PONE-D-21-32646Phenotypic and genotypic detection of extended spectrum beta lactamase enzyme in Klebsiella PneumoniaePLOS ONE

Dear Dr. Anoar,

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.

==============================Please address the reviewers recommendations and prior to submission make sure that the manuscript has been well revised by several people. In its current form it has gramatical and spelling errors and the names of the bacteria contains spelling mistakes and it is not italics. Please, pay attention to the details. ==============================

Please submit your revised manuscript by Dec 30 2021 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: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Monica Cartelle Gestal, PhD

Academic Editor

PLOS ONE

Journal Requirements:

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

1. 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 

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 

https://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 more 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 sensitive information, data are owned by a third-party organization, etc.) 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. 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: Yes

Reviewer #2: Partly

**********

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

Reviewer #1: No

Reviewer #2: Yes

**********

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

**********

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: No

Reviewer #2: No

**********

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: N0 Line number Reviewer’s Comments/Suggestions

1 Abstract Most results of antibiotic not clarify clearly in abstract section

Keywords Need to arrange alphbetically

2 The manuscript contains many grammatical errors that must be corrected especialy the discussion and introduction section need too much correction

3 highlighted in Green Correct the word

4 highlighted in Red Delete word or character

5 Many Word not writed in fully form like” EBLS,ICU,U.S.A,MICs,OPD)and others, also the term EBLS sometimes writed “ESBLS” other palces writed “ESBLs” it must write in unique and scinetific style

6 Highlighted in Yellow Give a space

7 Results - İn this sectio the concentration of each antibiotiv must mentioned inside the (table 4).

- (P-value with 0.00001) this wrong value (correct the value).

8 Discussion The authors mentioned in this section this wrong reference lined with yellow” The other drug such as amoxicillin-clavulanic acid also shows high resistance rate (96.29%), the same result was reported in Erbil , Najaf and Duhok / Iraq (Gupta etal.(2003), (Aljanaby etal.(2018), (Qadir (2019). Respectively. So Gupta and his collegous study founded in U.S.A

9 References All the refernce not in one unique style; the year of publication sometime after the name of authors and sometimes after the title of article, sometiems after the year of publication come comma others semicolon

10 Others important notice - Many word wtrited wrongly like „standardise,Fifty four,30 µg must become

30µg (without any space),TEM and SHV writed with different format like balSHV,blasCTM

- Table 1,2 need to re-type in word format not in picture foramt

- Chi-sequare and correlation analysis test mentioned in statistical anlalysis section but actualy not calculate for the data (for comparision), the authors must delete these characters , also the authors must mentioned which version of M.soft excel they used

- Table 3, 4,5 ,6 and 7 must re-type again with word format adn without coluration .

- The manuscript not contanin conclusion and any Acknowledgement.

Reviewer #2: After reading the manuscript titled: I suggest the need for major revisions.

I believe that the presented research is very relevant and worth publishing, however the authors need to pay attention to a few issues detailed below. First of all, spelling inconsistencies, such as VITEK / Vitek, are noticeable. The authors do not pay attention to the correct spelling of the name of the microorganisms (no italics, no capital letters), the names of the authors cited are often written in lower case. Punctuation errors are also noticeable.

Introduction:

1) “Extended-spectrum beta-lactamase (ESBL)-producing bacteria is plasmid-mediated enzymes…” – should be corrected, bacteria aren’t enzymes!

2) “…evolutionary families based on their amino acid sequence TEM and sulphydryl variable SHV were the major types…” is this one sentence?

3) ” The fact that patients most likely to become infected with ESBL-producing Enterobacteriaceae are those…” – Enterobacteriaceae should be in italics

4) “It is estimated that Klebsiella species cause 8% of all hospital-acquired infections...” – Klebsiella should be in italics

5) “Antimicrobial resistance in Klebsiella Pneumoniae…” – pneumoniae should be lowercase

6) “Combinations of all types of bla genes were reported in this species, this may be due to either carriage of an antibiotic-resistant plasmid encoding an array of antibiotic resistance genes or due to acquisition of transposons containing different bla genes on the same plasmid” – bla should be in italics

7) “Many different techniques exist for confirming ESBL production , Phenotypic tests for ESBL detection” – this sentences should be separated by a period, not a comma. Do not put spaces in front of the punctuation marks

8) “(Schwarz etal.(2010)” – too much brackets

9) “(shariif etal.(2017).” – too much brackets, write surnames with capital letters

10) “Another confirming method involves at least an eight-fold reduction in the MICs of ceftazidime or cefotaxime in the presence of clavulanic acid, The isolates then reported as resistant to all penicillins, cephalosporins and aztreonam (muhamed & Abas 2019).” - Separate sentences with a period and not with a comma, and write surnames with a capital letter

11) “(philippon etal.(2011).” – surnames with a capital letter

Methods

1) shon etal.(2013). – surnames with a capital letter

2) biomeireux – company name should be write: bioMérieux

3) “Vitek® 2 biomeireux machine was used for the identification of all isolated Klebsiella according to the manufacturer’s recommendations” – which card was used?

4) tryptic soya broth - who is the medium’s producer?

5) Eppendoruf – correct to Eppendorf

6) “Antibiotic susceptibility pattern of Klebsiella pneumoniae isolates were performed according to the Kirby–Bauer disk diffusion method (Bauer etal.(1966) by using 15 commonly used antibiotic agents and all of the inoculated plates were aerobically incubated at 37°C for 18–24 hours, and the results were interpreted based on the instruction provided by the CLSI (2018 ).” - please mention here the antibiotics and their concentration

7) “disks” – correct to “discs” in each place

8) “Mueller-Hinton Agar plate” – no information about producer

9) VITEK or Vitek – please standardize

10) “Then let it to dissolve well and leave it for 15 minute at room temperature and mixed by vortexing, stock primer diluted 1:10 (10 μL of stock primer with 90 μL of DNA and RNA free distil water) to prepare working primer in concentration 10 pmol/μL (Ali& Ismael (2017).” - please correct the syntax so that it doesn't look like an instruction

Discussion

1) “this indicate that UTI is the most common infection in hospitals and Klebsiella is the second most common isolated bacteria” – Klebsiella should be in italics

2) “ICU samples . this indicates” – remove space before period and start sentence with a capital letter

**********

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: No

Reviewer #2: No

[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: manuscript-26-10-2021.docx

Attachment

Submitted filename: renamed_36ab1.docx

Phenotypic and genotypic detection of extended spectrum beta lactamase enzyme in Klebsiella Pneumoniae

PONE-D-21-32646R1

Dear Dr. Anoar,

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.

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,

Monica Cartelle Gestal, PhD

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

**********

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

**********

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: Yes

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: 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: (No Response)

Reviewer #2: (No Response)

**********

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: Yes: JALEEL SAMANJE

Reviewer #2: No

Attachments

Attachment

Submitted filename: Revised article 21-1-2022.docx