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PONE-D-20-21797

Phenotypic and genotypic profile of isoniazid resistance in pulmonary and extrapulmonary tuberculosis in Pakistan; A retrospective study of laboratory based surveillance 2015-19

PLOS ONE

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Hasnain Seyed Ehtesham

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PLOS ONE

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2. The study design section in your manuscript states that “This is a retrospective five-year (January 2015-December 2015) laboratory based surveillance study”. Please check that these dates are correct.

Additional Editor Comments (if provided):

Minor Revision

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: The manuscript reflects a large retrospective 5 year study of INH resistance in defined provinces of Pakistan and thus addresses gaps in understanding the factors that identify INHresistance, the effect on mising out INHand RFP resistance and the connection of INHand RFP resistance patterns to fluoroquinolones and PZA. In my opinion, the manuscript provides valuable comprehensive regional information.

The manuscript is well drafted and the discussion is well constructed. However there are multiple minor edits that are needed all through the manuscript. Attention is drawn to a typo error in line 124, wrt the 5 year duration. December 2015 should be replaced with December 2019 and to the subheading Discussion (not Discussions)

While undoubtedly the manuscript focusses on INH, there is a constant comparison of findings of RFP resistance patterns. Might it be warranted that RFP should also find a place in the title.

The laboratory methods need some more detailing in light of the discussion line 328 to 332 where mention is made of using Gene XpertMTB/Rif and WGS to confirm all RFP resistant cases. If this was undertaken with isolates from the present study, then this confirmation should be mentioned briefly in the Laaboratory Methods section citing the reference.

Sixty four percent of the patients tested here were retreateated patients. and 45% had previous treatment regimen for new patients. Therefore amplification of resistance is likely to have taken place. Would the authors like to speculate why INH resistance is sizeable also in new INHcases

In fig.2 RsHR TB in pulmonary TB patients, there is a significant drop between 2016 and 2017 aven 2018. Is there a reason for this trend.

It would be nice to know the annual variation if any in the proportion of inh and katG mutations in the different strata of patients. Is the proportion of katG mutations overall increasing temporally in the bacterial population?

The argument for programme adoption of genotypic technologies starting from Xpert like molecular testing platform for INH and extending to WGS and deep sequencing for confirming RFP and more so is an apt one and constitutes an important message of the manuscript. However the authors should attempt to shorten the lengthy discussion without omitting the essential points for enhancing readibility.

The value of such a laboratory study would be greatly increased if treatment outcomes could be linked to the genotypic and phenotypic DR findings. This could be a message for the design of future studies.

Reviewer #2: The retrospective study addresses an important aspect of TB control. However, the discussion needs to be more focussed, relevant to the results obtained. Statements like "It is critical to have a simple, accurate (>90% sensitivity) and affordable test to rapidly detect INH and FQ resistance" are sweeping statements, that state the obvious, and could be avoided.

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Reviewer #1: No

Reviewer #2: No

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Isoniazid resistance profile and associated levofloxacin and pyrazinamide resistance in rifampicin resistant and sensitive isolates from pulmonary and extrapulmonary tuberculosis patients in Pakistan: A laboratory based surveillance study 2015-19

PONE-D-20-21797R1

Dear Dr. Tahseen,

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.

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Kind regards,

Hasnain Seyed Ehtesham

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

I have gone through this revised manuscript and also the Authors response to the comments of both the reviewers. This manuscript was sent for minor revision and Authors have made the necessary changes addressing the comments of both the reviewers. All issues have been addressed. Error in the fig 2 has been corrected and another figure is replaced with the new one. Authors have shortened the discussion part and re-arranged the text to provide more clarity to the readers.

I recommend this manuscript for publication.

Reviewers' comments: