The lower respiratory tract microbiome of critically ill patients with COVID-19

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-23

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33980943

DOI Digital object identifier for electronic documents.

10.1038/s41598-021-89516-6

URI

Authors

Gaibani P, Viciani E, Bartoletti M, Lewis RE, Tonetti T, Lombardo D, Castagnetti A, Bovo F, Horna CS, Ranieri M, Viale P, Re MC, Ambretti S

Journal

Scientific reports

Year

2021

COVID-19 infection may predispose to secondary bacterial infection which is associated with poor clinical outcome especially among critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a 16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia. Lung microbiome of critically ill patients with COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant Acinetobacter baumannii (CR-Ab) infection. In conclusion, SARS-CoV-2 infection and antibiotic pressure may predispose critically ill patients to bacterial superinfection due to opportunistic multidrug resistant pathogens.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-23

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): WikiWorks, Claregrieve1, Peace Sandy, Joiejoie

Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Lung Pulmo,Lung,lung

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 2019 novel coronavirus,2019 novel coronavirus infection,2019-nCoV,2019-nCoV infection,beta-CoV,beta-CoVs,betacoronavirus,coronavirus disease 2019,SARS-coronavirus 2,SARS-CoV-2,severe acute respiratory syndrome coronavirus 2,severe acute respiratory syndrome coronavirus 2 infectious disease,β-coronavirus,β-CoV,β-CoVs,COVID-19,cOVID-19

Group 0 name Corresponds to the control (unexposed) group for case-control studies: COVID-19 negative patients with pneumonia

Group 1 name Corresponds to the case (exposed) group for case-control studies: COVID-19 patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: COVID-19 Critically Ill Subjects

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Group 1 sample size Number of subjects in the case (exposed) group: 24

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-23

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy, WikiWorks

Source: Figure 3

Description: The figure shows the microbial taxa with significant differences between the COVID-19 positive (red) and negative patients (green) (LDA score>2) with their original identification codes.

Abundance in Group 1: increased abundance in COVID-19 patients

NCBI	Quality Control	Links
Acinetobacter
Acinetobacter schindleri
Enterobacteriaceae
Peptacetobacter hiranonis
Aquipseudomonas alcaligenes
Sphingobacterium

Revision editor(s): Claregrieve1, Peace Sandy, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-1-23

Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): WikiWorks, Claregrieve1, Peace Sandy, Aleru002

Source: Figure 3

Description: The figure shows the microbial taxa with significant differences between the COVID-19-positive (red) and negative patients (green) (LDA score>2) with their original identification codes.

Abundance in Group 1: decreased abundance in COVID-19 patients

NCBI	Quality Control	Links
Actinomyces
Atopobium
Campylobacter
Candidatus Nanosynbacter lyticus
Capnocytophaga
Catonella
Gemella
Granulicatella
Haemophilus influenzae
Haemophilus parainfluenzae
Hoylesella nanceiensis
Lacticaseibacillus zeae
Leptotrichia
Megasphaera
Moryella
Neisseria
Oribacterium
Porphyromonas
Prevotella
Prevotella melaninogenica
Prevotella pallens
Prevotellaceae
Rothia mucilaginosa
Selenomonas
Streptococcaceae bacterium RF32
Streptococcus
TM7 phylum sp. oral clone CW040
Tannerella
Veillonella
Veillonella dispar
Veillonella parvula
candidate division SR1 bacterium

Revision editor(s): WikiWorks, Claregrieve1, Peace Sandy, Aleru002