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

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

doi:10.1038/s41598-020-60992-6

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.

Highlights

The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging
Throat swab samples of 48 paediatric patients and seven controls were subjected to meta-transcriptomics analysis (Fig. 1)
We used an expansive meta-transcriptomics approach to characterize the microbial pathogens associated with paediatric ARI

Summary

Introduction

The diversity of pathogens associated with acute respiratory infection (ARI) makes diagnosis challenging. 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. Identifying the diversity of pathogens responsible for ARIs remains challenging because they involve a diverse set of viruses, bacteria, and fungal pathogens, with co-infection among them commonplace[4,5] Traditional testing methods such as PCR, serological typing, bacterial culture and antibody detection, are regarded as the “gold standard” and widely used in ARI diagnosis[6,7]. Total RNA sequencing (“meta-transcriptomics”) has successfully revealed the entire “infectome” (viruses, bacteria and eukaryotes) present within an organism and provided relevant data on genome sequence, gene expression, Environmental Sciences and School of Medical Sciences, The University of Sydney, New South Wales, 2006, Australia. The total spectrum of microbes present in patient throat swabs samples were identified, which involved both complex and diagnostically challenging cases

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Conclusion