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Culture-independent genomic typing of bacterial pathogens


In the past, diagnosis and investigation of infectious microorganisms relied on growing them on a culture plate or in culture media, which is a slow process. Now, diagnostic laboratories largely employ the use of culture-independent diagnostic tests (CIDTs), which can identify the pathogens responsible for many types of infections within hours without having to culture bacteria.

But while CIDTs are already replacing traditional diagnostic culture for many important diseases of public health concern, they currently provide limited information, typically confirming the presence or absence of pathogens. A culturing process is therefore still necessary to determine the detailed genetic and phenotypic information that describes the subtype of the organism, its antimicrobial resistance profile and the genes involved in pathogenicity or resistance. Without this culture process, crucial information is lost for tracing the source and spread of outbreaks, recognising particularly virulent organisms, or monitoring antimicrobial resistance.

This project investigated a method to support a test that could generate ‘typing’ information for a specific pathogen directly from the clinical sample, without having to culture. Such a test will eventually ensure that patients receive a quick diagnosis and suitable treatment plan without compromising the ability of public health laboratories to protect the public.

Using a metagenomics approach, investigators from the Institute of Environmental Science and Research (ESR) developed a custom amplicon-sequencing panel for typing Neisseria gonorrhoeae from clinical samples. The test allows species identification and informs about antimicrobial resistance genes carried by the gonococcus present in the clinical sample. A computational pipeline was developed to test the sensitivity and specificity of the amplicon panel. This approach is applicable to future amplicon panel development for other organisms.

Collaborations are continuing with the University of Oxford in the UK and the Molecular Epidemiology Unit, Queensland Health in Australia to test this amplicon panel on clinical samples in their collection.


  • Investigated a new method to generate rapid diagnostic data for public health outcomes

  • Produced an amplicon panel for short and long read sequencing technologies for species identification and typing of antimicrobial resistance in Neisseria gonorrhoeae from clinical samples

  • Improved capacity in understanding communicable disease metagenomics and bioinformatics


  • Dr Jenny Draper (formerly ESR, NSW Health Pathology, Australia) - Science lead
  • Dr Xiaoyun (Una) Ren (ESR) - Co-lead researcher
  • Dr Christina Straub (ESR) - Postdoctoral scientist
  • Dr Joep de Ligt (ESR) - Project advisor
  • Dr Xochitl Morgan (University of Otago) - Project advisor
  • Associate Professor Paul Gardner (University of Otago) - Project advisor

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