Risk factors for surgical site infections using a data-driven approach

J. M. van Niekerk; M. C. Vos; A. Stein; L. M. A. Braakman-Jansen; A. F. Voor in ‘t holt; J. E. W. C. van Gemert-Pijnen

doi:10.1371/journal.pone.0240995

Peer Review History

Original SubmissionMay 15, 2020
16 Jun 2020 Decision Letter - Francesco Di Gennaro, Editor PONE-D-20-14495 Risk factors for surgical site infections using a data-driven approach PLOS ONE Dear Dr. van Niekerk, 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 Jul 31 2020 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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The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. 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 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? 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: In this work, Authors conducted a robust data-driven approach to identify risk factors for surgical site infections after digestive system, orthopedic or thoracic surgery procedures. Overall, the work is well written and clear. The statistical analysis is appropriate and well performed. The major limitation of this work is the lack of certain information that could have influenced the final result of multivariable analysis. However, this work is worth for publication after few minor revisions Introduction 1) Lines 48-49: Many research have been conducted until now in order to identify risk factors for SSI. However, one important point often overlooked is the importance of clinical setting. Indeed, risk factors for SSI could importantly differ between low income countries and high income countries. A recent interesting work addressed this topic (Di Gennaro F, et al. Maternal caesarean section infection (MACSI) in Sierra Leone: a case-control study. Epidemiol Infect . 2020 Feb 27;148:e40. doi: 10.1017/S0950268820000370.) and could be cited, along with a brief paragraph discussing this point. Discussion 1) The antibiotic use as a risk factor for SSI is interesting but controversial. In fact, although many guidelines suggest to limit the use of the antibiotic prophylaxis at the day of the surgery, often antibiotics are prescribed several days before and after the surgical day. In my opinion Authors should give a possible explanation for this very important result possibly based on their data. 2) Did any data regarding the reason for surgical procedures were available? It is widely accepted that the cause of surgical procedure (infection, cancer, prosthetic implantation, etc) and the general clinical condition of patient (immunocompromised, severely undernourished, etc) are significant predictors of SSI. If these information are not available, this point should be included among limitations. Reviewer #2: In this manuscript Johan Magnus van Niekerk and co-authors tried to identify major risk factors for surgical site infections from digestive, thoracic and orthopaedic system surgeries. To reach this aim they previously identified some known risk factors in literature and then they compared them with data extrapolated from a database of a large tertiary care hospital in the Netherlands. This study could give an important contribution on prevention of surgical site infection by identifying modifiable risk factors and subsequently preventative actions. The title and abstract are appropriate for the content of the text. There are my comments sorted by section. Methods: • line 93: I think that could be useful to clarify how the nosocomial infection index was obtained, in particular which parameters where included to determine it. • Line 192-205: I think that this paragraph should be removed. It appears too technical and probably not necessary for the purpose of the article. Discussion: • Lines 240-241: when you talk about antibiotic usage before surgery do you refer to their use in a broad sense or there are particular class of antibiotics related to a major risk? It could be interesting to examine which classes are related to a major risk for SSI. • Lines 256-257: there is a repetition, you just defined the general risk factors in lines 225-228 ****** 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
21 Sep 2020 Author Response Response to reviewers – PONE-D-20-14495 Risk factors for surgical site infections using a data-driven approach Johan Magnus van Niekerk, Margreet C. Vos, Alfred Stein, Annemarie Braakman-Jansen, Anne F. Voor in ’t holt, Lisette van Gemert-Pijnen We are grateful for your valuable comments which helped us to improve our manuscript. We sincerely appreciate the time you spent reviewing this manuscript. We revised our manuscript in accordance with your comments. Please find our responses to the comments below. Reviewer #1: Introduction 1. Lines 48-49: Many research have been conducted until now in order to identify risk factors for SSI. However, one important point often overlooked is the importance of clinical setting. Indeed, risk factors for SSI could importantly differ between low income countries and high income countries. A recent interesting work addressed this topic (Di Gennaro F, et al. Maternal caesarean section infection (MACSI) in Sierra Leone: a case-control study. Epidemiol Infect . 2020 Feb 27;148:e40. doi: 10.1017/S0950268820000370.) and could be cited, along with a brief paragraph discussing this point. We welcome this suggestion and consider the introduction as more rounded because of this addition. The following text was added to the introduction, and the suggested research article cited: L51 – L53: “Risk factors in low-income countries also include unemployment and level of education due to the disparity in socioeconomic status [20].” Discussion 1. The antibiotic use as a risk factor for SSI is interesting but controversial. In fact, although many guidelines suggest to limit the use of the antibiotic prophylaxis at the day of the surgery, often antibiotics are prescribed several days before and after the surgical day. In my opinion Authors should give a possible explanation for this very important result possibly based on their data. Although the data regarding the timing and administration of surgical antibiotic prophylaxis were not available for this study, the reviewer’s comment led us to further investigate the relationship between the occurrence of SSI and the time between J01 antibiotics prescription time and surgery. The occurrence of SSI seems to vary for different times between antibiotics prescription and surgery (Fig 1), but hypotheses regarding this relationship should be evaluated using case-control studies with specific data regarding the reason for the prescription, the type of antimicrobials and the timing of the administration thereof. Fig 1. The occurrence of SSI for the time between the J01 antibiotics prescription start time and the start time of the surgery by decile. m, minutes; h, hours; d, days; #SSI, number of SSI occurrences; %SSI, percentage of SSI occurrences. 1The vertical axis starts at 75% to increase visibility. 2The horizontal axis stipulates the endpoints of the respective deciles of the distribution of the time between prescription and surgery. We added the following text to the discussion section to further share our insight with the readers: L280 – L283: “Systemic antibiotics are typically prescribed to stabilise patients before undergoing surgery. A possible explanation for the increased occurrence of SSI associated with antimicrobials prescribed before surgery could be that these patients were not completely stabilised before surgery which increased their risk of SSI.” 2. Did any data regarding the reason for surgical procedures were available? It is widely accepted that the cause of surgical procedure (infection, cancer, prosthetic implantation, etc) and the general clinical condition of patient (immunocompromised, severely undernourished, etc) are significant predictors of SSI. If these information are not available, this point should be included among limitations. We were hoping to include this information in the study but soon realised that these data were only available in free text field information, and there was no way to extract these data efficiently. We added the following sentence to the Limitations section: L288 – L290: “Surgeries were aggregated into three broad groups of surgical procedures which serve as a proxy for the reason for surgery but leads to the loss of information regarding the exact reasons for the surgery.” L294-295: “A comprehensive list of variables related to the nutritional and immunological alterations of the patients was not included in the analyses as they were not available from the data.” Reviewer #2: Methods 1. line 93: I think that could be useful to clarify how the nosocomial infection index was obtained, in particular which parameters where included to determine it. Thank you for bringing this to our attention. The references to the two articles which describe the nosocomial infection index, used as outcome variables in our study, are now provided immediately after the algorithm is mentioned for the first time. We also now refer to Streefkerk et al. in the text to make this referral clearer. 2. Line 192-205: I think that this paragraph should be removed. It appears too technical and probably not necessary for the purpose of the article. This paragraph referred to was added as supplementary material (S2 Formulae) instead. Discussion 1. Lines 240-241: when you talk about antibiotic usage before surgery do you refer to their use in a broad sense or there are particular class of antibiotics related to a major risk? It could be interesting to examine which classes are related to a major risk for SSI. Antibiotics in J01 Anatomical Therapeutic Chemical were used this study. This definition is specified in the variable definition table, but the legend was not complete. We agree with the reviewer that delving deeper into the subclasses of antibiotics is of great importance, although not in the scope of this study. The following changes were made to the manuscript: L101-103: The following text was added to the methods section where the data are described: “Data regarding the prescription of antimicrobials, in the J01 class of the Anatomical Therapeutic Chemical (ATC) classification system [28], were also included.” L161-L162: The following text was to the legend of the variable definition table: “ATC, Anatomical Therapeutic Chemical; WHO, World Health Organization.” 2. Lines 256-257: there is a repetition, you just defined the general risk factors in lines 225-228 Thank you, we have removed the repetition. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0240995.r002
7 Oct 2020 Decision Letter - Francesco Di Gennaro, Editor Risk factors for surgical site infections using a data-driven approach PONE-D-20-14495R1 Dear Dr. Johan, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Francesco Di Gennaro Academic Editor PLOS ONE Additional Editor Comments (optional): Dear Authors congratulations! Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy 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 ****** 5. 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 ****** 6. 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: (No Response) Reviewer #2: (No Response) ****** 7. 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. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: Yes:** Mariani Michele Fabiano https://doi.org/10.1371/journal.pone.0240995.r003
Formally Accepted
9 Oct 2020 Acceptance Letter - Francesco Di Gennaro, Editor PONE-D-20-14495R1 Risk factors for surgical site infections using a data-driven approach Dear Dr. van Niekerk: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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. Francesco Di Gennaro Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0240995.r004

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