Modulation of potential respiratory pathogens by pH1N1 viral infection

Study information

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

23167452

DOI Digital object identifier for electronic documents.

https://doi.org/10.1111/1469-0691.12054

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

Keywords:

Cell motility, chemotaxis, microbiota, pH1N1, pneumonia

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

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

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

Subjects

Location of subjects

China

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

Throat Gula,Throat,throat

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Influenza A (H1N1) 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

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).

raw counts

Statistical test

DESeq2

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

0.05

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	Links
Bacillota
Pseudomonadota
Bacillaceae
Moraxellaceae
Pseudomonadaceae
Acinetobacter
Pseudomonas
Bacillus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

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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	Quality Control	Links
Bacteroidota
Prevotellaceae
Veillonellaceae
Neisseriaceae
Neisseria
Prevotella
Veillonella

Revision editor(s): Claregrieve1, WikiWorks

Signature 3

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	Links
Bacillaceae
Moraxellaceae
Pseudomonadaceae

Revision editor(s): Claregrieve1, WikiWorks

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	Links
Neisseriaceae
Prevotellaceae
Veillonellaceae

Revision editor(s): Claregrieve1, WikiWorks

Signature 5

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	Links
Acinetobacter
Bacillus
Pseudomonas

Revision editor(s): Claregrieve1, WikiWorks

Signature 6

EditHistoryDelete

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Reviewed Marked as Reviewed by Fatima on 2022/04/6

Curated date: 2021/06/09

Curator: Claregrieve1

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	Links
Neisseria
Prevotella
Veillonella

Revision editor(s): Claregrieve1, WikiWorks