Microbes and MinIONs: Beating Bad Bugs using Genomics

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1. Project summary (maximum 150 words)

Antibiotics are critical in modern medicine and have saved countless lives. However, bacteria are quickly developing resistance against antibiotics also known as superbugs. Current diagnostics struggle to rapidly identify treatment options which causes high economic burden and mortality not only impacting Queensland, but globally. My research endeavours to uncover the mechanisms bacteria utilise to evade antibiotics and develop techniques to rapidly detect antibiotic resistance. Bacteria frequently acquire resistance by changing their DNA which subsequently modifies a component an antibiotic recognizes to kill the bacteria. Alarmingly, bacteria have the ability to give DNA to other bacteria which can encode resistance to multiple antibiotics! Using a device called the MinION, I have been able to identify bacteria in samples and rapidly determine if they harbour antibiotic resistance. I hope that in the near future, genomics will be used as a common practice to quickly diagnose infections and beat these superbugs!

2. How does your project benefit Queensland? (maximum 500 words)

Antimicrobial resistance, which encompasses antibiotic resistance, is estimated to contribute to 700,000 deaths per annum. If current trends continue, this could lead to 10,000,000 mortalities per year and an economic burden of $US 100 trillion globally in 20501. The World Health Organisation (WHO)2 and Centers for Disease Control (CDC)3 warn of bacteria that have acquired resistance to a multitude of antibiotics, becoming difficult to treat or untreatable and modern medicine moving closer to a post-antibiotic era.

In Australia, the economic burden of hospital-acquired infections is estimated to be approximately $942 million per year4. Rapid diagnosis of infections would reduce this high economic burden via providing accurate treatment and decreasing the time required in the hospital. One condition triggered by an infection requiring a rapid and accurate diagnostic is sepsis. Sepsis is commonly due to a bacterial infection which causes the immune system attack tissues and organs. In Queensland, more than 20,000 people were treated for sepsis in 2017/18 and approximately 10% of cases were fatal5.

Although I could bombard you with more statistics, the stories of how these infections have impacted individuals and families are truly what motivates my research! One particular incident which has resonated with me and occurred in Queensland would have to be the inspiring story of Matthew Ames. In 2012, Matthew initially had typical flu-like symptoms: sore throat, muscle aches and joint pains. However, this was not caused by the flu but was the result of a streptococcal A infection which led to toxic shock and the subsequent amputation of all four limbs. Matthew is extremely lucky to be alive considering he was given a 1% chance of survival. However, if this infection had been diagnosed earlier, this scenario could have been prevented.

The MinION device (Oxford Nanopore Technologies) is not limited to diagnosing infections in hospitals. This could also be applied to detecting diseases in agriculture (crops and livestock), an extremely important industry in Queensland. The technology has the capacity to detect differing diseases including those caused by viruses, fungi and parasites. Another advantage of this device is its portability and has the potential to diagnose infections in rural locations.

Overall, this research has multiple benefits for Queensland as rapidly diagnosing infections will reduce mortality, economic burden and this device has the potential to detect a vast array of diseases.

1.   O’Neill J. Tackling Drug-Resistant Infection Globally: An Overview of Our Work. The Review on Antimicrobial Resistance 2016. https://amr-review.org/.

2.   World Health Organisation. Antimicrobial resistance: a global report on surveillance 2014. 2014. http://www.who.int/drugresistance/documents/surveillancereport/en/.

3.   Centers for Disease Control and Prevention. Antibiotic Resistance Threats in the United States, 2013. 2013. https://www.cdc.gov/drugresistance/threat-report-2013/index.html.

4.   Graves N et al. The economic rationale for infection control in Australian hospitals Healthcare Infection. 2009:81-88.

5.  Queensland Government. New take on sepsis awareness. 2018. https://www.health.qld.gov.au/news-alerts/doh-media-releases/releases/new-take-on-sepsis-awareness.

3. What STEM promotion/engagement activities do you do/have you done? (maximum 500 words)

I have primarily promoted STEM via participating in programs offered through the Institute for Molecular Bioscience (IMB) and teaching. Since 2016, I have been involved in the IMB science ambassador program. This program has enabled me to speak to the public and students, including high school students, about my research and how I became a scientist. The ambassador program includes participating in events to raise awareness of certain research topics, tours through our institute, attending career information nights to give guidance to students or simply discussing this over coffee. Another opportunity to interact with students was participating in the IMB student society (SIMBA, President: 2014-2015) and due to these involvements, I was nominated for a 2016 IMB Impact Award for Service & Support.

Teaching is essential for inspiring our future generation in STEM. I have been tutoring since 2014 through the University of Queensland which has allowed me to strengthen my communication skills, provide guidance to students and encourage them to pursue a career in STEM. In 2016, I won a tutoring award through the School of Chemistry and Molecular Biosciences by ranking in the top 10% of tutors based on student and staff evaluations.

I believe it is a great opportunity to meet someone in the career you are potentially interested in. This was not an option available to me when I was in school and found it daunting pursuing this career path. I never had a chance to talk to anyone in this field and am in fact the first scientist in my family. Furthermore, there was a lack of female scientist role models. However, I was passionate about science and enrolled in a Bachelor of Biomedical Science degree at the University of Queensland. I’m glad I can share my story via the IMB ambassador program, tutoring and recently I participated in the STEM “speed dating” – National Youth Science Forum at the University of Queensland. Even if the students aren't too fascinated by science, they always seem to be entertained by my science earrings!

I’m also passionate about communicating my research to the scientific community. Poster presentations at Australian conferences include the Australian Society for Microbiology (2016, 2018 (Top tweet of conference)) and Solutions for Drug-Resistant Infections (2017). International conferences comprise of the Applied Bioinformatics and Public Health Microbiology (2017, Cambridge) and the American Society for Microbiology Microbe (2017, New Orleans). I had the immense privilege of being an invited speaker to London Calling 2018 (London, https://nanoporetech.com/resource-centre/evaluating-extensively-drug-resistant-klebsiella-pneumoniae-resistome-minion-direct). Competitions I’ve participated in consists of the 3 Minute Thesis (2016, Top 3 students of IMB, 5th in Inter-institute round), HealthHack (2016, 1st Place) and the Brisbane Life Science ECR symposium (2018, Pitch Collaboration Runner up Prize).

Thank you for your consideration of this application and supporting women in STEM! If you wish to find out more, follow me on Twitter: @Miranda_E_Pitt.



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I'm a postdoctoral researcher at the Institute for Molecular Bioscience (The University of Queensland). My research strives to uncover the mechanisms bacteria utilise to evade antibiotics and ident...

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