Network News
June 2024
GA-PGCOE’s 2nd Annual CAPE Meeting
On June 5-6, 2024, the GA-PGCOE hosted its 2nd Annual Meeting at the Georgia Tech Research Institute in Smyrna, GA. The meeting brought together Center Investigators and key stakeholders to discuss significant progress and future directions within the Center and in public health genomics. The meeting featured a total of six outside speakers, including Ellie Click and John Barnes from the Centers for Disease Control and Prevention, Kelsey Florek from the Wisconsin State Laboratory of Hygiene, U.S. Army Captain Kevin Caspary with the 4th Weapons of Mass Destruction Civil Support Team, Robert Petit from Wyoming Department of Public Health, and Ryker Penn from the Houston Health Department.
Key discussion topics included program accomplishments, universal IRB planning, reviewing and unifying Center priorities, and presenting a draft charter document. Notable outcomes from the meeting included insights from guest presentations and project presentations followed by collaborative discussion for each of the five CDC focus areas (wet lab, data, bioinformatics, field studies, and genomic surveillance) and a reception that fostered networking opportunities. The meeting concluded with a Center-wide self-evaluation, emphasizing continuous improvement and strategic planning for the upcoming year.
GA-PGCOE Internship
Chloe Burjak is currently pursuing her Master of Science in Epidemiology at the University of Georgia. Her six week internship (June 3 – July 15, 2024) at GA-DPH with GA-PGCOE Director Arun Ramaiah was funded by the GA-PGCOE program. Her work is focused on improving plasmid detection in short-read based de novo genome assemblies and enhancing the accuracy of identifying antimicrobial resistance (AMR) genes. Burjak participated in the several public health training courses and has had opportunities to interact with many public health experts from different backgrounds. Looking ahead, Burjak plans to leverage her internship experience in bioinformatics to advance public health science within the field of epidemiology.
August 2024
ASM Microbe Conference
Brooke Talbot presented a 15-minute oral presentation at the annual ASM Microbe Conference, this year held in Atlanta, GA. Her presentation, Investigation of Genomic Signatures of Recurrence among Methicillin-Resistant Staphylococcus aureus Bloodstream Infections, demonstrated the power of using AMD technologies and evolutionary principles to differentiate recurrent bloodstream infections and test for risk factors that lead to relapse of infection. She also got to highlight the usefulness of Bactopia for applied epidemiology in hospital and healthcare settings.
AMD Seminar
At the AMD Seminar, held on 31 July 2024 on CDC’s Atlanta campus, GTRI researchers Samantha Lie-Tjauw and Micah Halter presented a talk titled "Empowering Public Health Response and Epidemiologic Investigations Through Data Linkage and Automated Workflows."
The Georgia Tech Research Institute (GTRI) is partnering with Georgia Department of Public Health (GDPH) to link genomic and epidemiologic data from multiple, siloed sources. GTRI is currently focused on the automated development of an Antimicrobial Resistance Log (AR Log) for the Healthcare Acquired Infections (HAI) team at GDPH. The AR Log is automatically produced as the aggregation of case data from several actors in a single tabular format for easy readability and analysis. This enhanced and streamlined data output allows GDPH to respond more quickly and with deeper insight into epidemiological research questions for infectious outbreaks caused by antimicrobial-resistant organisms.
Nextstrain Training
We are excited to share the success of our Nextstrain training workshops for DPH epidemiologists and DPHL bioinformaticians, hosted by our academic partners at UGA this past June. The first virtual workshop focused on Nextstrain builds for bioinformaticians, providing essential skills for integrating these tools into their workflows. The second workshop introduced epidemiologists to Nextstrain Narratives. Ten dedicated participants joined us at UGA, gaining valuable insights and hands-on experience. We're pleased to announce that all training materials will soon be available on our upcoming website. Stay tuned for more updates!
September 2024
Researchers and engineers at the Georgia Tech Research Institute (GTRI) are studying how robust antimicrobial resistant (AMR) genomic analysis pipeline cases can be flagged rapidly using modernized data linkage methods and the automation of manual, human-in-the-loop workflows. The GA PGCoE, also known as GTRI's Center for Applied Pathogen Epidemiology and Outbreak Response (CAPE) team, in partnership with the Georgia Department of Public Health (GDPH), are developing infrastructure built on Amazon Web Services. The CAPE infrastructure is being built with discoverability in mind, taking into consideration the varying needs of different public health professionals. Read more here.
AMD Seminar Presentation: Balanced and Well-spread Subsampling for Better Phylogenetic Inferences in Epidemiology: Applied Molecular Epidemiology Research Group (Bahl Lab)
Guppy Stott, Bioinformatics PhD Candidate (University of Georgia)Study Abstract: Over the past decade, the rapid development of novel sequencing technologies has led to the proliferation of large sequencing datasets, presenting new problems for phylogenetics. While some efforts focus on more complex tools that can handle these large datasets, Bayesian phylogenetic approaches using tools like BEAST still require down-sampling. However, common subsampling strategies often do not consider the systemic biases introduced in the dataset by variation in sequence availability. We built a new tool to answer two questions: How do we subsample large datasets representative of a broader outbreak? And how do different subsampling strategies affect our phylodynamic interpretations?
Association of Public Health Laboratories (APHL) Training Connects Public Health Bioinformaticians and AWS Professionals
An AMD Academy training, organized by the Association of Public Health Laboratories (APHL), took place from August 20-22, 2024, at Amazon's second headquarters in Arlington, VA. Tatyana Kiryutina from the Georgia Public Health Laboratory (GPHL) attended this program. The advanced bioinformatic training included sessions led by Amazon Web Services (AWS) professionals who provided insights on modern cloud architecture. Participants engaged in interactive exercises, such as building solutions for public health scenarios using AWS services. This exercise helped Tatyana understand which AWS services are most relevant to public health out of the many available options. The training also introduced a user-friendly tool called Easy Genomics, which will enable Public Health Labs to scale their bioinformatics capacity with limited technical expertise. Overall, the training facilitated networking among bioinformaticians and highlighted efficient pipeline building techniques using Nextflow, Seqera Platform, and AWS services for the implementation and application in PGCOE projects.
19th Annual Georgia Emerging Infections Program (EIP) conferenceGroup photo at EIP conference.
Pictured from left to right: Jason Harrison, Dr. Arun Ramaiah and Keri Smith
Georgia Public Health Laboratory (GPHL) staff members attended the 19th Annual Georgia Emerging Infections Program (EIP) conference on August 16th, 2024, held in Atlanta. This state-level meeting provided an opportunity to learn and discuss topics including H5N1, meningococcal disease, antibiotic resistance, and wastewater surveillance. This event also facilitated networks among laboratorians, public health epidemiologists, health care staff, and clinical microbiology communities statewide.
November 2024
AMD DAYS 2024
Georgia Public Health Laboratory (GPHL) staff member Dr. Arun Ramaiah, and his team attended the AMD DAYS 2024 symposium on September 24th – 25th, 2024, in Decatur, Georgia. Members listened to advanced molecular and bioinformatics presentations, presented posters and were able to network with several public health researchers. Part of the PGCOE network wide collaboration and knowledge sharing, Keri Smith from GPHL had the pleasure of meeting with Sarah Namugenyi from the Minnesota Department of Health and discussed the RSV whole-genome sequencing (WGS) they had developed. The GPHL team also participated in the PGCOE Site Director meeting.
ARLN ANNUAL MEETING 2024
Dr. Arun Ramaiah, along with two Georgia Public Health Laboratory (GPHL) staff members attended the ARLN Annual Meeting 2024 from November 6th – 8th, 2024, at CDC Headquarters in Atlanta. Members participated in laboratory sessions related to advanced molecular and bioinformatics techniques and their applications in antimicrobial resistance organisms. Folks from all 50 states were part of this annual meeting with presentations from the CDC ARX team and public health partners. This provided an opportunity to learn more about the program and facilitating relationships with several public health researchers. During this meeting Dr. Arun Ramaiah met Dr. Ketan Patel from CDC AMD.
