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Erschienen in: Critical Care 1/2024

Open Access 01.12.2024 | Matters Arising

Bias caused by sample selection for lower respiratory tract microbiome research

verfasst von: Mingqiang Wang, Xiaojie Li

Erschienen in: Critical Care | Ausgabe 1/2024

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This comment refers to the article available online at https://​doi.​org/​10.​1186/​s13054-024-04922-2.
Mingqiang Wang and Xiaojie Li are contributed equally.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Dear Editor,
We read the article by Imbert et al. [1] published on Critical Care with great interest. The authors described the characteristics of the lower respiratory tract microbiota (specifically bacteria and fungi) in patients with ARDS caused by COVID-19, influenza A, and bacterial pneumonia. Here, we offer two suggestions for the authors to consider.
Firstly, we have doubts about whether endotracheal aspirates (ETAs) can characterize the lower respiratory tract microbiota of these diseases. COVID-19 and influenza A virus primarily cause interstitial pneumonia. Over the past three years, we have encountered numerous COVID-19 patients, and a common characteristic among them is the minimal presence of sputum, particularly in cases of pure viral infection, which becomes even more apparent after negative fluid balance. Consequently, we often say that ARDS caused by COVID-19 is not typical ARDS, as these patients exhibit minimal alveolar exudation [2]. In this scenario, obtaining ETA specimens from COVID-19 patients may not represent the majority of typical COVID-19 cases. These ETA specimens could either be: 1. upper respiratory tract contaminants aspirated into the lower respiratory tract rather than originating from the lower respiratory tract; or 2. patients who not only have COVID-19 but also concurrent other infections. Here, we recommend bronchoalveolar lavage fluid as the preferred sample for studying the lower respiratory tract microbiota, as outlined in the design of an ongoing prospective, multicenter study (NCT06114784).
Secondly, there is another bias in the sample collection process of this study. The COVID-19 samples for this study were collected during the early stages of the pandemic in 2020. At that time, the sample collection and processing procedures strictly adhered to sterile protocols, including inactivation of the viruses (which seems less likely to be implemented in bacterial pneumonia). It is unclear whether the processing of ETA samples for COVID-19 in this study was the same as for other ETA samples. Different processing procedures for lower respiratory tract samples with very low microbial content can significantly affect the conclusions of the experiments.
We believe that if the author could answer or partially answer these two questions, it would enhance the credibility of this study. High quality samples are the guarantee of obtaining reliable results. Meanwhile, we suggest that researchers need to carefully consider the potential biases caused by sample types and sample processing.

Declarations

None.

Competing interests

The authors declare no competing interests..
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://​creativecommons.​org/​licenses/​by/​4.​0/​. The Creative Commons Public Domain Dedication waiver (http://​creativecommons.​org/​publicdomain/​zero/​1.​0/​) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Literatur
1.
Zurück zum Zitat Imbert S, Revers M, Enaud R, et al. Lower airway microbiota compositions differ between influenza, COVID-19 and bacteria-related acute respiratory distress syndromes. Crit Care. 2024;28:133.CrossRefPubMedPubMedCentral Imbert S, Revers M, Enaud R, et al. Lower airway microbiota compositions differ between influenza, COVID-19 and bacteria-related acute respiratory distress syndromes. Crit Care. 2024;28:133.CrossRefPubMedPubMedCentral
2.
Zurück zum Zitat Oldani S, Ravaglia C, Bensai S, et al. Pathophysiology of light phenotype SARS-CoV-2 interstitial pneumonia: from histopathological features to clinical presentations. Pulmonology. 2022;28(5):333–44.CrossRefPubMed Oldani S, Ravaglia C, Bensai S, et al. Pathophysiology of light phenotype SARS-CoV-2 interstitial pneumonia: from histopathological features to clinical presentations. Pulmonology. 2022;28(5):333–44.CrossRefPubMed
Metadaten
Titel
Bias caused by sample selection for lower respiratory tract microbiome research
verfasst von
Mingqiang Wang
Xiaojie Li
Publikationsdatum
01.12.2024
Verlag
BioMed Central
Erschienen in
Critical Care / Ausgabe 1/2024
Elektronische ISSN: 1364-8535
DOI
https://doi.org/10.1186/s13054-024-04934-y

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