Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India

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The diagnostic landscape for enteric fever relies on traditional methods such as the Widal test and blood culture, each with inherent limitations regarding sensitivity and turnaround time. Methods The study will employ an Analytical Observational Study design conducted at Acharya Vinoba Bhave Rural Hospital in central India over a two-year period. Participants will include adults above 18 years admitted to the ward or Intensive Care Unit (ICU) with acute febrile illnesses. Inclusion criteria encompass a wide age range, ensuring a diverse study population. Peripheral blood samples will be collected for Salmonella PCR, Widal testing, and blood culture. Dot-PCR for Typhi will be employed, and DNA extraction will follow strict protocols. Data will be systematically recorded, and statistical analyses, including sensitivity, specificity, and comparative assessments, will be conducted to evaluate diagnostic performance. Expected Outcome It is anticipated that Salmonella PCR will exhibit superior sensitivity and specificity compared to traditional diagnostic methods, offering a more rapid and accurate identification of enteric fever cases. The study aims to contribute valuable evidence supporting the incorporation of Salmonella PCR into routine diagnostic algorithms, potentially revolutionizing the approach to enteric fever diagnosis. Moreover, insights gained from the study are expected to inform clinical practices, enhance patient management, and potentially reduce the economic burden associated with misdiagnosis or delayed diagnosis of enteric fever. The outcomes of this research are poised to impact public health strategies, providing a foundation for more effective and efficient diagnostic protocols in the context of enteric fever. 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F1000Research 2024, 13 :542 ( https://doi.org/10.12688/f1000research.145892.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Study Protocol Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] Dr.Khadija Hamdulay https://orcid.org/0009-0001-2737-2301 1 , Rajendra Ravekar 1 , Ashwini Tayade 1 Dr.Khadija Hamdulay https://orcid.org/0009-0001-2737-2301 1 , Rajendra Ravekar 1 , Ashwini Tayade 1 PUBLISHED 28 May 2024 Author details Author details 1 Medicine, Datta Meghe Institute of Higher Education and Research, Wardha, Maharashtra, 442001, India Dr.Khadija Hamdulay Roles: Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing Rajendra Ravekar Roles: Investigation, Methodology, Supervision, Validation, Visualization Ashwini Tayade Roles: Investigation, Supervision, Validation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Datta Meghe Institute of Higher Education and Research collection. Abstract Background Enteric fever, predominantly caused by Salmonella enterica serotype Typhi, remains a significant global health concern, particularly in resource-limited settings. The diagnostic landscape for enteric fever relies on traditional methods such as the Widal test and blood culture, each with inherent limitations regarding sensitivity and turnaround time. Methods The study will employ an Analytical Observational Study design conducted at Acharya Vinoba Bhave Rural Hospital in central India over a two-year period. Participants will include adults above 18 years admitted to the ward or Intensive Care Unit (ICU) with acute febrile illnesses. Inclusion criteria encompass a wide age range, ensuring a diverse study population. Peripheral blood samples will be collected for Salmonella PCR, Widal testing, and blood culture. Dot-PCR for Typhi will be employed, and DNA extraction will follow strict protocols. Data will be systematically recorded, and statistical analyses, including sensitivity, specificity, and comparative assessments, will be conducted to evaluate diagnostic performance. Expected Outcome It is anticipated that Salmonella PCR will exhibit superior sensitivity and specificity compared to traditional diagnostic methods, offering a more rapid and accurate identification of enteric fever cases. The study aims to contribute valuable evidence supporting the incorporation of Salmonella PCR into routine diagnostic algorithms, potentially revolutionizing the approach to enteric fever diagnosis. Moreover, insights gained from the study are expected to inform clinical practices, enhance patient management, and potentially reduce the economic burden associated with misdiagnosis or delayed diagnosis of enteric fever. The outcomes of this research are poised to impact public health strategies, providing a foundation for more effective and efficient diagnostic protocols in the context of enteric fever. READ ALL READ LESS Keywords Enteric Fever, Salmonella PCR, Diagnostic Accuracy, Widal Test, Analytical Observational Study, Central India Corresponding Author(s) Dr.Khadija Hamdulay ( [email protected] ) Close Corresponding author: Dr.Khadija Hamdulay Competing interests: No competing interests were disclosed. Grant information: The author(s) declared that no grants were involved in supporting this work. Copyright: © 2024 Hamdulay DK et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Hamdulay DK, Ravekar R and Tayade A. Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.12688/f1000research.145892.1 ) First published: 28 May 2024, 13 :542 ( https://doi.org/10.12688/f1000research.145892.1 ) Latest published: 28 May 2024, 13 :542 ( https://doi.org/10.12688/f1000research.145892.1 ) Introduction Enteric fever, predominantly caused by Salmonella enterica serotype Typhi, continues to pose a significant public health challenge, particularly in resource-limited settings. 1 Current diagnostic methods, such as the Widal test and blood culture, have sensitivity, specificity, and turnaround time limitations, necessitating a search for more accurate and efficient diagnostic modalities. 2 Polymerase Chain Reaction (PCR) technology has emerged as a promising tool for detecting bacterial pathogens, offering potential advantages in terms of sensitivity and rapidity. 3 Previous studies have highlighted the diagnostic potential of Salmonella PCR in various clinical settings, demonstrating its ability to complement traditional methods. 4 However, limited research has been conducted in the context of enteric fever, particularly in the central Indian region. This study protocol aims to address this gap by conducting an Analytical Observational Study to systematically evaluate the diagnostic efficacy of Salmonella PCR and compare it with routine laboratory parameters, including Widal test and blood culture. The study will be conducted at Acharya Vinoba Bhave Rural Hospital (AVBRH), a tertiary care teaching hospital in central India. The research design, encompassing two years, adheres to ethical guidelines and seeks to enroll a diverse cohort of adult patients admitted with acute febrile illnesses. Aim Salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever. Objectives 1. To diagnose enteric fever in patients with acute febrile Illness by Widal and blood culture test. 2. To perform Salmonella PCR in diagnosed cases of enteric fever. 3. To compare Salmonella PCR with typhi dot, Widal and blood culture. Methods Study design This study will employ an Analytical Observational Study design to assess the diagnostic efficacy of Salmonella Polymerase Chain Reaction (PCR) and its comparison with routine laboratory parameters in cases of enteric fever. Study population The study will include individuals above the age of 18 years who are admitted to the ward or Intensive Care Unit (ICU) with acute febrile illnesses. The participants will be selected based on predefined inclusion and exclusion criteria. Participants Inclusion criteria: • Individuals aged 18 years and above. • Patients admitted to the ward or ICU with acute febrile illnesses. Exclusion criteria: • Individuals below the age of 18 years. • Patients admitted with a confirmed diagnosis other than enteric fever (e.g., malaria, dengue). • Those who refuse to participate in the study. Place of study The study will be conducted at Acharya Vinoba Bhave Rural Hospital (AVBRH), a tertiary care teaching hospital located in Sawangi, Meghe, in the rural sector of Wardha district, Central India. The outpatient medicine department at AVBRH will be the primary site for participant enrollment and data collection. This setting has been chosen due to its accessibility, relevance to the study population, and the availability of necessary facilities for conducting the required diagnostic tests. Ethical approval will be obtained from the Institute’s review board before the initiation of the study, ensuring adherence to ethical guidelines and standards. The study will span two years, from March 2023 to March 2025, during which data will be systematically collected and analyzed to fulfill the study objectives. Ethics and consent The research protocol got approval from the Datta Meghe Institute of Higher Education and Research (Deemed to be university) Institutional ethical committee in the meeting held on 11-07-2022 with DMIMS (DU)/IEC/2022/28. All the participants will be educated about the research, and written and verbal informed consent will be obtained from all the participants before the intervention. Sample size consideration In an Analytical Observational Study context, the sample size is calculated using a specific formula. The formula, represented as Z 2 1-a/2 Sens(1-Sens) > 2d X Prev, considers various parameters for precise determination. Alpha (a) is set at 0.05, representing the significance level. The estimated sensitivity (Sens) is designated as 0.99, indicating the test’s ability to identify true positive cases correctly. The prevalence of the disease (Prev) is defined as 0.5, reflecting the anticipated frequency of the condition within the population. Additionally, an estimation error (d) of 0.03 is considered. By applying this formula, the minimum number of diseases required for the study is calculated to be 43, and correspondingly, the minimum total sample size needed is 86. These calculations are pivotal for ensuring the statistical robustness of the analytical observational study, facilitating reliable and meaningful conclusions. Procedure The data collection process for this study involves a systematic series of steps designed to gather relevant information and conduct diagnostic tests among eligible participants. To begin, potential participants meeting the study’s inclusion criteria are identified, and informed consent is obtained from those willing to contribute to the research. A thorough clinical assessment is conducted, encompassing detailed medical history, symptom evaluation, and physical examinations. Blood sample collection is a critical step with strict adherence to aseptic techniques. Two milliliters of blood are drawn into an EDTA vial for Salmonella PCR, while an additional 3 milliliters are collected in plain tubes for the Widal test. Proper labeling and documentation ensure the integrity of the collected samples. Subsequently, the Widal agglutination test is performed on the blood samples, utilizing commercially manufactured colored antigens for Salmonella Typhi O and H antigens. Results are interpreted based on observed agglutination reactions and titers. Simultaneously, blood culture procedures are initiated by drawing 5 milliliters of blood and placing it into Brain Heart Infusion (BHI) broth under strict sterile conditions. With all aseptic precautions nearly 30-40 ml of blood was sent for culture and automated mics. Daily monitoring for bacterial growth is undertaken, and blind subculture is implemented without observable progress. Verification of bacterial identity is accomplished through biochemical testing and specialized antisera. Specifically, for Typhi, a dot-PCR is conducted using the appropriate primers, following standard PCR procedures, including DNA extraction, amplification, and gel electrophoresis. Additionally, polymerase chain reaction (PCR) for Salmonella is executed by extracting total DNA from blood samples using SDS and proteinase K. Real-time PCR techniques are employed for accurate and efficient detection, incorporating positive controls ( Salmonella typhi DNA) and negative controls (DNA from E. coli , A. baumannii , and S. pneumoniae ) to ensure the reliability of results. Strict ethical considerations are maintained throughout the data collection process, including participant confidentiality, privacy protection, and compliance with institutional ethical review board approvals. All pertinent data, including clinical information, test results, and participant demographics, are meticulously recorded in a structured database. The study spans from March 2023 to March 2025, during which these procedures will be carried out to fulfill the research objectives. Outcome measures Primary outcome The primary outcome measure of this study is the diagnostic accuracy of Salmonella Polymerase Chain Reaction (PCR) in identifying enteric fever among patients with acute febrile illnesses. The primary focus is assessing the sensitivity, specificity, positive predictive value, and negative predictive value of Salmonella PCR compared to the reference standards of Widal testing and blood culture. Secondary outcomes: 1. Comparative diagnostic performance: • Evaluate and compare the diagnostic performance of Salmonella PCR with routine laboratory parameters, including Widal test and blood culture. • Assess the concordance and discrepancies between the results of Salmonella PCR, Widal test, and blood culture. 2. Clinical utility and practicality: • Explore the practicality and feasibility of implementing Salmonella PCR in routine clinical settings. • Examine the turnaround time for Salmonella PCR compared to traditional diagnostic methods. 3. Impact on patient management: • Investigate the impact of Salmonella PCR results on patient management and clinical decision-making. • Assess whether using Salmonella PCR leads to more timely and accurate interventions. 4. Cost-effectiveness analysis: • Conduct a preliminary cost-effectiveness analysis comparing the expenses associated with Salmonella PCR and routine laboratory parameters. • Evaluate the economic implications of incorporating Salmonella PCR into the diagnostic algorithm for enteric fever. 5. Subgroup analysis: • Explore the diagnostic performance of Salmonella PCR in specific subgroups, such as age categories or severity of illness. • Identify potential variations in sensitivity and specificity across different patient characteristics. Data management Efficient data management is integral to the study’s success, ensuring the collected information’s accuracy, security, and confidentiality. Standardized data collection forms and electronic databases will be employed, accompanied by unique identifiers to protect participant confidentiality. Trained personnel will ensure timely and precise data entry, incorporating validation checks and double-entry verification processes to minimize errors. Electronic data will be securely stored on restricted-access servers, with regular backup procedures to prevent data loss. Physical copies of data, if any, will be stored in locked and secure locations. Adherence to institutional and ethical guidelines for data security will be paramount, including encryption and password protection for electronic databases. Periodic data quality checks, audit trails, and the establishing of a Data Monitoring Committee will contribute to ongoing quality control. The study will use statistical software R Studio 4.3.1 to analyze exploratory data and identify patterns and trends. Reports will be generated for internal use and dissemination, with considerations for anonymized data-sharing aligned with ethical guidelines. A robust data archiving plan will be implemented for long-term storage, ensuring accessibility and compliance with data retention policies. Through these measures, the study aims to uphold the integrity and reliability of the collected data, facilitating accurate analysis and contributing to the overall success of the research. Statistical methods The statistical analysis for this study will encompass a multifaceted approach to assess the diagnostic accuracy of Salmonella Polymerase Chain Reaction (PCR) and compare its outcomes with routine laboratory parameters in cases of enteric fever. The initial steps involve descriptive statistics to summarize participant demographics and baseline characteristics. Diagnostic accuracy measures will be calculated for Salmonella PCR, Widal test, and blood culture, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Receiver operating characteristic (ROC) curves and the area under the curve (AUC) will be utilized to gauge overall diagnostic performance. Comparative analyses will be conducted using statistical tests like McNemar’s test to discern differences between Salmonella PCR and routine laboratory parameters. Subgroup analyses based on factors such as age, gender, and illness severity will be performed to explore potential variations in diagnostic accuracy. The study will also evaluate the practicality and feasibility of implementing Salmonella PCR in routine clinical settings and assess its impact on patient management. Cost-effectiveness analysis will compare the economic implications of Salmonella PCR with routine parameters. Regression analysis, if applicable, will identify factors influencing diagnostic outcomes. The statistical analyses will be executed using R studio Version 4.3.1, and results will be presented transparently, adhering to predetermined significance levels. Visual representations will be created to illustrate key findings. The study aims to derive comprehensive insights into the diagnostic utility of Salmonella PCR, contributing to evidence-based advancements in clinical practice and diagnostic protocols. Dissemination After the completion of the study, we will publish it in an indexed journal or conference. Study status The study has not yet started after the publication of the protocol; we will start recruitment in the study. Discussion The emergence of enteric fever, driven primarily by Salmonella enterica serotype Typhi, presents a persistent public health challenge globally. 1 Diagnostic accuracy is paramount for effective clinical management and preventing complications associated with this infectious disease. 5 The proposed study protocol seeks to address existing limitations in diagnostic methodologies by evaluating the diagnostic efficacy of Salmonella Polymerase Chain Reaction (PCR) and comparing it with routine laboratory parameters such as the Widal test and blood culture. The choice of Salmonella PCR as a diagnostic tool is grounded in its potential to overcome some of the limitations associated with traditional methods. Previous research has indicated that PCR-based assays can provide enhanced sensitivity and specificity, facilitating early and accurate detection of bacterial pathogens. 6 This aligns with the study’s primary aim of determining the diagnostic accuracy of Salmonella PCR in identifying cases of enteric fever. Including routine laboratory parameters, specifically the Widal test and blood culture, allows for a comprehensive comparison, considering established diagnostic practices. Despite being widely used, Widal testing has faced criticism for its variable sensitivity and specificity. 2 While considered a gold standard, blood culture is constrained by longer turnaround times and potential false negatives, especially in patients receiving prior antibiotic treatment. 7 The study’s analytical observational design aims to provide robust evidence regarding the diagnostic performance of Salmonella PCR in a real-world clinical setting. This research will contribute valuable insights into the potential utility of PCR as a complementary or alternative diagnostic tool for enteric fever. The comprehensive data collection approach, including dot-PCR for Typhi, will further enhance our understanding of the molecular characteristics of Salmonella strains prevalent in the study population. The findings from this study may have implications for clinical practice, guiding healthcare professionals in selecting appropriate diagnostic methods for enteric fever. The potential inclusion of cost-effectiveness analysis will add a practical dimension to the discussion, addressing the economic feasibility of incorporating Salmonella PCR into routine diagnostic algorithms. While the study’s proposed setting, Acharya Vinoba Bhave Rural Hospital, offers a unique perspective from central India, it is essential to acknowledge potential limitations such as regional variations in bacterial strains and healthcare infrastructure. Additionally, the study duration of two years may not capture long-term trends, necessitating ongoing surveillance. Data availability No data are associated with this article. References 1. Crump JA, Mintz ED: Global trends in typhoid and paratyphoid fever. Clin. Infect. Dis. 2010; 50 : 241–246. PubMed Abstract | Publisher Full Text | Free Full Text 2. House D, Wain J, Ho VA, et al. : Serology of Typhoid Fever in an Area of Endemicity and Its Relevance to Diagnosis. J. Clin. Microbiol. 2001; 39 : 1002–1007. PubMed Abstract | Publisher Full Text | Free Full Text 3. Schluger NW, Kinney D, Harkin TJ, et al. : Clinical utility of the polymerase chain reaction in diagnosing infections due to Mycobacterium tuberculosis. Chest. 1994; 105 : 1116–1121. Publisher Full Text 4. Kumar R, Gupta N: Shalini: Multidrug-resistant typhoid fever. Indian J. Pediatr. 2007; 74 : 39–42. Publisher Full Text 5. Parry CM, Hien TT, Dougan G, et al. : Typhoid fever. N. Engl. J. Med. 2002; 347 : 1770–1782. Publisher Full Text 6. Kariuki S, Revathi G, Muyodi J, et al. : Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya. J. Clin. Microbiol. 2004; 42 : 1477–1482. PubMed Abstract | Publisher Full Text | Free Full Text 7. Parry CM, Threlfall EJ: Antimicrobial resistance in typhoidal and nontyphoidal salmonellae. Curr. Opin. Infect. Dis. 2008; 21 : 531–538. Publisher Full Text Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 28 May 2024 ADD YOUR COMMENT Comment Author details Author details 1 Medicine, Datta Meghe Institute of Higher Education and Research, Wardha, Maharashtra, 442001, India Dr.Khadija Hamdulay Roles: Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing Rajendra Ravekar Roles: Investigation, Methodology, Supervision, Validation, Visualization Ashwini Tayade Roles: Investigation, Supervision, Validation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information The author(s) declared that no grants were involved in supporting this work. Article Versions (1) version 1 Published: 28 May 2024, 13:542 https://doi.org/10.12688/f1000research.145892.1 Copyright © 2024 Hamdulay DK et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Hamdulay DK, Ravekar R and Tayade A. Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.12688/f1000research.145892.1 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 1 VERSION 1 PUBLISHED 28 May 2024 Views 0 Cite How to cite this report: Abraham D. Reviewer Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r322560 ) The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-322560 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 12 Sep 2024 Dilip Abraham , Christian Medical College Vellore, Vellore, Tamil Nadu, India Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.159910.r322560 This is a protocol document for a study that aims to compare PCR for Salmonella Typhi against other methods like blood culture, Widal and Typhidot. The rationale for the study is well described in the abstract and ... Continue reading READ ALL This is a protocol document for a study that aims to compare PCR for Salmonella Typhi against other methods like blood culture, Widal and Typhidot. The rationale for the study is well described in the abstract and the introduction. However, the authors have not described the rationale for using other diagnostic modalities like Widal and Typhidot when it is well documented that this is inferior in sensitivity and specificity to blood culture. The authors have also not described how they would interpret a Widal; if this is a hospital study, paired sampling to observe an increase in titres might not be possible. The authors have not explained why they have excluded patients less than 18 years. Individuals less than 18 years form a huge part of the burden of typhoid in India and they are also the target of the TCV vaccine. The sampling frame is not ideal for the study design; patients admitted to the ward would just be a subset of the patients with typhoid and the reviewer would suggest including outpatients as well. The authors have described the methods for Widal and blood culture, but they have not described satisfactorily the Salmonella PCR method which is the major focus of the study. There is no description of the targets other than “appropriate primers” that they are planning to use. This is problematic because even if they will be developing new primers, that process should be detailed in brief. They have not referenced any article that have examined this work earlier, and there are multiple articles regarding this. In the data analysis section, they have stated that diagnostic accuracy measures will be carried out in for PCR, Widal and blood culture. In that case, which would be the gold standard method they are comparing this against? If they do not consider blood culture to be the gold standard, they have not stated any plans to do a latent class analysis. In the discussion, they have stated that “blood culture is constrained by longer turnaround times and potential false negatives, especially in patients receiving prior antibiotic treatment.” If that is so, how would PCR be any better than blood culture considering bacteremia even at the height of Typhoid is ~ 1 bacteria/ml. If they are planning to enrich the blood prior to PCR, this should be described. Is the rationale for, and objectives of, the study clearly described? Yes Is the study design appropriate for the research question? No Are sufficient details of the methods provided to allow replication by others? No Are the datasets clearly presented in a useable and accessible format? Not applicable Competing Interests: No competing interests were disclosed. Reviewer Expertise: Clinical microbiology, wastewater surveillance, gut microbiome I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Abraham D. Reviewer Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r322560 ) The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-322560 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Njarekkattuvalappil SK. Reviewer Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r288462 ) The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-288462 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 14 Jun 2024 Swathi Krishna Njarekkattuvalappil , Bharati Vidyapeeth Medical College (Deemed University), Pune, Maharashtra, India Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.159910.r288462 This is a protocol paper which details a study about to take place. The objectives 1 & 2 of the study seem to be inappropriate. From the text, what we understand is that the primary objective of the study ... Continue reading READ ALL This is a protocol paper which details a study about to take place. The objectives 1 & 2 of the study seem to be inappropriate. From the text, what we understand is that the primary objective of the study is to estimate the diagnostic accuracy of Salmonella PCR as compared to a composite score of Widal + blood culture. Hence the objectives need to be re-framed. The study design is mentioned as 'analytical observational' study. But it is not clear as to what type of analytical observational study is planned. In analytical observational studies, researchers try to establish an association between exposure(s) and outcome(s). Depending on the direction of enquiry, these studies can be directed forwards (cohort studies) or backwards (case–control studies). (1) If it is a diagnostic accuracy (DA) study, it should be explicitly mentioned what type it is- DA case-control, DA cross sectional or DA comparative studies. (2) Inclusion criteria needs to be more specific. Are you going to do a blood culture, Widal and PCR on all febrile illness cases? Is there any duration of fever cut off? And are these tests going to be done in series or in parallel? In calculating the sample size, why was a prevalence of 0.5 used? There is already indexed literature on prevalence of laboratory confirmed typhoid in India. (3) One of the secondary outcomes expected is mentioned as a cost-effectiveness analysis of Salmonella PCR for typhoid diagnosis. How is this analysis planned? With current methodology in the manuscript, it seems to lack those details. Enteric fever involves both typhoid and paratyphoid. Are you considering paratyphi also here or are you excluding those? Is the rationale for, and objectives of, the study clearly described? No Is the study design appropriate for the research question? No Are sufficient details of the methods provided to allow replication by others? Partly Are the datasets clearly presented in a useable and accessible format? Not applicable References 1. Ranganathan P, Aggarwal R: Study designs: Part 3 - Analytical observational studies. Perspect Clin Res . 2019; 10 (2): 91-94 PubMed Abstract | Publisher Full Text 2. Chassé M, Fergusson DA: Diagnostic Accuracy Studies. Semin Nucl Med . 2019; 49 (2): 87-93 PubMed Abstract | Publisher Full Text 3. John J, Van Aart CJ, Grassly NC: The Burden of Typhoid and Paratyphoid in India: Systematic Review and Meta-analysis. PLoS Negl Trop Dis . 2016; 10 (4): e0004616 PubMed Abstract | Publisher Full Text Competing Interests: No competing interests were disclosed. Reviewer Expertise: Infectious disease epidemiology, operational research I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Njarekkattuvalappil SK. Reviewer Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r288462 ) The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-288462 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Comments on this article Comments (0) Version 1 VERSION 1 PUBLISHED 28 May 2024 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 Version 1 28 May 24 read read Swathi Krishna Njarekkattuvalappil , Bharati Vidyapeeth Medical College (Deemed University), Pune, India Dilip Abraham , Christian Medical College Vellore, Vellore, India Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Abraham D. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 12 Sep 2024 | for Version 1 Dilip Abraham , Christian Medical College Vellore, Vellore, Tamil Nadu, India 0 Views copyright © 2024 Abraham D. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This is a protocol document for a study that aims to compare PCR for Salmonella Typhi against other methods like blood culture, Widal and Typhidot. The rationale for the study is well described in the abstract and the introduction. However, the authors have not described the rationale for using other diagnostic modalities like Widal and Typhidot when it is well documented that this is inferior in sensitivity and specificity to blood culture. The authors have also not described how they would interpret a Widal; if this is a hospital study, paired sampling to observe an increase in titres might not be possible. The authors have not explained why they have excluded patients less than 18 years. Individuals less than 18 years form a huge part of the burden of typhoid in India and they are also the target of the TCV vaccine. The sampling frame is not ideal for the study design; patients admitted to the ward would just be a subset of the patients with typhoid and the reviewer would suggest including outpatients as well. The authors have described the methods for Widal and blood culture, but they have not described satisfactorily the Salmonella PCR method which is the major focus of the study. There is no description of the targets other than “appropriate primers” that they are planning to use. This is problematic because even if they will be developing new primers, that process should be detailed in brief. They have not referenced any article that have examined this work earlier, and there are multiple articles regarding this. In the data analysis section, they have stated that diagnostic accuracy measures will be carried out in for PCR, Widal and blood culture. In that case, which would be the gold standard method they are comparing this against? If they do not consider blood culture to be the gold standard, they have not stated any plans to do a latent class analysis. In the discussion, they have stated that “blood culture is constrained by longer turnaround times and potential false negatives, especially in patients receiving prior antibiotic treatment.” If that is so, how would PCR be any better than blood culture considering bacteremia even at the height of Typhoid is ~ 1 bacteria/ml. If they are planning to enrich the blood prior to PCR, this should be described. Is the rationale for, and objectives of, the study clearly described? Yes Is the study design appropriate for the research question? No Are sufficient details of the methods provided to allow replication by others? No Are the datasets clearly presented in a useable and accessible format? Not applicable Competing Interests No competing interests were disclosed. Reviewer Expertise Clinical microbiology, wastewater surveillance, gut microbiome I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Abraham D. Peer Review Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r322560) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-322560 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Njarekkattuvalappil S. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 14 Jun 2024 | for Version 1 Swathi Krishna Njarekkattuvalappil , Bharati Vidyapeeth Medical College (Deemed University), Pune, Maharashtra, India 0 Views copyright © 2024 Njarekkattuvalappil S. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Not Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This is a protocol paper which details a study about to take place. The objectives 1 & 2 of the study seem to be inappropriate. From the text, what we understand is that the primary objective of the study is to estimate the diagnostic accuracy of Salmonella PCR as compared to a composite score of Widal + blood culture. Hence the objectives need to be re-framed. The study design is mentioned as 'analytical observational' study. But it is not clear as to what type of analytical observational study is planned. In analytical observational studies, researchers try to establish an association between exposure(s) and outcome(s). Depending on the direction of enquiry, these studies can be directed forwards (cohort studies) or backwards (case–control studies). (1) If it is a diagnostic accuracy (DA) study, it should be explicitly mentioned what type it is- DA case-control, DA cross sectional or DA comparative studies. (2) Inclusion criteria needs to be more specific. Are you going to do a blood culture, Widal and PCR on all febrile illness cases? Is there any duration of fever cut off? And are these tests going to be done in series or in parallel? In calculating the sample size, why was a prevalence of 0.5 used? There is already indexed literature on prevalence of laboratory confirmed typhoid in India. (3) One of the secondary outcomes expected is mentioned as a cost-effectiveness analysis of Salmonella PCR for typhoid diagnosis. How is this analysis planned? With current methodology in the manuscript, it seems to lack those details. Enteric fever involves both typhoid and paratyphoid. Are you considering paratyphi also here or are you excluding those? Is the rationale for, and objectives of, the study clearly described? No Is the study design appropriate for the research question? No Are sufficient details of the methods provided to allow replication by others? Partly Are the datasets clearly presented in a useable and accessible format? Not applicable References 1. Ranganathan P, Aggarwal R: Study designs: Part 3 - Analytical observational studies. Perspect Clin Res . 2019; 10 (2): 91-94 PubMed Abstract | Publisher Full Text 2. Chassé M, Fergusson DA: Diagnostic Accuracy Studies. Semin Nucl Med . 2019; 49 (2): 87-93 PubMed Abstract | Publisher Full Text 3. John J, Van Aart CJ, Grassly NC: The Burden of Typhoid and Paratyphoid in India: Systematic Review and Meta-analysis. PLoS Negl Trop Dis . 2016; 10 (4): e0004616 PubMed Abstract | Publisher Full Text Competing Interests No competing interests were disclosed. Reviewer Expertise Infectious disease epidemiology, operational research I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Njarekkattuvalappil SK. Peer Review Report For: Analytical observational study of salmonella PCR and its comparison with routine laboratory parameters in cases of enteric fever in tertiary care hospital in central India [version 1; peer review: 2 not approved] . F1000Research 2024, 13 :542 ( https://doi.org/10.5256/f1000research.159910.r288462) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/13-542/v1#referee-response-288462 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. Consider the following examples, but note that this is not an exhaustive list: Examples of 'Non-Financial Competing Interests' Within the past 4 years, you have held joint grants, published or collaborated with any of the authors of the selected paper. You have a close personal relationship (e.g. parent, spouse, sibling, or domestic partner) with any of the authors. You are a close professional associate of any of the authors (e.g. scientific mentor, recent student). You work at the same institute as any of the authors. 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