peaks between 20 and 40 years of age, and the date of isolation with a peak corresponding to the 1990s.
MSTs of the genomes in clusters 1 and 3 showed that, although there are obvious instances of migration between hospitals, genomes clustered well according to the hospital of origin and the date of isolation.
Regardless of the profile, the date of isolation introduction also correlated with outcomes.
Historically, IIVs were numbered according to date of isolation [37], [38].
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