PNTD-D-25-01911

The typhoid Mary legacy: genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales

PLOS Neglected Tropical Diseases

Dear Dr., Chattaway,

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Kind regards,

Sanjai Kumar

Guest Editor

PLOS Neglected Tropical Diseases

Stuart Blacksell

Section Editor

PLOS Neglected Tropical Diseases

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-4304-636XX

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-1765-0002

Additional Editor Comments:

Please address the following comments and submit a revised manuscript for review.

Reviewer 1:

This manuscript titled “The typhoid Mary legacy: genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales” by Nisbet et al., represents significant scientific merit with important public health implications. Exceptional 20-year surveillance dataset (2004-2023) with 8,297 cases. Authors presented novel findings about carriage dynamics make substantial contributions to the field.

There are some comments to improve the manuscript:

1. Provide better justification for the 3-week threshold and discuss limitations

2. Authors needs to address methodological limitations around carriage definition and potential surveillance biases

3. Include more discussion of immunological factors that might explain age-related carriage patterns

4. Fig 1 showed data for 2006-2023. Is there any reason 2004-2005 data were excluded?

5. Please check typographical errors, like in Line 505: "Welsh"(less...)

Reviewer 3:

This manuscript examines enteric fever surveillance data from England and Wales spanning 2004-2023, with a focus on understanding bacterial carriage dynamics of typhoidal Salmonella (S. Typhi and S. Paratyphi A/B). The study analyzed 8,297 cases and identified that approximately 2.7% of infections progressed to carriage (persistence >3 weeks), with only 0.1% becoming chronic carriers (>12 months). Key findings revealed that carriage risk was significantly elevated in elderly patients (ages 81-90) and those without recent foreign travel, while patients aged 21-30 and those infected with S. Paratyphi A had reduced carriage odds. Importantly, phylogenomic analysis found no distinct genetic signatures associated with carriage isolates, suggesting that host immune factors rather than bacterial genotype play a more critical role in determining whether infections persist long-term.

The manuscript is organized and written well, with no need for extensive language edits.

The study acknowledges substantial missing data across multiple variables (referenced in S1 Table), which required multiple imputation for statistical analysis. While I believe the authors used appropriate statistical methods to address this, missing data can still introduce bias and reduce the analytical power of the study overall.(less...)

Figure 3:

The 28-day travel window prior to disease onset may not capture all travel-associated cases, as the authors note that extending this to 60 days previously identified an additional 12% of cases as travel-related. This could affect the accuracy of travel versus non-travel associations with carriage.

What was the rationale for limiting the travel window to 28 days?

Figure 5:

Despite concluding that host immune factors likely play a greater role than bacterial genotype in carriage, the study lacks direct examination of patient immune status, comorbidities, or other host characteristics beyond age. The hypothesis about immune function is inferred rather than directly tested.

Are any data available that can be included (such as comorbidities, general immune status) to begin to infer additional host factors, other than age?(less...)

Figure 7:

Only 46% of S. Typhi cases, 36% of S. Paratyphi A cases, and 55% of S. Paratyphi B cases had publicly available high-quality genomes for phylogenetic analysis. This incomplete coverage could potentially miss important genetic patterns that may be associated with trends in carriage among the cases studied.

Are further studies planned to analyze these data as more genomes become publicly available? I believe this future re-analysis, combined with any additional subject data (underlying health conditions, etc. as mentioned above) will provide interesting additional data regarding carriage trends.(less...)

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Reviewers' comments:

Reviewer's Responses to Questions

Key Review Criteria Required for Acceptance?

As you describe the new analyses required for acceptance, please consider the following:

Methods

-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?

-Is the study design appropriate to address the stated objectives?

-Is the population clearly described and appropriate for the hypothesis being tested?

-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?

-Were correct statistical analysis used to support conclusions?

-Are there concerns about ethical or regulatory requirements being met?

Reviewer #1: -Yes

-Yes

-Yes

-Yes

-Yes

-No

Reviewer #2: (No Response)

Reviewer #3: Figure 7:

Only 46% of S. Typhi cases, 36% of S. Paratyphi A cases, and 55% of S. Paratyphi B cases had publicly available high-quality genomes for phylogenetic analysis. This incomplete coverage could potentially miss important genetic patterns that may be associated with trends in carriage among the cases studied.

Are further studies planned to analyze these data as more genomes become publicly available? I believe this future re-analysis, combined with any additional subject data (underlying health conditions, etc. as mentioned above) will provide interesting additional data regarding carriage trends.

**********

Results

-Does the analysis presented match the analysis plan?

-Are the results clearly and completely presented?

-Are the figures (Tables, Images) of sufficient quality for clarity?

Reviewer #1: -Yes

-Yes

-Yes

Reviewer #2: (No Response)

Reviewer #3: Figure 3:

The 28-day travel window prior to disease onset may not capture all travel-associated cases, as the authors note that extending this to 60 days previously identified an additional 12% of cases as travel-related. This could affect the accuracy of travel versus non-travel associations with carriage.

What was the rationale for limiting the travel window to 28 days?

Figure 5:

Despite concluding that host immune factors likely play a greater role than bacterial genotype in carriage, the study lacks direct examination of patient immune status, comorbidities, or other host characteristics beyond age. The hypothesis about immune function is inferred rather than directly tested.

Are any data available that can be included (such as comorbidities, general immune status) to begin to infer additional host factors, other than age?

**********

Conclusions

-Are the conclusions supported by the data presented?

-Are the limitations of analysis clearly described?

-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?

-Is public health relevance addressed?

Reviewer #1: -Yes

-No

-Yes

-Yes

Reviewer #2: (No Response)

Reviewer #3: While there are clear limitations to this study, as mentioned above, this analysis spanning 20 years of data in England and Wales captures a robust set of data examining long term trends, seasonal changes and the overall temporal stability of this disease (with post-pandemic incidence increase noted). Overall, this study highlights a few key public health findings, relating to socioeconomic impacts on the spread of this disease, as well as the higher disease burden in more deprived communities – informing where more intervention through vaccination may be needed. Importantly, the authors openly discuss the challenges and limitations of the data and do not overextend their conclusions.

**********

Editorial and Data Presentation Modifications?

Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.

Reviewer #1: (No Response)

Reviewer #2: (No Response)

Reviewer #3: Accept

**********

Summary and General Comments

Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.

Reviewer #1: This manuscript titled “The typhoid Mary legacy: genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales” by Nisbet et al., represents significant scientific merit with important public health implications. Exceptional 20-year surveillance dataset (2004-2023) with 8,297 cases. Authors presented novel findings about carriage dynamics make substantial contributions to the field.

There are some comments to improve the manuscript:

1. Provide better justification for the 3-week threshold and discuss limitations

2. Authors needs to address methodological limitations around carriage definition and potential surveillance biases

3. Include more discussion of immunological factors that might explain age-related carriage patterns

4. Fig 1 showed data for 2006-2023. Is there any reason 2004-2005 data were excluded?

5. Please check typographical errors, like in Line 505: "Welsh"

Reviewer #2: (No Response)

Reviewer #3: This manuscript examines enteric fever surveillance data from England and Wales spanning 2004-2023, with a focus on understanding bacterial carriage dynamics of typhoidal Salmonella (S. Typhi and S. Paratyphi A/B). The study analyzed 8,297 cases and identified that approximately 2.7% of infections progressed to carriage (persistence >3 weeks), with only 0.1% becoming chronic carriers (>12 months). Key findings revealed that carriage risk was significantly elevated in elderly patients (ages 81-90) and those without recent foreign travel, while patients aged 21-30 and those infected with S. Paratyphi A had reduced carriage odds. Importantly, phylogenomic analysis found no distinct genetic signatures associated with carriage isolates, suggesting that host immune factors rather than bacterial genotype play a more critical role in determining whether infections persist long-term.

The manuscript is organized and written well, with no need for extensive language edits.

The study acknowledges substantial missing data across multiple variables (referenced in S1 Table), which required multiple imputation for statistical analysis. While I believe the authors used appropriate statistical methods to address this, missing data can still introduce bias and reduce the analytical power of the study overall.

**********

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Reviewer #1: No

Reviewer #2: Yes: ANKIT PURIANKIT PURI

Reviewer #3: No

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Attachments

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Submitted filename: PLos one typoid Mary review.docx

Attachment

Submitted filename: PNTD-D-25-01911 manuscript review 02.10.2026.docx

Dear Dr. Chattaway,

We are pleased to inform you that your manuscript 'The typhoid Mary legacy: genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales' has been provisionally accepted for publication in PLOS Neglected Tropical Diseases.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

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Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Neglected Tropical Diseases.

Best regards,

Sanjai Kumar

Guest Editor

PLOS Neglected Tropical Diseases

Stuart Blacksell

Section Editor

PLOS Neglected Tropical Diseases

Shaden Kamhawi

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-4304-636XX

Paul Brindley

co-Editor-in-Chief

PLOS Neglected Tropical Diseases

orcid.org/0000-0003-1765-0002

***********************************************************

None.