PONE-D-21-13891

Genomic insights into methicillin-resistant Staphylococcus pseudintermedius isolates from dogs and humans of the same sequence types reveals diversity in prophages and pathogenicity islands.

PLOS ONE

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: A thorough description of the MRSP genome from both dogs and humans. This manuscript is well written, informative and gives initial insight into an interesting gap in knowledge about host adaptation in this important pathogen. Thank you for this manuscript.

I only have minor comments which are typographical in nature.

Line 69 - important c.f. importance

Line 93 - Should this be 'stored' in TSB?

Line 144 - This sentence doesn't appear to be complete?

Line 146 - sp. detection

Line 177 - '...difference in...' c.f. '...different of...'

Line 200 - isolate should be singular

Line 279 - Should this be Figure 3 references for the prophage in these strains?

Line 371-2 - Table 2 appears to show that int-6 is present in both ST112 and ST111 but this sentence suggests it is just in ST112. There are also 4 ST183 isolates in the table with no integrases (n=2 canine, n=2 human).

Line 374-376 - int8 is listed in the table as being present in canine ST185 and ST121 (n=3 total) but this sentence appears to suggest that it is only present in human isolates.

Line 382 - sp. eBURST

Reviewer #2: The present study by Phumthanakorn et al reports the whole genome sequencing and comparative genomics of six methicillin-resistant Staphylococcus pseudintermedius (MRSP) isolates from dogs (n=3) and humans (n= 3), belonging to ST45, ST112, and ST181. The main objective of the study was to determine the genetic similarities and differences between human and animal MRSP strains of a same sequence type (ST). The authors have analyzed the integrated prophages, pathogenicity island, plasmids, transposable elements and various genes linked to antibiotic resistance and virulence in the sequenced strains. Similar to previous studies, some of the eight prophages identified in this study were ST-specific. All sequences have been submitted to the NCBI GenBank, and findings are nicely presented in figures and tables. Overall, the study is important and I do not have major comments. Here are my minor comments-

1. As mentioned in the paper “AH18-ST45 harbored two additional genes (spsP and spsQ) that were absent in VB88-ST45 and a different spsO genes”. This finding needs to be discussed in detail in the light of a recent study by Zukancic et al 2020 (mSphere) where spsP/spsQ gene deletion has been studied across all S. pseudintermedius sequence types.

2. Method section: Line 82-87. There are repetitive sentences about the isolation source of the dog and human strains sequenced in this study. It appears to be a typing error.

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Reviewer #1: No

Reviewer #2: No

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Genomic insights into methicillin-resistant Staphylococcus pseudintermedius isolates from dogs and humans of the same sequence types reveals diversity in prophages and pathogenicity islands.

PONE-D-21-13891R1

Dear Dr. Prapasarakul,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Yung-Fu Chang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: No