genomics

This project aimed to address the problems associated with the reliability of E. amylovora-specific diagnostics by identifying new diagnostic targets and developing a new diagnostic protocol that can be used as the international standard.

What is the biosecurity problem?

Fire blight, caused by the bacterium Erwinia amylovora, is a destructive disease of apple and pear trees. Fire blight is estimated to cost the United States fruit industry over $100 million a year in crop losses and disease control.

E. amylovora is not currently found in Australia and as such is a major biosecurity threat to the Australian pomefruit industry. Accurate diagnosis of this bacterium is crucial for quarantine testing, incursion detection and incursion management. A number of the internationally accepted PCR tests for identification of E. amylovora used by research laboratories around the world have been found to be unreliable by Australian standards. False negative and false positive PCR results have been observed during routine testing for E. amylovora with some of these tests.

The main outputs of this project were to:
 

• evaluate available E. amylovora-specific PCR diagnostics
• identify and characterise endemic bacteria found on Fire Blight hosts in Australia
• conduct genomic sequencing of four genetically diverse strains of E. amylovora in order to identify the pan-genome of E. amylovora (the whole genome of the species consisting of core and flexible genomes) to determine the amount of intra-species genetic diversity
• identify new chromosomal diagnostic targets for the detection of E. amylovora using the E. amylovora pan-genome
• detect genetically diverse strains of E. amylovora core sequences of DNA that are conserved between all strains of E. amylovora (but are not present or conserved in closely related bacteria) need to be targeted, and
• validation of new diagnostic targets (PCR and/or micro array analysis)
   

Who are the end-users of your research?

The end users of this research are the Australian apple and pear industry, state and federal quarantine agencies and associated diagnostic laboratories.

Rachel Powney in the glasshouse at Cornell University

Professor Steven Beer, Jean Bonasera, Rachel Powney and Brendan Rodoni in the Beer Lab at Cornell University