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

Study information

Needs review

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 Uniform resource identifier for web resources.

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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Curated date: 2021/07/14

Curator: Claregrieve1

Revision editor(s): WikiWorks753, Claregrieve1

Subjects

Location of subjects: Italy

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-COVID-19 pneumonia patients
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: Patients positive for SARS-CoV-2 by RT-PCR on nasopharyngeal swabs or lower respiratory tract samples
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

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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Curated date: 2021/07/14

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Source: Figure 3

Description: Differential microbial abundance between COVID-19 positive patients and non-COVID pneumonia patients by LEfSe

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

NCBI	Links
Enterobacteriaceae
Acinetobacter ⚠
Acinetobacter schindleri ⚠
Sphingobacterium ⚠
Peptacetobacter hiranonis
Pseudomonas alcaligenes ⚠

Revision editor(s): Claregrieve1

Signature 2

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Curated date: 2021/07/14

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Source: Figure 3

Description: Differential microbial abundance between COVID-19 positive patients and non-COVID pneumonia patients by LEfSe

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

NCBI	Links
Catonella
TM73TM73
Oribacterium
Tannerella
Moryella
RF32RF32
Selenomonas
Atopobium
SR1SR1
Haemophilus parainfluenzae
Veillonella
Campylobacter
Gemella
Hoylesella nanceiensis
Prevotella pallens
CW040CW040
Megasphaera
Prevotella
Rothia mucilaginosa
Lacticaseibacillus zeae
Leptotrichia
Veillonella parvula
Prevotellaceae
Prevotella melaninogenica
Capnocytophaga
Porphyromonas
Actinomyces
Neisseria
Granulicatella
Veillonella dispar
Haemophilus influenzae
Streptococcus

Revision editor(s): Claregrieve1