Assessment of utilization of automated systems and laboratory information management systems in clinical microbiology laboratories in Thailand

Preeyarach Klaytong; Panida Chamawan; Voranadda Srisuphan; Krittiya Tuamsuwan; Phairam Boonyarit; Adisak Sangchankoom; Archawin Rojanawiwat; Aekkawat Unahalekhaka; Kulsumpun Krobanan; Pimrata Leethongdee; Orapan Sripichai; Vanaporn Wuthiekanun; Paul Turner; Direk Limmathurotsakul

doi:10.1371/journal.pone.0320074

Peer Review History

Original SubmissionDecember 26, 2024
26 Dec 2024 Author Response https://doi.org/10.1371/journal.pone.0320074.r001
14 Jan 2025 Decision Letter - Benjamin M. Liu, Editor Dear Dr. Limmathurotsakul, 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. 1. The authors made it clear Thailand is not LMIC. However, Abstract's Introduction states: little is known about how data are generated, managed and analyzed in those laboratories in low and middle-income countries (LMICs). This knowledge gap cannot be filled by this study. So the authors would better not ask this question as it will cause confusion. Please correct this across the manuscript. For example, line 343-344: "Our findings can support the global initiative to strengthen microbiology laboratory capacity in LMICs". 2. Line 359-361 in Discussion: "Although the automated systems for bacterial identification and AST are increasingly utilized, utilization of both conventional methods and automated systems for these two steps is still common." There are no references for this statement. More references are needed, with this reference (PMID: 34142857) as an example (citing is optional). Please submit your revised manuscript by Feb 28 2025 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. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. 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Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: No Reviewer #2: Yes ****** Reviewer #1: Dear Authors Though your manuscript and work is good but i suggest some changes. 1.Your title is a little bit confusing and doesn't provide the goal of the study. 2. Please make some changes in key words. 3. Delete the repeated citation in line 65 and make it whole with reference number 3. 4. The language quality and level must get enhance by a native speaker. 5. Some of introduction sentences is not related to the subject. provide better introduction. 6. Where is the conclusion part? 7. In Study participants section you have mentioned inviting laboratory staff from clinical microbiology laboratories, was it random or you did it based on something? 8. Discussion section is more like introduction part, you should mention about other related studies ( if there are any) and compare your research. 9. Explain more about the goal of the study. Kind regards Reviewer #2: This manuscript although seems very basic to the standrads of international publications but has weight when it comes to understanding the present requirements in clinical set up. Health care system is rapidly improving and also evolving with the big data. One of the main concern is on how to maintain and handle big data for patient benefit. In this scenario, this manuscript presents valid observation based on multi-location data to guide towards need of a better network based data handling. 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Revision 1
10 Feb 2025 Author Response Re: PLOS ONE Decision: Revision required [PONE-D-24-59742] - [EMID:5b975ce039a7bcd5] Dear Editor, Thank you for your e-mail concerning the above manuscript. We are grateful for the helpful comments made by the reviewers, and have addressed them as detailed below. Editor's comments: 1. The authors made it clear Thailand is not LMIC. However, Abstract's Introduction states: little is known about how data are generated, managed and analyzed in those laboratories in low and middle-income countries (LMICs). This knowledge gap cannot be filled by this study. So the authors would better not ask this question as it will cause confusion. Please correct this across the manuscript. For example, line 343-344: "Our findings can support the global initiative to strengthen microbiology laboratory capacity in LMICs". Answer. The sentence in the abstract has been revised as follows, “Here, we aim to understand the systems involved in generating, managing and analyzing blood culture data in these laboratories in an upper-middle income country.” The sentence in the discussion has been removed and the discussion has been revised for clear difference between upper-middle-income and lower-middle-income and low-income countries as follows, “The data on utilization of automated systems, capacity of automated blood culture systems, and the use of LIMS across different levels of public hospitals in Thailand can serve as one example to support the rational installation and enhancement of clinical microbiology laboratories in other upper-middle-income countries. The capacity of clinical microbiology laboratories can be increased through multifaceted interventions, including advocacy, commitment of funding, enhancing education and training, care for the laboratory workforce, metrics for monitoring, etc. [21]. Many lower-middle and low-income countries may require financial and non-financial support from various international and national organizations to increase capacity on clinical microbiology laboratories [22]. ” 2. Line 359-361 in Discussion: "Although the automated systems for bacterial identification and AST are increasingly utilized, utilization of both conventional methods and automated systems for these two steps is still common." There are no references for this statement. More references are needed, with this reference (PMID: 34142857) as an example (citing is optional). Answer. The new reference (PMID: 34142857) and the reference no. 21 (PMID: 31275940) have been added for the statement. Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Answer. Revised as suggested. 2. Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified (1) whether consent was informed and (2) what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information. Answer. The ethics statement has been revised as follows, “Ethical permission for this study was obtained from both of the Oxford Tropical Research Ethics Committee (OxTREC 553-23) and the Institute for the Committee of the Faculty of Tropical Medicine, Mahidol University (TMEC 23-049). Individual participant consent was obtained online prior to completing the questionnaire, and the Ethics Committee approved this process.” 3. Thank you for stating the following financial disclosure: [The study was supported by Ministry of Public Health Thailand and Wellcome Trust of Great Britain (224681/Z/21/Z). For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. Answer. The following sentence has been added for clarity, “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” 4. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Answer. The data has been made open-access, and the sentence has been revised as follows, “The dataset generated for this study is available at https://doi.org/10.6084/m9.figshare.28028285.” 5. We note that Figure 1 in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. 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. Figure 1 has been removed. Reviewer #1: Dear Authors Though your manuscript and work is good but i suggest some changes. 1.Your title is a little bit confusing and doesn't provide the goal of the study. Answer. The title has been revised to include the goal of the study as follows, “Assessment of Utilization of Automated Systems and Laboratory Information Management Systems in Clinical Microbiology Laboratories in Thailand” 2. Please make some changes in key words. Answer. The keyword “low and middle-income countries” has been changed to “upper-middle-income countries” for clarity. 3. Delete the repeated citation in line 65 and make it whole with reference number 3. Answer. The repeated citation in line 65 has been deleted as suggested. 4. The language quality and level must get enhance by a native speaker. Answer. The manuscript's language has been revised by co-author Paul Turner, a native English speaker. 5. Some of introduction sentences is not related to the subject. provide better introduction. Answer. We would like to maintain the sentences in the introduction because they provide background on why we conducted the study and why we assessed the barriers following the implementation of AMASS. 6. Where is the conclusion part? Answer. A conclusion paragraph has been added as follows, “In conclusion, various automated systems for blood culture and LIMS are utilized in Thailand. However, barriers to data management and analysis are common. These challenges are likely present in other upper-middle-income countries. To improve efficiency, quality and benefits of clinical microbiology laboratories, we propose that guidance and technical support for automated systems, LIMS, and data analysis are required.” 7. In Study participants section you have mentioned inviting laboratory staff from clinical microbiology laboratories, was it random or you did it based on something? Answer. We requested all clinical microbiology laboratories in all 127 public referral hospitals to participate the study. No randomization was performed. The sentence has been revised for clarity, “We invited laboratory staff from all 127 clinical microbiology laboratories (one each from 127 public referral hospitals) to complete the online survey via three rounds of email invitation.” 8. Discussion section is more like introduction part, you should mention about other related studies (if there are any) and compare your research. Answer. Additional references and sentences have been added as follows, “A recent study in Kenya, a lower-middle-income country, also suggests that multiple issues need to be targeted simultaneously and continuously at the health system level to sustain and provide routine blood culture testing in the country [23].”, “Although the automated systems for bacterial identification and AST are increasingly utilized, utilization of both conventional methods and automated systems for these two steps is still common in other upper-middle-income and high-income countries [25, 26].” and “A study from Uganda, a low-income country, describes the use of a Microsoft Access database to record clinical and laboratory data, the problem of connectivity, and the transition to a web-based data management system that can serve as the basis for responsive and sustainable public health surveillance [30].” 9. Explain more about the goal of the study. Answer. The sentence has been revised for clarity as follows, “The goal of this study is to assess the utilization of automated systems and LIMS for blood culture specimens, and the barriers to data analysis in Thailand.” Kind regards Reviewer #2: This manuscript although seems very basic to the standrads of international publications but has weight when it comes to understanding the present requirements in clinical set up. Health care system is rapidly improving and also evolving with the big data. One of the main concern is on how to maintain and handle big data for patient benefit. In this scenario, this manuscript presents valid observation based on multi-location data to guide towards need of a better network based data handling. I am happy to see these kind of studies which involves enormous amount of time and compilation which might yield a small conclusion but in a positive manner to focus on priorities and necessities. I recommend to accept this MS which can be a valuable resource for patient data handling and management. Answer. We are grateful for the comment. All contributing authors have reviewed and concurred with the revised manuscript. Yours, Direk Limmathurotsakul Attachments Attachment Submitted filename: response_to_reviewers LIMS 20250204.docx https://doi.org/10.1371/journal.pone.0320074.r003
13 Feb 2025 Decision Letter - Benjamin M. Liu, Editor Assessment of utilization of automated systems and laboratory information management systems in clinical microbiology laboratories in Thailand PONE-D-24-59742R1 Dear Dr. Limmathurotsakul, 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, Benjamin M. Liu, MBBS, PhD, D(ABMM), MB(ASCP) Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0320074.r004
Formally Accepted
Acceptance Letter - Benjamin Liu, Editor PONE-D-24-59742R1 PLOS ONE Dear Dr. Limmathurotsakul, 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. Benjamin M. Liu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0320074.r005

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