Guest Editors
Chuan Kok Lim
Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity
Dr. Chuan Kok Lim is a medical virologist at the Victorian Infectious Diseases Reference Laboratory (VIDRL) at the Peter Doherty Institute for Infection and Immunity in Melbourne. He earned his fellowships in microbiology and infectious diseases (FRCPA, FRACP) in 2016 and completed his PhD in 2022. Currently, he is the co-lead for Viral Infectious Diseases at the Doherty Institute and a co-director at the Centre for Pathogen Genomics at the University of Melbourne. His role and research focus on improving public health responses to emerging pathogens through translational virology and viral genomics.
Prashanth Ramachandran
Department of Infectious Diseases, University of Melbourne, Doherty Institute for Infection and Immunity
Prashanth is a clinician-scientist specializing in neuroinfectious diseases and neuroimmunology. He holds an NHMRC Investigator Grant (EL1) and leads a laboratory in the Department of Infectious Diseases at the Peter Doherty Institute for Infection and Immunity. He completed a fellowship in neuroimmunology and neuroinfectious diseases at the University of California, San Francisco (UCSF), where he also earned his PhD through the University of Melbourne. His doctoral research focused on applying metagenomic next-generation sequencing and host transcriptomics to investigate neuroinflammatory diseases. Following his fellowship, he joined the UCSF Neurology Department as a faculty member. In 2022, he returned to Australia to continue his research at the Doherty Institute, where he integrates clinical and genomic approaches to advance the understanding and diagnosis of central nervous system infections and immune-mediated neurological disorders.The Ramachandran Lab is a translational laboratory bridging clinical medicine and scientific innovation to develop novel diagnostic tools for neuroinflammatory conditions. The lab aims to understand the underlying mechanisms and pathology of these disorders through advanced technologies such as metagenomic next-generation sequencing, targeted pathogen enrichment, host transcriptomics, aneuploidy detection, and phage immunoprecipitation sequencing.
Collection Overview
Next-generation sequencing (NGS) plays a crucial role in identifying and characterizing emerging pathogens, particularly during early disease outbreaks. The sequencing of SARS-CoV-2 was rapidly scaled up during the COVID-19 pandemic, significantly contributing across various One Health sectors. It aided in the genomic characterization of new variants, tracked virus evolution in humans and animal hosts, and supported wastewater surveillance. Emerging pathogens can be analyzed by examining convergent mutations, pathogen evolution, host adaptation, and functional predictions. This approach has important implications for public health risk assessment, diagnostics, and treatment predictions. NGS has established itself as the new "gold standard" for pathogen genomics and should be accessible to all countries.
In recent years, significant technological advancements have been made in areas such as metagenomics, automation of library preparation, bioinformatic analyses, and artificial intelligence. Various pathogen discovery approaches have been explored in clinical and public health settings. This collection aims to present a selection of techniques from wet labs and bioinformatics that can enhance the identification and characterization of emerging pathogens, improve laboratory efficiency, expand access to pathogen genomics methodologies, and foster knowledge exchange. It serves as a guide for laboratories looking to establish a pathogen genomic facility and offers opportunities for advanced genomics laboratories to share their approaches.
Articles
Abstracts
Long-read platform as an effective tool in Biodiversity genomics and the discovery of emerging pathogens
Balaji Chattopadhyay*1
1Ashoka University, Sonipat, Haryana, India.
Ng-Amp-Seq: a high-throughput amplicon sequencing methodology for AMR surveillance in N. gonorrhoeae isolates using a multiplex PCR panel
Samantha Webster*1,
Amy Jennison*1,
Olivia Jessop2,
Una Ren3,
Sharon Biggs2,
Mitchell Sullivan2,
David Whiley4,
Rikki Graham2
1Public and Environmental Health Reference Laboratories, Queensland Health ,
2Public and Environmental Health Reference Laboratories, Queensland Health; University of Queensland Centre for Clinical Research,
3ESR NZ,
4University of Queensland Centre for Clinical Research