PONE-D-20-00432

Pragmatic accuracy of loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital

PLOS ONE

Dear Dr. Phinyo,

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.

I have received the reviews of your manuscript. While your paper addresses an interesting question, both reviewers expressed significant concern about your study and did not recommend publication in its present form.  Please see reviewers’ insightful comments below and address their comments carefully.  In particular, both reviewers have questions regarding the performance of the TB LAMP test performed in this study compare to the other TB LAMP tests in other published literature as well as WHO endorsed commercial LAMP test.  Both reviewers also felt that the effects and definition of a gold standard for TB testing which is not itself perfect should be discussed and reconsidered.

We would appreciate receiving your revised manuscript by Apr 18 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Baochuan Lin, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

1. When submitting your revision, we need you to address these additional requirements.

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.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2.  We note that you have indicated that data from this study are available upon request. PLOS only allows data to be available upon request if there are legal or ethical restrictions on sharing data publicly. For information on unacceptable data access restrictions, please see http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions.

* In your revised cover letter, please address the following prompts:

a) If there are ethical or legal restrictions on sharing a de-identified data set, please explain them in detail (e.g., data contain potentially identifying or sensitive patient information) and who has imposed them (e.g., an ethics committee). Please also provide contact information for a data access committee, ethics committee, or other institutional body to which data requests may be sent.

b) If there are no restrictions, please upload the minimal anonymized data set necessary to replicate your study findings as either Supporting Information files or to a stable, public repository and provide us with the relevant URLs, DOIs, or accession numbers. Please see http://www.bmj.com/content/340/bmj.c181.long for guidelines on how to de-identify and prepare clinical data for publication. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories.

We will update your Data Availability statement on your behalf to reflect the information you provide.

[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: No

Reviewer #2: No

**********

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

Reviewer #1: Yes

Reviewer #2: No

**********

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: No

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: 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 an important and interesting study on a newly emerging POC technology of TB diagnosis evaluated under actual condition. However, the paper is confused due to a poor study design. There are two serious concerns in this study that make the paper unacceptable.

1. The study aims to evaluate usefulness of a LAMP method in a practical setting in Thailand. The LAMP method is now available as an only commercial kit TB-LAMP assay (Loopamp™MTBC Detection Kit, Eiken Chemical Company Ltd., Japan) as endorsed by WHO in 2016. It seems that the method used in this study is a unique system at least partially. So, it is important to state explicitly that the target to be evaluated was an in-house LAMP and not one commercially available LAMP recommended by WHO.

2. In evaluating the sensitivity of the method, the authors used culture negative (clinically defined) cases, as well as bacteriologically confirmed cases, as a gold standard of the cases of TB. It may be difficult to admit the clinical diagnosis as a diagnostic basis for such a study as this, apart from clinical practice. Vice versa, the definition of the gold (conventional) standard for specificity (non-cases) should be reconsidered. The following paper may be of use in revising the paper; Kaku et al: Accuracy of LAMP-TB Method for Diagnosing Tuberculosis in Haiti. Jpn. J. Infect. Dis., 69, 488–492, 2016.

Reviewer #2: I think this paper has the potential to contribute more information to an ongoing area of research – that is, the performance of cheaper alternative diagnostic testing for TB in areas of high prevalence of disease. However, I cannot recommend publication of the results without major revision as I believe the diagnostic performance is misrepresented and the citations are misrepresenting the work of the other authors. I believe the authors just need to take greater care in summarizing the background to the current and in selecting the correct statistical methods. I’ve called out a few examples where the text mis-represents the citations, but a thorough re-look by the authors at all citations should be done.

Abstract/Background

“proven diagnostic performance” – this is both vague and too specific at the same time

“most of the results were validated” – the results aren’t validated, the assay is validated

The language surrounding people with possible TB needs to be updated throughout the paper - avoid the use of terms like "TB suspects" that increase the stigma surrounding this disease. http://www.stoptb.org/assets/documents/resources/publications/acsm/LanguageGuide_ForWeb20131110.pdf

The paper states repeatedly that there is little work published from resource-challenged settings, but this claim is not supported. Even the references given cite studies in such decentralized settings. Maybe it just hasn’t been done in Thailand? A better summary of the literature needs to be included. How does this compare to other studies? How is the TB LAMP test performed in this study compare to the TB LAMP tests in other published literature? A better focus on properly relating the current study to the body of work in the literature rather than trying to claim it is quite novel would actually strengthen the paper. There is merit in replication or demonstrating an important diagnostic in a new geographical area.

In-house vs commercialized kit is mentioned but not explained. And the position of this paper (what LAMP testing approach is used) is not properly placed in the context of what other papers are using and the potential impact on sensitivity/specificity.

The sensitivity/specificity of LAMP in other papers, settings, etc needs to be stated with numbers and not just alluded to. A proper, specific summary of the literature is lacking.

“In 2016, WHO suggested the use of LAMP assay for the diagnosis of pulmonary tuberculosis” – this is not quite right, WHO recommendations are very specific and it is important to get that right. From the abstract of the citation provided: “WHO recommends that TB-LAMP can be used as a replacement for microscopy for the diagnosis of pulmonary TB in adults with signs and symptoms of TB”. This needs to be stated correctly. Also, given the paper has mentioned in-house vs commercialized kits, it needs to be clarified that the WHO guidance refers only to the Eiken LAMP kit.

“LAMP assay has a low cost per test, does not required advanced technological facilities, and can be routinely practiced in general hospital laboratories [3].” Reference 3 doesn’t support this statement – it doesn’t say anywhere that the LAMP assay has a low cost per test. It says “Costs can be kept to a minimum if testing is limited to specimens from the most high-risk patients based on proper clinical assessments and national testing algorithms based on public health policies.” There are other publications on the cost of the LAMP assay for TB diagnosis. The authors might explain better the infrastructure/training needed for LAMP based on this reference and others.

Reference 5 doesn’t appear to really relate to the sentences it comes after. Reference 3 would make a lot more sense as it is a detailed overview of TB diagnostics including many molecular diagnostics.

Setting

The paper needs to do more to state what sets this setting apart from (or ties it to) other studies. See the methods section describing setting in reference 22 for how attributes of the specific site can be expressed in the context of the needs of LAMP.

Study Design

This is not a cross-sectional design, it is a prospective design. The plan was to prospectively enroll 120 patients.

“New patients who were clinically suspected of 109 pulmonary TB (coughing for more than two weeks with or without hemoptysis), aged more than 18 years old were consecutively invited into the study regardless of nation status.” Suggest re-writing to something more like: ‘Adults more than 18yrs of age with symptoms indicative of pulmonary TB (coughing…) and no history of TB were consecutively enrolled regardless of national status.’ If patients were ‘invited’ but not enrolled, we need numbers on how many declined.

“Samples with contaminated culture results or samples from patients who were previously documented as TB cases were excluded.” Were the patients excluded or the samples?

Methods

A map of which samples were used for what tests would be quite helpful. Highlight if any of the reference tests (smear, LJ culture, MGIT culture) were performed on the same sputum as LAMP.

Make it clear somewhere that smear-negative refers to AFB smear-negative.

Study size estimation

This has no purpose here – the study is done. Sample size estimation is for study planning purposes, for securing funding and making sure the plan has statistical validity.

Statistical analysis

The first four sentences are unnecessary.

The authors need to state what method was used to obtain the 95% CI for the sens/spec/PPV/NPV/LR+. It is clear from my testing that the Clopper Pearson binomial exact test was used, the authors should include the reference (usually found in the software documentation).

Kappa statistics are for inter-reader reliability, not for comparison of correlations between tests. It includes the concept that agreement may happen by chance when two people are guessing. However, it is not appropriate for comparison of diagnostic results because there isn’t guessing – the samples should not agree by chance but because they are or are not TB and the sensitivities of tests objectively vary. Spearman’s correlation can be used, but I think what you actually want is McNemar’s test. The desire is to compare the diagnostic performance (i.e. accuracy) between tests – McNemar’s test will do that. Alternatively Spearman’s correlation can look at the [objective] agreement between tests.

Results

Table 1 is dedicated to showing the patient clinical characteristics by culture status. The p-values shown test whether these characteristics differ significantly dependent on culture status. It is expected that gender, nationality, and age should not differ. Whereas it is also expected that chest x-rays and sputum quality would differ.

“The baseline demographic data between culture188 positive and negative patients were comparable except for the presence of cavitary lesions on 189 chest radiographs and the character of collected sputum (Table 1).”

Age, nationality, and gender are demographic data.

Chest x-ray and sputum quality are clinical characteristics.

Table 2 – re-check the NPV for parallel testing

There are a lot of LAMP-positive and AFB smear-positive patients with negative culture. Especially given that the tests are done on different sputum samples, these should be considered patients with probable TB and not used in assessing sensitivity and specificity.

There are too few smear-negative, culture-positive patients to assess sensitivity. Specificity should not be stratified by smear status, only sensitivity. For the reason above (that smear-positive, culture-negative patients shouldn’t be included in estimations of sensitivity/specificity of LAMP), what the paper is calling ‘smear-negative specificity’ should in fact be reported as the actual specificity of LAMP.

Table 2 – the p-values shown have no real meaning! If you want to compare accuracy of tests, you cannot do a p-value over the final accuracy measures among a bunch of tests. You need to compare tests 1 against another by using 2x2 grids and McNemar’s test. So, if you want to compare the accuracy of LAMP to the accuracy of AFB stain, you use the grid in Table 3 and McNemar’s test:

46 5

5 59 McNemar test p-value: 1.000

Discussion

“This study had demonstrated the pragmatic performance of the LAMP test, which was comparable to that of the conventional smear microscopy and the fluorescence microscopy.” Not true, the performance of LAMP as evaluated in this study was below that of smear microscopy.

“Although the sensitivity and specificity of the LAMP test were lower than that of the acid fast stain and the fluorescence stain, the comparative statistical test revealed non-significant results” This is still true when McNemar’s test is performed, but the right statistical tests need to be used in the paper. Furthermore, a non-significant result doesn't mean no difference, it means the difference is likely smaller than the power of the study to detect.

Put PPV/NPV in the context of the local prevalence of disease! State from the literature or reliable source what the prevalence of TB is in the hospital’s area of Thailand. I would suggest giving the readers an example: Given that prevalence and a group of 1000 patients, state how many would be true positives, false positive, true negatives, and false negatives. You can therefore assess what burden the different accuracies will place on the hospital. I.e. if the specificity is quite low and the sensitivity is higher, is that better? If the sensitivity is high and the specificity is lower, is that better? Relate this to the LR+.

“In the clinical context of TB diagnosis, both the LAMP test and the smear microscopy are considered as a diagnostic test which would normally be done in TB suspects with high pre-test probability [14]” – this is not what the reference says.

“Therefore, a serial test relying on both the result from the LAMP test and the acid-fast stain would be more appropriate for use as a rule-in test as it carried higher specificity and positive likelihood ratio than other methods.” Authors should define ‘rule-in’ test and what is generally expected of such a test. Should note the increased cost of such an approach.

The effect of a gold standard which is not itself perfect should be discussed. Also the variability between sputum samples should be discussed.

A better look at the differences between this study and others with better test performance needs to be done.

“Currently, the WHO only supported the use of two rapid molecular tests for the diagnosis of 294 pulmonary tuberculosis, which were Xpert MTB/RIF and the LAMP test” – as the concept of LAMP test from a kit and other LAMP tests has been raised, and the variability of accuracy depending, it needs to be clear that the WHO recommendation is only for the Eiken LAMP test kit!

**********

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: Toru Mori

Reviewer #2: Yes: Christen M Gray

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

PONE-D-20-00432R1

Pragmatic accuracy of in-house loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital

PLOS ONE

Dear Dr. Phinyo,

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.

Both reviewers agreed that the revised manuscript showed significant improvement, however, one of the reviewers still have concerns regarding clarity of the LAMP assay and discussion that need to be address carefully. Please see reviewer #2 insightful comments below.  In addition, the quality of the language needs to be improved to maintain the quality of published work, since PLoS ONE does not perform copyediting of manuscripts at any later stage in the publication process.  There are quite a few awkward sentences throughout the manuscript.  Please have a fluent, preferably native, English-language speaker thoroughly copyedit your manuscript for language usage, spelling, and grammar.  Personally, at a more detailed level, I found several issues need to be addressed, please see specific comments below.

Specific comments:

1. Abstract and Tables:  Change the format 95%CI to be consistent with the rest of the manuscript, for example“95%CI 78.3,97.5” should be “95%CI 78.3-97.5”.
2. Line 80, implicated has negative meaning, suggest changing to implemented.
3. Line 162, change M. tuberculosis to Mycobacterium tuberculosis since this is the first time you mentioned the bacteria. Also all the “M.” need to be italicized in M. tuberculosis throughout the manuscript.
4. Line 192 – 193, should the “smear-positive and culture-positive results” be “smear-positive and culture-negative results”?
5. Line 243 – 246:  These sentences need reference(s).

We would appreciate receiving your revised manuscript by Jun 27 2020 11:59PM. When you are 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.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter.

To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'.

Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

We look forward to receiving your revised manuscript.

Kind regards,

Baochuan Lin, Ph.D.

Academic Editor

PLOS ONE

[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: (No Response)

**********

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: Partly

**********

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

Reviewer #1: Yes

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 #1: (No Response)

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: No

**********

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: The reviewer is pleased to see that all of his comments are well addressed and the manuscript has been revised accordingly.

Reviewer #2: The English of the paper needs further work to be clear to the intended audience. While the main portion of the paper has been improved, further clarity around the assay (compared to other similar assays) is needed. Finally, the discussion requires heavy revision as it contains unsupported conclusions.

**********

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: Yes: Christen M Gray

[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 to be viewed.]

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 us at figures@plos.org. Please note that Supporting Information files do not need this step.

Attachments

Attachment

Submitted filename: PONE-D-20-00432_R1_review comments.pdf

Attachment

Submitted filename: PONE-D-20-00432_second review.docx

PONE-D-20-00432R2

Pragmatic accuracy of an in-house loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital

PLOS ONE

Dear Dr. Phinyo,

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.

Specifically, the reviewer still has concerns that need to be addressed carefully. Please see reviewer's insightful comments below.

Please submit your revised manuscript by Jul 24 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:

• 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Baochuan Lin, Ph.D.

Academic Editor

PLOS ONE

[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 #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: 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 #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: The manuscript is much improved after the second revision. Some minor problems remain, but these are specific rather than general and should be able to be easily addressed.

- The use of ‘This’ at the beginning of sentences in the Background is not very clear.

- Some of the other corrections have also reduced clarity rather than enhanced, I have made a note for each instance for ease of author correction in the annoted pdf that I have attached to this review.

- Line 84, ‘More affordable in-house LAMP assays were later developed’ – this is still a problematic assertion as the first reference (the original reference for the sentence) is dated 2008 which is published prior to the availability and endorsement of the commercial TB-LAMP assay being compared. Also, none of the now 5 references compare affordability of the commercialized assay to an in-house assay to the commercial assay. Suggest the authors change to ‘An in-house LAMP assay may be more affordable…”

- Line 331, the authors state that no patients with HIV infection were included – was HIV testing performed on all patients? Were they confirmed to be HIV negative? Or should this say more simply that HIV testing was not performed?

- Line 341, authors should remove ‘Sensitivity and specificity would be improved if higher quality sputum is obtained’ – the authors have no way to confirm that. And, no support has been given as to why specificity would, even hypothetically, change.

- In the previous review, I noted that if the Kappa statistic 95% CI is displayed, then the Spearman Rho in the same table should also have the 95% CI. However, in retrospect, I realize that Spearman’s Rho should not have a 95% CI as one cannot be calculated for this method. Suggest removing and making a note.

**********

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: Christen M Gray

[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-20-00432_R2_reviewed.pdf

Pragmatic accuracy of an in-house loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital

PONE-D-20-00432R3

Dear Dr. Phinyo,

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.  Please spell out M. tuberculosis on line 153 since this is the first time the name of the bacteria was mentioned.

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,

Baochuan Lin, 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

**********

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: 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 #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: The authors have done much to improve the manuscript and have addressed all of my concerns.

One very tiny thing: M. tuberculosis should be fully written out the first time it appears in the text and the abbreviation given. This occurs on the 2nd mention.

**********

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: Christen M Gray