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Bold MIRU-VNTR profiles are the most frequent profiles.
However, the most frequent profiles in any given time period varied.
The association of the 5 most frequent profiles with clinical features at diagnosis and during the disease course was examined, showing no statistically significant associations.
For reasons of compatibility with available inference tools, each profile is encoded as a one-letter amino acid, therefore only the twenty most frequent profiles have been conserved for this analysis.
Only the 20 most frequent profiles are considered (see Materials and Methods for details) and trees are inferred using the GTR+Γ4 and the CAT+Γ4 (Additional file 1: Figure S9) models.
'Profiles 50%' refers to the most frequent profiles, observed on 50% of the actual cows in herds 2 ρ = relative penalty reduction The stochastic optimisation method was chosen due to its simplicity: finding alternative solutions was straightforward for the issues under study, with a number of parameters (three) smaller than when using evolutionary algorithms [ 10].
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The second and third most frequent profile are the unskilled answerers (21%) and occasional contributors (10.6%).
Often the founder is also the most frequent profile in a complex (in terms of isolates in which is found).
Contrarily, in bacteria isolated from children, this MDR profile was the third most frequent profile (7.8%), and for this group the most frequent MDR profile included resistance to "CPS" (14.1%).
The next most frequent profile is the one of patients with invasive cancer and chemotherapy sessions (n=20,006, 35%) for a mean cost of 15,780€.
The most frequent profile was the resistance to penicillin alone (n = 42), followed by the cross-resistance to β-lactams (n = 20) and the multidrug resistance (n = 13).
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