Real time pathogen genomics for diagnostics in the Pacific
MWC is partnering with New Zealand-trained Pacific colleagues to develop diagnostics and tools for infection control and public health in the Pacific Islands.
Sakiusa Baleivanualala working in the Department of Microbiology and Immunology. Image courtesy of Antonella Gianfelice
MWC researchers from across the Infectious Diseases network are working through a large-scale four-year project exploring how to spot and stop the rise and travel of pathogens in and across the Pacific using next generation sequencing (NGS).
Pathogens rarely have respect for international borders. With significant bidirectional movement of people between New Zealand and the Pacific Islands, this is an important route for transmission of pathogens. Improved control of infection in the Pacific therefore has benefits for the entire region.
The project, employing real time pathogen genomics for diagnostics and surveillance in the Pacific, is led by immunologist and clinical microbiologist Professor James Ussher along with early and mid-career researchers from across institutions. Lupeoletalalelei Isaia and Sakiusa Baleivanualala, two MWC early career researchers and PhD candidates from the University of Otago have expertise in NGS analysis of priority anti-microbial resistant (AMR) pathogens and AMR in the Pacific. They will be working in Samoa and Fiji during the project.
NSG technology grew in fame through its use of metagenomic sequencing to rapidly identify SARS-CoV-2 as the cause of an outbreak of severe pneumonia in Wuhan at the end of 2019. It continued to play a crucial role in identifying novel variants of SARS-CoV-2.
Until recently, genomic sequencing required expensive equipment and bioinformatics expertise which limited its use to areas with access to specialist sequencing facilities. Now with advances in chemistry increasing accuracy and lower cost disruptive technologies, pathogen genomics is in reach of diagnostic laboratories.
Lupeoletalalelei and Sakiusa are collaborating with the Communicable Diseases Research Centre at Fiji National University and Tupua Tamasese Mea’ole Hospital in Samoa where they will be using some of the latest sequencing technology, the Oxford Nanopore Technologies MinION. This small USB-sized device can be taken into the field. It plugs into a standard well-powered computer and provides sequencing data in real time. Professor Ussher says the tool could be used to quickly identify outbreaks and help prevent transmission of hospital-acquired infection such as by multidrug-resistant organisms.
Another application of NSG which the team is exploring is its use for culture-independent genotypic resistance testing of Mycobacterium tuberculosis. Mycobacterium tuberculosis is an important challenge due to its higher incidence in the Pacific and emerging drug resistance.
Professor Ussher says the bacterium is very slow growing and the strain can be resistant to front-line drugs. “If you start a person on a course of anti-TB agents, without knowing whether the strain is resistant, you might drive further resistance and transmission to other people.”
NGS does not rely on the slow process of growing bacteria in culture. After someone has been diagnosed via a PCR test, the MinION could be used to predict whether the bacteria are likely susceptible or resistant to the planned anti-TB therapy.
NGS could also be used to detect novel and difficult to diagnose pathogens which may be causing life-threatening diseases such as severe community-acquired pneumonia, meningitis, or encephalitis.
The MWC researchers will continue to work on the fundamental science in New Zealand and the Pacific, sequencing samples and developing protocols suited to the local situations to establish NGS capability across the region.