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Changing bacterial pathogen diagnostics in public health

A novel genomics approach is being developed that could help to diagnose and treat a significant health problem in New Zealand.

Gonorrhoea, caused by Neisseria gonorrhoeae, is the second most common sexually transmittable disease worldwide. The emergence of antimicrobial resistance to every class of antibiotics used to treat gonorrhoea in the past is a growing public health concern, here and overseas.

In New Zealand, gonorrhoea is currently diagnosed using a culture-independent approach (CIDT), with no bacterial cultures available for further typing of other characteristics such as antimicrobial resistance. This means that rather than tracking antimicrobial resistance in N. gonorrhoeae on a regular basis, it is only surveyed every few years on a national scale using whole genome sequencing. We therefore lack contemporary information to make informed decisions about accurate treatment of the infection.

Postdoctoral fellow Dr Christina Straub joined the Genomics Aotearoa project on Culture-independent genomic typing of bacterial pathogens, based at ESR, to develop a genomics approach to managing the infection. This will allow finer resolution, faster response time and better surveillance to counteract the spread of multi-resistant pathogens or “superbugs”.

N gonorrhoeae

Drug-resistant Neisseria gonorrhoeae. Photo: Centers for Disease Control and Prevention

The approach involves developing a custom amplicon panel for directly typing bacterial pathogens from clinical samples and predicting antimicrobial phenotypes using a metagenomics approach. The goal of the project is a genomic method to identify N. gonorrhoeae directly from clinical samples, along with information such as antimicrobial resistance.

Christina explains: “This fast and cost-efficient diagnosis will provide the ability for tailored treatment, ultimately lowering the burden on the public health system, when compared to currently used tests. The results will also be comparable to publicly available global epidemiological data, minimising the current surveillance gap and contributing to our ability to understand the evolution, emergence and spread of antibiotic resistant N. gonorrhoeae.”

Christina Straub

Christina Straub

Christina’s career path

After a Bachelor’s degree in Cell Biology/Physiology, Christina did a Master’s degree in Zoology at the University of Salzburg, Austria, studying fire salamander populations. “During my research on amphibians, I learned about the devastating impact a pathogen can have on an organism, when chytrid fungus, which causes the disease chytridiomycosis in amphibians, ravaged across Europe and worldwide, rapidly diminishing amphibian populations."

Christina then moved to New Zealand to pursue a PhD in the lab of Prof. Paul Rainey at Massey University. She says working with bacterial pathogens is exciting, since it allows the study of evolution in real time thanks to short generation times. “My project focused on Pseudomonas syringae, a bacterial plant pathogen also found on kiwifruit. I investigated the type and extent of interactions of co-occurring bacteria with the pathogen P. syringae pv. actinidiae (Psa, bacterial canker of kiwifruit) on the kiwifruit leaf surface. During this time, I acquired skills in plant pathology, population genetics and comparative genomics, bioinformatics skills in genome assembly, and started working on a high performance computing cluster.“ After receiving a Zespri postdoctoral scholarship, Christina further investigated the role of commensal P. syringae in the evolution of Psa.

“Fascinated by the rampant bacterial evolution of pathogens and the problem of evolving superbugs in human pathogens, I was ready for a new challenge and joined the exciting project of making use of metagenomics in clinical diagnostics as a GA postdoctoral scientist based at ESR.”

Christina’s areas of expertise:

  • Microbiology
  • Genome assembly
  • Population genetics
  • Comparative genomics
  • Phylogenetic analysis
  • Metagenomics
  • Plant pathology