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

• Published in: Scientific reports 2020-03, Vol.10 (1), p.3963, Article 3963
• Main Authors: Li, Ci-Xiu, Li, Wei, Zhou, Jun, Zhang, Bing, Feng, Yan, Xu, Chang-Ping, Lu, Yi-Yu, Holmes, Edward C., Shi, Mang
• Format: Article
• Language: English
• Subjects: 45; 45/90; 45/91; 631/326/596/2142; 692/699/255/2514; Abundance; Antimicrobial resistance; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - pathogenicity; Concurrent infection; DNA viruses; DNA Viruses - classification; DNA Viruses - genetics; DNA Viruses - pathogenicity; Drug Resistance, Microbial - genetics; Epidemiology; Female; Fungi; Fungi - classification; Fungi - genetics; Fungi - pathogenicity; Genomes; Genotypes; Humanities and Social Sciences; Humans; Infections; Male; Metagenome - genetics; Metagenomics; multidisciplinary; Nucleotide sequence; Pathogens; Phylogeny; Respiratory diseases; Respiratory tract infection; Respiratory Tract Infections - microbiology; Respiratory Tract Infections - virology; RNA viruses; RNA Viruses - classification; RNA Viruses - genetics; RNA Viruses - pathogenicity; Science; Science (multidisciplinary); Species diversity; Transcriptomics; Viruses - classification; Viruses - genetics; Viruses - pathogenicity
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-60992-6

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.