Proteus mirabilis

Dear Dr. Yusuf,

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Overall assessment

This manuscript addresses an important and underrepresented topic: the phenotypic and genomic epidemiology of multidrug-resistant Proteus mirabilis in a military referral hospital in Ethiopia. The study is timely and potentially valuable because genomic data on P. mirabilis from sub-Saharan Africa remain limited, and the authors combine antimicrobial susceptibility testing, ESBL/carbapenemase phenotyping, whole-genome sequencing, MLST, resistance gene detection, plasmid replicon analysis, virulence profiling, and phylogenomics. The manuscript reports a very high MDR burden among 99 clinical isolates, with 25 selected isolates undergoing WGS, and identifies ESBL determinants including blaPER-13, blaVEB-6, and blaCTX-M-65, as well as multiple non-β-lactam resistance genes and plasmid replicons .

However, several substantial issues need to be addressed before the manuscript can be considered suitable for publication in PLOS ONE. The main concerns relate to the representativeness of the sequenced subset, insufficient methodological detail, overinterpretation of genomic epidemiology and plasmid-mediated transmission, incomplete reporting of sequencing quality metrics, unclear genotype–phenotype concordance analysis, limited statistical treatment, and figure quality. The study has merit, but the current version requires major revision to strengthen reproducibility, interpretation, and presentation.

Major comments

1. The study includes 99 non-duplicate P. mirabilis isolates, but only 25 were sequenced. The authors state that these were “representative ESBL- and/or carbapenemase-producing isolates” chosen to represent specimen types and hospital wards within sequencing capacity. This selection is understandable, but it introduces enrichment bias because the sequenced subset is not a random or complete representation of the full isolate collection.

The manuscript should clearly present how the 25 isolates compare with the full 99-isolate collection in terms of specimen type, ward, ESBL status, carbapenemase status, resistance profile, age group, and patient category. A table comparing the sequenced and non-sequenced isolates would greatly improve transparency.

The authors should also revise language suggesting that genomic findings reflect the entire hospital population. Statements such as “endemic hospital circulation,” “plasmid-mediated dissemination,” and “horizontal dissemination across hospital units” should be presented more cautiously unless supported by denser sampling, temporal clustering, SNP distance thresholds, plasmid reconstruction, or epidemiological linkage data.

2. The methods mention FastQC, fastp, Shovill/SKESA, QUAST, BUSCO, AMRFinderPlus, MLST, Snippy, IQ-TREE, and ABRicate. However, the manuscript does not provide isolate-level sequencing quality metrics. For reproducibility and confidence in downstream analyses, the authors should include a supplementary table with, at minimum:

coverage depth, total reads, genome size, number of contigs, N50, GC content, BUSCO completeness, contamination/species confirmation result if available, and assembly accession or SRA run ID per isolate.

This is especially important because the authors discuss genotype–phenotype discordance and suggest that short-read assembly limitations may explain missing ESBL genes. Without assembly quality metrics, it is difficult to judge whether gene absence is biological or technical.

3. The AST section is too brief. The authors should specify the full antibiotic panel, disk potencies, interpretive criteria, quality control strains, incubation conditions, and whether intermediate isolates were consistently grouped with resistant isolates as “non-susceptible.” The tables state that percentages represent intermediate plus resistant isolates, but the methods should explicitly define this approach.

For Proteus mirabilis, the authors should also ensure that all antibiotics interpreted are appropriate for the species and clinical context. If intrinsic resistance was considered or excluded for any drug classes, this should be stated.

4. The manuscript states that ESBL detection was performed using the double-disk synergy test and carbapenemase production using mCIM. More detail is needed. For ESBL testing, the authors should specify which disks were used, distances between disks, the positive interpretation criteria, and QC strains. For carbapenemase testing, the authors should specify whether eCIM was performed. If eCIM was not done, the authors should avoid implying definitive carbapenemase class or mechanism.

The finding that 6 isolates were mCIM-positive but the genomic results do not clearly report carbapenemase genes needs further explanation. Were carbapenemase genes detected by AMRFinderPlus? If not, this discrepancy should be explicitly presented and discussed, including possible mechanisms such as porin alteration, ESBL/AmpC plus permeability changes, or limitations of gene detection.

5. The section on ESBL genotype–phenotype concordance is promising but incomplete. The authors report that among 20 phenotypically ESBL-positive sequenced isolates, 17 carried ESBL genes, and that five isolates carried ESBL genes but were phenotypically ESBL-negative. This should be presented as a 2 × 2 table with sensitivity, specificity, positive predictive value, negative predictive value, and overall agreement, with confidence intervals if possible.

The statement that there was “high concordance (85.0%)” is somewhat misleading because it only refers to ESBL-positive phenotypic isolates and does not account for the five genotype-positive/phenotype-negative isolates. The authors should calculate concordance across all 25 sequenced isolates and interpret discordance carefully.

6. The authors conclude that the data support endemic hospital circulation with partial clonal expansion and plasmid-mediated dissemination. However, the manuscript does not provide pairwise SNP distances, temporal distribution, ward admission overlap, patient movement data, or clear cluster definitions. The phylogeny alone, especially from 25 selected isolates, is insufficient to support strong transmission claims.

The authors should provide pairwise SNP distances within and between major ST clusters, define what constitutes a cluster, and include sampling dates if available. If such data are unavailable, the wording should be softened to indicate that the observed clustering is “consistent with” possible lineage expansion, rather than evidence of transmission.

7. The manuscript identifies IncQ1 and Col-type plasmid replicons and suggests plasmid-mediated dissemination. However, short-read replicon detection does not prove that ESBL genes are plasmid-located or transferred on those plasmids. The authors should avoid implying direct plasmid carriage of specific genes unless they provide contig-level co-localization, plasmid reconstruction, MOB-suite analysis, long-read sequencing, or conjugation evidence.

At minimum, the authors should report whether ESBL genes and replicon markers occurred on the same contigs or assembled plasmid bins. If not assessed, this should be stated as a limitation and the interpretation revised.

8. The manuscript uses Fisher’s exact or chi-square tests but does not always specify which test was used for each comparison. Given the small number of carbapenemase-positive isolates, Fisher’s exact test is appropriate. The authors should also consider multiple testing correction or clearly state that analyses are exploratory.

P-values alone are not enough. The authors should include effect sizes, such as odds ratios with confidence intervals, particularly for comparisons between ESBL-positive and ESBL-negative isolates and carbapenemase-positive and carbapenemase-negative isolates.

9. The current figures are difficult to read. Figure 2 and Figure 3 have small labels, crowded legends, and limited interpretability. The figure files embedded at the end of the manuscript appear cropped or low-resolution in places. For PLOS ONE, figures should be clear, self-contained, and readable without excessive zooming.

Figure 2 should be redesigned with larger labels, clearer legends, explicit annotation tracks, and a more informative caption explaining what each color track represents. Figure 3 should use a cleaner heatmap format with readable gene names and isolate labels. Figure 1 should also be improved, as the current plot contains limited information and could be replaced or supplemented by a clearer bar chart showing the distribution of resistance classes.

10. Several references appear problematic or mismatched. For example, some references cited for P. mirabilis virulence or resistance appear to concern other organisms or broader topics. The authors should carefully audit all references to ensure each citation supports the statement made. There are also formatting issues, including inconsistent spacing, duplicated Murray references, missing spaces before citations, and gene names not consistently formatted.

In addition, the manuscript contains several 2025 and 2026 references. The authors should confirm that all cited works are published, accessible, and correctly formatted with complete bibliographic details.

Minor comments

1. The abstract should clarify that WGS was performed only on a selected subset of 25 ESBL- and/or carbapenemase-associated isolates, not all 99 isolates.

2. The phrase “multidrug-resistance” should be corrected to “multidrug resistance” or “multidrug-resistant.”

3. Gene names should be consistently italicized where appropriate, and β-lactamase gene formatting should be standardized throughout.

4. The term “CRE+” in Table 3 should be reconsidered. Since the organism is Proteus mirabilis, and the phenotype refers to carbapenemase production, “carbapenemase-positive” or “mCIM-positive” may be clearer than “CRE+.”

5. The limitations section is useful but should be expanded to include the non-random WGS subset, lack of long-read sequencing, lack of plasmid-gene co-localization, lack of eCIM or carbapenemase gene confirmation, and limited epidemiological metadata.

Reviewer #2: The novelty of this study lies in its integrated genomic and phenotypic characterization of multidrug-resistant Proteus mirabilis isolates obtained from a military hospital environment, with particular emphasis on the diversity of ESBL determinants, plasmid-mediated dissemination, and population structure. Although antimicrobial resistance in P. mirabilis has been widely reported, comprehensive whole-genome epidemiological analyses from military healthcare settings remain limited.

The bioinformatic component appears to be the strongest aspect of the study; however, in my opinion, the overall novelty of the research is currently insufficient for publication in its present form. The study focuses primarily on a single area of investigation, which limits the broader scientific impact of the findings. Overall, the manuscript presents data mainly in an epidemiological context and offers limited scientific novelty.

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Reviewer #1: No

Reviewer #2: No

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Dear Dr. Yusuf,

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 Aug 22 2026 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.

• A 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.

As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only  the individual author can complete the verification step; PLOS staff cannot  verify ORCID iDs on behalf of authors.

We look forward to receiving your revised manuscript.

Kind regards,

Zhi Ruan, Ph.D.

Academic Editor

PLOS One

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: (No Response)

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2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #1: Yes

**********

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

Reviewer #1: N/A

**********

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

The PLOS Data policy

Reviewer #1: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

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Reviewer #1: The revised manuscript is substantially improved, and the authors have addressed several previous concerns. In particular, the manuscript now clarifies that whole-genome sequencing was performed on a selected subset of 25 isolates rather than all 99 isolates, expands the ESBL and carbapenemase phenotyping methods, adds some assembly-quality metrics, revises some transmission and plasmid-dissemination language, and expands the limitations section. These revisions strengthen the manuscript.

However, several important issues remain only partially addressed, and I recommend a further focused minor revision before acceptance.

First, the manuscript still does not provide a clear comparison between the 25 sequenced isolates and the full 99-isolate collection. Because the WGS subset was purposively selected and enriched for ESBL- and/or carbapenemase-associated phenotypes, the authors should add a supplementary table comparing the sequenced subset with the full collection by specimen type, ward/source, ESBL status, carbapenemase status, MDR profile, and key phenotypic resistance patterns.

Second, the sequencing-quality information remains incomplete. The added assembly metrics are useful, but Supplementary Table S2 should also include total reads, coverage depth, isolate-level SRA run IDs or assembly accessions, and species confirmation/contamination assessment if available. These details are important because the manuscript discusses genotype–phenotype discordance, and readers need enough information to assess whether gene absence may be biological or technical.

Third, the ESBL genotype–phenotype concordance analysis has not been adequately addressed. The previous review requested a 2 × 2 table with sensitivity, specificity, positive predictive value, negative predictive value, and overall agreement. The revised manuscript provides a narrative description but does not provide this table. Based on the numbers reported, 20 sequenced isolates were phenotypically ESBL-positive, 17 of these carried ESBL-associated genes, and five phenotypically ESBL-negative isolates carried ESBL-associated genes. Therefore, the overall agreement appears to be 17/25, or 68%, and should not be described as high or substantial without qualification. This analysis should be clearly presented and interpreted cautiously.

Fourth, carbapenemase genotype–phenotype interpretation remains underdeveloped. The authors clarified that mCIM was performed and that eCIM was not used, which is helpful. However, the manuscript should clearly state whether carbapenemase genes were detected among the six mCIM-positive isolates. If no carbapenemase genes were detected, this should be explicitly discussed as phenotype–genotype discordance. If genes were detected, they should be reported isolate by isolate.

Fifth, the antimicrobial susceptibility testing methods still require more complete reproducibility details. The Methods should list the full antibiotic panel, disk potencies, interpretive criteria, and whether any antibiotics were excluded or interpreted cautiously because of intrinsic resistance or species-specific considerations for Proteus mirabilis.

Sixth, some interpretation of phylogeny and hospital circulation remains too strong. Without pairwise SNP distances, sampling dates, patient movement data, ward overlap, or defined genomic clusters, the authors should avoid wording that suggests proven endemic circulation or transmission. Wording such as “is consistent with possible circulation” or “suggests possible lineage expansion” would be more appropriate.

Seventh, plasmid interpretation should remain limited to replicon detection. The authors correctly acknowledge that short-read data cannot confirm plasmid structure or gene–plasmid co-localization. Any remaining wording implying plasmid-mediated dissemination of specific ESBL genes should be removed unless supported by contig-level co-localization, plasmid reconstruction, MOB-suite analysis, long-read sequencing, or conjugation data.

Eighth, the statistical analysis remains limited. The authors now state that Fisher’s exact test was used and that comparisons involving carbapenemase-positive isolates are exploratory, which is appropriate. However, p-values from very small groups should not be overemphasized. Where feasible, odds ratios with confidence intervals should be added for the main comparisons, or the authors should explicitly state that effect-size estimates were not reported because of instability due to sparse cells.

Ninth, the figures remain a concern. Although the authors state that the figures were improved, the submitted versions still appear cropped or difficult to read, especially the phylogeny and virulence heatmap. Figure 2 should be regenerated with readable isolate labels, clear metadata tracks, larger legends, and a caption explaining all colour annotations. Figure 3 should be presented as a clean heatmap with legible gene names and isolate labels. Final figure files should be checked at publication size.

Tenth, the references and formatting still need careful checking. Some citations appear mismatched to the statements they support. For example, a statement on P. mirabilis flagellar systems and virulence appears to cite a reference concerning E. coli CTX-M-27 plasmids, which does not support that claim. The authors should re-audit all references, especially those cited for P. mirabilis virulence, plasmids, ESBL epidemiology, and recent 2025/2026 claims.

Finally, the manuscript requires a careful final language and formatting edit. There are still missing spaces, inconsistent section numbering, and awkward phrases such as “extensive multidrug-resistant associated.” The plasmid section numbering also appears inconsistent. These issues should be corrected before acceptance.

The manuscript contains valuable data and is potentially suitable for publication after a focused minor revision. The remaining issues do not require major new experiments, but they do require clearer reporting, improved figures, more cautious interpretation, completion of requested supplementary information, and correction of residual citation and formatting problems.

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Reviewer #1: No

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Genomic Epidemiology of Multidrug-Resistant and ESBL-Producing Proteus mirabilis in a Military Referral Hospital in Ethiopia

PONE-D-26-15733R2

Dear Dr. Yusuf,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Zhi Ruan, Ph.D.

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments: