Prevalence of fungal infections in a patient cohort in The Gambia: Identification and characterization of three priority fungal species in patients with symptoms suggestive of TB

Zackary Salem-Bango; Mary Basiru Njai; Zainab Tambajang; Tessa Rose Cornell; Jayne Sutherland; Karen Forrest; Omai Garner; Behzad Nadjm; Saffiatou Darboe; Basil Sambou; Sheikh Jarju

doi:10.1371/journal.pone.0347766

Peer Review History

Original SubmissionDecember 4, 2025
11 Mar 2026 Decision Letter - Rajeev Singh, Editor -->PONE-D-25-64712-->-->Prevalence of fungal infections in a patient cohort in The Gambia: Identification and characterization of three priority fungal species in patients with symptoms suggestive of TB-->-->PLOS One Dear Dr. Salem-Bango, 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 Apr 25 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.. 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If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.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? 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Is there more information available on sociodemographic data? such as comorbidities, presence or not of cavitation in the chest xRay, socioeconomic data, housing conditions? What do you mean by TB status? Was TB confirmed for all samples? Were there ambulatory patients? hospitalized? The discussion could be extended on the public health implications of the multiplex PCR. With these results, what would be the application of this tool? and how should it be used, in which group could it be applied for a better target of population at risk? Authors state that low coinfection rate in may have been due to the small size of our study. However it seems that the samples tested might have had a low pre-test probability for fungal infections- What is the info/literature available on who to test? Reviewer #2: It is a good study. Would have been great to include a large sample size. What will be the cost of this multiplex assay in low-resource setting? . ****** -->6. 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Revision 1
30 Mar 2026 Author Response Dear Dr. Singh and Reviewers, We sincerely thank you for your thoughtful evaluation of our manuscript entitled “Prevalence of fungal infections in a patient cohort in The Gambia: Identification and characterization of three priority fungal species in patients with symptoms suggestive of TB” and for the constructive comments provided. We appreciate the opportunity to revise our work and have carefully addressed each point raised. Below, we provide a detailed, point-by-point response to the reviewers’ comments and indicate where changes have been made in the revised manuscript. ________________________________________ Reviewer #1 We thank the reviewer for the positive assessment of our manuscript and for the helpful suggestions to strengthen the work. Comment 1: “Is there more information available on sociodemographic data? such as comorbidities, presence or not of cavitation in the chest xRay, socioeconomic data, housing conditions?” Response: We agree that additional sociodemographic and clinical data would enhance the interpretation of our findings. Unfortunately, detailed socioeconomic, clinical and housing data were not systematically collected as part of the parent data sets that our samples derived from—so we were not able to include this in our analysis and demographics figures. ________________________________________ Comment 2: “What do you mean by TB status? Was TB confirmed for all samples? Were there ambulatory patients? hospitalized?” Response: We appreciate this request for clarification. We have revised the manuscript to clearly define “TB status” as sputum positivity via GeneXpert (Page 4, Lines 124-125). We have also clarified that patients were recruited from a mix of ambulatory and inpatient settings, though the data set we utilized did not specify which category each patient fell into (Page 8, Lines 236-238). ________________________________________ Comment 3: The discussion could be extended on the public health implications of the multiplex PCR. With these results, what would be the application of this tool? and how should it be used, in which group could it be applied for a better target of population at risk? Authors state that low coinfection rate in may have been due to the small size of our study. However it seems that the samples tested might have had a low pre-test probability for fungal infections- What is the info/literature available on who to test? Response: Thank you for this important suggestion. We believe that this has been partially addressed in (Page 3, Lines 69-74). We have included additional discussion on (Page 9, Lines 293-294). Regarding which group this test could be utilized in, we have included an additional statement in (Page 10, Lines 336-338). We based our sample size off of several previous works: For Aspergillus sp., Lakoh et al demonstrated that 11.6% of patients presenting with respiratory symptoms had pulmonary aspergillosis in Sierra Leone. Granted, the HIV positivity rate in their sample population was ~50% which likely impacted the aspergillosis rate in comparison to our data set. This is discussed in (Page 10, Lines 303-305). For Histoplasma sp., Cornell et al had demonstrated a high seroprevalence in The Gambia (~30%). In Nigeria, Ekeng et al had demonstrated that in patients with a presumptive TB diagnosis, ~13% tested positive for pulmonary histoplasmosis. 35% of their patients were HIV positive. This is discussed in (Page 9, Lines 300-301). For Pneumocystis jirovecci, Wills et al showed a >20% prevalence of PJP pneumonia in patients with HIV in this region. This is discussed in (Page 9, Lines 298-299). Unfortunately, due to this being a secondary study utilizing samples derived from parent works, we were not able to include as many samples from HIV positive individuals as we had originally hoped. We agree that testing patients with HIV, as well as TB like symptoms, would’ve likely led to higher positive results. We discuss this in (Page 10, Lines 330-331). ________________________________________ Reviewer #2 We thank the reviewer for their positive feedback and constructive suggestions. Comment 1: “Would have been great to include a large sample size.” Response: We agree that a larger sample size would strengthen the study. We discussed this in our “Limitations” section. Future work will reflect clinical implementation of this assay and we hope that data derived from this will allow for consideration of a larger group of patients. ________________________________________ Comment 2: “What will be the cost of this multiplex assay in low-resource setting?” Response: Thank you for highlighting this important aspect. We have included an approximate cost of $6.00 USD per sample in (Page 9, Lines 291-292) ________________________________________ Additional Revisions and Journal Requirements • We have updated the Data Availability Statement to include the required third-party contact details. • We have added the Role of the Funder statement to our cover letter “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” • We have carefully reviewed and updated the reference list for completeness and accuracy. • We have ensured that the manuscript complies with PLOS ONE formatting guidelines. • We have completed and included the Inclusivity in Global Research questionnaire as Supporting Information. • All changes in the manuscript are highlighted in the tracked changes version. ________________________________________ We believe that these revisions have significantly strengthened the manuscript and addressed all reviewer concerns. We are grateful for the reviewers’ insightful comments and the opportunity to improve our work. Sincerely, Dr. Zackary Salem-Bango and co-authors Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0347766.r002
7 Apr 2026 Decision Letter - Rajeev Singh, Editor Prevalence of fungal infections in a patient cohort in The Gambia: Identification and characterization of three priority fungal species in patients with symptoms suggestive of TB PONE-D-25-64712R1 Dear Dr. Salem-Bango, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support.... 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, Rajeev Singh Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0347766.r003
Formally Accepted
Acceptance Letter - Rajeev Singh, Editor PONE-D-25-64712R1 PLOS One Dear Dr. Salem-Bango, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@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 Dr. Rajeev Singh Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0347766.r004

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