Modulation of potential respiratory pathogens by pH1N1 viral infection

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 6 April 2022
study design
case-control
Citation
PMID
URI
Authors
Leung RK, Zhou JW, Guan W, Li SK, Yang ZF, Tsui SK
Journal
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
Year
2013
While much effort has been made to characterize influenza A pdm09 virus (pH1N1), the flu that was responsible for the fourth influenza pandemic, there is a lack of study on the composition of bacteria that lead to secondary infection. In this study, we recruited pneumonia patients with and without pH1N1 infection and characterized their oropharyngeal microbiota by the unbiased high-throughput sequencing method. While there were no significant differences in common bacterial pneumonia-causative agents (Acinetobacter and Streptococcus species), previously unreported Pseudomonas species equipped with chemotaxis and flagellar assembly genes significantly increased (>20-fold) in the pH1N1-infected group. Bacillus and Ralstonia species that also increased significantly (5-10-fold) were also found to possess similar signaling and motility genes. In contrast, no such genes were found in oral commensal Prevotella, Veillonella and Neisseria species, which decreased significantly, or in either Acinetobacter or 10 out of 21 Streptococcus species, including Streptococcus pneumoniae. Our results support the notion that pH1N1 infection provides a niche for previously unnoticed potential respiratory pathogens that were able to access the lower respiratory tract with weakened immunity.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): WikiWorks753, LGeistlinger, Fatima, Claregrieve1

Subjects

Location of subjects Country from which study subjects were recruited
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
Throat Gula,Throat
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
influenza A (H1N1) influenza A (H1N1)
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pneumonia patients without any influenza A infection
Group 1 name Corresponds to the case (exposed) group for case-control studies
Pneumonia patients with pH1N1 infection
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Positive lab test (real-time PCR or cell culture) and criteria for pneumonia simultaneously met, with pH1N1 infection
Group 0 sample size Number of subjects in the control (unexposed) group
11
Group 1 sample size Number of subjects in the case (exposed) group
11

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
WMS
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05



Signature 1

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1a-c

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients

Abundance in Group 1: increased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Firmicutes
Proteobacteria
Bacillaceae
Moraxellaceae
Pseudomonadaceae
Acinetobacter
Pseudomonas
Bacillus

Revision editor(s): Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1a-c

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients

Abundance in Group 1: decreased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Bacteroidetes
Prevotellaceae
Veillonellaceae
Neisseriaceae
Neisseria
Prevotella
Veillonella

Revision editor(s): Claregrieve1

Signature 3

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1b

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level

Abundance in Group 1: increased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Bacillaceae
Moraxellaceae
Pseudomonadaceae

Revision editor(s): Claregrieve1

Signature 4

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1b

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the family level

Abundance in Group 1: decreased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Neisseriaceae
Prevotellaceae
Veillonellaceae

Revision editor(s): Claregrieve1

Signature 5

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1c

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level

Abundance in Group 1: increased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Acinetobacter
Bacillus
Pseudomonas

Revision editor(s): Claregrieve1

Signature 6

Reviewed Marked as Reviewed by Fatima on 6 April 2022

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 1c

Description: Relative microbial abundance of pH1N1-infected and uninfected pneumonia patients at the genus level

Abundance in Group 1: decreased abundance in Pneumonia patients with pH1N1 infection

NCBI Links
Neisseria
Prevotella
Veillonella

Revision editor(s): Claregrieve1