Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia

Rhiannon L. Wallace; Dieter M. Bulach; Amy V. Jennison; Mary Valcanis; Angus McLure; James J. Smith; Trudy Graham; Themy Saputra; Simon Firestone; Sally Symes; Natasha Waters; Anastasia Stylianopoulos; Martyn D. Kirk; Kathryn Glass

doi:10.1371/journal.pone.0236889

Peer Review History

Original SubmissionMay 14, 2020
17 Jun 2020 Decision Letter - Iddya Karunasagar, Editor PONE-D-20-14286 Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia PLOS ONE Dear Dr. Glass, 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 Aug 01 2020 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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PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. For a full list of recommended repositories, see http://journals.plos.org/plosone/s/data-availability#loc-omics or http://journals.plos.org/plosone/s/data-availability#loc-sequencing. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "The CampySource Project Team comprises three working groups and a reference panel. The working groups focus on: food and animal sampling, epidemiology and modelling, and genomics. The reference panel includes expert representatives from government and industry. The study is supported by the following partner organisations: the Australian National University, Massey University, University of Melbourne, Queensland Health, Queensland Health Forensic and Scientific Services, New South Wales Food Authority, New South Wales Health, Hunter New England Health, Victorian Department of Health and Human Services, Food Standards Australia New Zealand, Commonwealth Department of Health and AgriFutures Australia–Chicken Meat Program. CampySource is also supported by collaboration with the following organisations: ACT Health, Sullivan Nicolaides Pathology, University of Queensland, Primary Industries and Regions South Australia, Department of Health and Human Services Tasmania, Meat and Livestock Australia, and New Zealand Ministry for Primary Industries. The CampySource Project Team consists of: Nigel P French, Massey University, New Zealand; Mary Valcanis, The University of Melbourne; Dieter Bulach, The University of Melbourne; Emily Fearnley, The Australian National University and South Australian Department for Health and Wellbeing; Russell Stafford, Queensland Health; Amy Jennison, Queensland Health; Trudy Graham, Queensland Health; Keira Glasgow, Health Protection NSW; Kirsty Hope, Health Protection NSW; Themy Saputra, NSW Food Authority; Craig Shadbolt, NSW Food Authority; Arie H Havelaar, The University of Florida, USA; Joy Gregory, Department of Health and Human Services, Victoria; James Flint, Hunter New England Health; Simon Firestone, The University of Melbourne; James Conlan, Food Standards Australia New Zealand; Ben Daughtry, Food Standards Australia New Zealand; James J Smith, Queensland Health; Heather Haines, Department of Health and Human Services, Victoria; Sally Symes, Department of Health and Human Services, Victoria; Barbara Butow, Food Standards Australia New Zealand; Liana Varrone, The University of Queensland; Linda Selvey, The University of Queensland; Tim Sloan-Gardner, ACT Health; Deborah Denehy, ACT Health; Radomir Krsteski, ACT Health; Natasha Waters, ACT Health; Kim Lilly, Hunter New England Health; Julie Collins, Hunter New England Health; Tony Merritt, Hunter New England Health; Rod Givney, Hunter New England Health; Joanne Barfield, Hunter New England Health; Ben Howden, The University of Melbourne; Kylie Hewson, AgriFutures Australia–Chicken Meat Program; Dani Cribb, The Australian National University; Rhiannon Wallace, The Australian National University; Angus McLure, The Australian National University; Ben Polkinghorne, The Australian National University; Cameron Moffatt, The Australian National University; Ma 485 rtyn Kirk, The Australian National University; and Kathryn Glass, The Australian National University." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "This work was funded by a National Health and Medical Research Council grant (NHMRC GNT1116294), AgriFutures, Australian Government Department of Health, Food Standards Australia New Zealand, New South Wales Food Authority and Queensland Health. The National Health and Medical Research Council provided research fellowship funding for Martyn D. Kirk (APP1145997). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Additionally, because some of your funding information pertains to commercial funding, we ask you to provide an updated Competing Interests statement, declaring all sources of commercial funding. In your Competing Interests statement, please confirm that your commercial funding does not alter your adherence to PLOS ONE Editorial policies and criteria by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests. If this statement is not true and your adherence to PLOS policies on sharing data and materials is altered, please explain how. Please include the updated Competing Interests Statement and Funding Statement in your cover letter. We will change the online submission form on your behalf. 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We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 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 ****** 4. 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Here, the authors perform a molecular characterization using whole-genome sequencing of 616 Campylobacter spp isolates collected from different retail products in a two years period. The material, methods and results sections are very well written, and the discussion and conclusions are justified by the results obtained. Limitations are also well taken into consideration in the discussion section. Minor comments: - As in table 2, in Tables 3 and 4 it should be included in the legend the years of sample collection (2017-2019). The same in figure legends 1, 2 and 3. In this way the reader don´t miss the period time of the study at any moment of the paper. - As a suggestion, “Results” section may be divided into subsections, for instance: • Phylogeny • AMR prevalence • Presence of AMR genes and point mutations by species • Phylogeny and AMR ****** 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 [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. 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Revision 1
24 Jun 2020 Author Response Monday June 22nd, 2020 Dear editor and reviewers, Thank you for taking the time to review our manuscript (PONE-D-20-14286) entitled " Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia ". The comments have been very helpful in improving our manuscript. Comments from the Editor and Reviewer 1 are copied below (in black) and our responses are in blue. References to line numbers in the reponse to reviews are those in the final (unmarked) ‘Manuscript’. Responses to the Editor’s recommendations: Some minor changes have been recommended. Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The title page has been re-formatted to follow PLOS ONE’s style requirements. Specifically, the spacing on the title page and the author affiliations (components are now listed small to large) have been revised. All files uploaded as part of this revision have been named as suggested by the editor and include: ‘Response to Reviewers’ ‘Revised Manuscript with Track Changes’ ‘Manuscript’ Line 201- Changed “Table S1” to “S1 Table” 2. We note that you are reporting an analysis of a microarray, next-generation sequencing, or deep sequencing data set. PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. Next generation sequencing data has been deposited to NCBI’s SRA. Our sequence data is now publicly available. The reviewer link has been removed from line 202 and replaced with a link to the sequence data (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA591966). 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "The CampySource Project Team comprises three working groups and a reference panel. The working groups focus on: food and animal sampling, epidemiology and modelling, and genomics. The reference panel includes expert representatives from government and industry. The study is supported by the following partner organisations: the Australian National University, Massey University, University of Melbourne, Queensland Health, Queensland Health Forensic and Scientific Services, New South Wales Food Authority, New South Wales Health, Hunter New England Health, Victorian Department of Health and Human Services, Food Standards Australia New Zealand, Commonwealth Department of Health and AgriFutures Australia–Chicken Meat Program. CampySource is also supported by collaboration with the following organisations: ACT Health, Sullivan Nicolaides Pathology, University of Queensland, Primary Industries and Regions South Australia, Department of Health and Human Services Tasmania, Meat and Livestock Australia, and New Zealand Ministry for Primary Industries. The CampySource Project Team consists of: Nigel P French, Massey University, New Zealand; Mary Valcanis, The University of Melbourne; Dieter Bulach, The University of Melbourne; Emily Fearnley, The Australian National University and South Australian Department for Health and Wellbeing; Russell Stafford, Queensland Health; Amy Jennison, Queensland Health; Trudy Graham, Queensland Health; Keira Glasgow, Health Protection NSW; Kirsty Hope, Health Protection NSW; Themy Saputra, NSW Food Authority; Craig Shadbolt, NSW Food Authority; Arie H Havelaar, The University of Florida, USA; Joy Gregory, Department of Health and Human Services, Victoria; James Flint, Hunter New England Health; Simon Firestone, The University of Melbourne; James Conlan, Food Standards Australia New Zealand; Ben Daughtry, Food Standards Australia New Zealand; James J Smith, Queensland Health; Heather Haines, Department of Health and Human Services, Victoria; Sally Symes, Department of Health and Human Services, Victoria; Barbara Butow, Food Standards Australia New Zealand; Liana Varrone, The University of Queensland; Linda Selvey, The University of Queensland; Tim Sloan-Gardner, ACT Health; Deborah Denehy, ACT Health; Radomir Krsteski, ACT Health; Natasha Waters, ACT Health; Kim Lilly, Hunter New England Health; Julie Collins, Hunter New England Health; Tony Merritt, Hunter New England Health; Rod Givney, Hunter New England Health; Joanne Barfield, Hunter New England Health; Ben Howden, The University of Melbourne; Kylie Hewson, AgriFutures Australia–Chicken Meat Program; Dani Cribb, The Australian National University; Rhiannon Wallace, The Australian National University; Angus McLure, The Australian National University; Ben Polkinghorne, The Australian National University; Cameron Moffatt, The Australian National University; Martyn Kirk, The Australian National University; and Kathryn Glass, The Australian National University." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. No funding information has been included in the acknowledgements section. Only those who have supported this study in the form of supervision, management, materials, resources and writing, or a combination of these, have been mentioned in the acknowledgements. The acknowledgements section has been revised (line 461) so that it is now clear that those mentioned in this section were partners. Some partner organizations provided a financial contribution, and these have been declared in the funding statement. Currently, your Funding Statement reads as follows: "This work was funded by a National Health and Medical Research Council grant (NHMRC GNT1116294), AgriFutures, Australian Government Department of Health, Food Standards Australia New Zealand, New South Wales Food Authority and Queensland Health. The National Health and Medical Research Council provided research fellowship funding for Martyn D. Kirk (APP1145997). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Additionally, because some of your funding information pertains to commercial funding, we ask you to provide an updated Competing Interests statement, declaring all sources of commercial funding. We have updated our Competing Interests statement. The only source of commercial funding for this work was AgriFutures. In your Competing Interests statement, please confirm that your commercial funding does not alter your adherence to PLOS ONE Editorial policies and criteria by including the following statement: "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests. If this statement is not true and your adherence to PLOS policies on sharing data and materials is altered, please explain how. Please include the updated Competing Interests Statement and Funding Statement in your cover letter. Our updated Funding Statement can be found at the end of this letter, following our responses to the reviewer’s comments. We will change the online submission form on your behalf. Please know it is PLOS ONE policy for corresponding authors to declare, on behalf of all authors, all potential competing interests for the purposes of transparency. PLOS defines a competing interest as anything that interferes with, or could reasonably be perceived as interfering with, the full and objective presentation, peer review, editorial decision-making, or publication of research or non-research articles submitted to one of the journals. Competing interests can be financial or non-financial, professional, or personal. Competing interests can arise in relationship to an organization or another person. Please follow this link to our website for more details on competing interests: http://journals.plos.org/plosone/s/competing-interests 4. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. The data being presented is not a core part of the research being presented in our study. Thus, both sentences have been removed. Response to Reviewer #1 comments Reviewer #1: I really liked reading the manuscript entitled “Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia”. Here, the authors perform a molecular characterization using whole-genome sequencing of 616 Campylobacter spp isolates collected from different retail products in a two years period. The material, methods and results sections are very well written, and the discussion and conclusions are justified by the results obtained. Limitations are also well taken into consideration in the discussion section. Minor comments: - As in table 2, in Tables 3 and 4 it should be included in the legend the years of sample collection (2017-2019). The same in figure legends 1, 2 and 3. In this way the reader don´t miss the period time of the study at any moment of the paper. Revised as suggested. The titles of Tables 1, 3 & 4 now include the years of sample collection. - As a suggestion, “Results” section may be divided into subsections, for instance: • Phylogeny • AMR prevalence • Presence of AMR genes and point mutations by species • Phylogeny and AMR As suggested, we divided the results section into the following subsections: ‘ST prevalence by source’ (line 206), ‘AMR prevalence over time’ (line 239), ‘AMR prevalence by species’ (line 264) and ‘Phylogeny and AMR’ (line 284). Our updated Funding Statement is copied below. This work was funded by a National Health and Medical Research Council grant (NHMRC GNT1116294), with partner funding from AgriFutures, Australian Government Department of Health, Food Standards Australia New Zealand, New South Wales Food Authority and Queensland Health. Additional funding was provided by ACT Health. The National Health and Medical Research Council provided research fellowship funding for Martyn D. Kirk (APP1145997). Yours sincerely, Rhiannon Wallace Rhiannon.wallace@anu.edu.au https://doi.org/10.1371/journal.pone.0236889.r002
16 Jul 2020 Decision Letter - Iddya Karunasagar, Editor Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia PONE-D-20-14286R1 Dear Dr. Glass, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Iddya Karunasagar Academic Editor PLOS ONE Additional Editor Comments (optional): All reviewer comments have been addressed satisfactorily. 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 ******** 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: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) ****** 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: (No Response) ****** 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: (No Response) ****** 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) ****** 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 https://doi.org/10.1371/journal.pone.0236889.r003
Formally Accepted
20 Jul 2020 Acceptance Letter - Iddya Karunasagar, Editor PONE-D-20-14286R1 Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia Dear Dr. Glass: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Iddya Karunasagar Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0236889.r004

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