Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
18 10 2023
18 10 2023
Historique:
received:
03
06
2023
accepted:
14
10
2023
medline:
23
10
2023
pubmed:
19
10
2023
entrez:
18
10
2023
Statut:
epublish
Résumé
Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted to the intensive care unit (ICU) with severe community acquired pneumonia (CAP) between 2019 and 2021 in comparison with a control group of 6 patients undergoing digestive surgery. As a second objective, the diagnostic capabilities of metagenomics was also studied in a small group of selected patients. The lung microbiome of patients with viral (5 with Influenza A and 8 with SARS-CoV-2) pneumonia at admission showed a similar diversity as the control group (p = 0.140 and p = 0.213 respectively). Contrarily, the group of 12 patients with pneumococcal pneumonia showed a significant lower Simpson´s index (p = 0.002). In the control group (n = 6) Proteobacteria (36.6%), Firmicutes (24.2%) and Actinobacteria (23.0%) were the predominant phyla. In SARS-CoV-2 patients (n = 8), there was a predominance of Proteobacteria (mean 41.6%) (Moraxella and Pelomonas at the genus level), Actinobacteria (24.6%) (Microbacterium) and Firmicutes (22.8%) mainly Streptococcus, Staphylococcus and Veillonella. In patients with Influenza A pneumonia (n = 5) there was a predominance of Firmicutes (35.1%) mainly Streptococcus followed by Proteobacteria (29.2%) (Moraxella, Acinetobacter and Pelomonas). In the group of pneumococcal pneumonia (n = 12) two phyla predominated: Firmicutes (53.1%) (Streptococcus) and Proteobacteria (36.5%) (Haemophilus). In the 7 patients with non-pneumococcal bacterial pneumonia Haemophilus influenzae (n = 2), Legionella pneumophila (n = 2), Klebsiella pneumoniae, Streptococcus pyogenes and Leptospira were detected by metagenomics, confirming the diagnosis done using conventional microbiological techniques. The diversity of the respiratory microbiome in patients with severe viral pneumonia at ICU admission was similar to that of the control group. Contrarily, patients with pneumococcal pneumonia showed a lower grade of diversity. At initial stages of SARS-CoV-2 infection, no important alterations in the pulmonary microbiome were observed. The analysis of bacterial microbiome showed promising results as a diagnostic tool.
Identifiants
pubmed: 37853062
doi: 10.1038/s41598-023-45007-4
pii: 10.1038/s41598-023-45007-4
pmc: PMC10584954
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
17724Informations de copyright
© 2023. Springer Nature Limited.
Références
Jain, S. et al. Community-acquired pneumonia requiring hospitalization among U.S. adults. N. Engl. J. Med. 373, 415–427 (2015).
doi: 10.1056/NEJMoa1500245
pubmed: 26172429
pmcid: 4728150
Prina, E., Ranzani, O. T. & Torres, A. Community-acquired pneumonia. Lancet 386, 1097–1108 (2015).
doi: 10.1016/S0140-6736(15)60733-4
pubmed: 26277247
pmcid: 7173092
Dickson, R. P. The microbiome and critical illness. Lancet Respir. Med. 4, 59–72 (2016).
doi: 10.1016/S2213-2600(15)00427-0
pubmed: 26700442
Kitsios, G. D. et al. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients. Front. Microbiol. 9, 1413 (2018).
doi: 10.3389/fmicb.2018.01413
pubmed: 30042738
pmcid: 6048198
Mu, S. et al. Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia. Front. Cell Infect. Microbiol. 11, 684965 (2021).
doi: 10.3389/fcimb.2021.684965
pubmed: 34737971
pmcid: 8560692
Natalini, J. G., Singh, S. & Segal, L. N. The dynamic lung microbiome in health and disease. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-022-00821-x (2022).
doi: 10.1038/s41579-022-00821-x
pubmed: 36385637
pmcid: 9668228
Dickson, R. P., Erb-Downward, J. R. & Huffnagle, G. B. Towards an ecology of the lung: New conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir. Med. 2, 238–246 (2014).
doi: 10.1016/S2213-2600(14)70028-1
pubmed: 24621685
pmcid: 4004084
Bassis, C. M. et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. mBio 6, e00037 (2015).
doi: 10.1128/mBio.00037-15
pubmed: 25736890
pmcid: 4358017
Es, C. et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Respir. Crit. Care Med. 184, 957–963 (2011).
doi: 10.1164/rccm.201104-0655OC
Faner, R. et al. The microbiome in respiratory medicine: Current challenges and future perspectives. Eur. Respir. J. 49, 1602086 (2017).
doi: 10.1183/13993003.02086-2016
pubmed: 28404649
Dickson, R. P., Erb-Downward, J. R. & Huffnagle, G. B. The role of the bacterial microbiome in lung disease. Expert Rev. Respir. Med. 7, 245–257 (2013).
doi: 10.1586/ers.13.24
pubmed: 23734647
pmcid: 4007100
Sole, M. L. et al. Pulmonary microbiome of patients receiving mechanical ventilation: Changes over time. Am. J. Crit. Care 30, 128–132 (2021).
doi: 10.4037/ajcc2021194
pubmed: 33644803
pmcid: 8344366
Pettigrew, M. M., Tanner, W. & Harris, A. D. The lung microbiome and pneumonia. J. Infect. Dis. 223, S241–S245 (2021).
doi: 10.1093/infdis/jiaa702
pubmed: 33330898
Metlay, J. P. et al. Diagnosis and treatment of adults with community-acquired pneumonia. An official clinical practice guideline of the American Thoracic Society and Infectious Diseases Society of America. Am. J. Respir. Crit. Care Med. 200, e45–e67 (2019).
doi: 10.1164/rccm.201908-1581ST
pubmed: 31573350
pmcid: 6812437
Avalos-Fernandez, M. et al. The respiratory microbiota alpha-diversity in chronic lung diseases: First systematic review and meta-analysis. Respir. Res. 23, 214 (2022).
doi: 10.1186/s12931-022-02132-4
pubmed: 35999634
pmcid: 9396807
Sze, M. A. et al. The lung tissue microbiome in chronic obstructive pulmonary disease. Am. J. Respir Crit. Care Med. 185, 1073–1080 (2012).
doi: 10.1164/rccm.201111-2075OC
pubmed: 22427533
pmcid: 3359894
Cuthbertson, L. et al. Lung function and microbiota diversity in cystic fibrosis. Microbiome 8, 45 (2020).
doi: 10.1186/s40168-020-00810-3
pubmed: 32238195
pmcid: 7114784
Heul, A. V., Planer, J. & Kau, A. L. The human microbiota and asthma. Clin. Rev. Allergy Immunol. 57, 350–363 (2019).
doi: 10.1007/s12016-018-8719-7
pmcid: 7449604
Richardson, H., Dicker, A. J., Barclay, H. & Chalmers, J. D. The microbiome in bronchiectasis. Eur. Respir. Rev. 28, 190048 (2019).
doi: 10.1183/16000617.0048-2019
pubmed: 31484665
pmcid: 9489022
Smith, D. J. et al. Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics. Eur. Respir. J. 44, 922–930 (2014).
doi: 10.1183/09031936.00203013
pubmed: 25034564
Drengenes, C. et al. Laboratory contamination in airway microbiome studies. BMC Microbiol. 19, 187 (2019).
doi: 10.1186/s12866-019-1560-1
pubmed: 31412780
pmcid: 6694601
Liu, H.-X. et al. Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects. Int. J. Cancer 142, 769–778 (2018).
doi: 10.1002/ijc.31098
pubmed: 29023689
Yu, G. et al. Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. Genome Biol. 17, 163 (2016).
doi: 10.1186/s13059-016-1021-1
pubmed: 27468850
pmcid: 4964003
Hanada, S., Pirzadeh, M., Carver, K. Y. & Deng, J. C. Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. Front. Immunol. 9, 2640 (2018).
doi: 10.3389/fimmu.2018.02640
pubmed: 30505304
pmcid: 6250824
Yildiz, S., Mazel-Sanchez, B., Kandasamy, M., Manicassamy, B. & Schmolke, M. Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. Microbiome 6, 9 (2018).
doi: 10.1186/s40168-017-0386-z
pubmed: 29321057
pmcid: 5763955
Han, Y., Jia, Z., Shi, J., Wang, W. & He, K. The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis. Bioimpacts 12, 139–146 (2022).
doi: 10.34172/bi.2021.23378
pubmed: 35411293
Lloréns-Rico, V. et al. Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host. Nat. Commun. 12, 6243 (2021).
doi: 10.1038/s41467-021-26500-8
pubmed: 34716338
pmcid: 8556379
Shen, Z. et al. Genomic diversity of severe acute respiratory syndrome–coronavirus 2 in patients with coronavirus disease 2019. Clin. Infect. Dis. 71, 713–720 (2020).
doi: 10.1093/cid/ciaa203
pubmed: 32129843
Vientós-Plotts, A. I., Ericsson, A. C., Rindt, H. & Reinero, C. R. Respiratory dysbiosis in canine bacterial pneumonia: Standard culture vs. microbiome sequencing. Front. Vet. Sci. 6, 354 (2019).
doi: 10.3389/fvets.2019.00354
pubmed: 31681810
pmcid: 6798064
Dickson, R. P. et al. Lung microbiota predict clinical outcomes in critically ill patients. Am. J. Respir. Crit. Care Med. 201, 555–563 (2020).
doi: 10.1164/rccm.201907-1487OC
pubmed: 31973575
pmcid: 7047465
de Roux, A. et al. Mixed community-acquired pneumonia in hospitalised patients. Eur. Respir. J. 27, 795–800 (2006).
doi: 10.1183/09031936.06.00058605
pubmed: 16585087
Tikhomirova, A. & Kidd, S. P. Haemophilus influenzae and Streptococcus pneumoniae: Living together in a biofilm. Pathog. Dis. 69, 114–126 (2013).
doi: 10.1111/2049-632X.12073
pubmed: 23913525
Du, S. et al. Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia. Front. Med. 16, 389–402 (2022).
doi: 10.1007/s11684-021-0856-3
pubmed: 34302613
Bousbia, S. et al. Repertoire of intensive care unit pneumonia microbiota. PLoS One 7, e32486 (2012).
doi: 10.1371/journal.pone.0032486
pubmed: 22389704
pmcid: 3289664
Rovery, C. et al. PCR detection of bacteria on cardiac valves of patients with treated bacterial endocarditis. J. Clin. Microbiol. 43, 163–167 (2005).
doi: 10.1128/JCM.43.1.163-167.2005
pubmed: 15634966
pmcid: 540121