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Culture-independent genomic typing of bacterial pathogens

In the past, diagnosis and investigation of infectious micro-organisms relied on growing them on a culture plate or in culture media, which is a slow and expensive process.

Now, culture-independent diagnostic tests (CIDTs) can identify the pathogens responsible for many types of infection by detecting specific molecules produced by the microbes. However, while CIDTs are much more efficient and are already being used to diagnose many diseases, they provide limited information – usually just whether or not a specific pathogen is present in the sample.

CIDTs are already replacing traditional diagnostic culture for many important diseases. However, culture is still necessary to determine the “typing” information that describes the organism’s lineage and which important genes it carries, such as toxins or resistance to antibiotics.

When CIDTs are performed without follow-up culture – which is already happening – we lose the crucial information needed for tracing the source and spread of outbreaks, recognising particularly virulent organisms,  or monitoring particular strains of a pathogen.

This project aims to develop a new test to generate this ‘typing’ information for a specific pathogen directly from the sample, without culture. Developing this new method eliminates one of the main downsides of culture-independent diagnostic tests, ensuring that patients receive quick and easy diagnoses without compromising the ability of public health laboratories to protect the public.

This project will initially involve primary investigators from one Crown Research Institute and one university, and will make use of a postdoc hosted at ESR; further collaborations are already under discussion and will be developed as the project progresses.


  • Develop a new method to generate rapid diagnostic data for public health outcomes
  • Embed skillsets to generate rapid diagnostic data for public health outcomes
  • Improved capacity in understanding communicable disease metagenomics and bioinformatics


  • Dr Xiaoyun (Una) Ren (Institute of Environmental Science and Research Ltd) – lead researcher
  • Dr Christina Straub (ESR)
  • Dr Xochitl Morgan (University of Otago)
  • Dr Paul Gardner (University of Otago) - Project Advisor

  • Associate Professor Patrick Biggs (Massey University) - Project Advisor

  • Dr Joep de Ligt (ESR)