{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T21:09:27Z","timestamp":1792271367207,"version":"4.4.0"},"update-to":[{"DOI":"10.12688\/wellcomeopenres.14851.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T00:00:00Z","timestamp":1542758400000}}],"reference-count":38,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T00:00:00Z","timestamp":1542758400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["106698"],"award-info":[{"award-number":["106698"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007421","name":"Li Ka Shing Foundation","doi-asserted-by":"publisher","award":["SM40"],"award-info":[{"award-number":["SM40"]}],"id":[{"id":"10.13039\/100007421","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    We have previously shown that PCR following enrichment culture is the most sensitive method to detect\n                    <ns4:italic>Burkholderia pseudomallei<\/ns4:italic>\n                    in environmental samples. Here we report an evaluation of the published consensus method for the culture of\n                    <ns4:italic>B. pseudomallei<\/ns4:italic>\n                    from Lao soil in comparison with our conventional culture method and with PCR with or without prior broth enrichment.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    One hundred soil samples were collected from a field known to contain\n                    <ns4:italic>B. pseudomallei<\/ns4:italic>\n                    and processed by: (i) the conventional method, (ii-iii) the consensus method using media prepared in either Laos or Thailand, and (iv) the consensus method performed in Thailand, as well as by (v) PCR following direct extraction of DNA from soil and (vi) PCR following broth pre-enrichment.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    The numbers of samples in which\n                    <ns4:italic>B. pseudomallei<\/ns4:italic>\n                    was detected were 42, 10, 7, 6, 6 and 84, respectively. However, two samples were positive by the consensus method but negative by conventional culture, and one sample was negative by PCR following enrichment although\n                    <ns4:italic>B. pseudomallei<\/ns4:italic>\n                    was isolated by the conventional culture method.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions\/Discussion:<\/ns4:bold>\n                    The results show that no single method will detect all environmental samples that contain\n                    <ns4:italic>B. pseudomallei.<\/ns4:italic>\n                    People conducting environmental surveys for this organism should be aware of the possibility of false-negative results using the consensus culture method. An approach that entails screening using PCR after enrichment, followed by the evaluation of a range of different culture methods on PCR-positive samples to determine which works best in each setting, is recommended.\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.14851.2","type":"journal-article","created":{"date-parts":[[2018,11,21]],"date-time":"2018-11-21T10:25:39Z","timestamp":1542795939000},"page":"132","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Evaluation of consensus method for the culture of Burkholderia pseudomallei in soil samples from Laos"],"prefix":"10.12688","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9189-7244","authenticated-orcid":false,"given":"David 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N.","family":"Newton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Premjit","family":"Amornchai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3074-0742","authenticated-orcid":false,"given":"Vanaporn","family":"Wuthiekanun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sayan","family":"Langla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7240-5320","authenticated-orcid":false,"given":"Direk","family":"Limmathurotsakul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2018,11,21]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"15008","DOI":"10.1038\/nmicrobiol.2015.8","article-title":"Predicted 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pseudomallei in soil","author":"D Dance","year":"2018"}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,5]],"date-time":"2018-12-05T05:20:12Z","timestamp":1543987212000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,11,21]]},"references-count":38,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.14851.2","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.16288.r34299","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.16288.r34299","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,21]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.16180.r34076, Ya-Lei Chen, Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan, 25 Oct 2018, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v1#referee-response-34076","order":0,"name":"referee-response-34076","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>David A. B. Dance<\/b>; \n<i>Posted: 16 Nov 2018<\/i>; Evaluation of consensus method for the culture of \n<i>Burkholderia pseudomallei<\/i> in soil samples from Laos\n<b>Response to Referees\u2019 Comments<\/b>&nbsp;\n<i>We are grateful to the referees for taking the time to read and comment on our manuscript, which has enabled us to make improvements in Version 2.&nbsp; Our responses are given in italics below.<\/i>&nbsp;\n<b>Referee 1<\/b>&nbsp;This manuscript is valuable to remind us that the isolation strategy for \n<i>B. pseudomallei<\/i> in the environment should strictly consider its own physiochemical parameters. Consensus methodology has shown successful isolation of&nbsp;\n<i>B. pseudomallei<\/i> from Thai soil but, in this report, it shows a worse isolation from Lao soil. I believe that \n<i>B. pseudomallei<\/i> strains exhibit many genomovars, morphovars and even pathovars in different areas that are endemic to melioidosis because B. pseudomallei accommodate in different soil condition through a long-term evolution by geographical seclusion. Thus, different isolation methods used in different places are reasonable. However, several concerns have to be considered:1. Even if the soil was collected from same place, it was very difficult to ensure that presence or absence of \n<i>B. pseudomallei <\/i>or any organisms that were antagonistic to \n<i>B. pseudomallei<\/i> can be found in different pieces (sub-sample). Actually, the distribution of \n<i>B. pseudomallei<\/i> in soil sample is very uneven.&nbsp;\n<i>We agree with the referee about this, which is why we went to considerable lengths to ensure that the sub-samples were as representative as possible by using the \u20182D Japanese slab-cake\u2019 method, as mentioned in the \u2018Methods\u2019 section.&nbsp; We have added a paragraph in the \u2018Results and discussion\u2019 section to address this and other limitations of the study raised by the referees.<\/i>2. The suspect isolates were chosen following the colony morphology from consensus and ASH methods. However, this technique is experience-dependent because \n<i>B. pseudomallei<\/i> colony morphovars have been widely reported in these media. Several atypical morphologies such as smaller, moisturized or mucoid could appear in environmental isolates but they probably were ignored and seldom found in clinical isolates, usually appearing a dry and winkled colony morphology.&nbsp;\n<i>Again, we agree about this and have included this in the discussion of the limitations referred to above.<\/i>3. The fragment of \n<i>orf2<\/i> stretch of the TTSS could be amplified by soil organisms that are not related to \n<i>B. pseudomallei<\/i>. In other words, false positive probably existed in ES\/qPCR method.\n<i>We are not clear of the referee\u2019s evidence for this.&nbsp; This target has been widely used by others for the detection of B. pseudomallei in both clinical and environmental samples and is generally believed to be highly specific. However, since we accept that there are probably \u2018near-neighbours\u2019 of B. pseudomallei in the environment that have not yet been fully characterised, we have included this in the paragraph on limitations as above.<\/i>&nbsp;4.&nbsp;In Fig. 1, the proportion of positive sample in ES\/qPCR is 84 or 85?\n<i>This was 84 of the 85 samples positive by any method as shown in the figure, the discrepancy being the result of the single sample that was negative by ES\/qPCR but positive by conventional culture.<\/i>5.&nbsp;In the statistical analysis, there is no mention of how to calculate 95% CI.\n<i>We have added a statement in the \u2018Statistical analysis\u2019 section that says \u201cThe confidence intervals for sensitivities were estimated by using the ci command in STATA\u201d.<\/i>Overall, I agree with the authors\u2019 conclusion that \n<i>B. pseudomallei<\/i> in a new environment would be to use enrichment culture followed by PCR as a screening method. Repeatedly isolation for \n<i>B. pseudomallei<\/i> by selective media from PCR positive sample is needed.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2#referee-comment-3733","order":1,"name":"referee-comment-3733","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.16288.r34299, Rasana W Sermswan, Melioidosis Research Center, Faculty of Medicine, Khon Kaen University\u00a0(KKU), Khon Kaen, Thailand, 05 Dec 2018, version 2, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/3-132\/v2#referee-response-34299","order":2,"name":"referee-response-34299","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the Wellcome core grant to the Mahidol-Oxford Tropical Medicine Research network (106698\/Z\/14\/Z ) and by a seed award from the Lee Ka Shing Foundation to the University of Oxford (SM40). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"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"}]}}