Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China

Wei Yan; Deshun Xu; Liping Chen; Xiaofang Wu

doi:10.1371/journal.pone.0304621

Peer Review History

Original SubmissionMarch 10, 2024
8 Apr 2024 Decision Letter - Mabel Kamweli Aworh, Editor PONE-D-24-09010Antimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou,ChinaPLOS ONE Dear Dr. Xu, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by May 23 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information. Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”). 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments : In addressing the reviewer's comments please address the following additional issues. 1. In your revision, please provide line numbers on the revised manuscript to make it easier for reviewers to review the revised manuscript. 2. Please engage the services of a native English speaker to revise the manuscript for typographical and grammatical errors. Delete any Chinese inscriptions in the manuscript, especially in the results section. Define any abbreviations upon first use in the manuscript. 3. Genes should be italicized and written in small letters all through the manuscript. 4. In discussing your results, do not repeat them; rather, provide a possible explanation for your findings while comparing them to the reports of other similar studies. 5. In the second paragraph of the discussion section, please italicize "Escherichia coli" and any other bacteria mentioned in the manuscript. Please italicize "Salmonella" all through the manuscript. 6. Highlight the main limitations of the current study in the last paragraph of the discussion section, please. [Note: HTML markup is below. Please do not edit.] 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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: N/A ****** 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 ****** 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: No Reviewer #2: No ****** 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: The authors have a good study question but were not able to properly put it in writing. There is no justification for the study, the methodology was not properly referenced for reproducibility and there were several grammatical and writing errors. Also, all authors referenced in the article need to be fully stated in the reference section and not stating et al., in places where the full names are supposed to be written. Not to say that there were scientific names that were not italicized and confusing species of Salmonella in the result section. Authors need to proof-read, justify the document and pay attention to details. Reviewer #2: General Comments: Personally, I would like to see the letter of approval, especially since the author claims that the consent was given orally. The paper could benefit from a thorough revision, particularly in terms of punctuation. The lack of line numbers makes it challenging to pinpoint specific areas where punctuation is missing. Additionally, there are several acronyms that are not fully spelled out. I also noticed possible translation errors, as it appears the author may have translated the paper from another language to English. I recommend a careful review to ensure accurate translation. Finally, the author should pay much attention on their discussion because they did not discuss all results, and the conclusion is weak. Abstract: The authors have failed to state the purpose of their study, despite attempting to define the problem. This is a crucial element that could engage the reader’s interest in the article. Introduction: The sentence, “Multi-drug resistant bacteria and even super bacteria have emerged, which lead to the emergence of new epidemiological and clinical characteristics of the disease,” seems redundant and does not add value. It appears to repeat previously mentioned information. The preceding sentence could also be restructured and potentially supplemented with a citation. Results: It was disappointing to see that the authors did not reference the supplemental material, which, in my opinion, could have been effectively utilized in their results to strengthen their arguments. Discussion: The authors should consider using more direct language, as exemplified by their use of the vague term “some strains.” The discussion lacks depth and fails to highlight the practical implications of the results. There are no recommendations beyond drug resistance. Apparently, the genomic results are not discussed at all, and they applied genomic sequencing without a clear plan of how the results might be useful. Conclusion: The conclusion is weak. It merely restates the methods without summarizing the results or discussing their potential benefits to the community. It gives the impression that the authors were more interested in applying the methods and maintaining records than in the study’s purpose. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-24-09010.pdf Attachment Submitted filename: REVIEW genome characteristics of S.enteritidis.pdf Attachment Submitted filename: PONE-D-24-09010 REVIEWERS COMMENT.pdf https://doi.org/10.1371/journal.pone.0304621.r001
Revision 1
22 Apr 2024 Author Response Dear editors: Thank you very much for your letter and the comments from the referees about our paper submitted to PLOS ONE (PONE-D-24-09010). We have carefully addressed all of the comments from the reviewers, as outlined in the point-by-point responses attached below. We hope that you find the revised manuscript now acceptable for publication in PLOS ONE. The English in this document has been checked by at least two professional editors, both native speakers of English. For a certificate, please see: http://www.textcheck.com/certificate/axviDO Thanks for your attention Yours Sincerely Deshun Xu Responses to the editor’s comments: (Q: as comments, A: as our responses) Q: Can authors please justify the article? Kindly proof read and ensure proper spacing after a comma or full stops. Pay attention to details! A: We had ensured proper spacing after a comma or full stops and revised other details in the manuscript. INTRODUCTION Q: Line 41 “Salmonella is a zoonotic pathogen. It is also an important pathogenic factor 42 causing foodborne diseases [2,3] and the main cause of bacterial food poisoning [4]. 43 Contaminated food and water source or infected individuals by Salmonella can 44 become the source of infection and spread to the outside, posing a serious threat to 45 human and animal health[1]”. Any reason for starting the referencing numbers with 2, 3 and 4 before “1”? If none please correct it accordingly. A: We have made corrections it accordingly in the manuscript. Q: Line 48 – 49 “gastroenteritis type, septicemia type (typhoid type) and 49 local infection type” Kindly reference this statement A: We have added references “Mingfeng SH, Rongxing C, Kai ZH, Hongjian CH. Etiological and clinical characteristics of 92 children with Salmonella enteritis[J].Chin J Nosocomiol, 2022, 32(14): 2212-2217.” in the manuscript. Q: Authors need to state clearly the justification for the study as dearth of information of the said topic in the region studied. A: We added justification for the study in the introduction: There have been no previous reports on the drug resistance and genetic characteristics of S. enteritidis in the Huzhou area。 METHODOLOGY Q: The authors need to cite references for the methodology “as described by ……” for reproducibility. A: We added 2 references in the manuscript: “ Bacteria were isolated according to the methods described in Diagnostic Criteria for Infectious Diarrhea (WS271-2007) and National Standards for Food Safety (GB4789.4-2016) ”. Q: Lines 86 – 88 Ethics statement This study was approved by the human research ethics committee of the Huzhou Center for Disease Control and Prevention. kindly state the approval number A: We added the approval number(HZ2020007) in the manuscript. Q: Line 151 “and the 7 housekeeping genes were aroC 152 (5), dnaN (2), hemD (3), hisD (7), purE(6), sucA (6) and thrA (11).” These values when added gives 40 as against 43 stated. Any reason for the discrepancy?Nothing was said about the statistical analysis in the methodology or none was carried out? A: The data in parentheses represent an identifier for every unique allele sequence, rather than the number of strains, and were used to determine the ST genotype of the strain. We removed these data so as not to cause any misunderstanding. Statistical analysis is rarely used in this paper. RESULT Q: Can authors confirm the species of Salmonella especially in the result because there are several confusing names? A: We have made careful modifications as required. Q: If authors are not stating a specific species or simple sp. there is no need italicizing the Salmonella A: We have made careful modifications as required. REFERENCES Q: While writing the authors of articles cited, kindly write out the names of all authors and desist from using et al., in the reference section. Check online for the names of all authors. If truly these articles were downloaded and read before citing them, the authors should have all the names of the authors of articles cited in this study. See lines 286, 289, 301, 310, 314, 317, 320, 324, 327, 330, 333, 338, 342, 348, 351, 356, 362, 365, 368,371, 374, 381, 387 A: We have made careful modifications as required. The names of all authors have been written out in the reference section. Q:5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. A: Supplementary Material had been submitted at the time of initial submission of the paper. Q: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. A: We have carefully checked the references. Additional Editor Comments : In addressing the reviewer's comments please address the following additional issues. Q: 1. In your revision, please provide line numbers on the revised manuscript to make it easier for reviewers to review the revised manuscript. A: We have added line numbers to the manuscript as requested. Q: 2. Please engage the services of a native English speaker to revise the manuscript for typographical and grammatical errors. Delete any Chinese inscriptions in the manuscript, especially in the results section. Define any abbreviations upon first use in the manuscript. A: The English in this document has been checked by at least two professional editors, both native speakers of English. For a certificate, please see: http://www.textcheck.com/certificate/axviDO Q: 3. Genes should be italicized and written in small letters all through the manuscript. A: We have made the changes as requested. Q: 4. In discussing your results, do not repeat them; rather, provide a possible explanation for your findings while comparing them to the reports of other similar studies. A: We removed the same content as the results from the discussion and added comparisons with similar studies to the discussion. Q: 5. In the second paragraph of the discussion section, please italicize "Escherichia coli" and any other bacteria mentioned in the manuscript. Please italicize "Salmonella" all through the manuscript. A: We have made the changes as requested. Q: 6. Highlight the main limitations of the current study in the last paragraph of the discussion section, please. A: The main limitations of the current study were added in the last paragraph of the discussion section. 5. Review Comments to the Author Q: Reviewer #1: The authors have a good study question but were not able to properly put it in writing. There is no justification for the study, the methodology was not properly referenced for reproducibility and there were several grammatical and writing errors. Also, all authors referenced in the article need to be fully stated in the reference section and not stating et al., in places where the full names are supposed to be written. Not to say that there were scientific names that were not italicized and confusing species of Salmonella in the result section. Authors need to proof-read, justify the document and pay attention to details. A: We have carefully revised the above content as required. Reviewer #2: General Comments: Q: Personally, I would like to see the letter of approval, especially since the author claims that the consent was given orally. The paper could benefit from a thorough revision, particularly in terms of punctuation. The lack of line numbers makes it challenging to pinpoint specific areas where punctuation is missing. Additionally, there are several acronyms that are not fully spelled out. I also noticed possible translation errors, as it appears the author may have translated the paper from another language to English. I recommend a careful review to ensure accurate translation. Finally, the author should pay much attention on their discussion because they did not discuss all results, and the conclusion is weak. A: We had submitted the human research ethics committee of the Huzhou Center for Disease Control and Prevention(approval number: HZ2020007). The name of file is “approval document(English)”. And asked to modify the relevant content. The English in this document has been checked by at least two professional editors, both native speakers of English. For a certificate, please see: http://www.textcheck.com/certificate/axviDO Abstract: Q: The authors have failed to state the purpose of their study, despite attempting to define the problem. This is a crucial element that could engage the reader’s interest in the article. A: the purpose of study were added in abstract: This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1 2021, to December 30, 2023. Introduction: Q:The sentence, “Multi-drug resistant bacteria and even super bacteria have emerged, which lead to the emergence of new epidemiological and clinical characteristics of the disease,” seems redundant and does not add value. It appears to repeat previously mentioned information. The preceding sentence could also be restructured and potentially supplemented with a citation. A: We removed “Multi-drug resistant bacteria and even super bacteria have emerged, which lead to the emergence of new epidemiological and clinical characteristics of the disease,” and the sentence was also rearranged. Results: Q: It was disappointing to see that the authors did not reference the supplemental material, which, in my opinion, could have been effectively utilized in their results to strengthen their arguments. A: Supplementary material file had been submitted at the time of initial submission of the paper. Discussion: Q: The authors should consider using more direct language, as exemplified by their use of the vague term “some strains.” The discussion lacks depth and fails to highlight the practical implications of the results. There are no recommendations beyond drug resistance. Apparently, the genomic results are not discussed at all, and they applied genomic sequencing without a clear plan of how the results might be useful. A: By analyzing the relationship between drug resistance genes and drug resistance phenotypes, we found that 12 strains, including S2021237, carried sul2 gene, but were sensitive to trimethoprim-sulfamethoxazole. In addition, 4 strains, including S2023209, were resistant to chloramphenicol but no chloramphenicol resistance genes were found. At the same time, we removed the expression of ambiguous terms in the text. Conclusion: Q: The conclusion is weak. It merely restates the methods without summarizing the results or discussing their potential benefits to the community. It gives the impression that the authors were more interested in applying the methods and maintaining records than in the study’s purpose. A: We reformatted the conclusion section. Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0304621.r002
9 May 2024 Decision Letter - Mabel Kamweli Aworh, Editor PONE-D-24-09010R1Antimicrobial Resistance and Genome Characteristics of Salmonella enteritidis from Huzhou, ChinaPLOS ONE Dear Dr. Xu, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jun 23 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. We look forward to receiving your revised manuscript. Kind regards, Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN Academic Editor PLOS ONE Journal Requirements: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] 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 ******** 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: Authors have responded to all questions raised earlier and the manuscript can be accepted for publication. Reviewer #2: I appreciate the current revised version, as it addresses most of the problems stated in the first version. I would also recommend it for publication. A. However, the authors made a strong statement in lines 75 and 76: "There have been no previous reports on drug resistance and genetic characteristics of S enteriditis in the Huzhou area." Unless the authors are 100% sure there is none, I suggest revising this statement. Based on a few searches, I realized that some co-authors have indeed contributed to previous works that include drug resistance in the Huzhou area. Nevertheless, these studies did not specifically investigate the genetic characteristics of S. enteriditis. See articles: 1. Prevalence and Serotyping of Salmonella in Retail Food in Huzhou, China (D. Xu et al., 2024) 2. Characterization of Clinical Salmonella entericas Strains in Huzhou, China (D. Xu et al., 2022) B. Furthermore, a review (though it is not a big issue) of the known genetic characteristics of S. enteriditis in other areas of China would be appreciated. Example articles: 1. The Resistance and Virulence Characteristics of Salmonella Enteritidis Strain Isolated from Patients with Food Poisoning Based on the Whole-Genome Sequencing and Quantitative Proteomic Analysis (B. Xu et al., 2023) 2. Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident (Hou et al., 2024) Bibliography: Hou, Z., Xu, B., Liu, L., Yan, R., & Zhang, J. (2024). Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food.Poisoning Incident. Polish Journal of Microbiology, 73(1), 69–89. https://doi.org/10.33073/PJM-2024-008 Xu, B., Hou, Z., Liu, L., Yan, R., Zhang, J., Wei, J., Du, M., Xuan, Y., Fan, L., & Li, Z. (2023). The Resistance and Virulence Characteristics of Salmonella Enteritidis Strain Isolated from Patients with Food Poisoning Based on the Whole-Genome Sequencing and Quantitative Proteomic Analysis. Infection and Drug Resistance, 16, 6567–6586. https://doi.org/10.2147/IDR.S411125 Xu, D., Chen, L., Lu, Z., & Wu, X. (2024). Prevalence and Serotyping of Salmonella in Retail Food in Huzhou China. Journal of Food Protection, 87(2), 100219. https://doi.org/10.1016/J.JFP.2024.100219 Xu, D., Ji, L., Yan, W., & Chen, L. (2022). Characterization of Clinical Salmonella entericas Trains in Huzhou, China. Canadian Journal of Infectious Diseases and Medical Microbiology, 2022. https://doi.org/10.1155/2022/7280376 ******** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0304621.r003
Revision 2
13 May 2024 Author Response Dear editors: Thank you very much for your letter and the comments from the referees about our paper submitted to PLOS ONE (PONE-D-24-09010). We have carefully addressed all of the comments from the reviewers, as outlined in the point-by-point responses attached below. We hope that you find the revised manuscript now acceptable for publication in PLOS ONE. Thanks for your attention Yours Sincerely Deshun Xu Responses to the editor’s comments: (Q: as comments, A: as our responses) Q: However, the authors made a strong statement in lines 75 and 76: "There have been no previous reports on drug resistance and genetic characteristics of S enteriditis in the Huzhou area." Unless the authors are 100% sure there is none, I suggest revising this statement. A: We have put "There have been no previous reports on drug resistance and genetic characteristics of S enteriditis in the Huzhou area. "changed to “As far as we know, there have been few previous reports on the drug resistance and genetic characteristics of S.enteritidis in the Huzhou area”. Q: Based on a few searches, I realized that some co-authors have indeed contributed to previous works that include drug resistance in the Huzhou area. Nevertheless, these studies did not specifically investigate the genetic characteristics of S. enteriditis. See articles: 1. Prevalence and Serotyping of Salmonella in Retail Food in Huzhou, China (D. Xu et al., 2024) 2. Characterization of Clinical Salmonella entericas Strains in Huzhou, China (D. Xu et al., 2022) A: These two manuscripts are previous research conducted by our research group. One manuscript focuses on the Prevalence and Serotyping of Salmonella in Retail Food in Huzhou, while the other paper examines the Characterization of Clinical Salmonella entericas Strains in Huzhou. However, it is important to note that these studies did not specifically investigate the genetic characteristics of S. enteriditis. Q: B. Furthermore, a review (though it is not a big issue) of the known genetic characteristics of S. enteriditis in other areas of China would be appreciated. Example articles: 1. The Resistance and Virulence Characteristics of Salmonella Enteritidis Strain Isolated from Patients with Food Poisoning Based on the Whole-Genome Sequencing and Quantitative Proteomic Analysis (B. Xu et al., 2023) 2. Isolation, Identification, Antimicrobial Resistance, Genotyping, and Whole-Genome Sequencing Analysis of Salmonella Enteritidis Isolated from a Food-Poisoning Incident (Hou et al., 2024) A: These two manuscripts have been cited in the article, with References 35 and 42 respectively. Attachments Attachment Submitted filename: Response to Reviewers.doc https://doi.org/10.1371/journal.pone.0304621.r004
15 May 2024 Decision Letter - Mabel Kamweli Aworh, Editor Antimicrobial Resistance and Genome Characteristics of Salmonella enteritidis from Huzhou, China PONE-D-24-09010R2 Dear Dr. Xu, 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. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN Academic Editor PLOS ONE Additional Editor Comments (optional): All reviewer's comments have been addressed. Reviewers' comments: https://doi.org/10.1371/journal.pone.0304621.r005
Formally Accepted
22 May 2024 Acceptance Letter - Mabel Kamweli Aworh, Editor PONE-D-24-09010R2 PLOS ONE Dear Dr. Xu, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Mabel Kamweli Aworh Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0304621.r006

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