PONE-D-21-37300Molecular and microbiological evidence of bacterial contamination of intraocular lenses commonly used in canine cataract surgeryPLOS ONE

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Reviewers' comments:

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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

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

Reviewer #1: Yes

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

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Reviewer #1: Yes

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Reviewer #1: Yes

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Reviewer #1: This study investigated the presence of bacteria and/or bacterial DNA contamination in presumably sterile and commercially available canine IOLs and their packaging fluid. I appreciate your efforts in this important and emerging area of research. The manuscript is well-written, concise, and informative. The number of products sampled for each manufacturer is relatively small, but as a descriptive pilot study this is adequate. Further clarification regarding negative controls and data filtering methods are necessary before publication.

Materials & Methods:

For consistency, please have the order of experiments in the Materials & Methods match the Results. For example, if conventional bacterial culture is mentioned first in the Materials & Methods, please list it first in the Results.

Although the authors have used negative controls to assess the presence of environmental contaminants, which can significantly influence samples from sites with low microbial biomass, it is not clear if contaminant filtering analysis was conducted to discount the possibility of reagent/environmental contaminants impacting the results. Information regarding subtractive filtering should be provided in the manuscript. More information is provided below.

Results:

Table S1 – “Uncultured” bacterium is likely inappropriate terminology for microbiome data. Consider renaming to unidentified or unlisted bacterium.

Discussion:

243-249: As mentioned above, subtractive filtering to remove contaminants is important for low biomass samples, especially since the negative controls closely resemble the IOL and fluid packaging samples in this study. Several methods have been developed to identify and remove contaminating DNA, and this should be utilized and described in the manuscript. For example, Decontam is an open-source R package that identifies contaminants in microbiome data to censor contaminant taxa from the dataset allowing researchers to generate more accurate profiles of microbial communities. Following the use of any subtractive filtering technique, the read count of each sample should be assessed to determine whether the minimum cutoff based on the rarefaction curve has been met. Samples with very low read counts should be excluded from further analysis.

Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6(1):226.

https://doi.org/10.1186/s40168-018-0605-2

Zinter MS, Mayday MY, Ryckman KK, Jelliffe-Pawlowski LL, DeRisi JL. Towards precision quantification of contamination in metagenomic sequencing experiments. Microbiome. 2019;7(1):62.

https://doi.org/10.1186/s40168-019-0678-6

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Reviewer #1: No

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Molecular and microbiological evidence of bacterial contamination of intraocular lenses commonly used in canine cataract surgery

PONE-D-21-37300R1

Dear Dr. Ericsson,

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,

Paula V Morais, 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

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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

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

Reviewer #1: 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

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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

**********

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: Dear Authors,

Thank you for addressing my comments. I have no further concerns or comments prior to publication.

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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: No

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