Use of multiplex PCR in pleural effusion: is it necessary to change the paradigm of culture-based methods?
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The microbiological diagnosis of pleural effusion is based largely on classical microbiology methods, but these methods have a high rate of false negative results. Some previous studies have shown improved diagnostic performance for pathogens such as Streptococcus pneumoniae using molecular biology methods. We present the use of a multiplex PCR platform (BIOFIRE FILMARRAY Pneumonia Panel) for the aetiological diagnosis of pleural effusion in paediatric pneumonia. We present a case series of 17 pleural fluid samples that were processed by culture-based microbiology and molecular biology methods. Microbiological isolation was successful in four cases (25 %) through traditional culture methods. In contrast, the molecular biology panels allowed for detection in 16 out of 17 cases (94 %). The results from these panels led to a change in management for nine out of the 17 cases (52 %). This study found an increase in aetiological diagnosis in complicated pneumonia in children by using molecular biology methods, which led to a significant change in patient management.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. All comments by the reviewers have been satisfactorily addressed.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
The manuscript is describing an application of multiplex PCR in pleural effusion. It is interesting and well written. Overall, the methodology is sound, the results well presented and the literature sources of good quality and relevance. Few minor corrections: Abstract: provide values and statistics Abstract: At the end provide a sentence about the medical importance of your findings. Methods: provide more details about the statistical tests that were used. The Discussion needs more references of similar studies. Are you sure there are only two? What about non-empyema cases? All microbial genus names have to be in italics
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
Comments to Author
The manuscript is describing an application of multiplex PCR in pleural effusion. It is interesting and well written. Overall, the methodology is sound, the results well presented and the literature sources of good quality and relevance. Few minor corrections: Abstract: provide values and statistics Abstract: At the end provide a sentence about the medical importance of your findings. Methods: provide more details about the statistical tests that were used. The Discussion needs more references of similar studies. Are you sure there are only two? What about non-empyema cases? All microbial genus names have to be in italics
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
In this manuscript by London-Ruiz et al, the authors evaluate a multiplex-pcr platform to identify the etiological agents of pleural effusion in pediatric pneumonia. They use this platform on 17 cases identifying the agent and compare this method with the standard procedure of bacterial cultures. The authors reach the conclusion that this method is worthy to be considered for implementation in clinical diagnosis. Although the results presented in the table are clear, there are a few things that should be clarified before the manuscript is suitable for publication. Major points: 1. The authors decided to use the BIOFIRE® FILMARRAY® Pneumonia Panel following manufacturer's recommendations. However, as they state in line 166 this platform is not FDA approved for use in pleural fluid samples. Why did the …
Comments to Author
In this manuscript by London-Ruiz et al, the authors evaluate a multiplex-pcr platform to identify the etiological agents of pleural effusion in pediatric pneumonia. They use this platform on 17 cases identifying the agent and compare this method with the standard procedure of bacterial cultures. The authors reach the conclusion that this method is worthy to be considered for implementation in clinical diagnosis. Although the results presented in the table are clear, there are a few things that should be clarified before the manuscript is suitable for publication. Major points: 1. The authors decided to use the BIOFIRE® FILMARRAY® Pneumonia Panel following manufacturer's recommendations. However, as they state in line 166 this platform is not FDA approved for use in pleural fluid samples. Why did the authors select this platform then? Are others more suitable for the clinical samples interrogated? 2. If this platform is not approved, the authors need to explain how they controlled the pcr samples. What positive and negative controls were used? How can they identify false positive/negative results in coinfections and in single species infection? How where the samples stored prior to analyses? These details should be included in the materials and methods and discussed as it is known that storage conditions of PE samples can affect PCR results. Minor points: 1. Have the authors, following the kit's recommendation, performed semi-quantitative analysis for the most common bacteria identified? Did they check for presence of resistance genes? 2. The authors should discuss the impact of anaerobes (if any) in pediatric pneumonia as has been the case in adults. 3. Reference missing in line 50. 1. Methodological rigour, reproducibility and availability of underlying data Reproducibility will be very difficult with these specific clinical samples. 2. Presentation of results Results are presented in a clear way with the table provided. However the authors could make a graph with the bacteria identified as a percentage of samples to help readers. 3. How the style and organization of the paper communicates and represents key findings Key findings are clearly presented 4. Literature analysis or discussion Certain points can be added to the discussion (see Major points 1, 2)
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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