The scope of these studies covers a very wide range of strain rates, multiple species, various ages, and in some cases direct intervention.
The notable advances highlighted in this study, in comparison to previous investigations of hospital outbreaks of K. pneumoniae, are the use of the large-scale WGS data to deduce the bacterial isolates involved in the outbreaks and to use these data to retrospectively define the scope of outbreak strains across the hospital over a protracted period.
We propose a reconstruction that uses the mapping between displacement gradients and Lagrange strains to approximate the geometrically nonlinear result within the scope of the linear strain theory if the linear strains are substituted for the Lagrange strains.
The estimated strain-specific CDSs and core CDSs for the species, beyond the scope of eight sequenced strains if the genomes of additional strains were sequenced (i.e. n→ ∞), were extrapolated by fitting the data for the n = 1→8 comparison combinations above to an exponential decay functions as per [ 12].
By extrapolation of this function, the core, pan-genome and strain-unique CDSs for the entire species, beyond the scope of the eight sequenced strains, could be predicted [ 12].
It is unrealistic to suggest phasing-out of this strain, given the scope of shared resources built around it, however, continuing on the road of "strain-unawareness" will result in profound waste of effort, particularly where translational research is concerned.
NGS combined with phylogenetic analysis, however, was able to delineate the scope of contamination by differentiating those strains associated with the spiced-meat outbreak from strains epidemiologically unrelated to this event despite the remarkable genetic identity linking these two strain sets.
The comparatively small size of the Frankia secretomes may reflect the narrow scope of carbon sources utilized by Frankia strains, especially strains CcI3 and ACN, which have less than half of the solute-binding proteins found in EAN (Table 1, Additional File 2).
Scope of the product line.
To infer the temporal scope of the Outbreak Lineage 1 strains, we estimated the time of the most recent common ancestor (TMRCA) of sequenced Outbreak Lineage 1 isolates using Bayesian phylogenetic methods implemented in BEAST (Fig 2A) (Drummond & Rambaut, 2007).
