Lab Matters Fall 2024 | Page 102

APHL 2024 POSTER ABSTRACTS

From Scattered Sheets to Actionable Insights : Establishing a Robust NGS QA Database

M . Gomaa , V . Aoki , P . Dykema , Washington State Department of Health

Introduction : Next generation sequencing ( NGS ) represents a revolution for diagnostics and surveillance . However , as NGS methodology expands , a major challenge faced by public health laboratories ( PHLs ) are the robust NGS quality management systems requirements , which are crucial for the delivery of reliable results . Traditionally , PHLs rely on manual data entry and scattered excel sheets , hindering efficient data collection , analysis and utilization . The current study describes the development and implementation of a consolidated NGS QA database at the Washington State Public Health Laboratories ( WA PHL ). The construction of the NGS QA database is useful to overcome these challenges and provide actionable insights for meaningful quality improvement .

Methods : This project utilizes a multi-pronged approach :

• Data Integration : Integrating disparate data sources , including LIMS ( StarLIMS ) and legacy excel sheets , using dedicated tools and middleware platforms for seamless data ingestion .

• Structured Database Design : Implementing a well-defined database schema with clear data validation rules to ensure consistency and quality .

• Interactive Power BI Dashboards : Developing real-time dashboards visualizing key NGS quality metrics across all workflow phases ( pre-analytic , analytic , post-analytic ) for the past ten years .

• Automated Updates : Implementing automated data refresh mechanisms for both the database and dashboards , eliminating manual intervention .

• Smart Data Entry Form : Creating a web-based data entry form that mirrors lab workers ’ existing data entry , but directly integrates data into the established database , optimizing data capture , improves fidelity and minimizes errors .

• Cost Analysis Module : Integrating a cost-analysis module into the Power BI dashboard for real-time monitoring of test costs and informed annual budgeting .

Results :

• Improved access to comprehensive NGS quality information through user-friendly dashboards .

• Continuous process control and compliance monitoring by tracking and detecting trends in NGS QA indicators .

• More accurate budget forecasting through real-time cost monitoring .

Conclusion : This project demonstrates the critical role of a robust NGS QA database in empowering laboratories like the WA PHL to continuously improve their quality management systems , optimize costs and ultimately deliver reliable , high-quality NGS testing for public health benefit . Our approach can serve as a model for other laboratories transitioning from manual processes and scattered data sheets to automated processes with actionable insights in the NGS era .

Presenter : Mohamed Gomaa , spockegypt @ gmail . com

Genomic Analysis of the New Delhi metallo-βlactamase ( blaNDM ) Producing Carbapenem-resistant Enterobacterales Informs the Clonal Transmission of Emerging Lineages in Georgia

A . Ramaiah , T . Kiryutina , G . Tiga , K . Dugger , A . Bedada , S . Woods , E . Daley , T . Parrott , N . Balakrishnan , Georgia Department of Public Health

New Delhi metallo-β-lactamase ( NDM ) is a plasmid-encoded class B carbapenamase enzyme in bacteria capable of hydrolyzing a wide variety of drugs such as carbapenems , penicillins , cephalosporins and monobactams . NDM has been reported worldwide , with the highest prevalence in the Indian subcontinent and Middle East . NDM-producing carbapenem-resistant Enterobacterales ( CRE ) were recently reported from different regions of the United States and are being considered an emerging public health threat . Genomic surveillance of CRE is essential for better understanding of variant and clonal transmission within and between healthcare settings for effective containment of these pathogens . Thus , between January 2020 - December 2023 , a total of 3920 CRE isolates submitted to the Georgia Public Health Laboratory ( GA PHL ) for phenotypic ( using MALDI-TOF and mCIM ) and genotypic characterization ( β-Lactamase Streck ARM-D Kit ) were used for surveillance and outbreak detection . Among 3920 isolates , 4.4 % tested positive for blaNDM by β-Lactamase Streck PCR . Whole genome sequencing ( WGS ) libraries were prepared for these isolates with Illumina DNA Prep and Nextera XT kits ( Illumina Inc ) and sequenced on MiSeq . Paired-end raw reads were assembled and antimicrobial resistance ( AR ) was characterized using bioinformatics methods . Escherichia spp ., Citrobacter spp ., Enterobacter spp ., Klebsiella spp ., Proteus spp ., Providencia spp . and Serratia spp . were commonly identified . The assembled bacterial genome size ranged from 3.9 Mb to 6.8 Mb ( median , 5.3 Mb ) with GC content ranging from 38 % to 59 % ( median , 55 %). Among sequenced strains , 52 % were positive of blaNDM-1 , followed by blaNDM-5 ( 43 %) and blaNDM-7 ( 5 %). We identified E . coli , K . pneumoniae and E . cloacae were the predominantly circulating strains with most prevalent sequence types ( STs ; E . coli : ST167 , ST405 , ST127 ; K . pneumoniae : ST16 , ST147 , ST307 ; E . cloacae ST78 ) documented , indicating the transmissibility of genetically related clonal strains in the facilities . Consistent with epidemiological data , the core genome single nucleotide polymorphisms based phylogenetic analysis revealed specific clusters of closely related species within Enterobacterales harboring the blaNDM variant and within-species clusters of closely related genomes predominated by one sequence type . These clusters could be of potential interest for assisting outbreak investigation and understanding clonal dissemination within the healthcare facilities . WGS provides valuable , near real-time , epidemiologic-informed genomic subtyping approaches to support public health action and targeted infection prevention interventions such as containment strategy in healthcare settings to prevent the transmission of blaNDM-containing CRE .

Presenter : Arunachalam Ramaiah , arunachalamphd @ gmail . com