PONE-D-21-16017

72-Hour Transport Recovery of Antimicrobial Resistant Neisseria gonorrhoeae Isolates Using the InTray® GC Method

PLOS ONE

Dear Dr. Keely S Paris,

Your manuscript "72-Hour Transport Recovery of Antimicrobial Resistant Neisseria gonorrhoeae Isolates Using the InTray® GC Method" have been assessed by external reviewers and me. Although the data of potential interest, the paper is unfortunately not acceptable for publication in the present form. There are several essential issues as outlined by reviewers that will need to be addressed. The reviewers are overall positive that with significant revision, the quality of the paper may be improved. Therefore, I invite you to revise your paper, considering the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Dr. Supram Hosuru Subramanya, Ph.D.

Academic Editor

PLOS ONE

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2. Thank you for stating the following in the Financial Disclosure section:

"CCB and KSP acknowledge funding from National Institute of Allergy and Infectious Diseases (K01AI136725). All study procedures were funded and conducted by BioMed Diagnostics Inc. (https://biomeddiagnostics.com/). "

We note that one or more of the authors have an affiliation to the commercial funders of this research study : BioMed Diagnostics Inc.

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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: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: 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

Reviewer #3: Yes

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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

Reviewer #3: 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: Gonorrhea incidence is on the rise as is the level of antibiotic resistance in the circulating strains. It is important to develop techniques that maintain viability during transport of this organism. In this study, Paris et. al assessed bacterial recovery of clinical isolates of N. gonorrhoeae in transport conditions using InTray GC (the current standard developed by BioMed Diagnostics), 72 hours after an initial period of incubation. The purpose of this study was also to receive approval from the US FDA to modify the intended use to extend the allowable times that the InTray GC device could be used to transport specimens. The study is rigorous and well written, however there are some concerns that must be addressed:

1. The central finding in this paper is that the recovery is good after 72h in InTrayGC. However, the fact that most of the strains seem to “grow” (in terms of % recovered) during the 72 hours in the InTrayGC (the strain that grew the most, 0197, increased by 1 log) could likely confound any quantitation of the initial bacterial load that was present in the sample. While it is evident that the authors are focused on recovery, this confounder should be at least addressed in the discussion.

2. Continuing from above, the different strains grow to different extents. What do the authors make of this finding?

3. L78- It is not clear why the authors chose to test the particular strains #0165, #0181, #0197, #0202, and #0175. While they provide different MIC values for antibiotics in Table S1 to demonstrate the differences in the strains, how do the authors deflect the criticism that the strains were “cherry picked”? Some reasoning for why they chose these strains would be useful information to provide. Additionally, highlighting the unbiased nature of the process that lead to the selection of these 5-6 strains would allay some of the skepticism associated with strain selection (perhaps they are phylogenetically well spaced out on a tree? Or this is part of a standard set of strains used to test any new method in the field?).

4. L 97- To an uninitiated reader, it is not clear why the 72-hour time point was chosen for InTray GC and 24 hours for Eswab. It would help if appropriate literature describing the current standard in the field was cited.

5. L180 – “the same strain failed”. The word “as” is a typo

6. Figure 3 does not need the 48 and 72 hr timepoints on the X axis

Reviewer #2: The manuscript by Paris and colleagues investigates the recovery of Neisseria gonorrhoeae from two transport systems. The BioMed Diagnostics InTray GC system and Copan Diagnostics Liquid Amies Elution Swab (ESwab) were inoculated with a standard inoculum of six different N. gonorrhoeae strains (five clinical isolates from the CDC FDA specimen bank and one ATCC strain) and held at various times and temperatures to simulate transport conditions from a clinic to a laboratory. There was a 19.3% increase in CFU/ml from GC InTray plates and a 24.8% decrease in CFU/ml from the Eswab system at 72 hours. The data confirms previous studies reporting similar findings and will be used by BioMed Diagnostics to seek a modification from the US Food and Drug Administration to extend the allowable times that the GC InTray can be used to transport clinical specimens.

Comments

General comment: Review the manuscript for consistent use of Neisseria gonorrhoeae and N. gonorrhoeae. The full bacterial name should only be spelled out when it is first used in the manuscript and subsequently referred to as N. gonorrhoeae. There is no need to put N in paratheses as written on line 20.

Line 53: Does the sentence refer to culture being necessary to identify outbreaks of antimicrobial resistant (AMR) N. gonorrhoeae or simply gonorrhea outbreaks? Non-culture methods would be more useful for gonorrhea outbreaks and culture being need for AMR outbreaks.

General comment for the Methods section: Were the strains confirmed to be N. gonorrhoeae following initial recovery from the supplier? The methods used to confirm the identity of the strains should be added.

Reviewer #3: REVIEW NOTES FOR MANUSCRIPT NUMBER- PONE-D-21-16017

The manuscript is well and clearly written, with figures and tables that are easy to comprehend. It describes a research study, assessing the recovery of six Neisseria gonorrhoeae clinical isolates that are inoculated into two different transport devices, the BioMed Diagnostics’ InTray GC and the Copan Diagnostics’ Liquid Amies Elution Swab (ESwab) Collection and Transport System.

The approach used is appropriate. Assessment of recovery from both systems was done after 24h for the ESwab and after 72h for the BioMed Diagnostics’ InTray GC. Each system was assigned to a separate experimental group while a third group consisted of a control group made up of the same clinical samples inoculated unto standard chocolate agar plates to confirm viability of the clinical isolates. Both systems were subjected to the same temperature conditions. The ability of each system to maintain viability of the isolates was determined by comparing the CFU/ml at initial time zero and the CFU/ml at the end point time.

The ability of the InTrayGC system to maintain and transport viable gonococcal isolates for recovery after more than 24hrs has been confirmed by earlier studies (Papp et al., 2016; Beverly et al., 2000). However, the work under review was done to obtain approval from the FDA to use the InTrayGC system to transport clinical specimen for an extended period (up to 72hrs) before recovery of isolates of Neisseria gonorrhoeae. The methods used were chosen to demonstrate viability based on FDA standards.

The study results show that the InTrayGC system can maintain N. gonorrhoeae clinical isolates for up to 72h for recovery of viable isolates.

This study is important in that Neisseria gonorrhoeae is a very fastidious organism that is easily lost to temperature fluctuations during transportation of clinical specimens. There is a need to develop and assess appropriate transport systems to overcome this weakness.

ABSTRACT AND INTRODUCTION

The main research question and the key findings of this study are clearly summarized. Other current literature on the topic has been referenced

FIGURES AND TABLES

All the associated text supports the information in the tables and figures. The figures are clear and readable, captions are complete and accurate.

METHODS

The experiments used are appropriate and the data is enough to support the conclusions that were arrived at, although the assessment of more specimen would have given more weight to the data. However, the author may need to explain why the InTray GC system was incubated here. The system is described as a transport system, when in actuality, incubating the system before transportation has a strong positive influence on isolate survival/viability.

Limitations were addressed adequately; data was collected and interpreted correctly. This study can be replicated.

RESULTS, DISCUSSION AND CONCLUSIONS

The results, discussion and conclusion are well described and clearly written

MINOR COMMENTS/EDITS

Line 66. Space between the end of the sentence and the parenthesis ie. (7) is missing

Line 193. Space between the & and C is missing

Line 261. (ref 6.). The reference title was not complete

Line 233. Typo at “used”, it should be “use”

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Reviewer #1: Yes: aditya bandekar

Reviewer #2: No

Reviewer #3: No

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72-Hour transport recovery of antimicrobial resistant Neisseria gonorrhoeae isolates using the InTray® GC method

PONE-D-21-16017R1

Dear Dr. Keely S Paris,

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,

Supram Hosuru Subramanya, 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 #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: 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 #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: 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 #1: Yes

Reviewer #2: Yes

Reviewer #3: 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 #1: Yes

Reviewer #2: Yes

Reviewer #3: 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 #1: (No Response)

Reviewer #2: The revised manuscript properly addresses comments from the reviewers. This reviewer does not have any additional comments for consideration.

Reviewer #3: (No Response)

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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.

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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: aditya bandekar

Reviewer #2: No

Reviewer #3: No