Peer Review History
| Original SubmissionMay 14, 2020 |
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PONE-D-20-14308 Taenia species in smallholder farms in Gauteng, South Africa: seroprevalence in pigs, and farmers’ knowledge and practices PLOS ONE Dear Dr. Daniel Nenene Qekwana 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. Many thanks for submitting your manuscript to PLOS One Your manuscript was reviewed by three experts in the field, and they have recommended some modifications be made prior to acceptance If you could write a detailed response to reviewers, that will help to expedite review when resubmitted. I wish you the best of luck with your revisions Hope you are keeping safe and well in these difficult times Many thanks Simon Please submit your revised manuscript by Jul 13 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. Please include the following items when submitting your revised 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Simon Clegg, PhD Academic Editor PLOS ONE 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 PLOS ONE style templates can be found at http://www.plosone.org/attachments/PLOSOne_formatting_sample_main_body.pdf and http://www.plosone.org/attachments/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please include additional information regarding the survey or questionnaire used in the study and ensure that you have provided sufficient details that others could replicate the analyses. For instance, please describe the pretesting of this tool in further detail, including the number of participants and whether or not they provided written informed consent before consultation. 3.Please amend either the title on the online submission form (via Edit Submission) or the title in the manuscript so that they are identical. 4. Your ethics statement must appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please move it to the Methods section and delete it from any other section. Please also ensure that your ethics statement is included in your manuscript, as the ethics section of your online submission will not be published alongside your manuscript. 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. (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: Partly Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: Yes Reviewer #3: 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: Yes Reviewer #3: 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: Yes Reviewer #2: No Reviewer #3: 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 manuscript describes a study which undertook serology on pigs living in a region of South Africa as well as a survey of farmers knowledge and attitudes related to the transmission of Taenia solium. While the manuscript’s title and abstract correctly refer to the serological outcomes as providing evidence of infection with Taenia spp, rather than T. solium specifically, all other aspects of the paper are presented as if the work was relevant specifically to T. solium. Unfortunately, the study did not obtain any direct evidence that any of the pigs involved actually had T. solium infection. The serological test that was used in the study is unable to differentiate infection with T. solium from infection with T. hydatigena. Infection with T. hydatigena has no relevance as a zoonotic infection nor would it have any relevance to the survey that was conducted. The value of the study would have been increased enormously had the Ag-ELISA positive pigs been purchased and Taenia infection, or more importantly, T. solium infection been confirmed at necropsy. The limitations to the interpretation of the serological data in relation to T. solium place a major constraint on the importance of the study. Nevertheless, the results are worthy of publication, but the many interpretations and analyses relating to T. solium are not warranted. The valuable data about both seroprevalence and farming practices are publishable as statements of fact, without the extensive analyses that assume the data relates to T. solium when this has not been determined. Hence my recommendation is that the manuscript be re-drafted and shortened substantially. The following are some notes to be considered if a revised manuscript is prepared. Line 101. Add full stop. Lines 111-114. Reference 33 does not provide the methodology that was used for the commercial Ag-ELISA. The commercially available test uses a methodology significantly different to the in-house test developed by the Institute for Tropical Medicine in Belgium which was used in the work described in Reference 33. The test’s specificity and sensitivity, referred to in Reference 11, uses the in-house test methodology and not the commercial kit. To my knowledge there has been no proper evaluation of the sensitivity and specificity of the commercial kit. There have been numerous reports of the sensitivity and specificity of the B158/B60 Ag-ELISA, several of which have found the test to have a substantially lower specificity for detection of T. solium infection than the single reference chosen to be cited here. The choice of this single reference gives a biased impression of the test’s performance. Lines 284-6. The authors cannot attribute the prevalence of pigs infected with Taenia spp to the conditions they describe because they have no idea whether any were actually infected with T. solium. It is possible that all the positives were infected with T. hydatigena or, given the occurrence of false positive pigs in the Ag-ELISA, they may be pigs with no Taenia infection at all. The authors should qualify these interpretations by stating “If the Ag-ELISA positive pigs were infected with T. solium….” and include a statement indicating that the test positive animals may instead harbour T. hydatigena, in which case it would be an indication of the presence of dogs in the community which were not regularly treated with a taeniacide which had access to offal from pigs, sheep or goats. Lines 288-291. It is incorrect to say that they would need carcass dissection plus PCR to differentiate animals infected with T. solium and T. hydatigena. For the vast majority of infections with either of these two parasites the identity of the species involved is clear based on the cysticercus morphology and site of encystment. It is recommended that the words ‘coupled with PCR’ be deleted. Lines 296-298. Care needs to be exercised in commenting on the results of other publications which involved use of serology for determining the prevalence of T. solium. For may years the Ag-ELISA test was used and the fact that the test is not species specific was virtually ignored and the results assumed to relate to T. solium. Recent detailed evaluations of the test’s performance have revealed that there is a high proportion of animals that are positive in the test that have neither T. solium nor T. hydatigena infected. For example, Chembensofu et al 2017 (DOI 10.1186/s13071-017-2520-y) found that from 30 pig carcasses that were fully dissected and found negative for T. solium, the Ag-ELISA returned ten positives, of which two were infected with T. hydatigena. That is 8/30 (26.6%) animals that had neither T. solium nor T. hydatigena infection tested false positive in Ag-ELISA. With a false positive rate of this magnitude, it is not inconceivable that all 9 Ag-ELISA positive animals from the 126 that were tested in the study described in this manuscript may have no Taenia infection at all… Lines 352-353. The sharing of the environment of children and pigs with dogs has nothing whatsoever to do with transmission of T. solium. Lines 400-401. It is difficult to understand which authors did what – it appears that the letters refer to authors’ Christian names. It is suggested to use all the authors’ initials. Reviewer #2: MANUSCRIPT REVIEW REPORT Dear Editor (PLOS ONE) Kindly find a REVIEW REPORT for a manuscript titled “Taenia spp. in smallholder farms in Gauteng, South Africa: seroprevalence in pigs, and farmers’ knowledge and practices”. The report contains general comments as well as specific comments for the different sections. GENERAL COMMENTS The authors of this manuscript are reporting findings on the epidemiology of an important zoonotic parasite of pigs. Somewhere, in the introduction (lines 64 – 66) and in the discussion (lines 280-283) the authors clearly indicate that similar studies have been done in the same area. In my opinion, results of an undertaking reported here are just a duplication of something which has already been reported and doesn’t add any value. It is however upon the journal Editorial Board to decide on the fate of this manuscript. Technically, the article is fairly well written although there are some minor language problems and some study design issues which are raised in section reviews. COMMENTS BY SECTION TITLE The authors need to recast the title, they could write it better than the way it is currently ABSTRACT Line 15-16: The sentence “Poor agricultural practices, and sanitary practices, and lack of…………” should be re-written to reduce the number of “ands” Line 22-25: The sentence “Descriptive statistics were run and logistic regression models were used to assess the relationship between socio demographic and pig farming conditions and knowledge of porcine cysticercosis and neurocysticercosis.” should be re-written to reduce the number of “ands” INTRODUCTION Lines 64 – 66: the authors could not clearly indicate the rationale of conducting the study MATERIALS AND METHODS In line 86 the authors indicate the use of mixed method which are not evident in the subsequent part of the study design. In line 86-87 the authors state that they used purposive sampling to identify farms and farmers to participate in this study, they should clearly explain/reason justification for this. Line 87-90: the authors explain the selection procedure of pigs to be involved in the study and they eventually refer to the step as being probability, THIS IS SERIOUS. Line 87-88: the authors indicate that all pigs that met criteria in all the selected farms were sampled, what was the essence of calculating the sample size then? The authors also need to state the number of farms from which pigs were sampled; Line 90-95: the authors explain the selection procedure of farmers. It is not clear whether these were the owners of the farms where pigs were sampled or otherwise. Line 98: the authors indicate that the calculated sample size was 185 pigs, but in Line 101: they indicate they sampled 126 pigs, this needs explanation. Lines 103-114: The authors do not consider “Blood collection and processing” and “Serological analysis” as part of data collection, can they give a reason to this? Lines 128-131: The pretesting of the questionnaire doesn’t seem to make sense as the population to which it was tested is very different in characteristics from farmers. The authors need to defend their decision. Line 150: The sentence “The open-ended questions were analyzed using thematic analysis” should be cancelled. RESULTS Generally this section is poorly organized, the flow is not good In several occasions there is double presentation of results in text and in table DISCUSSION Generally the discussion is poorly organized References “7” cited in line 280 and reference “36” cited in line 283 indicate that similar works were conducted in the same area. This is a weakness as resources devoted in this study could be deployed elsewhere CONCLUSIONS The third word in line 385 (training) does sound good to me as it is linked to imparting farmers knowledge on epidemiology of the parasite Ethical considerations Line 389-390: Check this “The Animal Ethics Committee Research Ethics Committee” Line 393-394: I am doubting on the statement that; “Signed informed consent was obtained from each respondent before the questionnaires were administered”. This implies that all farmers could read and write Acknowledgements Line 396: The statement “The author would like to acknowledge the Gauteng……….” Indicates that this manuscript is single authored Reviewer #3: The manuscript is interesting and very well written. I have a few comments: All the manuscript always refers to Taenia spp, but since all the study was performed in pigs and since it also states human neurocysticercosis, I recommend to change spp for solium, mainly because it is more accurate even though the species was not identified but Taenia saginata is only found in cattle and it does not cause neurocysticercosis in humans and using T. soliun more precise in educational terms. An exception is lines 290-291 The authors should include the concept of KAP because they use it but it is not included as a specific issue such as in lines 117, 127, 157. The reference to the statistic test cited on lines 182-183 should be provided. Line 210 does not state pigs in numbers between 10 and 20. The authors should add: 11-20 pigs, 48% Line 228, if not plain water, what other source/type of water did the farmers use? Table 3. farming purpose “all three” should be moved two lines below Line 310 eliminate “of age” The subject of KAP should also be included in the paragraph that starts on line 359 In acknowledgments I would add to the farmers that participated in the study ********** 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. 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. |
| Revision 1 |
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PONE-D-20-14308R1 Knowledge, practices and seroprevalence of Taenia species in smallholder farms in Gauteng, South Africa PLOS ONE Dear Dr. Qekwana, 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. ============================== Many thanks for submitting your manuscript to PLOS One It was reviewed by the same experts in the field, and they have requested some more minor changes be made prior to acceptance. If you could make these changes and write a response to reviewers, that will greatly expedite revision upon resubmission I wish you the best of luck with your changes Hope you are keeping safe and well in these difficult times Thanks Simon ============================== Please submit your revised manuscript by Oct 30 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. Please include the following items when submitting your revised 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols We look forward to receiving your revised manuscript. Kind regards, Simon Clegg, PhD Academic Editor PLOS ONE 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: (No Response) Reviewer #3: 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 #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #3: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #3: 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 #3: 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: I am disappointed with the authors' responses to several of the comments I made on the manuscript. In many places they choose to argue, in effect, that I was wrong. This would be entirely acceptable if they were correct and I was not, but when the opposite is the case, it is galling. For example, in response to my indicating that the value of the manuscript would have been enhanced had they purchased the serologically positive pigs and shown that they were actually infected with T. solium, the authors simply provide a list of excuses as to why they did not do it. The fact they did not do it is the only thing that is relevant, not why they could not, or choose not. In response to my criticism about the lack of specificity of the serological test uses, the authors respond by citing a reference that specifies the test had a specificity of 67% for T. solium. That is exactly my point. That is a very poor specificity, and there is certainly a possibility that all 9 of the 126 animals that the authors found positive may well have had no T. solium infection at all. As the authors choose to cite two papers about the performance of the B158/B60 Ag-ELISA in relation to diagnosis of T. solium infection in pigs, and recognise that the test is also positive in pigs infected with T. hydatigena, for balance they should add the test’s sensitivity for diagnosis of T. hydatigena infection. This information is in the literature and I believe they will find that the test’s performance for T. hydatigena is just a good as it is for T. solium. The authors’ response to my statement that the commercial test they used is not the same as the in-house test they cite in relation to the test’s performance, they firstly accept this is true but make excuses about what they perceive as small differences in the methodology used in the kit form of the test. They are not small differences, and they certainly have potential to affect the test’s performance. The authors’ response to my comment that it is not necessary to invoke the use of PCR to differentiate T. solium and T. hydatigena cysts was to cite Chembensofu et al 2017 who claimed to have found numerous instances of T. solium cysts in the liver and lungs of pigs in Zambia and that Chembensofu et al validated their results by PCR. It is interesting to note that Chembensofu et al provided no actual data to support their extraordinary claims about cysts in ‘unusual’ locations, nor any information about what controls were used in their PCRs. The authors of the present manuscript seem unaware of the publication by Gauci et al 2019 https://doi.org/10.1371/journal.pntd.0007408 who, in response to the Chembensofu et al publication, investigated ‘lesions’ in the tissues of pigs from T. solium endemic areas of Nepal and Uganda, such as the liver and lung, that could possibly have been confused with being caused by T. solium. No T. solium cyst was found in any organ other than in the striated muscles and the brain. Numerous ‘lesions’ in other body organs were confirmed as being caused by a T. hydatigena or nematodes, as well as other causes. Gauci et al presented actual PCR results, and specified that tissue from the same animal and organ where a suspect lesion was found, but containing no lesion, was used as a negative control in the PCRs. I make two points here. Firstly, by statement that PCR is not required to differentiate T. solium and T. hydatigena cysts stands as correct. Secondly, it is annoying that the authors choose to argue against the point I made in my original review in relation to this matter, when they are clearly ignorant of the recent relevant literature. This is especially surprising because the two Belgian-based authors have a long history in the T. solium field. The changes that have been made to the manuscript are adequate in relation to the (lack of) specificity of the serological studies they performed and the limitations this imposes on the interpretation of their results. I reiterate what I said in my original review, which was that the study would have been so much more meaningful if they had obtained actual evidence that any of the pigs were infected with T. solium. The authors’ reliance on poor quality serology was a major flaw in the study design and has resulted in a substantial reduction in the potential value of the study. Reviewer #3: (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 Reviewer #3: 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. |
| Revision 2 |
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Knowledge, practices and seroprevalence of Taenia species in smallholder farms in Gauteng, South Africa PONE-D-20-14308R2 Dear Dr. Qekwana, 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, Simon Clegg, PhD Academic Editor PLOS ONE Additional Editor Comments: Many thanks for resubmitting your manuscript to PLOS One As you have addressed all the comments, and the manuscript reads well, I have recommended the manuscript for publication You should hear from the Editorial office soon It was a pleasure working with you, and I wish you the best of luck for your future research Hope you are keeping safe and well in these difficult times Thanks Simon |
| Formally Accepted |
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PONE-D-20-14308R2 Knowledge, practices and seroprevalence of Taeniaspecies in smallholder farms in Gauteng, South Africa Dear Dr. Qekwana: 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. Simon Clegg Academic Editor PLOS ONE |
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