Lab Matters Fall 2024 | Page 113

APHL 2024 POSTER ABSTRACTS

Establishing Surge Capacity Infrastructure for Whole Genome Sequencing During Healthcare-associated Infection Outbreaks

F . Knight , A . Laufer Halpin , P . Gable , T . Ewing , M . Keckler , G . McAllister , Centers for Disease Control and Prevention

Background : Whole genome sequencing ( WGS ) is critical for responding to healthcare-associated infection ( HAI ) outbreaks . Bacterial isolates can be sequenced to determine whether cases are genetically related and help identify potential reservoirs of the outbreak strain . Despite the increased granularity that WGS provides relative to other testing modalities , there are limitations to consider , including instrument throughput and turnaround time , cost , reagent shelf life and regulatory reporting requirements . Moreover , training new personnel and maintaining competencies in wet-lab ( e . g ., DNA extraction , library preparation , sequencing ) and dry-lab ( e . g ., bioinformatics , data analysis ) components of WGS are time- and resource-intensive . Thus , we face challenges in ensuring preparedness to handle unexpected , time-sensitive surges in sequencing requests . In the case of a major HAI outbreak , activating a continuity of operations plan ( COOP ) to triage and prioritize sequencing for efficient outbreak responses alongside routine laboratory operations may become necessary . Having procedures and infrastructure in place beforehand is critical for handling a surge response rapidly while maintaining appropriate standards of laboratory quality and safety and protecting the public ’ s health .

Methods : Using data from past outbreaks for which CDC ’ s Division of Healthcare Quality Promotion Clinical and Environmental Microbiology Branch ( CEMB ) provided testing , we conducted an analysis to inform laboratory emergency response planning . CEMB subject matter experts selected variables to better understand surge capacity and needs , including target pathogen , originating state , date ( s ) outbreak occurred , total sample and isolate counts and number of isolates sequenced per outbreak .

Results : Preliminary analysis of outbreak data indicated that from 2017-2023 , CEMB provided WGS for 82 outbreaks . Of these , 42 involved antimicrobial-resistant ( AR ) organisms and 40 were non-AR . CEMB received > 3,360 samples during that time ( 1-282 samples per outbreak ), including clinical specimens / isolates , environmental samples / isolates and medical devices / products . These outbreaks encompassed > 14 genera and > 22 species of HAI organisms , with the most common genera being Pseudomonas ( n = 13 / 82 outbreaks ; 16 %), non-tuberculous Mycobacteria ( n = 13 ; 16 %), Staphylococcus ( n = 10 ; 12 %), Acinetobacter ( n = 9 ; 11 %) and Klebsiella ( n = 9 ; 11 %). Discussions with wet-lab staff indicated that CEMB can currently process ~ 180 isolates per week under surge conditions ( i . e ., sequencing 24 / 7 by two staff on two instruments ).

Conclusion : This project assesses the capacity and resources needed to support WGS surge testing for HAI outbreaks . Our review of historical outbreak data can inform prioritization of sequencing for specific HAI organisms and recommendations for maintaining testing capacity ( e . g ., training additional surge staff to support core personnel ), guidance for alternative laboratory activation ( e . g ., CDC core facilities or state / local labs ) and development of a data management system . Further COOP development will include analysis of additional variables such as outbreak size / duration and samples received vs . isolates tested , as well as considerations for maintaining staff resilience and avoiding laboratorian burnout .

Presenter : Frances Knight , uqo5 @ cdc . gov

INSPIRE : Readiness – Enhancing State Infectious Disease Preparedness and Response Capabilities for Future Threats

S . Christian , M . Haviland , Association of State and Territorial Health Officials

Public health agencies work tirelessly to prepare for and respond to public health threats , including infectious disease outbreaks and natural disasters . Preparedness plans , training and exercises are a few tools health agencies utilize to ensure communities are ready to respond in the face of an impending threat . While advanced preparedness planning is invaluable , current emergencies also serve as a critical learning opportunity to inform future public health response efforts . ASTHO , in partnership with the Centers for Disease Control and Prevention ’ s Division of Preparedness and Emerging Infections , Emergency Preparedness and Response Program , embarked on an initiative to understand effective policies , practices and resources utilized by state and territorial health agencies during the COVID-19 response , to share key strategies for consideration for enhanced preparedness planning for future infectious disease outbreaks .

During the initial data collection phase of the project , ASTHO convened specialized peer networks and various public health and healthcare associations to reflect on experiences and identify tools and model practices related to workforce , data systems management and training utilized or adopted during the COVID-19 response . Through an extensive literature review and incorporating resources identified during convenings with key partners , ASTHO worked to identify the best mechanism to socialize the compilation of synthesized promising practices , lessons learned and other operational challenges captured during the data collection phase .

ASTHO determined that a stagnant document would not adequately illustrate the innovative solutions used by health agencies . From this assessment , INSPIRE : Readiness was designed as an ever-evolving discovery hub where peers can learn about successful strategies for overcoming similar gaps and challenges and apply those insights to their health agency needs . The site is organized into a landing page featuring a description of the product / uses , along with four domain pages : Workforce , Training / Resources , Data Systems and Management and Equity . Each domain page focuses on common factors contributing to public health readiness gaps and challenges . The subdomains cover the following areas : Relate ( Common Ground and Challenges ), Be Inspired ( Success Stories and Innovations ), Discover ( Tools and Resources for Progress ) and Take Action ( Implement Solutions and Share Your Journey ).

INSPIRE : Readiness is a hub where the ASTHO community and other public health professionals can learn from their peers about successful strategies for overcoming similar gaps , learn from each other ’ s experiences , discover new methods and apply those insights to their health agency needs .

This poster will summarize the initiative ’ s key results , highlighting the project ’ s evolution over the past two years and the process of creating INSPIRE : Readiness . ASTHO will engage participants in a review of the project findings , the journey to INSPIRE : Readiness and curated examples of identified promising practices and lessons learned , focusing on actionable strategies to inform real-world implementation .

Presenter : Sidnie Christian , schristian @ astho . org