Seasonality and weather dependance of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil

Sebastião Pires Ferreira Filho; Milca Severino Pereira; Jorge Luiz Nobre Rodrigues; Raul Borges Guimarães; Antônio Ribeiro da Cunha; José Eduardo Corrente; Antônio Carlos Campos Pignatari; Carlos Magno Castelo Branco Fortaleza

doi:10.1371/journal.pone.0255593

Peer Review History

Original SubmissionFebruary 18, 2021
11 May 2021 Decision Letter - Aleksandra Barac, Editor PONE-D-21-05493 Seasonality and weather dependance of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil. PLOS ONE Dear Dr. Fortaleza, 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 Jun 25 2021 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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Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. 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: No Reviewer #2: Yes Reviewer #3: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reviewer #3: 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: No Reviewer #2: Yes Reviewer #3: 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: No Reviewer #2: Yes Reviewer #3: 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: Many hospital-acquired blood stream infections worldwide have been attributed to Acinetobacter baumannii complex. The focus of this study was to assess the impact of seasons, weather parameters and climate control on the incidence as well as carbapenem-resistance in A. baumannii complex bloodstream infections in hospitals from three regions of Brazil with different climatic conditions. A major strength of this manuscript is the use of Box-Jenkins models, which allows for identifying seasonality in the dependent series (seasonally differencing it if necessary) from even retrospective datasets. Notwithstanding, the manuscript has a number of flaws that makes it not suitable for publication in the present state, but of major concern is the methodology section. The data sources from which the entire results are based on are missing. The author’s stated that monthly incidence rates between 2006 and 2015 were studied, however failed to show yearly distribution of ABBSI in hospitals from the study sites. Much emphasis was laid on these raw data but none was showed, not in terms of charts or tables. Other minor issues have been highlighted in the manuscript. Reviewer #2: PONE-D-21-05493 Report In this manuscript the authors analyzed the seasonal changes of ABBSI in different climates, and its relationship with antibiotic resistance and climate control in hospitals. The manuscript seems scientifically sound, and contains some interesting results that can be considered for publication in PONE. However, before the decision of acceptance for publication is running, a very major revison of the manuscript is required. Specifically, the following points should be addressed by the authors: 1、In general, there is a lack of explanation of replicates and statistical methods used in the study. It is expected that the author can give a more detailed explanation or basis why SARIMA is selected in the time series analysis and multivariate Poisson regression models, is selected in the weather-dependent model. 2、Another major question needs to be explained by the author: why only three hospitals are selected, and is the argument for the conclusion sufficient? In addition, whether it is possible to increase the number of hospital cases selected in the same city (that is, under the same climatic conditions) to see if more interesting results can be obtained, and further confirm the conclusion. Reviewer #3: Review on “Seasonality and weather dependence of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil.” The study aims to determine the seasonal weather control of Acinetobacter baumannii complex bloodstream infections (ABBSI) in hospitals from different climatic regions of Brazil. The study conducted hospitals in three climatic zones of Brazil viz. Cfa, subtropical climate, humid (Botucatu São Paulo State, Southeast); Aw, tropical climate with dry winter (Goiânia Goiás State, Middle-west); and As, tropical with dry summer (Fortaleza, Ceará State, Northeast region). The values of monthly averaged climate parameters viz. temperature, relative humidity, and rainfall have been obtained from the INPE climate dataset. The monthly incidence rates of ABBSI (per 10,000 patient-days) have been calculated for Carbapenem-susceptible and Carbapenem-resistant cases separately and for climate control units and non-climate control units. The analysis using Seasonal Autoregressive Integrated Moving Average has been made. The study is novel and valuable. It would have a wider readership if it published in PLOS-One. Having said that, I feel the study requires major revision. My comments are mentioned below. 1. It is not clearly stated in the manuscript that why the authors intended to do such a study. The motivation and significance of the study need to be brought out clearly in the manuscript before its publication. 2. The authors have selected the hospitals in different climatic zone to understand the impact of the weather on ABBSI. The elevation and proximity of the ocean differ for all these stations. The author needs to justify how their experiment design does not affect by these factors in the revised manuscript. For the better readership of this paper, it will be helpful if authors supplement a detailed description of the SARIMA model in the revised manuscript. 3. Table 2 shows that ABBSI per (10000 patients-days) are more in climate control units than non-climate control units for Carbapenem-susceptible and Carbapenem-resistant cases. However, in conclusion, they have stated that “Strict temperature control may be a tool for prevention of A. baumanii infections in healthcare settings.” – It is confusing and need proper analysis and explanation. 4. The temperature, relative humidity, and rainfall have been analyzed to understand their impact on ABBSI incidences. Relative humidity and rainfall do not vary significantly over all three stations, as seen from the monthly average dataset. Therefore the variation of temperature has importance. However, it will be valuable if authors perform this study for non-rainy months and rainy months. The author needs to check spelling and grammar before submitting the revised manuscript. There are some typo-grammatical errors in the manuscript. ****** 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. 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: No Reviewer #3: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-21-05493_reviewer.pdf Attachment Submitted filename: PONE-review.docx https://doi.org/10.1371/journal.pone.0255593.r001
Revision 1
13 Jul 2021 Author Response RESPONSE TO REVIEWERS To the Editor and Reviewers – We thank you for extensively reading our manuscript and for your excellent comments. Whenever possible, we followed your recommendations and changed the manuscript accordingly. Changes in the revised manuscript are presented in red types (in the “track changes version”). We address each comment and recommendation bellow. Editorial team We note that Figure 1 in your submission contain map 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. Authors’ response: Figure 1 was generated in ArcGis (ESRI, Redlands, CA) and its copyrights belong to the authors. We included that information as a note in the figure. Reviewer #1 Reviewer #1: Many hospital-acquired blood stream infections worldwide have been attributed to Acinetobacter baumannii complex. The focus of this study was to assess the impact of seasons, weather parameters and climate control on the incidence as well as carbapenem-resistance in A. baumannii complex bloodstream infections in hospitals from three regions of Brazil with different climatic conditions. A major strength of this manuscript is the use of Box-Jenkins models, which allows for identifying seasonality in the dependent series (seasonally differencing it if necessary) from even retrospective datasets. Notwithstanding, the manuscript has a number of flaws that makes it not suitable for publication in the present state, but of major concern is the methodology section. The data sources from which the entire results are based on are missing. The author’s stated that monthly incidence rates between 2006 and 2015 were studied, however failed to show yearly distribution of ABBSI in hospitals from the study sites. Much emphasis was laid on these raw data but none was showed, not in terms of charts or tables. Other minor issues have been highlighted in the manuscript. Authors’ response: We thank Reviewer #1 for her/his comments. The data used for analysis were obtained in laboratory files in the study hospitals, and validated in accordance to databases from the infection control committee’s in every study hospital. We clarified that topic in the methodology section. A new figure (Figure 2) presenting time series of monthly ABBSI incidence was included. Also, we included a statement informing that raw data are submitted as supplementary file. We included the type of study in the abstract (ecologic study). Reviewer #2 In this manuscript the authors analyzed the seasonal changes of ABBSI in different climates, and its relationship with antibiotic resistance and climate control in hospitals. The manuscript seems scientifically sound, and contains some interesting results that can be considered for publication in PONE. However, before the decision of acceptance for publication is running, a very major revison of the manuscript is required. Specifically, the following points should be addressed by the authors: 1、In general, there is a lack of explanation of replicates and statistical methods used in the study. It is expected that the author can give a more detailed explanation or basis why SARIMA is selected in the time series analysis and multivariate Poisson regression models, is selected in the weather-dependent model. 2、Another major question needs to be explained by the author: why only three hospitals are selected, and is the argument for the conclusion sufficient? In addition, whether it is possible to increase the number of hospital cases selected in the same city (that is, under the same climatic conditions) to see if more interesting results can be obtained, and further confirm the conclusion. Authors’ response: We expanded explanations on the reasons for using Box-Jenkins models and Poisson regression. We used only three hospitals because, previously to 2013, there was no countrywide data on incidence of healthcare-associated pathogens. Those three hospitals agreed to share their data. We are aware that this does not provide a wide or representative sample of the country, but those were the data available for our analysis. We attempted to compare those hospitals from different areas rather than providing a representative overview of ABBSI incidence in Brazil. We included this limitation in the discussion section. Reviewer #3 The study aims to determine the seasonal weather control of Acinetobacter baumannii complex bloodstream infections (ABBSI) in hospitals from different climatic regions of Brazil. The study conducted hospitals in three climatic zones of Brazil viz. Cfa, subtropical climate, humid (Botucatu São Paulo State, Southeast); Aw, tropical climate with dry winter (Goiânia Goiás State, Middle-west); and As, tropical with dry summer (Fortaleza, Ceará State, Northeast region). The values of monthly averaged climate parameters viz. temperature, relative humidity, and rainfall have been obtained from the INPE climate dataset. The monthly incidence rates of ABBSI (per 10,000 patient-days) have been calculated for Carbapenem-susceptible and Carbapenem-resistant cases separately and for climate control units and non-climate control units. The analysis using Seasonal Autoregressive Integrated Moving Average has been made. The study is novel and valuable. It would have a wider readership if it published in PLOS-One. Having said that, I feel the study requires major revision. My comments are mentioned below. 1. It is not clearly stated in the manuscript that why the authors intended to do such a study. The motivation and significance of the study need to be brought out clearly in the manuscript before its publication. 2. The authors have selected the hospitals in different climatic zone to understand the impact of the weather on ABBSI. The elevation and proximity of the ocean differ for all these stations. The author needs to justify how their experiment design does not affect by these factors in the revised manuscript. For the better readership of this paper, it will be helpful if authors supplement a detailed description of the SARIMA model in the revised manuscript. 3. Table 2 shows that ABBSI per (10000 patients-days) are more in climate control units than non-climate control units for Carbapenem-susceptible and Carbapenem-resistant cases. However, in conclusion, they have stated that “Strict temperature control may be a tool for prevention of A. baumanii infections in healthcare settings.” – It is confusing and need proper analysis and explanation. 4. The temperature, relative humidity, and rainfall have been analyzed to understand their impact on ABBSI incidences. Relative humidity and rainfall do not vary significantly over all three stations, as seen from the monthly average dataset. Therefore the variation of temperature has importance. However, it will be valuable if authors perform this study for non-rainy months and rainy months. The author needs to check spelling and grammar before submitting the revised manuscript. There are some typo-grammatical errors in the manuscript. Authors’ response: 1. We included the following statement in the discussion: Rather than providing an overview of A. baumannii seasonality in Brazil, we were interested in investigating differences in ABBSI seasonal behavior in hospitals from different areas. We believe that this statement clarifies the intention of our study (as well as its limitations, such as those provided by the study design). 2. We included a more detailed description of the SARIMA model in the methods section (please see response to Reviewer #2). 3. The incidence was higher in climate controlled units because they were intensive care units, therefore harboring more severilly ill patients with invasive devices. However, we changed the conclusion section in order to avoid confusing messages. 4. We did preliminar analyes of rainy vs. non-rainy months and colder vs warmer seasons. They presented no statistical significance and did not relevantly expand our inferences. So we preferred to exclude them. As for typos and other errors, we performed an extensive revision of the manuscript. We thank Reviewer #3 for her/his comments and recommendations. We believe that the peer review process is a rich opportunity for important discussion on scientific relevance and methodology, and that reviewers’ comments and recommendations helped us improving our manuscript. We thank once again the reviewers and editor. Yours, The authors Attachments Attachment Submitted filename: PLOStiao_RESPONSE TO REVIEWERS.docx https://doi.org/10.1371/journal.pone.0255593.r002
21 Jul 2021 Decision Letter - Aleksandra Barac, Editor Seasonality and weather dependance of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil. PONE-D-21-05493R1 Dear Dr. Fortaleza, 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, Aleksandra Barac Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0255593.r003
Formally Accepted
10 Aug 2021 Acceptance Letter - Aleksandra Barac, Editor PONE-D-21-05493R1 Seasonality and weather dependance of Acinetobacter baumannii complex bloodstream infections in different climates in Brazil. Dear Dr. Fortaleza: 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. Aleksandra Barac Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0255593.r004

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