Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry

Victor Chaumeau; Martine Piarroux; Thithiworada Kulabkeeree; Sunisa Sawasdichai; Aritsara Inta; Wanitda Watthanaworawit; François Nosten; Renaud Piarroux; Cécile Nabet

doi:10.1371/journal.pone.0305167

Peer Review History

Original SubmissionMarch 20, 2024
16 Apr 2024 Decision Letter - Joseph Banoub, Editor PONE-D-24-11167Identification of Southeast Asian Anopheles mosquito species with MALDI-TOF mass spectrometryPLOS ONE Dear Dr. Chaumeau, 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 May 31 2024 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. 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: An interesting piece of work. It produces a widely available database that should prove of considerable value in analysis and control of mosquito thence malaria problems. There are some minor quibbles, e.g. does political instability in Myanmar cause increase in P.falsiparum and P.vivax due to changes in human migration, mosquito movement or change in control measures?, also it is implied that not only does MALDI-Tof analysis identify mosquito species but also infection states, past blood meal and mosquito age. However the overall technical description is clear and the data obtained justify the claims made. The realism expressed in the discussion as to how the identification procedure can be refined in the future is welcome; the comparison with previous efforts using smaller sample sizes and species types, plus the use of head extracts as opposed to other body parts and the benefits therein validate the value of this new data. The need for optimal sample storage and multiple specimens is correctly emphasized. The development of the algorithm and use to reject lower quality spectra is an integral part of the data appreciation, at first consideration the selection of 45 as the score threshold seemed counter-intuitive but detailed consideration of the data provided demonstrated the correctness of the selection. Reviewer #2: Dear author, Please find below some comments on your manuscript: p. 14, line 116: please mention the MALDI matrix used and the amount of protein extract spotted in the target plate. p. 16, line 152: more details are needed, like the noise filtering, intensity threshold, de-isotoping… p. 21, line 220: please precise the “predefined criteria for high quality spectra” Best, ****** 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. 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Revision 1
20 May 2024 Author Response Dear Editor, We are thankful for the review of the manuscript “Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry”. Below is a point-by-point answer to Editor’s and Reviewers’ comments: Journal requirements: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. Answer: The manuscript was revised to meet PLOS ONE’s style requirements. 2. Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Answer: The funding statement was amended to meet the journal requirements. The amended funding statement should read: “This research was funded by Wellcome (#220211), the Bill and Melinda Gates Foundation (#OPP1177406) and the Global Fund (#QSE-M-UNOPS-20864-003-32). There was no additional external funding received for this study.” 3. We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Answer: Funding-related text was removed from the manuscript. The amended funding statement is provided above. 4. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission. Answer: Base map of Figure 1 come from Openstreetmap, which is free to use, according to journal requirements. As requested by the journal, we have written the sentence “Base map and data from OpenStreetMap and OpenStreetMap Foundation”in Figure 1 legend. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Answer: The reference list was reviewed to meet the journal requirements. Additional references were cited in the Introduction section to give more background information on malaria on the Thailand-Myanmar border (references 3-12 in the revised version of the manuscript). Reviewers’ comments: Reviewer #1: An interesting piece of work. It produces a widely available database that should prove of considerable value in analysis and control of mosquito thence malaria problems. There are some minor quibbles, e.g. does political instability in Myanmar cause increase in P.falsiparum and P.vivax due to changes in human migration, mosquito movement or change in control measures?, also it is implied that not only does MALDI-Tof analysis identify mosquito species but also infection states, past blood meal and mosquito age. However the overall technical description is clear and the data obtained justify the claims made. The realism expressed in the discussion as to how the identification procedure can be refined in the future is welcome; the comparison with previous efforts using smaller sample sizes and species types, plus the use of head extracts as opposed to other body parts and the benefits therein validate the value of this new data. The need for optimal sample storage and multiple specimens is correctly emphasized. The development of the algorithm and use to reject lower quality spectra is an integral part of the data appreciation, at first consideration the selection of 45 as the score threshold seemed counter-intuitive but detailed consideration of the data provided demonstrated the correctness of the selection. Answer to reviewer #1: We thank the reviewer for her/his constructive feed-back on the manuscript. The manuscript was revised to address the points raised by the reviewer: “There are some minor quibbles, e.g. does political instability in Myanmar cause increase in P.falsiparum and P.vivax due to changes in human migration, mosquito movement or change in control measures?” Answer: Additional details were provided in the Introduction section to clarify our current understanding of how political instability in Myanmar affects malaria epidemiology in Karen state. The surge in malaria observed in recent years in Karen state is multi-factorial and remains largely unexplained. Entomological factors may be involved but there is currently no data available to support this hypothesis. Entomological factors are unlikely directly affected by the political context. Political instability has led to disruption of health services across the country and affected human behaviours. More specifically, the armed-conflict has disrupted access to early diagnosis and treatment (the main pillar of falciparum malaria elimination in this setting) and likely increased human exposures to vector bites (because fleeing civilians sought temporary shelters in forested areas and on the river banks which delimit the international border between Thailand and Myanmar, two typical habitats of the main local vectors) in the fighting areas. Mosquito bed nets have only a marginal impact on malaria in this region because the vectors bite mostly outdoors and at a time when people are not protected by mosquito bed nets; the efficacy of mosquito bed nets for malaria vector control is unlikely affected by political instability in Myanmar. Parasitological factors including a shift in Plasmodium spp. resistance to antimalarial drugs may also be involved and are the focus of active research. “Also it is implied that not only does MALDI-Tof analysis identify mosquito species but also infection states, past blood meal and mosquito age.” Answer: Assessment of infection states, past blood meal and mosquito age typically involves processing of different anatomical parts (e.g. the thorax, legs and abdomen) and analysing the data with protein profiling and machine learning. Additional details can be found in the cited references. These potential applications are out of the scope of the current study (mosquito species identification); therefore, they were not discussed in more details as part of this article. Reviewer #2: Dear author, Please find below some comments on your manuscript: p. 14, line 116: please mention the MALDI matrix used and the amount of protein extract spotted in the target plate. p. 16, line 152: more details are needed, like the noise filtering, intensity threshold, de-isotoping… p. 21, line 220: please precise the “predefined criteria for high quality spectra” Answer to reviewer #2: We thank the reviewer for her/his constructive feed-back on the manuscript. The manuscript was revised to address the points raised by the reviewer: “p. 14, line 116: please mention the MALDI matrix used and the amount of protein extract spotted in the target plate.” Answer: We have not performed a quantification of the proteins in the protein extracts to be spotted because this information is not useful to ensure quality mass spectra using MALDI-TOF. Indeed, we ensured a reproducible quality of mass spectra using our protocol without any quantification of proteins. “p. 16, line 152: more details are needed, like the noise filtering, intensity threshold, de-isotoping…” Answer: The pre-processing of mass spectra is standard, it includes a smoothing (python library pimzml), a baseline correction and a custom peak picking with selection of the 70 highest intensity peaks. Noise filtering and intensity threshold are not applied here, because there is a ranking of the highest intensity peaks instead. The de-isotoping is not applied using MALDI-TOF mass spectrometry. A specific comment has been added at lines 181-183 (version with tracked changes) of the method section. “p. 21, line 220: please precise the “predefined criteria for high quality spectra” Answer: The predefined criteria for high quality spectra are mentioned in the method section, in the paragraph about the construction of MSI2 reference database 189-197 (version with tracked changes). We referred to this method section after the cited sentence at lines 255 (version with tracked changes). Sincerely, Dr. Victor Chaumeau Attachments Attachment Submitted filename: rebutal_letter_20240521.docx https://doi.org/10.1371/journal.pone.0305167.r002
27 May 2024 Decision Letter - Joseph Banoub, Editor Identification of Southeast Asian Anopheles mosquito species with MALDI-TOF mass spectrometry PONE-D-24-11167R1 Dear Dr. Chaumeau, 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. If you have any questions relating to publication charges, 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, Joseph Banoub, Ph,D., D. Sc. Academic Editor PLOS ONE Additional Editor Comments (optional): Thank you very much for completing all the revisions required. Reviewers' comments: https://doi.org/10.1371/journal.pone.0305167.r003
Formally Accepted
31 May 2024 Acceptance Letter - Joseph Banoub, Editor PONE-D-24-11167R1 PLOS ONE Dear Dr. Chaumeau, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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. 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. Joseph Banoub Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0305167.r004

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