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

Study information

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

35579429

DOI Digital object identifier for electronic documents.

10.1128/spectrum.02311-21

URI

Authors

Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R

Journal

Microbiology spectrum

Year

2022

Keywords:

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

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 Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/08

Curator: Leenaa

Revision editor(s): Leenaa, Folakunmi, Omojokunoluwatomisin, Svetlana up

Subjects

Location of subjects: India

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: Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: COVID-19 symptoms measurement COVID-19 symptoms measurement,cOVID-19 symptoms measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: mild

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients showing breathing difficulty with SpO2 levels ranging between 91% and 93%.

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: 36

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

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: Mann-Whitney (Wilcoxon)

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: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/08

Curator: Leenaa

Revision editor(s): Leenaa

Source: Figure 3i-j

Description: Differentially abundant bacterial species between mild group and moderate group

Abundance in Group 1: decreased abundance in moderate

NCBI	Quality Control	Links
Halomonas sp.
Schaalia meyeri

Revision editor(s): Leenaa

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/10

Curator: Leenaa

Revision editor(s): Leenaa, Folakunmi

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients who succumbed to COVID-19 during hospital stay

Group 1 sample size Number of subjects in the case (exposed) group: 12

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/10

Curator: Leenaa

Revision editor(s): Leenaa

Source: Figure 3e

Description: Differentially abundant bacterial species between mild group and mortality group

Abundance in Group 1: increased abundance in mortality

NCBI	Quality Control	Links
Achromobacter xylosoxidans

Revision editor(s): Leenaa

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/10

Curator: Leenaa

Revision editor(s): Leenaa, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: moderate

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients showing respiratory distress with respiratory support requirement and SpO2 levels < 90%

Group 0 sample size Number of subjects in the control (unexposed) group: 36

Group 1 sample size Number of subjects in the case (exposed) group: 14

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/10

Curator: Leenaa

Revision editor(s): Leenaa

Source: Figure 3g

Description: Differentially abundant bacterial species between moderate group and severe group

Abundance in Group 1: increased abundance in severe

NCBI	Quality Control	Links
Leptotrichia buccalis

Revision editor(s): Leenaa

Experiment 4

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Folakunmi on 2024-3-25

Curated date: 2024/03/10

Curator: Leenaa

Revision editor(s): Leenaa, Folakunmi

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients who succumbed to COVID-19 during hospital stay