PONE-D-19-17181

Genomic comparison of diverse Salmonella serovars isolated from swine

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. 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

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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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3. 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

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4. 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

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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: Gupta et al., examined the genomic profiles of diverse Salmonella serovars from swine using whole genome sequencing. Overall there are some interesting pieces, but the paper needs some major revisions and editing. Many of the specific areas of concern or further consideration are provided below.

Title

Ln3: Please remove additional ‘+’ symbol after the author name Jonathan G. Frye.

Abstract

Ln44: “More than 75% of the genes were part of the core genome”, according to Ln252 it is ~ 42% please confirm.

Ln52: Expand CRISPR.

Ln55: The keywords Salmonella and serovar can be removed and add new keywords because these two are appearing in title and arrange the keywords in descending order.

Introduction

Ln73: Please remove the” >” symbol because” more than” is already written.

Ln76-78: In general objective and hypothesis are written at the end of the introduction. However, they are written at Ln76-78.

Ln78: were Salmonella serovars collected from swine swabs?

Materials and Methods

Ln108-110: what are concentrations used for antibiotics panel used? Which solvent did used for solubility?

Results

Ln143: “This study was the part of retrospective study” were the samples used in this study obtained from the McMillan et al., 2019 (ref # 22)? It is not clear in M&M section.

Ln152-157: Data not available in Table 1.

Ln156: Expand ‘ANI’.

LN158: Expand ‘SRA’.

Ln164: Expand ‘CLSI’.

Ln172: Please correct the sentence.

Ln177-179: The information related to ‘total number of AR genes’ is not available in Table 1.

Ln178: Please include the total number of genomes before ‘genome sequences’.

Ln179-Ln182: Please recheck the result, the gene variants Y and aa of aac6-I were not found in the table 2.

Ln184: According to table2, only seven isolates were resistance to beta-lactams. Please check.

Ln198: blaCARB-2 is 2/14 right?

Ln207-209: Please check the results, the gene “ereA” is not found in Agona. Please restructure the sentence.

Ln211: “both “only in Agona both sul1 and sul2 were detected but not in typhimurium were only sul1 were detected.

Ln213: Please remove ‘chloramphenicol resistant’ or rearrange the sentence because not all the fourteen are resistance to chloramphenicol.

Ln214-215: What is the need for writing cml or cat resistance genes here because they are not detected in the study.

Ln215-220: Data not available.

Ln221: How were integrons detected? This information is not available in M & M section.

Ln231: How were plasmids detected? This information is not available in M & M section.

Ln233-237: The replicon types such as IncII, IncFII, IncN, IncP6, col440II and IncQ were not found in table 2.

Ln240-241: Please provide the complete legend for Fig.1 Example what does arrows indicated?

Ln252: The total number of unique genes 2,324 is correct? From Fig.2 they are 2,517. Please make changes.

Ln255: Please include how floral diagram is created in the M & M section?

Ln265: Please remove’(ref)’

Ln266: I could see only 22 COG functions in figure 3.

Ln269-270: Suggestions to change Y-axis as percentages and keep only most abundant functions (may be top 10 + combining all other functions).

Ln273: Please include number of genes near “highest and lowest”.

Ln275: Expand ‘E’ completely.

Ln288: Please include exact percentage values for G and L.

Ln293-328: These results are based on supplementary tables and these are presented for each isolate and it is difficult to compare the results. A comprehensive information like table 2 will help to look over the results clearly.

Ln357-359: Fig.5 results were not discussed in results section.

Ln362: This is ten right?

Discussion

Discussion is well organized however it is too lengthy, restatement of data (restatement of results) observed in some places.

References

Too many references.

Figures

Except figure 2, none of the figures are in good quality they are not clearly visible for interpretation, in addition more information is needed to add in the legend for easy interpretation.

Reviewer #2: The manuscript reports an extensive genome analysis of 14 diverse Salmonella serotypes isolated from swine using whole genome sequencing. The results suggest that majority of the genes were part of core genome and dispensable genes were acquired for adaptability. Here, the authors have performed analysis using various bioinformatics tools to identify and predict genetic repertoire in salmonella serovars. I found this paper of broad relevance to the field, especially to antibiotic resistance and public health. However, I have provided general comments and suggestions below that are necessary to improve the manuscript.

Minor comments

1. The authors have stated high concordance between phenotypically confirmed resistances and detected ARGs, however they did not state why it was not well correlated. The authors need to explain.

2. The authors noticed two distinct pattern of CRISPR-cas3 gene, how did they validated the findings ?

3. The authors have showed clusters of orthologous genes in core and accessory genes (figure 4). Authors might also consider to show the distribution of cogs in unique genes.

4. Authors might consider to add a figure showing the distribution of pan genome (core genes, accessary genes and unique genes) content in each salmonella serotypes (for eg: serovars in x-axis and number of genes in y-axis).

5. The authors need to elaborate the materials and methods sections.

6. Authors should add cogs database reference (line 265)

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Reviewer #1: Yes: Nagaraju Indugu

Reviewer #2: No

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Attachments

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Submitted filename: CommentToAuthorsPlosOne.docx

Genomic comparison of diverse Salmonella serovars isolated from swine

PONE-D-19-17181R1

Dear Dr. Frye,

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

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

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: N/A

Reviewer #2: N/A

**********

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: Thr authors have addressed all the comments and substantially improved the manuscript. I have not further comments.

Reviewer #2: All comments are addressed well in the manuscript.

An extensive genome analysis of 14 diverse Salmonella serotypes isolated from swine using whole genome sequencing was reported well. Further the authors have included a figure showing the distribution of pan genome (core genes, accessary genes and unique genes) for the readers to understand the genome repertoire of the salmonella serotypes

The authors also modified figure 4 to include clusters of orthologous genes in unique genes, as suggested. The manuscript is well written in standard English and the authors have presented a good scientific research article.

I recommend for accepting the manuscript.

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If you choose “no”, your identity will remain anonymous but your review may still be made public.

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Reviewer #1: No

Reviewer #2: No