Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai

Study information

Reviewed Marked as Reviewed by Fatima on 2022/05/11

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

34103263

DOI Digital object identifier for electronic documents.

10.1016/j.jmii.2021.03.015

URI

Authors

Miao Q, Ma Y, Ling Y, Jin W, Su Y, Wang Q, Pan J, Zhang Y, Chen H, Yuan J, Wu H, Hu B

Journal

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

Year

2021

Keywords:

Antimicrobials, COVID-19, Escalation, Metagenomic sequencing, Superinfection

BACKGROUND: In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship. METHOD: This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19. RESULTS: The total population co-infection rate was 17/323 (5.3%) and 0/229 (0), 4/78 (5.1%), and 13/16 (81.3%) for the mild, severe, and critically severe subgroups, respectively. Proven fungal infection was significantly associated with a higher mortality rate (p = 0.029). In critically severe patients, the rate of antimicrobials and carbapenem usage were 16/16 (100%) and 13/16 (81.3%), respectively, in which the preemptive and empiric antimicrobial days accounted for 51.6% and 30.1%, respectively. Targeted therapy only accounted for 18.3%. MS was implemented to detect non-COVID-19 virus co-existence and the semi-quantitative surveillance of bacteremia, with clear clinical benefit seen in cases with MS-based precision antimicrobial management. Airway microbiome analysis suggested that the microbiota compositions in critically severe COVID-19 patients were likely due to intubation and mechanical ventilation. CONCLUSIONS: In the SPHCC cohort, we observed a non-negligible rate of super-infection, especially for the critically ill COVID-19 patients. Fungal co-infection requires intensive attention due to the high risk of mortality, and the clinical benefit of MS in guiding antimicrobial management warrants further investigation.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Rimsha, Claregrieve1, WikiWorks

Subjects

Location of subjects: China

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: Oropharynx Mesopharynx,Oral part of pharynx,Pars oralis pharyngis,Oropharynx

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-intubated patients with non-incubation viral pneumonia or non-incubation non-infectious diseases
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: Intubated patients with critically severe COVID-19 infection
Group 0 sample size Number of subjects in the control (unexposed) group: 54
Group 1 sample size Number of subjects in the case (exposed) group: 50

Lab analysis

Sequencing type: WMS

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: BGISEQ-500 Sequencing

Statistical Analysis

Statistical test: PERMANOVA

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)?: No

Alpha Diversity

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

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Text

Description: Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients

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

NCBI	Quality Control	Links
Acinetobacter
Klebsiella
Pelomonas sp.
Ralstonia
Sphingomonas

Revision editor(s): Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/17

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Text

Description: Differential abundance of airway microbiome between samples from critically ill intubated COVID-19 patients and samples from non-incubated viral pneumonia/non-infectious disease patients

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

NCBI	Quality Control	Links
Actinomyces
Haemophilus
Neisseria
Prevotella
Streptococcus
Veillonella

Revision editor(s): Claregrieve1

Experiment 2

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Reviewed Marked as Reviewed by Fatima on 2022/05/11

Curated date: 2021/06/20

Curator: Claregrieve1

Revision editor(s): Fatima, Rimsha, Claregrieve1, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Inbutation non-covid
Group 1 name Corresponds to the case (exposed) group for case-control studies: critically severe covid
Group 0 sample size Number of subjects in the control (unexposed) group: 20

Lab analysis

Statistical Analysis

Alpha Diversity

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