High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-03-03

AUTHORS

Ci-Xiu Li, Wei Li, Jun Zhou, Bing Zhang, Yan Feng, Chang-Ping Xu, Yi-Yu Lu, Edward C. Holmes, Mang Shi

ABSTRACT

The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. Traditional pathogen screening tests have a limited detection range and provide little additional information. We used total RNA sequencing (“meta-transcriptomics”) to reveal the full spectrum of microbes associated with paediatric ARI. Throat swabs were collected from 48 paediatric ARI patients and 7 healthy controls. Samples were subjected to meta-transcriptomics to determine the presence and abundance of viral, bacterial, and eukaryotic pathogens, and to reveal mixed infections, pathogen genotypes/subtypes, evolutionary origins, epidemiological history, and antimicrobial resistance. We identified 11 RNA viruses, 4 DNA viruses, 4 species of bacteria, and 1 fungus. While most are known to cause ARIs, others, such as echovirus 6, are rarely associated with respiratory disease. Co-infection of viruses and bacteria and of multiple viruses were commonplace (9/48), with one patient harboring 5 different pathogens, and genome sequence data revealed large intra-species diversity. Expressed resistance against eight classes of antibiotic was detected, with those for MLS, Bla, Tet, Phe at relatively high abundance. In summary, we used a simple total RNA sequencing approach to reveal the complex polymicrobial infectome in ARI. This provided comprehensive and clinically informative information relevant to understanding respiratory disease. More... »

PAGES

3963

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41598-020-60992-6

DOI

http://dx.doi.org/10.1038/s41598-020-60992-6

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https://app.dimensions.ai/details/publication/pub.1125323980

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/32127629


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