{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T02:20:10Z","timestamp":1789438810283,"version":"build-2803163510"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.19809.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T00:00:00Z","timestamp":1698883200000}}],"reference-count":31,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T00:00:00Z","timestamp":1698883200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["220540"],"award-info":[{"award-number":["220540"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["216457"],"award-info":[{"award-number":["216457"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    Background Melioidosis is a frequently fatal disease caused by an environmental bacterium\n                    <ns3:italic>Burkholderia pseudomallei<\/ns3:italic>\n                    . The disease is prevalent in northeast Thailand, particularly among rice field farmers who are at risk of bacterial exposure through contact with contaminated soil and water. However, not all exposure results in disease, and infection can manifest diverse outcomes. We postulate that genetic factors, whether from the bacterium, the host or the combination of both, may influence disease outcomes. To address this hypothesis, we aim to collect, sequence, and analyse genetic data from melioidosis patients and controls, along with isolates of\n                    <ns3:italic>B. pseudomallei<\/ns3:italic>\n                    obtained from patients. Additionally, we will study the metagenomics of the household water supply for both patients and controls, including the presence of\n                    <ns3:italic>B. pseudomallei.<\/ns3:italic>\n                    Methods BurkHostGEN is an ongoing observational study being conducted at Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand. We are obtaining consent from 600 melioidosis patients and 700 controls, spanning both sexes, to collect 1 mL of blood for host DNA analysis, 3 mL of blood for RNA analysis, as well as 5 L of household water supply for metagenomic analysis. Additionally, we are isolating\n                    <ns3:italic>B. pseudomallei<\/ns3:italic>\n                    from the melioidosis patients to obtain bacterial DNA. This comprehensive approach will allow us to identify\n                    <ns3:italic>B. pseudomallei<\/ns3:italic>\n                    and their paired host genetic factors associated with disease acquisition and severity. Ethical approvals have been obtained for BurkHostGEN. Host and bacterial genetic data will be uploaded to European Genome-Phenome Archive (EGA) and European Nucleotide Archive (ENA), respectively. Conclusions BurkHostGEN holds the potential to discover bacterial and host genetic factors associated with melioidosis infection and severity of illness. It can also support various study designs, including biomarker validation, disease pathogenesis, and epidemiological analysis not only for melioidosis but also for other infectious diseases.\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.19809.2","type":"journal-article","created":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T09:35:12Z","timestamp":1698917712000},"page":"347","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis 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P.J.","family":"Day","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Chewapreecha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2023,11,2]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"892-902","DOI":"10.1016\/S1473-3099(19)30157-4","article-title":"Global burden of melioidosis in 2015: a systematic review and data synthesis.","volume":"19","author":"E Birnie","year":"2019","journal-title":"Lancet Infect Dis."},{"key":"ref-2","doi-asserted-by":"publisher","DOI":"10.1038\/nrdp.2017.107","article-title":"Melioidosis.","volume":"4","author":"W Wiersinga","year":"2018","journal-title":"Nat Rev Dis Primers."},{"key":"ref-3","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofz498","article-title":"Clinical Epidemiology of 7126 Melioidosis Patients in Thailand and the Implications for a 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Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,9]],"date-time":"2023-11-09T07:35:13Z","timestamp":1699515313000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,2]]},"references-count":31,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.19809.2","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.22585.r69547","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.22585.r69547","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,2]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.22585.r69547, Sheila Nathan, Faculty\u00a0of\u00a0Science\u00a0and\u00a0Technology,\u00a0School\u00a0of\u00a0Biosciences\u00a0and\u00a0Biotechnology, National University of Malaysia, Bangi, Selangor, 03 Nov 2023, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2#referee-response-69547","order":0,"name":"referee-response-69547","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Claire Chewapreecha<\/b>; \n<i>Posted: 08 Nov 2023<\/i>; We are grateful for the reviewer's time and constructive comments. This helps enhance the clarity of our study protocol. Thank you immensely.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2#referee-comment-5514","order":1,"name":"referee-comment-5514","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.21941.r65464, Chiranjay Mukhopadhyay, Ranita Ghosh Dastidar, Department\u00a0of\u00a0Microbiology,\u00a0Kasturba\u00a0Medical\u00a0College\u00a0and\u00a0Hospital, Manipal Academy of Higher Education, Manipal, Karnataka, 12 Oct 2023, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v1#referee-response-65464","order":2,"name":"referee-response-65464","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Claire Chewapreecha<\/b>; \n<i>Posted: 30 Oct 2023<\/i>; #Authors: We sincerely thank the reviewers for their feedback and constructive insights, which have enhanced the clarity and readability of our study protocol. We really appreciate your time and support, and hope that our work will make a meaningful contribution to the genetic progress in our melioidosis community. A point-by-point response is provided below&nbsp;  ###### \n<i>#Reviewers: In the study protocol entitled \u201cBurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection\u201d by Kesorn Angchagun et al., the authors have emphasized that not all bacterial exposures lead to melioidosis. Acquisition and further the outcomes of melioidosis vary largely due to genetic factors of both the acquired bacteria and the genetic makeup of the individual. With this fact in focus, the authors have undertaken an initiative to perform a detailed genomic study hypothesizing that genetic factors of both bacteria and host (separately or combinatorially) determine the acquisition and outcome patterns of patients. The protocol includes comparative DNA and RNA level studies from the patient and control blood samples as well as comparing their HbA1c levels. The protocol also enables comparison of DNA from bacteria collected from patient sample and community water source in nearby areas of patients and controls by metagenomic analyses. It also collects and stores the patient PBMCs for future utilization as cell models. The sample collection procedure is already over but can continue further as well. The sequencing and analysis, when complete, will provide the opportunity to discover several novel bacterial and host genetic factors and also can be followed by all melioidosis-prone south eastern Asia and northern Australian regions and beyond for better understanding, prevention and cure of the disease. This study protocol can further serve as basic guideline for the study of many other infectious diseases and emerging tropical diseases and also help generate community database nationally and globally.After careful review of the manuscript, these reviewers feel that there are following minor concerns regarding the manuscript, which after being addressed can allow the approval of this protocol for indexing.For DNA extraction of environmental microbial community, emphasis has been on the plate-sweep culture from concentrated 5 litre of water (as shown in table 1). The disadvantages of single-colony pick method should be elaborated if any. Methods section, however, mentions the use of both plate-sweep and single-colony pick methods being used for sequencing using GridION (with ligation library preparation on a pool of up to 10 samples per flow cell) and Novaseq (as for patient sample isolation) respectively. Please clarify. The disadvantages and advantages of both plate-sweep and single-colony pick sequencing has been discussed.<\/i>  #Authors: We apologise for the lack of the rationale for using the dual plate-sweep and single-colony pick approach in the previous version. We have now provided a detailed explanation. To briefly summarise, the plate-sweep method ensure that all bacterial growth, including potentially unnoticed B. pseudomallei colonies due to competition with faster-growing microbes, is included for DNA extraction and analysis. This minimises bias associated with visual inspection and accommodates the potential presence of multiple B. pseudomallei clones or lineages, thereby preventing the oversight of minor populations. Additionally, for visible B. pseudomallei colonies, we perform conventional single-colony picks to complement the analysis. &nbsp;  \n<i>#Reviewers: 2. In section \u201cDiversity of B. pseudomallei in the household water supply of melioidosis and control group\u201d, it is mentioned that slow growth of B. pseudomallei can lead to overgrowth of other microbes and hence negative culture results due to invisible colonies. This section can be better aligned with the methods section for better clarification.<\/i>  #Authors: We thank the reviewers for this comment and have restructured the text to make the two sections aligned. &nbsp;  \n<i>#Reviewers: 3. Please mention clearly - Are all sequencing procedures done under BSL3 laboratory facilities or only DNA\/RNA extraction methods?<\/i>  #Authors: We appreciate this comment and have specifically outlined the procedure involved in BSL2, and BSL3 at the beginning of the sample processing section as &quot;sample processing adheres to Biosafety laboratory 3 (BSL3) guidelines for handling infectious materials (suspected B. pseudomallei presence) and Biosafety Laboratory 2 (BSL2) guidelines for handling sterile samples (processed DNA or RNA).&quot; &nbsp;  \n<i>#Reviewers: 4. In data analysis section, one of the infection severity groups includes, \u201ca healthy population with no or subclinical symptoms\u201d \u2013 please elaborate subclinical symptoms.<\/i>  #Authors: We thank the reviewer for this feedback and have defined a healthy population with no or subclinical symptoms as those who were healthy and did not seek healthcare to make this clearer. &nbsp;  \n<i>#Reviewers: 5. The definition for \u2018mild melioidosis\u2019 may be more clear.<\/i>  #Authors: We appreciate this comment and have defined \u201cmild melioidosis\u201d as a group with less severe melioidosis infection that required healthcare but recovered. &nbsp;  \n<i>#Reviewers: 6. Since a portion of the collected data has been reported in another preprint awaiting peer-review, assure that this does not create any conflict of interest amongst participating individuals or groups. A statement to that effect will be preferred that states these two groups are identical or have no conflicts<\/i>  #Authors: We thank the reviewer for pointing this and have now explicitly mentioned in the text that there are no publication conflicts.&nbsp; &nbsp;  \n<i>#Reviewers: 7. In sample collection section, preferred and alternative sites of phlebotomy are mentioned. Any information related to any expected differences in the HbA1c reports and amount of PBMC that can be collected that can vary based on the site of blood collection (for phlebotomy) if any should be mentioned (as a matter of fact if known or as an assumption).<\/i>  #Authors: Irrespective of the phlebotomy sites, PBMC and HbA1c were processed identically. However, we noted that the processing time between blood collection and storage are critical factor affecting the number of viable cells and have now included this specification in the protocol.  ###### Again, a heartfelt thank you for your help reviewing this study protocol.&nbsp; &nbsp; &nbsp;","URL":"https:\/\/wellcomeopenresearch.org\/articles\/8-347\/v2#referee-comment-5507","order":3,"name":"referee-comment-5507","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [216457, <a href=https:\/\/doi.org\/10.35802\/216457>https:\/\/doi.org\/10.35802\/216457<\/a>, an International Intermediate Fellowship award to CC; and 220540, a Sanger Review award to EED]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}