One future of clinical metagenomic sequencing for infectious diseases

Investigation of acute encephalitis syndrome with implementation of metagenomic next generation sequencing in Nepal

BACKGROUND

The causative agents of Acute Encephalitis Syndrome remain unknown in 68-75% of the cases. In Nepal, the cases are tested only for Japanese encephalitis, which constitutes only about 15% of the cases. However, there could be several organisms, including vaccine-preventable etiologies that cause acute encephalitis, when identified could direct public health efforts for prevention, including addressing gaps in vaccine coverage.

OBJECTIVES

This study employs metagenomic next-generation-sequencing in the investigation of underlying causative etiologies contributing to acute encephalitis syndrome in Nepal.

METHODS

In this study, we investigated 90, Japanese-encephalitis-negative, banked cerebrospinal fluid samples that were collected as part of a national surveillance network in 2016 and 2017. Randomization was done to include three age groups (< 5-years; 5-14-years; >15-years). Only some metadata (age and gender) were available. The investigation was performed in two batches which included total nucleic-acid extraction, followed by individual library preparation (DNA and RNA) and sequencing on Illumina iSeq100. The genomic data were interpreted using Chan Zuckerberg-ID and confirmed with polymerase-chain-reaction.

RESULTS

Human-alphaherpes-virus 2 and Enterovirus-B were seen in two samples. These hits were confirmed by qPCR and semi-nested PCR respectively. Most of the other samples were marred by low abundance of pathogen, possible freeze-thaw cycles, lack of process controls and associated clinical metadata.

CONCLUSION

From this study, two documented causative agents were revealed through metagenomic next-generation-sequencing. Insufficiency of clinical metadata, process controls, low pathogen abundance and absence of standard procedures to collect and store samples in nucleic-acid protectants could have impeded the study and incorporated ambiguity while correlating the identified hits to infection. Therefore, there is need of standardized procedures for sample collection, inclusion of process controls and clinical metadata. Despite challenging conditions, this study highlights the usefulness of mNGS to investigate diseases with unknown etiologies and guide development of adequate clinical-management-algorithms and outbreak investigations in Nepal.

Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance

The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for "widespread metagenomic monitoring" to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.

Forty Years of Molecular Diagnostics for Infectious Diseases

Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.