PONE-D-21-34537Could the type and severity of gross lesions in pig lymph nodes play a role in the detection of Mycobacterium avium?PLOS ONE

Dear Dr. Kaczmarkowska,

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.

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ACADEMIC EDITOR: As one of the reviewers have pointed out, this article needs robust and clear statistical section and inclusion of all p-values and their significance. This is particularly important since only a fraction of the total tested samples showed positivity for mycobacteria, and much fewer samples were confirmed as specific mycobacterial species. Secondly, the authors should clearly highlight and emphasize the strength/uniqueness as well as the limitations, such as the quality of the samples analyzed etc., on the manuscript. Finally, the article needs to be revised to remove redundant and irrelevant information in all sections, and  should focus  more on the main findings and their interpretations.==============================

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The paper entitled “Could the type and severity of gross lesions in pig….” by Kaczmarkowska et al. describes the development/validation of a simple tool for the rapid diagnosis of Mycobacterium avium complex members useful for the vets employed at slaughtering facility. I have appreciated the efforts put by the authors to validate such a kind of tool, but, despite the statistical approaches used in my opinion are in general quite correct (sometimes some values, e. g. Intervals of confidence and p-values are missing), an answer whit e certain degree of confidence about the presence or less of MAC members is far to be obtained, so it would be necessary in any case a more complex and expansive diagnostic assay to obtain a certain grade of confidence about the status of this specimens. Nevertheless I believe this kind of paper could be of some utility for those specifically employed in the slaughtering activity, so I encourage the authors to shorten the paper and to resubmit it in a new short version. Particularly the discussion section contains a lot of redundant or similar concepts that weigh down the text

Please, find here a few suggestions:

Row 59: I would say instead of “a collection” a “group”

Row 84: I would add a suggestion more appropriated , like the current European Union rules dedicated to this issue.

Row 149 and elsewhere: please report the centrifuge force as “g” and not as “rpm”.

Row 152: how many microliters of sediments have been inoculated?

Rows 185 187: suppose this model is based on the assumptions referred to the Ockham's razor? Could the author try to better explain this concept?

Row 251: there are any IC95% or similar? Maybe also correlated with a p-value?

Row 254-258: maybe here a further explanation about the model used could allow to the reader to better follow the explanation about low or high probability.

Row 268 Figure 6: It would be interesting if the authors report also the intervals of confidence for the model proposed.

Rows 300-301: Why PCR results here?

Rows 354-360: it sounds a little bit repetitive.

Reviewer #2: This study examined the size and type of tuberculous-like lymph node lesions found in 10,600 pigs at a slaughterhouse. The lymph nodes from 86 mandibular nodes with visible macroscopic changes and 113 without changes were further studied by examining a cross-section of the nodes and culturing M. avium on Lowenstein-Jensen and Stonebrink media and genotyping M. avium species using a commercial GenoType CM test. M. avium was found in 57% of lymph nodes with lesions but only 19% in unchanged lymph nodes suggesting a simple way to screen pigs to prevent entry of contaminated pork into the food chain. The following questions and comments should be addressed.

1. It was mentioned that visual inspection of the mandibular lymph nodes, as these appear to present with more frequent changes than mesenteric lymph nodes, by meat inspectors could serve to be a rapid and cost effective procedure for screening for macroscopic lesions (lines 287-298). How easy is it to access the mandibular lymph nodes to perform the inspection, i.e., how much time is involved to visually inspect these lymph nodes (minutes)?

2. Two subspecies of M. avium appear to be dominant in infecting pig lymph nodes, that being M. avium subspecies avium and M. avium subspecies hominissuis. Is there any difference in prevalence for these two types in infecting pigs and do both of these subspecies present a potential danger to humans? It was mentioned that humans may be infected with localized and pulmonary infections, particularly in immunocompromised individuals (lines 59-69). It was unclear from the GenoType CM test if it had the ability to distinguish between the subspecies avium and hominissuis as the Results only mention M. avium without differentiating the subspecies.

3. Staining included hematoxylin and eosin, presumably to assess lymphocytic infiltration common in granulomatous lesions. It was also mentioned that Kinyoun staining was used although it was not mentioned why (line 137). Kinyoun staining involving carbol fuchsin is generally used to stain mycobacteria red due to the presence of mycolic acid in order to detect acid fast bacilli. Was this the primary purpose for this staining and does M. avium stain positive with this technique?

Minor points

Line 216 “Necrosis separated by a thick one fibrous proliferation.” Unclear meaning

Line 392, “M. chelone” should be “M. chelonae”

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Reviewer #1: No

Reviewer #2: Yes: John S. Spencer

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Could the type and severity of gross lesions in pig lymph nodes play a role in the detection of Mycobacterium avium?

PONE-D-21-34537R1

Dear Dr. Kaczmarkowska,

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.

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Kind regards,

Selvakumar Subbian, Ph.D.

Academic Editor

PLOS ONE

 

Additional Editor Comments (optional):

 

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

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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: Yes

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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

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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: (No Response)

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Reviewer #2: Yes: John S. Spencer

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