Referee 1's review:

Summary of manuscript:
This manuscript is a descriptive comparison of the early disease progression of an intradermal infection by Yersinia pestis and Y. pseudotuberculosis. This inoculation route mimics the normal route of infection by the vector-borne pathogen Y. pestis but not the gastrointestinal pathogen Y. pseudotuberculosis. The authors focus almost exclusively on the tissue pathology at the inoculation site and draining lymph nodes but do show a limited set of data comparing the rate of dissemination of the two pathogens. As may be expected, there is a noticeable difference in the pathology by two days post infection in the draining lymph nodes between these two bacteria. A fairly large portion of the results and discussion is dedicated to application of cluster analysis and a multiple correspondence analysis system to define major histological patterns that are associated with each pathogen.

General comments:

It seems to this reviewer that this type of analysis would have the most impact if it were applied to the analysis of Y. pestis mutants to determine the role of specific genes to virulence. However, the authors make no mention of this application. Furthermore, while the differences between the pathology of Y. pestis and Y. pseudotuberculosis infections are quite dramatic, individual Y. pestis mutants may have a significantly more subtle phenotype. The authors should include some discussion addressing this application and the caveats that could arise with more subtle differences. Inclusion of an attenuated Y. pestis mutant to determine if their MCA system could differentiate a more subtle phenotype would significantly strengthen this paper.
If there are no page limits in PLoSONE, then why are the authors submitting Supporting Data figures? If figures include data that is important for the manuscript then they should be included as main figures.

Specific comments:
Page 5 and Figure 1:
-While the range of the inoculums was provided, it may be more useful to see the average dose (+/- standard error) for each species. It is unclear to the reader if one species was inoculated on the high end of this range and one was inoculated on the low end.
-According to the text, cfu in the tissues was not determined at day 0, but this value is shown on the graphs. If actual numbers were not obtained for the 0 hr time point, then this time point should be left off the graphs.
-If no data is available for the 0 hr time point, then it appears that both species are growing at the same rate in the injection site between 24 hrs and 48 hrs (the slopes appear very similar and both increase ~ one log), This would indicate that Y. pseudotuberculosis does not proliferate more efficiently than Y. pestis at the injection site.
-The authors state that the two Yersinia species translocate to the DLN at similar efficiencies. I am not sure if this is a valid statement. First, even though there are significantly higher numbers of Y. pseudotuberculosis than Y. pestis at the inoculation site, there are equal numbers of the two bacteria in the DLN at 24 hrs, suggesting that Y. pestis is actually more efficient at translocation. Second, the authors did not determine if one species arrives at the DLN at an earlier time than the other, which is another way to interpret translocation efficiency. I think at best the authors can state that they can re-isolate Y. pseudotuberculosis from the DLN by 24 hrs.
-While the authors stated that 63 total mice were analyzed, stating the number of mice examined at each time point for each strain would be more useful. Also, is it really valid to combine the results from 6 different experiments? Were Y. pestis and Y. pseudotuberculosis tested side-by-side in each of these experiments with similar results?
-Limits of detection should be included on the graphs.

Page 6, line 25: It is unclear whether 36 DLNs were collected for each time point or total. If 36 is the total number of DLNs, how many were collected at each time point.
Page 8, lines 19-22: The reader would greatly benefit from a better description of what each axis represents.
Page 10, Line 11: As stated earlier, I would argue that Y. pestis may drain more efficiently. There are similar numbers in the DLN at 24 hrs even though there appears to be a 1.5 log higher Y. pseudotuberculosis load in the inoculation site, which suggests that Y. pestis actually disseminates at a higher rate. However, without knowing if one species reaches the DLN at earlier time, perhaps a conclusion on efficiency of dissemination cannot be made.
Figure 4: This figure should include an example of the type I category and be relabeled Type I, Type II and Type III instead of Y. pseudotub. and Y. pestis.

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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.