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Our people-our expertise: Dr Sanmarié Schlebusch

Our people-our expertise

Dr Sanmarié Schlebusch

Qualifications | Research interests | Publications | Presentations | Awards | Grants and funding | Memberships

Dr Sanmarié Schlebusch is an experienced clinical microbiologist and the Chief Medical and Genomics Microbiologist at Forensic and Scientific Services, where she is the designated person responsible for clinical governance of the Public and Environmental Health laboratory, including Queensland Public Health and Infectious diseases REference Genomics (Q-PHIRE Genomics), She is also a Clinical Microbiologist at Pathology Queensland and both Vice Chair and Board Director for NATA. Previously Sanmarié was the Director of Microbiology at Mater Pathology in Brisbane, where she led the clinical validation and NATA accreditation for microbial whole genome sequencing, the first such accreditation achieved in Queensland.

Dr Schlebusch is internationally recognised for her pioneering of innovative technologies in clinical microbiology, including clinical metagenomics (RCPA PathWay, 114). 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 Royal College of Pathologists of Australasia to supervise and report on microbial genomics in laboratories, including pathogen identification, characterisation and phylogeny.

Sanmarié is currently undertaking research on the effects of antibiotics on the gut microbiome using a metagenomic approach. She further contributes to translational medicine and research as senior lecturer with the University of Queensland.

See more information about Dr Sanmarié Schlebusch at:


  • Graduate of the Australian Institute of Company Directors
  • Associate Fellow of the Australasian College of Health Services Management (AFCHSM)
  • Graduate Certificate in Business, Southern Cross University, Australia
  • Fellow of the Royal College of Pathologists of Australasia (FRCPA)
  • Australian Medical Council Certificate, Australian Medical Council
  • Bachelor of Medicine and Bachelor of Surgery, University of Pretoria, South Africa (MBChB)

Research interests and expertise

Dr Schlebusch is currently undertaking research with the University of Queensland: Assessing the effects of antibiotics on the gut microbiome – a metagenomic approach. 

The Gut and its microbiome in the Fight against Superbug Threats (GaimitFaST) research, which includes patients from the MERINO trials ( and patients admitted to the Royal Brisbane Hospital intensive care unit (ICU).

The human gut contains a vast array of micro-organisms that play an essential role in human health and disease. The use of antimicrobials has a detrimental effect on gut microbiota and increased risk for infection or colonisation with resistant organisms. The gastro-intestinal tract is a major reservoir for colonisation with multi-drug resistant pathogens. This study utilised whole genome sequencing on faecal samples or rectal swabs from hospitalised patients with a focus on three groups (no antibiotics, piperacillin-tazobactam or meropenem treatment), to describe the relative microbial diversity in each patient sample set collected over time and compared between groups. In addition, changes to key organisms and antimicrobial resistance genes will be assessed. This work will inform decisions around antibiotic usage and have implications for preventing antimicrobial resistance transfer. The project also involves enhancing laboratory methodology, bioinformatics pipelines, and clinical interpretation of metagenomic sequencing to support utilisation in healthcare.

This is a multi-site collaborative research project, which includes FSS as a collaborating site.

See more information at:


Smoll NR, Taylor C, Martin R, Wheatley S, Moore P, Finger M, Moore F, Schlebusch S, Khandaker G, (2021). SARS-CoV-2 public health investigation in an aged care facility and challenges with serological screening in low pre-test probability settings.  Communicable Diseases Intelligence, 45. DOI: 10.33321/cdi.2021.45.42

Brischetto A, Schooneveldt J, Schlebusch S, (2021). Evaluation of direct antimicrobial susceptibility testing using positive blood culture broth in an Australian laboratory. Pathology. DOI: 10.1016/j.pathol.2021.03.013

Pyke AT, Nair N, van den Hurk A, Burtonclay P, Nguyen S, Barcelon J, Kistler C, Schlebusch S, McMahon J, Moore F, (2021). Replication Kinetics of B.1.351 and B.1.1.7 SARS-CoV-2 Variants of Concern Including Assessment of a B.1.1.7 Mutant Carrying a Defective ORF7a Gene. Viruses, 13. DOI: 10.3390/v13061087

O'Toole Á, Hill V, Pybus OG et al. (2021) Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [version 1; peer review: 1 approved]. Wellcome Open Res 2021, 6:121. DOI: 10.12688/wellcomeopenres.16661.1

Stewart AG, Satlin MJ, Schlebusch S, Isler B, Forde BM, Paterson DL, Harris PNA, (2020). Completing the Picture - Capturing the Resistome in Antibiotic Clinical Trials. DOI: 10.1093/cid/ciaa1877

Stehlik P, Alcorn K, Jones A, Schlebusch S, Wattiaux A, Henry F, (2020). Repeat testing for SARS-COV-2: Persistence of viral RNA is common, and clearance is slower in older age groups. DOI: 10.1101/2020.08.27.20183483 [preprint]

Pyke AT, Choong K, Moore F, Schlebusch S, Taylor C, Hewitson G, McMahon J, Neelima Nair, Moore P, Finger M, Burtonclay P, Wheatley S, (2020). A Case of Japanese Encephalitis with a Fatal Outcome in an Australian Who Traveled from Bali in 2019. Tropical Medicine and Infectious Disease, 5(3) 133. DOI: 10.3390/tropicalmed5030133

Walczak A, Wilks K, Shakhovskoy R, Baird T, Schlebusch S, Taylor C, Reid D, Choong K, (2020). COVID-19 in a complex obstetric patient with cystic fibrosis. Infection, Disease & Health. ISSN 2468-0451. DOI: 10.1016/j.idh.2020.07.002

Moyniham KM, McGarvey T, Barlow A, Heney C, Gibbons K, Clark JE, Schlebusch S, Luregn J, (2020). Testing for Common Respiratory Viruses in Children Admitted to Pediatric Intensive Care: Epidemiology and Outcomes. Pediatric Critical Care Medicine, 21(6) e333-e341. DOI: 10.1097/PCC.0000000000002302

Arulkumaran N, Routledge M, Schlebusch S, Lipman J, Conway Morris A, (2020) Antimicrobial-associated harm in critical care: a narrative review. Intensive Care Medicine. DOI: 10.1007/s00134-020-05929-3


For publications prior to commencement at FSS see:


October 2020: SARS-Co-V-2 genomics Queensland. In: The McCormack Infection Meeting, online, Queensland.

November 2019: Invited speaker, The gut microbiome and emergence of antimicrobial resistance. In: National Antimicrobial Resistance Forum 2019, Brisbane, Qld.

September 2019: Invited speaker, New microbial diagnostics – clinical metagenomics. In: Short Course in Critical Infection 2019, Brisbane Qld.

August 2019: Invited speaker, Metagenomics in Healthcare. In: Pathology grand rounds, Pathology Queensland, Brisbane Qld.


  • Betty McGrath Fellowship, Mater Foundation, 2016 - 2018.


  • Member of the Australian Society for Microbiology (MASM).
  • Member of the Australian Society for Antimicrobials.
  • Member of Women's Health Queensland Inc.
  • Member of the Expert Reference Panel on SARS-CoV-2 Serological Testing for the Public Health Laboratory Network (PHLN), which provides advice on the use of serology for SARS-CoV-2 to inform the National response to COVID-19.
  • Member of the Communicable Diseases Genomics Network (CDGN) including the Expert Reference Panel on SARS-CoV-2 Genomics of the CDGN, providing advice on the potential use of SARS-CoV-2 genomics to inform the National response to COVID-19, in a manner that aligns with the capability and capacity of Australian laboratories, public health units and the state, territory and Australian governments.
  • Member of the Statewide Infection Clinical Network (SICN) Steering Committee, which was established to provide leadership and clinical expertise with respect to hospital infectious diseases and infection prevention and control, initially with a focus on COVID-19 preparedness and response.
  • Member of the Communicable Diseases Network Australia (CDNA) COVID-19 National Surveillance Working Party   Serosurveillance subgroup, which is responsible for developing the Australian COVID-19 Serosurveillance Strategy as part of the Australian National Plan for COVID-19.
  • Member of the Management Committee of Bloodstream Infections collaborative.

Dr Sanmarié Schlebusch
Principal Clinical Microbiologist
phone: +61 1800 000 377