Jason Kwong1,2,3, Ben Howden1,2,3
1 Department of Infectious Diseases, Austin Health, Heidelberg, Victoria
2 Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity
3 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity
To aid the process of outbreak identification and investigation, typing of isolates allows discrimination within a single species, and subsequently, identification of highly similar organisms more likely to be implicated in transmission. Historically, a number of different typing methods have been used, including traditional methods based on phenotypic appearance, such as serotyping, phage-typing, and antibiogram comparison. Molecular methods have also been popular, including pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and multi-locus sequence typing (MLST). Each of these methods have different levels of discriminatory power. More recently, with the availability of high-throughput DNA sequencing technology, whole-genome sequencing (WGS) has been used in microbial pathogen surveillance and outbreak identification and investigation, providing the highest level of discrimination to compare isolates. Whether it is the optimal typing method for all outbreaks remains a key question. As with all approaches, there are costs and benefits with using WGS, though its increasing use for both hospital and public health outbreaks warrants an understanding of the technology and its application in assessing infectious disease transmission.