PONE-D-24-04229Antimicrobial resistance and AmpC production in ESBL-producing Klebsiella pneumoniae and K. quasipneumoniae subsp. similipneumoniae: A retrospective study in Japanese clinical isolatesPLOS ONE

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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

Reviewer #4: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

Reviewer #4: 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

Reviewer #4: 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

Reviewer #4: No

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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: This is an important study with interesting findings, the manuscript is systematic and well put together, previous recommendations for corrections have been effected. In the discussion, it is always important to clearly state the health/public health implication of the work and how it has added to the body of knowledge. The minor issues raised in the review should be addressed. It is quite commendable and will add to the body of knowledge.

Reviewer #2: Great work.

Authors should consider that their work was done in a particular location and that should be stated where necessary, do not overgeneralize.

Further comments are included in the manuscript and a word document of same attached.

Reviewer #3: Lines 20-21

“The aim of this study is to evaluate the prevalence of various species, ESBL genotypes, 21 antimicrobial resistance patterns, and AmpC co-production in ESBL-producing Klebsiella”.

It is better for the authors to first introduce the basic concept of the work before going into the aim of the work. Also, the aim is too generic without a location attached to it.

Lins 54 to 56

“However, research on ESBL and AmpC co-producing K. pneumoniae is limited”. How is it limited? Internet search shows there are a lot of studies on this.

Lines 61-62

“the global epidemiology of ESBL-producing K. quasipneumoniae and K. variicola is ill62 understood” What do you mean by global epidemiology? This work is Japan focussed.

The work should be specific in its aims by attaching a location to it.

Lines 73-74

In this study, we 74 collected clinical isolates of ESBL-producing Klebsiella isolates and investigated.

Line 83-85

“In total, we collected 139 ESBL-producing Klebsiella isolates from two locations in Japan: Kameda Medical Center in the eastern part and Sapporo Clinical Laboratory in the northern part”

What is the basis for this? Which sampling technique was used?

Authors should present results in a way that shows significant differences or otherwise as set out under the statistics section.

The silence on significant differences that is obvious on the tables and body of results is obvious in the discussion too.

Reviewer #4: The authors provide useful information on the phenotypic and genotypic characterization of Klebsiella species from clinical isolates but needs to provide certain clarifications with major revisions. There are several repetitive presentations across the manuscript and authors should revisit their presentation style and revise the manuscript for a better outcome. Additionally, the manuscript will benefit from English editing for clarity.

- “The aim of this study is to evaluate the prevalence of various species, ESBL genotypes,

antimicrobial resistance patterns, and AmpC co-production in ESBL-producing Klebsiella” this is a bit confusing especially with the use of “prevalence” since the isolate were already identified and store as ESBL producing Klebsiella. I would suggest the use of “characterization” instead.

- The study provides interesting findings on the ESBL and AmpC genotypes in Klebsiella species from two healthcare facilities in Japan. The methodology session however needs to provide further information on the isolate sourcing. Were the isolates obtained from a repository and storage information? I am curious to know if there were some of the klebsiella species that were not confirmed even though they were stored as Klebsiella

- The authors need to provide acknowledgements for the facilities where the isolates were collected.

- The tables are followed by a verbatim report of the results presented in the Table. This is highly repetitive. The authors need to use either of the two methods.

- Table 3: it is not clear what the column “other” represents. If it is refereeing to the genotypes listed below it, then there is no need for this and it should be expunged. I suggest that the table should be presented in a clearer way. for example. To use “CTX-M-1group and CTX-M-1 alone” to differentiate where they occur tother with other genotypes and where it occurs alone rather than just “CTX-M-1” Also, “SHV group” should be reported in addition to “SHV alone”

- Table 5 does not add much value per se and should be expunged since the information has already been provided in line 258-264.

- The authors indicated that Phenotypic ESBL testing will be done in the methodology but made no mention of it in the result session or even in the supplementary table. It may be worthwhile to state how it compares with the ESBL genotyping.

- The discussions section needs to be improved to avoid repetition of results rather provide in-depth interrogation of the study findings for instance, the issue of co-production of ESBL and Amp C was briefly mentioned as a major complication of AMR but needs more elaborate discussion of the public health implication of co-production in clinical management of Klebsiella infections.

- The conclusion in its current state is a repetition of the results and lacks critical engagement with the study objectives, findings and implication.

Minor revisions

-The title gives prominence to K. quasipneumoniae subsp. Similipneumoniae even though there were very few isolates obtained and not much discussion around it in the discussion section

Pg 4 line 64- Correct to “Antimicrobial resistance pattern…”

- Pg 5 line 66: Add a full-stop after pneumonia

- Pg 5, line 72-80: Further information are needed in the methodology

-Pg 6 line 92: “further identification of Klebsiella species, detection……” This is confusing as it has been stated that MALDI-TOF was used for identification.

- Line 128: m-CIM…. Please write the full meaning of the acronym on first appearance

- Line 196-198: kindly expunge as this information has been provided in the methods section

-Line 213-215: same as above

Line 207: “The co-existing CTX….” This sentence lacks clarity. please rephrase.

-Line 219: “Within the CTX-M-9 group, coexisting CTX-M-9 and SHV were the most common genotype in K. pneumoniae (37/135, 27.4%).” This statement is unclear and needs to be rephrased for better clarity.

- Line 244-251- This paragraph does not seem to add any real value but merely states what can be clearly observed from the table> the authors need to choose either tables or description

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Reviewer #1: Yes: Rahab Charles-Amaza

Reviewer #2: No

Reviewer #3: No

Reviewer #4: Yes: Emelda Chukwu

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Attachments

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Submitted filename: Reviewers comment_ Rahab Charles Amaza_Feb 2024.docx

Attachment

Submitted filename: PONE-D-24-04229 REVIEW.pdf

Attachment

Submitted filename: PONE D 24 04229 Review.docx

Antimicrobial resistance and AmpC production in ESBL-producing Klebsiella pneumoniae and Klebsiella quasipneumoniae: A retrospective study in Japanese clinical isolates

PONE-D-24-04229R1

Dear Dr. Watanabe,

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,

Mabel Kamweli Aworh, DVM, MPH, PhD. FCVSN

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

Reviewer #4: 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

Reviewer #4: Yes

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

Reviewer #2: Yes

Reviewer #4: 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

Reviewer #4: 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

Reviewer #4: 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 a good job by attending to the concerns raised earlier. The findings are essential in advancing knowledge.

Reviewer #4: (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.

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: No

Reviewer #4: No

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