Molecular characterisation of emerging pathogens of unexplained infectious disease syndromes

ABSTRACT

Introduction: The discoveries of HIV and Helicobacter pylori in the 1980s were landmarks in identification of novel pathogens causing unexplained infectious syndromes using conventional microbiological technologies. In the last few decades, advancement of molecular technologies has provided us with more robust tools to expand our armamentarium in this microbial hunting process.

Areas covered: In this article, we give a brief overview of the most important molecular technologies we use for identification of emerging microbes associated with unexplained infectious syndromes, including 16S rRNA and other conserved targets sequencing for bacteria, internal transcribed spacer (ITS) and other target gene sequencing for fungi, polymerase and other gene sequencing for viruses, as well as deep sequencing. Then, we use several representative examples to illustrate how these techniques have been used for the discoveries of a few notable bacterial, fungal and viral pathogens associated with unexplained infectious syndromes in the last 20–30 years.

Expert opinion: In the past and present, characterization of emerging pathogens of unexplained infectious disease syndromes has relied on a combination of conventional culture- and phenotype-based technologies and nucleic acid amplification and sequencing. In the next era, we envisage more widespread adoption of next generation technologies that can detect both known and previously undescribed pathogens.

KEYWORDS:

• Infectious disease
• novel microbe
• bacterium
• virus
• fungus

Article highlights

• Conventional microbiological identification relies on culture- and phenotype-based methods.

• Molecular technologies, especially nucleic acid amplification and DNA sequencing have been increasingly utilized in the clinical microbiology laboratories.

• Common gene targets used for microbial identification include 16S rRNA gene for bacteria, internal transcribed spacer region for fungi, polymerase for viruses and many other conserved gene targets.

• Deep sequencing represents a promising tool for the rapid characterization of both known and emerging pathogens causing unexplained infectious disease syndromes in the future.

Declaration of interest

The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Reviewers disclosure

Peer reviewers on this manuscript have no relevant financial relationships or otherwise to disclose.

Additional information

Funding

This work is partly supported by the Consultancy Service for Enhancing Laboratory Surveillance of Emerging Infectious Diseases and Research Capability on Antimicrobial Resistance for Department of Health, HKSAR Government; and funding from the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the Ministry of Education of China.