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The manuscript is acceptable.
[# PeerJ Staff Note - this decision was reviewed and approved by Konstantinos Kormas, a PeerJ Section Editor covering this Section #]
Based on the reviewer comments, your manuscript needs minor revision.
Dear Authors
You are doing well
I hope for you all the success
Regard
Article content is within the Aims and Scope of the journal and article type.
The sources are adequately cited.
Conclusions are well stated, linked to the original research question & limited to supporting results.
Everything is ok
Nil
The Authors did not address all of my comments in their response file, except for the duplication of the text. However, I carefully reviewed the manuscript and found that some of the corrections I suggested have already been incorporated.
Please check the following sentence: “Species like K. pneumoniae and K. oxytoca are shown to cluster closely, suggesting a more recent common ancestry compared to more genetically distant species such as K. variicola and K. mitogenesis” (Lines 113-115). Fig. 1A indicates that K. pneumoniae and K. oxytoca are in the same cluster, while both K. variicola and K. michiganensis are in a separate cluster. Therefore, the sentence should be corrected as I suggested earlier.
Please review gene names throughout the text; they should be italicized.
No comment
No comment
Dear authors
Based on reviewer reports, your manuscript needs major revision. The Reviewers’ comments are all valuable, and some are very minor, and will help improve the article significantly. They should be addressed and your manuscript revised accordingly.
**PeerJ Staff Note:** It is PeerJ policy that additional references suggested during the peer-review process should only be included if the authors agree that they are relevant and useful.
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**Language Note:** The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Alternatively, you should make your own arrangements to improve the language quality and provide details in your response letter. – PeerJ Staff
The English language is excellent. The literature references and sufficient field background context were provided. The materials of the manuscript are within the scope of the journal. The text
The article content is within the Aims and Scope of the journal and article type. Also, a Rigorous investigation was performed to a high technical & ethical standard. The technical standard is high. Further, sufficient details and information are mentioned.
The conclusions and highlighting points are well described.
Dear Authors,
You are doing excellent work, and this manuscript reflects great effort and thoughtful research. The study is promising and contributes meaningfully to the field. However, there are a few important points that require further clarification and revision to enhance the overall quality and impact of the manuscript.
Line 34: Replace the phrase “golden era” and subjective tone with a more precise and formal opening. E.g., “The efficacy of antibiotics in modern medicine is increasingly compromised by the rise of antimicrobial resistance (AMR).”
Line 49: To enhance the introduction section, add the following reference: Al-Ouqaili, MTS, Al-Taei, SA, Al-Najja,r A. Molecular Detection of Medically Important Carbapenemases Genes Expressed by Metallo-β-lactamase Producer Isolates of Pseudomonas aeruginosa and Klebsiella pneumoniae. Asian Journal of Pharmaceutics • Jul -Sep 2018 (Suppl ) • 12 (3) | S991
Lines 34-49: Paragraphs 1 and 2 should be reorganized to more logically group together the global health impact, resistance mechanisms, and spread of K. pneumoniae. Consider separating background information (epidemiology, WHO classification) from mechanisms of resistance and virulence.
Line 49: Throughout the manuscript, ensure that Klebsiella pneumoniae (abbreviated as K. pneumoniae) is consistently written in italics, in accordance with scientific writing conventions for genus and species names.
Line 54: “The share of K. pneumoniae in the crisis of antibiotic resistance is incalculable” → Consider rephrasing to “K. pneumoniae plays a central role in the global antimicrobial resistance crisis.”
Line 60: To enhance the introduction section, add the following reference: Rawaa A. Hussein, Shaymaa H. AL-Kubaisy, Mushtak T.S. Al-Ouqaili. The influence of efflux pump, outer membrane permeability and β-lactamase production on the resistance profile of multidrug, extensively and pandrug-resistant Klebsiella pneumoniae. Journal of Infection and Public Health, Volume 17, Issue 11, 2024. https://doi.org/10.1016/j.jiph.2024.102544.
Line 67: Several sentences in this section are either grammatically incorrect or awkwardly phrased. Consider revising for clarity and flow. Example: “Understanding the mechanisms that render bacteria resistant to antibiotics is crucial and may play a key role in addressing this global challenge.”
Line 100: Species names such as Klebsiella pneumoniae, K. pneumoniae, K. oxytoca, etc., should be consistently italicised throughout the manuscript.
Lines 127-129: The distinction between Klebsiella pneumoniae sensu stricto and its phylogroups (Kp1–Kp7) needs clearer explanation for non-specialist readers.
Line 132: To enhance the Taxonomy section, add the following reference: Al-Ouqaili, MTS., Jal'oot, AS., Badawy, AS. Identification of an OprD and bla(IMP) Gene-mediated Carbapenem Resistance in Acinetobacter baumannii and Pseudomonas aeruginosa among Patients with Wound Infections in Iraq. Asian Journal of Pharmaceutics, volume 12, Issue 3, 2019 Page S959-S965.
Line 207: "For readability, consider organizing the virulence factors under subheadings such as: ‘Capsular Polysaccharide’, ‘Iron Acquisition Systems’, ‘Fimbrial Adhesins’, and ‘Outer Membrane Proteins’.”
Lines 208–210: "Please clearly distinguish between hypervirulent (hvKp) and classical (cKp) K. pneumoniae strains early in this section to guide readers unfamiliar with these terms."
Lines 210: To enhance the virulence factor section, add the following reference: Saki, M., Amin, M., Savari, M., Hashemzadeh, M., & Seyedian, S. S. (2022). Beta-lactamase determinants and molecular typing of carbapenem-resistant classic and hypervirulent Klebsiella pneumoniae clinical isolates from the southwest of Iran. Frontiers in microbiology, 13, 1029686. https://doi.org/10.3389/fmicb.2022.1029686
Lines 294–299: "The roles of genes like uge, wabG, ureA, etc., are listed but not always explained. Please briefly describe the pathogenic significance of each."
Line 313: To enhance the virulence factor section, add the following reference: Yalew, G. T., Muthupandian, S., Hagos, K., Negash, L., Venkatraman, G., Hagos, Y. M., Meles, H. N., Weldehaweriat, H. H., Al-Dahmoshi, H. O. M., & Saki, M. (2022). Prevalence of bacterial vaginosis and aerobic vaginitis and their associated risk factors among pregnant women from northern Ethiopia: A cross-sectional study. PloS one, 17(2), e0262692. https://doi.org/10.1371/journal.pone.0262692
Lines 548–549: "‘On the other hand, Immunotherapy is also considered as a rational alternative…’ could be revised for clarity and grammatical accuracy. For example: ‘Immunotherapy represents a promising alternative for managing MDR K. pneumoniae, by leveraging the host’s immune response rather than relying on antibiotics.’”
Lines 573–574: "Consider adding a clear transitional sentence to separate immunotherapy-based strategies from gene-editing tools like CRISPR-Cas, as the abrupt shift might confuse readers."
Line 576: To enhance the Prospectives section, add the following reference: Hekmat A. Owaid, Mushtak T.S. Al-Ouqaili, Molecular characterization and genome sequencing of selected highly resistant clinical isolates of Pseudomonas aeruginosa and its association with the clustered regularly interspaced palindromic repeat/Cas system, Heliyon, Volume 11, Issue 1, 2025, e41670, ISSN 2405-8440, https://doi.org/10.1016/j.heliyon.2025.e41670.
Line 580: "Define RNA-guided nucleases (RGNs) more clearly and explain their role in antimicrobial action with one illustrative example."
Line 584: Conclusion should be objective with further perspective, or should add at least a few sentences about future study/future perspective of it
Pathogenic Klebsiella pneumoniae poses a significant health threat worldwide. A comprehensive understanding of its mechanisms of multidrug resistance, virulence, and immune evasion is essential for developing new, effective strategies to combat K. pneumoniae infections. The literature review by Bilal Aslam and Sulaiman F Aljasir emphasizes these key aspects and falls within the scope of the PeerJ journal. The Introduction adequately introduces the subject and defines the goal of the review.
1. The English language needs improvement throughout the entire text.
2. One of my main concerns is the literature list. The most recent cited papers were published in 2022. I recommend expanding the list to include more recent articles, especially those that discuss high-risk K. pneumoniae clones or new therapies. Several excellent reviews on K. pneumoniae have been published over the past decade (some of which are cited by the authors). Therefore, to support the novelty of the manuscript, it is important to add more recent findings.
3. The authors mentioned in the Abstract (lines 19-22): “Multiple antibiotic-resistance genes and virulence genes across various Klebsiella species were studied to explore their evolutionary dynamics and genetic diversity.” However, the manuscript primarily contains information about AMR genes and virulence factors of K. pneumoniae. Therefore, this sentence should be revised, or the manuscript should include relevant data from other Klebsiella species.
In general, the manuscript is well-organized. However, the chapter on Virulence factors should be reorganized for clarity because some information is repeated, such as siderophores mentioned in lines 210, 235, and 291.
Moreover, the section on genome organization (Lines 177-206) should be revised entirely. The text is very similar to excerpts from the review paper by Wyres and Holt (2018). See the attached PDF file.
The Perspectives and Conclusions sections emphasize unresolved questions and future directions. To improve these chapters, a review of more recent literature is recommended, as mentioned earlier.
1. The numbering of figures differs between the text and the figure captions. Figure 2 is referred to in the text as Figure 1B, etc.
Figure 1 seems incomplete. The listed species should be assigned to specific branches. On which sequences (whole genome sequences, 16S rRNA) was the phylogenetic construction based? It should also be specified what software was used to generate a graphical map of the genome (Figure 2, or Figure 1B in the text).
2. Please correct the species names and gene names - they should be written in italics.
3.Line 112-114, Please correct this sentence as follows: Species like K. pneumoniae and K. variicola are shown to cluster closely, suggesting a more recent common ancestry compared to more genetically distant species such as K.oxytoca and K. michiganensis".
4. Lines 114-116 “This clustering indicates not only the evolutionary pathways of these bacteria but also their adaptation strategies to different environments or hosts (Fig 1A).” Could you please explain this issue in more detail (natural environments vs clinical settings).
5. Line 419 The sentence mentions plasmids harboring the blaNDM-5 gene and refers to Figure 2. However, Figure 2 shows the genomic organization of K. pneumoniae.
The article reviews the antibiotic-resistance and virulence genes across various Klebsiella species, emergence of resistant variants K. pneumoniae and describes the characteristics features of K. pneumoniae.
This review article falls short of extensive analysis of the recent developments and advancement in the relevant field. Much of the discussion is confined to their earlier publications.
The figures in the article are inappropriate and poorly designed. They are not acknowledged and explained clearly.
Novelty is not clear and much of the details are widely available information. Conclusions drawn are not linked to research objectives and supporting results are not provided.
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