Characterization of commercial poultry farms in Mexico: Towards a better understanding of biosecurity practices and antibiotic usage patterns

Erika Ornelas-Eusebio; Gary García-Espinosa; Karine Laroucau; Gina Zanella

doi:10.1371/journal.pone.0242354

Peer Review History

Original SubmissionJune 21, 2020
3 Aug 2020 Decision Letter - Iddya Karunasagar, Editor PONE-D-20-19059 Characterization of commercial poultry farms in Mexico: towards a better understanding of biosecurity practices and antibiotic usage patterns PLOS ONE Dear Dr. Ornelas Eusebio, 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. ============================== Some clarifications regarding methodology and data presentation. ============================== Please submit your revised manuscript by Sep 17 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. 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The following resources for replacing copyrighted map figures may be helpful: USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/ The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/ Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/ Landsat: http://landsat.visibleearth.nasa.gov/ USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/# Natural Earth (public domain): http://www.naturalearthdata.com/ Additional Editor Comments (if provided): Two reviewers have commented on the manuscript. Clarifications are needed regarding sample size and basis of farm selection and other issues. Please address all comments point by point. [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: Yes Reviewer #2: 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 Reviewer #2: No ****** 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 ****** 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: This is a nice draft, which is presented in a way that audience could understand clearly. My specific suggestions are below: Line 109: Please describe whether the farm selection was purposive or random within the mentioned categories/groups Line 263: The caption of the Figure probably merged with another sentence which should be in the next paragraph, please check Line 286: The caption of the Table probably merged with another sentence which should be in the next paragraph, please check Line 290: Table 2 can be presented in landscape style, some % seems break between lines Line 366: It seems that this should be the first paragraph of the discussion section as it contains the most important results of your paper Line 532: The first paragraph of the discussion section can be placed here, before limitation Line 579: This paragraph contains the same argument as the first paragraph of the discussion, seems repetition of idea Reviewer #2: Please refer to the attached document with more detailed remarks. IN particular I am missing a justification of the sample size. Furthermore please discuss the robustness of MCA for n= 43 and 19 (or 50) variables. ****** 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: Yes: Mahbub-Ul Alam Reviewer #2: Yes:** Sonja Hartnack [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: Review PONE-D-20-19059.docx https://doi.org/10.1371/journal.pone.0242354.r001
Revision 1
22 Oct 2020 Author Response *Reviewer #1: This is a nice draft, which is presented in a way that audience could understand clearly. My specific suggestions are below: Line 109: Please describe whether the farm selection was purposive or random within the mentioned categories/groups Authors: In lines 111-113 it is mentioned that we contacted veterinarians who provide technical support to poultry farms during a national congress on poultry farming. When the invitation to participate in the study was extended, we corroborate with the veterinarians in order to encompass the mentioned categories, hence the selection was purposive (as specified in lines 115-117 “We sought to include farms…”). Line 263: The caption of the Figure probably merged with another sentence which should be in the next paragraph, please check. Authors: The sentence “The dendrogram shows the categories of variables that most characterize the farms within each cluster”, corresponds to the legend of figure 2. Line 286: The caption of the Table probably merged with another sentence which should be in the next paragraph, please check. Authors: It has been checked. The table has a legend after the title (lines 292-295). Line 290: Table 2 can be presented in landscape style, some % seems break between lines. Authors: The table 2 has been edited; percentages should appear in the same line. Line 366: It seems that this should be the first paragraph of the discussion section as it contains the most important results of your paper Authors: Thank you for the suggestion, the change has been made. Line 532: The first paragraph of the discussion section can be placed here, before limitation Authors: Thank you for the suggestion, the change has been made. Line 579: This paragraph contains the same argument as the first paragraph of the discussion, seems repetition of idea. Authors: We agree, the last two ideas of the paragraph were removed, which were in fact a repetition of the last paragraph intended to conclude the article. Reviewer #2: Please refer to the attached document with more detailed remarks. In particular, I am missing a justification of the sample size. Furthermore, please discuss the robustness of MCA for n= 43 and 19 (or 50) variables. PLoS endorsed already many years ago the STROBE guidelines. Please make sure that the reporting of this cross-sectional study complies with the guidelines: https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0040297 Authors: We have checked the manuscript compliance according to the STROBE reporting guidelines. Please provide a justification for the sample size. What coverage of commercial farms do you expect by the 43 farms? Authors: The criteria used to establish the minimum and maximum of sample size was specified in the manuscript (lines 114-115). Minimum sample size was calculated for a prevalence and risk factor study that has already been published (10.1016/j.prevetmed.2020.104922.), and the maximum number of farms to visit was established considering time and resources available. We have specified this information in the manuscript (lines 114-115). In line with the sample size, please discuss the robustness of your results for n=43 and 29 variables. I understood that 20 cases for each variable are suggested (https://doi.org/10.1007/s11135-015-0206-0). Authors: We were not aware of the Giovanni di Franco (2016) paper and his suggestion about a threshold of 20 individuals per active variable category. To conduct the MCA we followed the recommendations issued by Husson et al. (2016), who implemented the R FactoMineR package we used. Husson’s recommendations are in line with those preconized in di Franco’s paper (i.e. eliminate low-frequency categories, recoding the variables in order to rebalance the distribution of the cases within the categories of each variable, balance the number of categories per single variable). We also excluded variables with less than 5% variability for which the answers were homogeneous. Husson et al. do not preconize a minimal number of cases per active variable. We are aware that if we took into account this threshold, some categories in our study would be below it and therefore should be excluded, however, if the threshold is 15, there would be fewer variable excluded. If that rule of thumb was to be applied even with much more poultry farms included in our study, it would have been very difficult to have 20 cases in each active category, for instance: farms with no footbaths at barn entrance, farms breeding other domestic species, farms implementing composting (which is a recently implemented practice on poultry farms in Mexico). We have specified that we followed recommendations provided by Husson, et al. 2016 in the results section (line 233-234). How many veterinarians or farmers refused to participate? Authors: There were no refusals, although, obtaining consent to visit the commercial poultry farms and to perform the on-farm interviews was difficult. We have specified it in line 113 and modified a passage in the discussion to take into account this fact (lines 541-544). Did you perform any pre-testing of the questionnaire? Authors: Yes, we did. The final draft of the questionnaire was pre-tested on five veterinarians specialized in poultry science in order to identify ambiguities in the questions and their relevance. Minor suggestions were made by the respondents (e.g. formulate open-ended instead of multiple-choice questions and increase options in the multiple-choice questions). Their recommendations were taken into account. L 105-107 Please formulate your research hypothesis in more precisely (e.g. similar to l. 25-27). Authors: The hypothesis has been reworded as suggested (lines 105-108). Attachments Attachment Submitted filename: Response_to_reviewers_PONE-D-20-19059-16092020.docx* https://doi.org/10.1371/journal.pone.0242354.r002
2 Nov 2020 Decision Letter - Iddya Karunasagar, Editor Characterization of commercial poultry farms in Mexico: towards a better understanding of biosecurity practices and antibiotic usage patterns PONE-D-20-19059R1 Dear Dr. Ornelas Eusebio, 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. 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 #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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #2: No ****** 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 #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 #2: All my comments have been adressed. Please consider to make the data set as well as your annotaed R code available. ****** 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 #2: Yes:** Sonja Hartnack https://doi.org/10.1371/journal.pone.0242354.r003
Formally Accepted
16 Nov 2020 Acceptance Letter - Iddya Karunasagar, Editor PONE-D-20-19059R1 Characterization of commercial poultry farms in Mexico: towards a better understanding of biosecurity practices and antibiotic usage patterns Dear Dr. Zanella: 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.0242354.r004

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