Meet a genomic epidemiologist
Dr. Nicole Pacchiarini, Public Health Wales
I recently had the pleasure of speaking with Dr. Nicole Pacchiarini, a Senior Epidemiological Scientist at Public Health Wales who leads the Genomic Epidemiology Unit. I hope you find her story as interesting as I did!
Overview
Educational path
Joint Hons Bachelor of Science (BSc), Cognitive Neuroscience and Psychology, The University of Manchester
Master’s Degree, Clinical Neuroscience, King’s College London
Doctor of Philosophy (Ph.D.) Neuroscience and Psychology, Cardiff University
Experience path
Information Analyst, Public Health Wales
Bioinformatician, Public Health Wales
Senior Epidemiological Scientist, Public Health Wales
Education and early career
Like many working in the field, genomic epidemiology wasn’t on Nicole’s radar during her schooling or the start of her career. After completing her PhD in Neuroscience and Psychology, she decided she was more interested in data analysis than laboratory-based work. That interest brought her into public health where her first role was as an information analyst with Public Health Wales (PHW) in the Blood borne viruses, Sexual health, Tuberculosis and Inequalities team located within the Communicable Disease Surveillance Centre (CDSC). Through this role she was exposed to a variety of public health data management and analysis functions as well as the investigative side of epidemiology.
Her moment of inspiration about the power of genomic epidemiology came through her involvement in tuberculosis investigations and cohort reviews. As she saw connections among cases come to light through genomics, she saw the power of genomics to shape both clinical and public health action. Just as exciting was the ability for genomics to cast doubt on an epidemiologic hypothesis – sometimes showing no genomic linkages for cases that may have overlapped in time and space.
Moving into genomic epidemiology
Pursuing her burgeoning interest in genomics further, she moved into a bioinformatics role with the Pathogen Genomics Unit at PHW, just before the COVID-19 pandemic. She was originally tasked with working on the existing HIV pipeline, but along with much of the public health workforce at the time, she was diverted into SARS-CoV-2 work. After spending a couple of years working on SARS-CoV-2 sequencing pipelines and outbreak investigations, she had the opportunity to move back into the CDSC to lead a new genomic epidemiology group which had been set up in response to the pandemic.
Through her bioinformatics and genomic epidemiology roles, she has been involved in many different investigations, including an epidemiological analysis of the first Omicron cases in Wales and the detection of a new recombinant lineage, facility-level SARS-CoV-2 outbreaks in a prison, and a Salmonella cluster among ruminants and the associated food supply chain.
Q&A with Nicole
What are some of the trainings and resources have you used along the way to learn about genomic epidemiology, bioinformatics, and the laboratory?
When I first joined Public Health Wales, I had only used MATLAB and a little R so the Epi R Handbook was a brilliant resource. When I moved to the Bioinformatician role, I found the Datacamp courses really useful for an introduction to programming languages I wasn’t previously familiar with such as Python and SQL. For Bioinformatics, I would also recommend the Software Carpentry Bioinformatics repository to get to grips with the Unix terminal. Finally, for general epidemiology, the ECDC Virtual Academy contains a huge range of resources for training that I found really helpful when moving from Neuroscience to Epidemiology.
What advice would you give to a student or professional that's interested in pursuing genomic epidemiology?
Keep an open mind! This is a very fast-moving field and you may need to pivot quickly to learn new programming languages, techniques and concepts. I would also say that the basics of epidemiology are also really important - so person, place and time are essential when using Genomics for outbreak response.
What are some words of wisdom for those interested in genomic epidemiology:
Don’t worry if you don’t have a specific Genomics or Bioinformatics educational background, lots of the scientists in this field come from varied backgrounds. I have colleagues who trained in medicine, biology and even geography! The most important thing is that you are keen to learn.
Hope for the future
We discussed where the field is going, and what genomic epidemiology teams might look like in the future. One of the main remits of teams right now is workforce development, and that’s an area where Nicole sees long-term needs. Even if genomics becomes more integrated into training programs for up-and-coming epidemiologists, there will always be new tools and methods being developed that need integration into epidemiologic practice. Genomic epidemiology teams along with bioinformatics teams fill a critical role in providing education and training to keep epidemiologists, health protection practitioners and clinicians educated in the latest analyses, methods, and nomenclature.
In addition to the training and enablement role, there are also opportunities for more advanced analyses which will become easier as programs mature. Along with more analyses of pathogens currently routinely sequenced, Nicole is excited about the growing diversity of pathogens where genomics is being used to guide disease surveillance and investigation. The sky truly is the limit when it comes to what pathogens could benefit from the insights gained through genomic epidemiology.
Genomic epidemiology teams are a critical component of the public health workforce and will be needed for the long-term. As highlighted in Nicole’s words of wisdom, if you have an interest in the field, find some training opportunities and dive into learning. No matter your background if you’re eager to learn, there are opportunities for you in the field.
I appreciate Nicole taking time to share her story with me! Do you incorporate genomic data into your work as an epidemiologist? If you’d like to share your career journey, reach out to krisandra@genomicepi.com.