Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli

Sayran Hamad Haji; Safaa Toma Hanna Aka; Fattma A. Ali

doi:10.1371/journal.pone.0259005

Peer Review History

Original SubmissionJuly 11, 2021
23 Jul 2021 Decision Letter - Abdelazeem Mohamed Algammal, Editor PONE-D-21-22590 Evaluation of carbapenemase-producing clinical isolates of Gram-negative bacilli using phenotypic and genotypic methods at hospitals in Erbil city, Kurdistan region of Iraq PLOS ONE Dear Dr. haji, 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. ACADEMIC EDITOR: A major revision is needed.The manuscript should be revised for English editing and grammar mistakes. Please submit your revised manuscript by Sep 06 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: http://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, Abdelazeem Mohamed Algammal, Prof, Ph.D 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. In your Methods section, please provide additional information on the verbal consent provided by the patients, including as to how this verbal consent was documented or witnessed. 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 5. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. 6. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1 in your text; if accepted, production will need this reference to link the reader to the Table. [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: Partly Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: No ****** 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: Yes Reviewer #2: Yes ****** 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: Comments to authors: - The current study is very interesting; however, the authors should address the following comments to improve the quality of the manuscript: - The manuscript should be revised for language editing and grammar mistakes by a native English speaker. - Please write the genes name in correct form all over the manuscript (the 1st 3 letters must be small and italic and the other 3 letter are capital and subscripted) Title: I think the work would benefit from the title that contains main conclusion of the study (should be derived from the conclusion), please modify the title. Abstract: - The abstract must illustrates the used methods and the most prevalent results (give more hints about methods and results). Besides, rephrase the main conclusion of your findings. Introduction: -Give a hint about different infections caused by common pathogenic members of Enterobacteriaceae (such as E. coli and K. pneumonia) and Pseudomonas aeruginosa, their virulence factors, and the mechanism of disease occurrence. - The introduction needs to be more informative: -The authors should illustrate the public heath importance concerning the emergence of multidrug-resistant (MDR) bacterial pathogens that reflecting the necessary of new potent and safe antimicrobial agents. Several studies proved the widespread MDR- bacterial pathogens; Authors could add the following paragraph: Multidrug resistance has been increased globally that is considered public health threat. Several recent studies reported the existence of multidrug-resistant bacterial pathogens from different origins including humans, poultry, cattle, and fish that increase the need for routine application of the antimicrobial susceptibility testing to detect the antibiotic of choice as well as screening of the emerging MDR strains. You should cite the following valuable studies: 1-PMID: 33177849 2-PMID: 32497922 3-PMID:33061472 4-PMID: 33947875 5-PMID: 32472209 6-PMID: 32994450 -Rephrase the aim of work to be clear and better sound. Material and methods -Table 1 must be placed in the results section. -It is not acceptable to illustrate the prevalence of the bacterial pathogens in the methods; it should be placed to the results section. -Where are the methods of the isolation and identification of 200 Gram-negative bacteria?? You must illustrate in details and support your methods with specific references. - Phenotype-based method for carbapenemases: should be modified to be: Phenotypedetection carbapenemases using Disc diffusion method. Rephrase this section; add more details, discuss in details and specific references. - Confirmation of carbapenemase production using commercial combination disk assay; add specific references to this section. -Molecular detection of genes should be modified: PCR-based detection of carbapenemase genes. Besides, add specific references. -Where are the statistical analyses? -Results: - Where are the results of phenotypic characters and the prevalence of the isolated bacterial pathogens from the examined samples? You must illustrate their prevalence in a new table. -Table 1 must be placed in the results section. - Illustrate in a new table the test results of the phenotypic MDR (illustrate the antimicrobial classes of the used antimicrobial agents). -Illustrate the distribution of the carbapenemase genes among the recovered isolates in a new table. - Please increase the resolution of all figures (1200 dpi). -Where are the statistical analyses? -Discussion: -The discussion is too long and poor; the authors are advised to illustrate the real impact of their findings without repetition of results. -Conclusion - Should be rephrased to be sounded. A real conclusion should focus on the question or claim you articulated in your study, whose resolution has been the main objective of your paper? Reviewer #2: - The current study has a significant impact, but it needs a major revision: - The manuscript should be revised for grammar mistakes. -The title is broad, please modify the title. -In the introduction: discuss the public health importance of the members of Enterobacteriaceae and other Gram negative bacterial pathogens. -Improve the aim of work. Methods: -Transfer Table 1 to the results. -Transfer the prevalence of bacterial species to the results section. -Discuss the isolation and identification of the bacterial pathogens. -Specific references should be added to all the used methods and techniques. -Where is the statistical analysis? -Results: - Discuss the prevalence of the retrieved isolates in a new table. - Transfer Table 1 to the results - Please increase the resolution of all figures (1200 dpi). -Where is the statistical analysis? -Discussion: -Very long; please improve ****** 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. https://doi.org/10.1371/journal.pone.0259005.r001
Revision 1
4 Sep 2021 Author Response Dear Dr. Abdelazeem Thank you for reviewing my manuscript. I appreciate your efforts and the efforts of the reviewers. I have worked hard to edit the revised manuscript and I hope I have done well I look forward to having my research accepted in PLOS ONE journal. Sayran H. Haji Author 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 I tried to be in accordance with the requirements of PLOS ONE style ------------------------------------------------------------------------------------ 2. In your Methods section, please provide additional information on the verbal consent provided by the patients, including as to how this verbal consent was documented or witnessed. I added regarding oral consent in the ethical issues section ------------------------------------------------------------------------------------ 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. My cover letter contains the DOI of the original, uncropped, unedited images of the blot /gel data published in a public data repository. https://data.mendeley.com/datasets/fhnkrf3jdr/1 ------------------------------------------------------------------------------------ 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. The minimal data set is available in public repository and include the relevant DOIs, within my revised cover letter. Dataset: https://data.mendeley.com/datasets/dp7g8rntyb/1 Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. I don’t have any ethical or legal restrictions We will update your Data Availability statement to reflect the information you provide in your cover letter. ------------------------------------------------------------------------------------ 5. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. I referenced all the Figures in my text to link the reader to the figure. ------------------------------------------------------------------------------------ 6. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1 in your text; if accepted, production will need this reference to link the reader to the Table. I referenced all the tables in my script to connect the reader to the figure. ------------------------------------------------------------------------------------ Reviewer #1: Comments to authors: - The current study is very interesting; however, the authors should address the following comments to improve the quality of the manuscript: - The manuscript should be revised for language editing and grammar mistakes by a native English speaker. I have checked for language editing and grammatical errors by native British speakers using online proofreading; Professional editing and proofreading services at your fingertips https://app.proofreadmyessay.co.uk/my-documents/ ------------------------------------------------------------------------------------ - Please write the genes name in correct form all over the manuscript (the 1st 3 letters must be small and italic and the other 3 letter are capital and subscripted) I corrected the name of the genes throughout the manuscript ------------------------------------------------------------------------------------ Title: I think the work would benefit from the title that contains main conclusion of the study (should be derived from the conclusion), please modify the title. I modified the title that contains main conclusion ------------------------------------------------------------------------------------ Abstract: - The abstract must illustrates the used methods and the most prevalent results (give more hints about methods and results). Besides, rephrase the main conclusion of your findings. More hints were given about the methods and results. Besides, I reformulated the main conclusion of the results. ------------------------------------------------------------------------------------ Introduction: -Give a hint about different infections caused by common pathogenic members of Enterobacteriaceae (such as E. coli and K. pneumonia) and Pseudomonas aeruginosa, their virulence factors, and the mechanism of disease occurrence. Hints were given about the common pathogenic members of Enterobacteriaceae in the introduction part ------------------------------------------------------------------------------------ - The introduction needs to be more informative: -The authors should illustrate the public heath importance concerning the emergence of multidrug-resistant (MDR) bacterial pathogens that reflecting the necessary of new potent and safe antimicrobial agents. Several studies proved the widespread MDR- bacterial pathogens; Authors could add the following paragraph: Multidrug resistance has been increased globally that is considered public health threat. Several recent studies reported the existence of multidrug-resistant bacterial pathogens from different origins including humans, poultry, cattle, and fish that increase the need for routine application of the antimicrobial susceptibility testing to detect the antibiotic of choice as well as screening of the emerging MDR strains. You should cite the following valuable studies: 1-PMID: 33177849 2-PMID: 32497922 3-PMID:33061472 4-PMID: 33947875 5-PMID: 32472209 6-PMID: 32994450 I have illustrated the public health importance of the emergence of multidrug-resistant (MDR) bacterial pathogens by adding your paragraph, and I really appreciate your help in providing these valuable studies, which I used as references. ------------------------------------------------------------------------------------ -Rephrase the aim of work to be clear and better sound. I paraphrased the aim of the work Material and methods -Table 1 must be placed in the results section. I have moved the table to the resulting part ------------------------------------------------------------------------------------ -It is not acceptable to illustrate the prevalence of the bacterial pathogens in the methods; it should be placed to the results section. I have moved the prevalence of bacterial pathogens to the results section. ------------------------------------------------------------------------------------ -Where are the methods of the isolation and identification of 200 Gram-negative bacteria?? You must illustrate in details and support your methods with specific references. The methods for isolating and identifying 200 Gram-negative bacteria have been explained with adding specific references. Furthermore, I added a new table to identify 200 Gram-negative bacteria. ----------------------------------------------------------------------------------- - Phenotype-based method for carbapenemases: should be modified to be: Phenotypedetection carbapenemases using Disc diffusion method. Rephrase this section; add more details, discuss in details and specific references. I have modified the phenotypic-based method for carbapenemes to the phenotype detection of carbapenemes using the disc diffusion method, and more details have been added to this section with references. ------------------------------------------------------------------------------------ - Confirmation of carbapenemase production using commercial combination disk assay; add specific references to this section. The phenotypic-based method has been combined with confirmation of carbapenemase production using commercial combination disk checked, because I think it was duplicated, and specific references were added ------------------------------------------------------------------------------------ -Molecular detection of genes should be modified: PCR-based detection of carbapenemase genes. Besides, add specific references. Molecular gene detection was changed to PCR-based detection of carbapenemase genes. Besides, specific references have been added. ------------------------------------------------------------------------------------ -Where are the statistical analyses? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Results: - Where are the results of phenotypic characters and the prevalence of the isolated bacterial pathogens from the examined samples? You must illustrate their prevalence in a new table. The results of the phenotypic characteristics and prevalence of bacterial pathogens isolated from the examined samples were added to a new table with a clear explanation of the correlation in the text. ------------------------------------------------------------------------------------ -Table 1 must be placed in the results section. Table 1 has been converted to Table 2 and moved to the result section. ----------------------------------------------------------------------------------- - Illustrate in a new table the test results of the phenotypic MDR (illustrate the antimicrobial classes of the used antimicrobial agents). I have developed a new table of MDR phenotypic test results identifying the antimicrobial classes of the antimicrobial agents used. ------------------------------------------------------------------------------------ -Illustrate the distribution of the carbapenemase genes among the recovered isolates in a new table. The distribution of carbapenemase genes among the recovered isolates is illustrated in a new table ------------------------------------------------------------------------------------ - Please increase the resolution of all figures (1200 dpi). I have increased the resolution. Hope it is clear now ------------------------------------------------------------------------------------ -Where are the statistical analyses? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Discussion: -The discussion is too long and poor; the authors are advised to illustrate the real impact of their findings without repetition of results. I've shortened the discussion and deleted all the duplicates as much as I can ------------------------------------------------------------------------------------ -Conclusion - Should be rephrased to be sounded. A real conclusion should focus on the question or claim you articulated in your study, whose resolution has been the main objective of your paper? The conclusion has been reformulated to be presented and includes the main resolution of my study. ------------------------------------------------------------------------------------ Reviewer #2: - The current study has a significant impact, but it needs a major revision: - The manuscript should be revised for grammar mistakes. I have checked for language editing and grammatical errors by native British speakers using online proofreading; Professional editing and proofreading services at your fingertips https://app.proofreadmyessay.co.uk/my-documents/ ------------------------------------------------------------------------------------ -The title is broad, please modify the title. I have modified and shortened the title ------------------------------------------------------------------------------------ -In the introduction: discuss the public health importance of the members of Enterobacteriaceae and other Gram-negative bacterial pathogens. The public health importance of the members of Enterobacteriaceae and other Gram-negative bacterial pathogens was discussed in the introduction part ------------------------------------------------------------------------------------ -Improve the aim of work. The purpose of the work has improved ------------------------------------------------------------------------------------ Methods: -Transfer Table 1 to the results. I have moved the table to the resulting part ------------------------------------------------------------------------------------ -Transfer the prevalence of bacterial species to the results section. I have moved the prevalence of bacterial pathogens to the results section. ------------------------------------------------------------------------------------ -Discuss the isolation and identification of the bacterial pathogens. The methods for isolating and identifying Gram-negative bacteria have been explained with adding specific references. Furthermore, I added a new table to identify 200 Gram-negative bacteria. ------------------------------------------------------------------------------------ -Specific references should be added to all the used methods and techniques. I added specific references to all the methods and techniques used ------------------------------------------------------------------------------------ -Where is the statistical analysis? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Results: - Discuss the prevalence of the retrieved isolates in a new table. The results of the prevalence of bacterial pathogens isolated from the examined samples were added to a new table with a clear explanation in the text. ------------------------------------------------------------------------------------ - Transfer Table 1 to the results Table 1 has been converted to Table 2 and moved to the result section. ------------------------------------------------------------------------------------ - Please increase the resolution of all figures (1200 dpi). I have increased the resolution. Hope it is clear now ----------------------------------------------------------------------------------- -Discussion: -Very long; please improve I've shortened and improved the discussion as much as I can________________________________________ Attachments Attachment Submitted filename: Response to Reviewers30.08.docx https://doi.org/10.1371/journal.pone.0259005.r002
7 Sep 2021 Decision Letter - Abdelazeem Mohamed Algammal, Editor PONE-D-21-22590R1Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilliPLOS ONE Dear Dr. haji, 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 submit your revised manuscript by Oct 22 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, Abdelazeem Mohamed Algammal, Prof, Ph.D Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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: (No Response) ******** 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 ****** 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 ****** 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: The authors have addressed some of my comments; however the have ignored a major comment concerning the introduction. Please address the following comment: The introduction needs to be more informative: -The authors should illustrate the public heath importance concerning the emergence of multidrug-resistant (MDR) bacterial pathogens that reflecting the necessary of new potent and safe antimicrobial agents. Several studies proved the widespread MDRbacterial pathogens; Authors could add the following paragraph: Multidrug resistance has been increased globally that is considered public health threat. Several recent studies reported the existence of multidrug-resistant bacterial pathogens from different origins including humans, poultry, cattle, and fish that increase the need for routine application of the antimicrobial susceptibility testing to detect the antibiotic of choice as well as screening of the emerging MDR strains. You should cite the following valuable studies: 1-PMID: 33177849 2-PMID: 32497922 3-PMID:33061472 4-PMID: 33947875 5-PMID: 32472209 6-PMID: 32994450 ****** 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: 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. https://doi.org/10.1371/journal.pone.0259005.r003
Revision 2
11 Sep 2021 Author Response 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 I tried to be in accordance with the requirements of PLOS ONE style ------------------------------------------------------------------------------------ 2. In your Methods section, please provide additional information on the verbal consent provided by the patients, including as to how this verbal consent was documented or witnessed. I added regarding oral consent in the ethical issues section ------------------------------------------------------------------------------------ 3. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels. In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions. My cover letter contains the DOI of the original, uncropped, unedited images of the blot /gel data published in a public data repository. https://data.mendeley.com/datasets/fhnkrf3jdr/1 ------------------------------------------------------------------------------------ 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. The minimal data set is available in public repository and include the relevant DOIs, within my revised cover letter. Dataset: https://data.mendeley.com/datasets/dp7g8rntyb/1 Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. I don’t have any ethical or legal restrictions We will update your Data Availability statement to reflect the information you provide in your cover letter. ------------------------------------------------------------------------------------ 5. Please ensure that you refer to Figure 1 in your text as, if accepted, production will need this reference to link the reader to the figure. I referenced all the Figures in my text to link the reader to the figure. ------------------------------------------------------------------------------------ 6. We note you have included a table to which you do not refer in the text of your manuscript. Please ensure that you refer to Table 1 in your text; if accepted, production will need this reference to link the reader to the Table. I referenced all the tables in my script to connect the reader to the figure. ------------------------------------------------------------------------------------ Reviewer #1: Comments to authors: - The current study is very interesting; however, the authors should address the following comments to improve the quality of the manuscript: - The manuscript should be revised for language editing and grammar mistakes by a native English speaker. I have checked for language editing and grammatical errors by native British speakers using online proofreading; Professional editing and proofreading services at your fingertips https://app.proofreadmyessay.co.uk/my-documents/ ------------------------------------------------------------------------------------ - Please write the genes name in correct form all over the manuscript (the 1st 3 letters must be small and italic and the other 3 letter are capital and subscripted) I corrected the name of the genes throughout the manuscript ------------------------------------------------------------------------------------ Title: I think the work would benefit from the title that contains main conclusion of the study (should be derived from the conclusion), please modify the title. I modified the title that contains main conclusion ------------------------------------------------------------------------------------ Abstract: - The abstract must illustrates the used methods and the most prevalent results (give more hints about methods and results). Besides, rephrase the main conclusion of your findings. More hints were given about the methods and results. Besides, I reformulated the main conclusion of the results. ------------------------------------------------------------------------------------ Introduction: -Give a hint about different infections caused by common pathogenic members of Enterobacteriaceae (such as E. coli and K. pneumonia) and Pseudomonas aeruginosa, their virulence factors, and the mechanism of disease occurrence. Hints were given about the common pathogenic members of Enterobacteriaceae in the introduction part ------------------------------------------------------------------------------------ - The introduction needs to be more informative: -The authors should illustrate the public heath importance concerning the emergence of multidrug-resistant (MDR) bacterial pathogens that reflecting the necessary of new potent and safe antimicrobial agents. Several studies proved the widespread MDR- bacterial pathogens; Authors could add the following paragraph: Multidrug resistance has been increased globally that is considered public health threat. Several recent studies reported the existence of multidrug-resistant bacterial pathogens from different origins including humans, poultry, cattle, and fish that increase the need for routine application of the antimicrobial susceptibility testing to detect the antibiotic of choice as well as screening of the emerging MDR strains. You should cite the following valuable studies: 1-PMID: 33177849 2-PMID: 32497922 3-PMID:33061472 4-PMID: 33947875 5-PMID: 32472209 6-PMID: 32994450 I have illustrated the public health importance of the emergence of multidrug-resistant (MDR) bacterial pathogens by adding your paragraph, and I really appreciate your help in providing these valuable studies, which I used as references. ------------------------------------------------------------------------------------ -Rephrase the aim of work to be clear and better sound. I paraphrased the aim of the work Material and methods -Table 1 must be placed in the results section. I have moved the table to the resulting part ------------------------------------------------------------------------------------ -It is not acceptable to illustrate the prevalence of the bacterial pathogens in the methods; it should be placed to the results section. I have moved the prevalence of bacterial pathogens to the results section. ------------------------------------------------------------------------------------ -Where are the methods of the isolation and identification of 200 Gram-negative bacteria?? You must illustrate in details and support your methods with specific references. The methods for isolating and identifying 200 Gram-negative bacteria have been explained with adding specific references. Furthermore, I added a new table to identify 200 Gram-negative bacteria. ----------------------------------------------------------------------------------- - Phenotype-based method for carbapenemases: should be modified to be: Phenotypedetection carbapenemases using Disc diffusion method. Rephrase this section; add more details, discuss in details and specific references. I have modified the phenotypic-based method for carbapenemes to the phenotype detection of carbapenemes using the disc diffusion method, and more details have been added to this section with references. ------------------------------------------------------------------------------------ - Confirmation of carbapenemase production using commercial combination disk assay; add specific references to this section. The phenotypic-based method has been combined with confirmation of carbapenemase production using commercial combination disk checked, because I think it was duplicated, and specific references were added ------------------------------------------------------------------------------------ -Molecular detection of genes should be modified: PCR-based detection of carbapenemase genes. Besides, add specific references. Molecular gene detection was changed to PCR-based detection of carbapenemase genes. Besides, specific references have been added. ------------------------------------------------------------------------------------ -Where are the statistical analyses? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Results: - Where are the results of phenotypic characters and the prevalence of the isolated bacterial pathogens from the examined samples? You must illustrate their prevalence in a new table. The results of the phenotypic characteristics and prevalence of bacterial pathogens isolated from the examined samples were added to a new table with a clear explanation of the correlation in the text. ------------------------------------------------------------------------------------ -Table 1 must be placed in the results section. Table 1 has been converted to Table 2 and moved to the result section. ----------------------------------------------------------------------------------- - Illustrate in a new table the test results of the phenotypic MDR (illustrate the antimicrobial classes of the used antimicrobial agents). I have developed a new table of MDR phenotypic test results identifying the antimicrobial classes of the antimicrobial agents used. ------------------------------------------------------------------------------------ -Illustrate the distribution of the carbapenemase genes among the recovered isolates in a new table. The distribution of carbapenemase genes among the recovered isolates is illustrated in a new table ------------------------------------------------------------------------------------ - Please increase the resolution of all figures (1200 dpi). I have increased the resolution. Hope it is clear now ------------------------------------------------------------------------------------ -Where are the statistical analyses? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Discussion: -The discussion is too long and poor; the authors are advised to illustrate the real impact of their findings without repetition of results. I've shortened the discussion and deleted all the duplicates as much as I can ------------------------------------------------------------------------------------ -Conclusion - Should be rephrased to be sounded. A real conclusion should focus on the question or claim you articulated in your study, whose resolution has been the main objective of your paper? The conclusion has been reformulated to be presented and includes the main resolution of my study. ------------------------------------------------------------------------------------ Reviewer #2: - The current study has a significant impact, but it needs a major revision: - The manuscript should be revised for grammar mistakes. I have checked for language editing and grammatical errors by native British speakers using online proofreading; Professional editing and proofreading services at your fingertips https://app.proofreadmyessay.co.uk/my-documents/ ------------------------------------------------------------------------------------ -The title is broad, please modify the title. I have modified and shortened the title ------------------------------------------------------------------------------------ -In the introduction: discuss the public health importance of the members of Enterobacteriaceae and other Gram-negative bacterial pathogens. The public health importance of the members of Enterobacteriaceae and other Gram-negative bacterial pathogens was discussed in the introduction part ------------------------------------------------------------------------------------ -Improve the aim of work. The purpose of the work has improved ------------------------------------------------------------------------------------ Methods: -Transfer Table 1 to the results. I have moved the table to the resulting part ------------------------------------------------------------------------------------ -Transfer the prevalence of bacterial species to the results section. I have moved the prevalence of bacterial pathogens to the results section. ------------------------------------------------------------------------------------ -Discuss the isolation and identification of the bacterial pathogens. The methods for isolating and identifying Gram-negative bacteria have been explained with adding specific references. Furthermore, I added a new table to identify 200 Gram-negative bacteria. ------------------------------------------------------------------------------------ -Specific references should be added to all the used methods and techniques. I added specific references to all the methods and techniques used ------------------------------------------------------------------------------------ -Where is the statistical analysis? Statistical analyzes for this study were designed using GraphPad Prism (version 5; GraphPad Software, San Diego, CA). The Chi-square test was applied to analyze the obtained data. ------------------------------------------------------------------------------------ -Results: - Discuss the prevalence of the retrieved isolates in a new table. The results of the prevalence of bacterial pathogens isolated from the examined samples were added to a new table with a clear explanation in the text. ------------------------------------------------------------------------------------ - Transfer Table 1 to the results Table 1 has been converted to Table 2 and moved to the result section. ------------------------------------------------------------------------------------ - Please increase the resolution of all figures (1200 dpi). I have increased the resolution. Hope it is clear now ----------------------------------------------------------------------------------- -Discussion: -Very long; please improve I've shortened and improved the discussion as much as I can Attachments Attachment Submitted filename: Response to Reviewers30.08.docx https://doi.org/10.1371/journal.pone.0259005.r004
29 Sep 2021 Decision Letter - Abdelazeem Mohamed Algammal, Editor PONE-D-21-22590R2Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilliPLOS ONE Dear Dr. haji, 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. ============================== ACADEMIC EDITOR: Please address all the reviewer comments, it is your last chance./>============================== Please submit your revised manuscript by Nov 13 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, Abdelazeem Mohamed Algammal, Prof, Ph.D Academic Editor PLOS ONE [Note: HTML markup is below. Please do not edit.] 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: (No Response) ******** 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 ****** 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 ****** 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: In the introduction section the authors reported several recent studies in the following paragraph, however they have cited only one reference.. How?? Please cite all references: Multidrug resistance has been increased globally that is considered public health threat. Several recent studies reported the existence of multidrug-resistant bacterial pathogens from different origins including humans, poultry, cattle, and fish that increase the need for routine application of the antimicrobial susceptibility testing to detect the antibiotic of choice as well as screening of the emerging MDR strains. You should cite the following valuable studies: 1-PMID: 33177849 2-PMID: 32497922 3-PMID:33061472 4-PMID: 33947875 5-PMID: 32472209 6-PMID: 32994450 Lines 438- 505; please add specific references. The following sentence is found instead of refrences; please revise and correct. Error! Reference source not found.. ****** 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: 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. https://doi.org/10.1371/journal.pone.0259005.r005
Revision 3
7 Oct 2021 Author Response Reviewer #1: In the introduction section the authors reported several recent studies in the following paragraph, however they have cited only one reference.. How?? Please cite all references: ________________________________________ With my appreciation, I have referred to all of the following valuable studies as references in the introduction, material methods, and results in the manuscript. 1-PMID: 33177849 reference number 30 2-PMID:33061472 reference number 3 3-PMID: 33947875 reference number 1 4-PMID: 32472209 reference number 22 5-PMID: 32994450 reference number 2 ________________________________________ Lines 438- 505; please add specific references. The following sentence is found instead of refrences; please revise and correct. Error! Reference source not found. ________________________________________ I have revised and corrected the error related to the reference source on lines 438-505. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0259005.r006
11 Oct 2021 Decision Letter - Abdelazeem Mohamed Algammal, Editor Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli PONE-D-21-22590R3 Dear Dr. haji, 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, Abdelazeem Mohamed Algammal, Prof, 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 ******** 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 ****** 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 ****** 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: The authors have carried out a significant changes to the manuscript. They have addressed all the suggested corrections and comments. Really, it's an interesting study that has a significant impact. Now, the manuscript could be accepted. Congratulations. ****** 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: No https://doi.org/10.1371/journal.pone.0259005.r007
Formally Accepted
21 Oct 2021 Acceptance Letter - Abdelazeem Mohamed Algammal, Editor PONE-D-21-22590R3 Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli Dear Dr. Haji: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Professor Abdelazeem Mohamed Algammal Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0259005.r008

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