Queensland Public Health and Infectious diseases REference (Q-PHIRE) Genomics is the state-wide reference centre for microbial and public health genomics. It provides cutting edge, rapid microbial genomics to support the Queensland response to health threats, including viruses and pandemics. Dr Sanmarié Schlebusch is Chief Medical and Genomics Microbiologist at Forensic and Scientific Services (FSS) and is responsible for clinical governance of the Public and Environmental Health laboratory, including Q-PHIRE Genomics.

“I think the job I do here is just the most interesting – when I started, I couldn’t believe that no one had ever told me about this type of role. I was born and raised in South Africa and went to medical school at the University of Pretoria. I did my internship with Johannesburg General Hospital then worked as a medical officer in community service and general practitioner for a few years before eventually embarking on training in microbiology.

“When I came over to Australia, I knew I had to decide what I was going to do long term. I really enjoy learning so I needed to choose something that was going to be really dynamic and that I would not lose interest in after 10 years. I had worked in laboratories as a medical student, so I was already thinking about pathology before I applied for a training position with microbiology. Three months after starting, I knew that microbiology was the field for me because it was so dynamic and so interesting. I have never looked back,” said Dr Schlebusch.

Dr Schlebusch is internationally recognised for her pioneering of innovative technologies in clinical microbiology, including clinical metagenomics. She is well-published and has been involved in several major research projects. She was amongst the first intake of clinical microbiologists accredited by the RCPA to supervise and report on microbial genomics in laboratories, including pathogen identification, characterisation and phylogeny.

“I have always been interested in new technology. In fact, I was the first microbiologist to pursue mass spectrometry for organism characterisation in Queensland before it became widely used. I remember after my first presentation to microbiologists and infectious diseases physicians in Queensland, they all said that it was interesting, but some saw it only as a research tool, and one person said it would never work!

“Later I went on to become very involved in whole genome sequencing (WGS) in Queensland and was the clinical lead for getting NATA/RCPA accreditation for microbial whole genome sequencing at Mater Pathology, the first such accreditation achieved in Queensland. I moved to FSS around two years ago when I saw a role come up which had a significant component of microbial WGS in the emerging infectious diseases laboratory for Queensland.

“I find my role so interesting and diverse because we test all the different aspects of an outbreak within one laboratory. When there is a large outbreak, it raises the question of “where are people getting their infection” and it is our role to help find out. Providing fast and accurate identification and typing of pathogens is essential for effective surveillance and outbreak detection. There are many ways to do this but one of the main ways is to sequence - to look at the genomes and compare them. To do this, various samples will be tested in the laboratory. This includes not only patient samples but also from kitchens, food, water etc., which allows us to trace the origins of the pathogen responsible for the outbreak.

“For example, it is possible to identify people linked with the same Salmonella infection. Public Health will find out where those people had meals, go to that restaurant and take samples. We may find that there is a link with the eggs which can then be traced back to a particular farm. We can then test samples collected at the farm and confirm if that is where the outbreak originated from. By doing this, we can then prevent more people from getting sick. We are doing something similar for COVID-19, providing sequencing for the whole of Queensland. By turning results around extremely quickly we have been able to help identify different clusters and help control the spread,” said Dr Schlebusch.