Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.
COVID-19
Holo-Seq
co-infection
disease outcome
disease sub-phenotype
host-pathogen interactions
metabolic pathways
nasopharyngeal RNA
pathogen genomics
respiratory virus oligo panel (RVOP)
transcriptionally active microbial isolates
Journal
Microbiology spectrum
ISSN: 2165-0497
Titre abrégé: Microbiol Spectr
Pays: United States
ID NLM: 101634614
Informations de publication
Date de publication:
29 06 2022
29 06 2022
Historique:
pubmed:
18
5
2022
medline:
2
7
2022
entrez:
17
5
2022
Statut:
ppublish
Résumé
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and
Identifiants
pubmed: 35579429
doi: 10.1128/spectrum.02311-21
pmc: PMC9241827
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0231121Références
Appl Microbiol Biotechnol. 2020 Sep;104(18):7777-7785
pubmed: 32780290
Adv Sci (Weinh). 2021 Oct;8(20):e2102785
pubmed: 34423593
Clin Infect Dis. 2020 Jul 28;71(15):713-720
pubmed: 32129843
Lancet. 2020 Feb 15;395(10223):497-506
pubmed: 31986264
Int J Infect Dis. 2021 Apr;105:540-550
pubmed: 33610778
Biol Proced Online. 2020 Jul 25;22:18
pubmed: 32728349
PLoS One. 2021 Jul 16;16(7):e0254707
pubmed: 34270621
Front Immunol. 2018 Sep 19;9:2065
pubmed: 30283438
mBio. 2015 Mar 03;6(2):e00037
pubmed: 25736890
Clin Microbiol Rev. 2010 Apr;23(2):382-98
pubmed: 20375358
Front Cell Infect Microbiol. 2018 Feb 28;8:57
pubmed: 29541629
ISME J. 2012 Mar;6(3):670-9
pubmed: 21975597
PLoS One. 2009;4(4):e5135
pubmed: 19352512
Nat Rev Immunol. 2016 May 27;16(6):341-52
pubmed: 27231050
Pathogens. 2021 Aug 31;10(9):
pubmed: 34578142
Front Cell Infect Microbiol. 2022 Jan 24;11:781968
pubmed: 35141167
Nat Commun. 2015 Jan 08;6:5975
pubmed: 25569306
mSystems. 2018 Oct 30;3(5):
pubmed: 30417108
Nat Rev Microbiol. 2021 Jul;19(7):409-424
pubmed: 34075212
NPJ Biofilms Microbiomes. 2021 Jul 22;7(1):61
pubmed: 34294722
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Sci Rep. 2017 Jul 18;7(1):5752
pubmed: 28720878
Microb Ecol. 1999 Nov;38(4):348-357
pubmed: 10758181
J Clin Microbiol. 2009 Feb;47(2):496-8
pubmed: 19052180
Lancet Microbe. 2020 Oct;1(6):e254-e262
pubmed: 33103132
Nat Microbiol. 2017 Aug 24;2:17121
pubmed: 28836573
Respir Res. 2006 Oct 11;7:125
pubmed: 17034639
Cell Metab. 2020 Sep 1;32(3):437-446.e5
pubmed: 32697943
J Cyst Fibros. 2010 Jan;9(1):51-8
pubmed: 19939747
Periodontol 2000. 2020 Jun;83(1):234-241
pubmed: 32385873
Front Immunol. 2020 Jul 10;11:1708
pubmed: 32754163
IDCases. 2020 May 30;21:e00855
pubmed: 32514399
ERJ Open Res. 2021 May 31;7(2):
pubmed: 34084788
mBio. 2021 Aug 31;12(4):e0177721
pubmed: 34399607
BMJ. 2021 Mar 9;372:n579
pubmed: 33687922
Bioinformatics. 2020 Feb 15;36(4):1303-1304
pubmed: 31553437
mBio. 2021 Oct 26;12(5):e0251021
pubmed: 34607452
Front Microbiol. 2020 Jul 31;11:1840
pubmed: 32849438
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
PLoS Pathog. 2012;8(5):e1002681
pubmed: 22615558
Front Microbiol. 2018 Aug 30;9:1892
pubmed: 30233503
Appl Environ Microbiol. 2013 Jan;79(1):177-84
pubmed: 23087033
Front Microbiol. 2021 May 28;12:653399
pubmed: 34122366
J Microbiol Immunol Infect. 2020 Aug;53(4):505-512
pubmed: 32482366
Signal Transduct Target Ther. 2021 May 13;6(1):191
pubmed: 33986253
Rev Esp Quimioter. 2018 Jun;31(3):268-273
pubmed: 29806765
Chem Phys Lipids. 2015 Sep;190:27-42
pubmed: 26148574
N Engl J Med. 2021 May 13;384(19):1866-1868
pubmed: 33761203
FEMS Microbiol Ecol. 1999 Nov 1;30(3):253-260
pubmed: 10525181
BMC Biol. 2019 Nov 7;17(1):87
pubmed: 31699101
J Infect. 2012 Oct;65(4):357-61
pubmed: 22406688
J Infect Dis. 2015 Dec 1;212(11):1690-1
pubmed: 25943204
Trends Microbiol. 2021 May;29(5):458-471
pubmed: 33004259
Mucosal Immunol. 2021 Mar;14(2):305-316
pubmed: 33244161
SN Compr Clin Med. 2020;2(8):1069-1076
pubmed: 32838147
Sci Rep. 2019 Sep 20;9(1):13639
pubmed: 31541147
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
EMBO Mol Med. 2020 Jul 7;12(7):e12560
pubmed: 32453917
Clin Infect Dis. 1996 Sep;23(3):569-76
pubmed: 8879782
Microorganisms. 2020 May 13;8(5):
pubmed: 32414211
Infect Immun. 2015 Jan;83(1):417-29
pubmed: 25385800
Nat Rev Immunol. 2020 Jun;20(6):375-388
pubmed: 32132681
J Oral Microbiol. 2010 Dec 21;2:
pubmed: 21523220
Sci Rep. 2021 Feb 26;11(1):4802
pubmed: 33637820
Nucleic Acids Res. 2010 Jul;38(12):e132
pubmed: 20403810
Clin Vaccine Immunol. 2009 Dec;16(12):1804-9
pubmed: 19828771
Rev Med Virol. 2021 Jan;31(1):1-10
pubmed: 32845042
Int J Antimicrob Agents. 2021 Feb;57(2):106272
pubmed: 33347989
Infect Dis Rep. 2012 Apr 10;4(1):e24
pubmed: 24470931
Sci Rep. 2021 Oct 29;11(1):21297
pubmed: 34716394
J Bacteriol. 2010 Oct;192(19):5002-17
pubmed: 20656903
Front Microbiol. 2017 Oct 10;8:1878
pubmed: 29067003
Front Microbiol. 2021 Jun 23;12:687513
pubmed: 34248910
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Eur Respir J. 2020 May 14;55(5):
pubmed: 32217650
Curr Biol. 2003 Jan 21;13(2):R47-9
pubmed: 12546801
Nat Methods. 2019 Jun;16(6):453-454
pubmed: 31133757
Clin Infect Dis. 2020 Dec 17;71(10):2669-2678
pubmed: 32497191
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nature. 2012 Jul 25;487(7408):477-81
pubmed: 22837003
Biol Sex Differ. 2020 May 25;11(1):29
pubmed: 32450906
Cell Rep. 2021 Aug 31;36(9):109637
pubmed: 34433082
EcoSal Plus. 2008 Sep;3(1):
pubmed: 26443740
BMJ. 2021 Mar 10;372:n436
pubmed: 33692022
Emerg Microbes Infect. 2021 Dec;10(1):1431-1440
pubmed: 34184973
Methods Mol Biol. 2016;1418:335-51
pubmed: 27008022
PLoS One. 2021 May 6;16(5):e0251170
pubmed: 33956882
JA Clin Rep. 2017;3(1):25
pubmed: 29457069
Appl Environ Microbiol. 1993 Aug;59(8):2594-601
pubmed: 16349018
Science. 2021 Nov 19;374(6570):995-999
pubmed: 34648303
Viruses. 2021 Jul 02;13(7):
pubmed: 34372500
Appl Environ Microbiol. 2005 Jun;71(6):3235-47
pubmed: 15933026
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508