Outbreak Detection Using Next Generation Genome Sequencing (NGS)

Project on Salmonella enterica serovar Typhimurium
Salmonella enterica is a zoonotic pathogen causing a variety of diseases in humans and animals. S. Typhimurium represents up to 50% of human and 20-25% of bovine and chicken isolates in Australia, posing a major public health threat.

Next Generation Genome Sequencing (NGS) has been increasingly employed to prospectively identify and track outbreaks. NGS has major advantages over other pathogen typing methods as it promises a standardised universal solution for high-resolution typing. This project will develop a genome-based method for Salmonella outbreak detection. Techniques include genome sequencing and bioinformatics.

Recent publications

  • Lam C et al, 2014, ‘Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia’, Emerg Infect Dis. 20:626.
  • Bart M et al, 2014, ‘Global population structure and evolution of Bordetella pertussis and their relationship with vaccination’, MBio, 5: e01074.
  • Octavia S, 2015, Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak’, J Clin Microbiol, 53:1063.
  • Fu S et al, 2015, ‘Defining the core genome of Salmonella enterica serovar typhimurium for genomic surveillance and epidemiological typing’, J Clin Microbiol, 53:2530. 

BABS academic responsible for this project:

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