Lab Matters Fall 2024 | Page 66

APHL 2024 POSTER ABSTRACTS

DIAGNOSTICS AND NEW DISEASE TECHNOLOGIES

Alinity m You-Create Lab-developed Test for Candida auris Using Commercially Available Reagents

M . Sasaki , X . Wang , D . Lucic , Abbott Molecular

Introduction : Lab developed tests ( LDTs ) play an important role in the realm of infectious diseases . Current molecular diagnostic platforms offer fully automated high-throughput performance capable of running LDTs . The Alinity m platform enables users to run LDTs concurrently with other FDA cleared or approved IVD assays with its Alinity m You-Create feature . Here , we investigated the performance of an LDT assay targeting Candida auris using commercially available reagents .

Methods : Alinity m You-Create LDT for C . auris was evaluated using Applied Biosystems TaqMan Fast Virus 1-Step Multiplex Master Mix , No ROX , ( ThermoFisher , Cat : 5555532 ) and primer set for C . auris from Fort Worth Diagnostics ( Ft . Worth , TX , Cat : CAUR ). Panels were prepared in Alinity m Transport Buffer Amies Buffer ( Copan , Cat : 480C ) using frozen aliquots of C . auris . Samples extraction utilized Alinity m Sample Prep Kit 1 or 2 .

Results : Alinity m You-Create for C . auris had 100 % detection of C . auris as low as 10 CFU / mL for all PCR buffers tested with either Alinity m Sample Prep 1 or 2 .

Conclusion : This study demonstrated successful implementation of an LDT for C . auris on the Alinity m platform using the Alinity m You-Create feature using commercially available PCR reagents . The Alinity m You-Create feature for C . auris has not been approved by FDA for use in the detection or diagnosis for C . auris and its safety and effectiveness has not been established .

Presenter : Mark Sasaki , mark . sasaki @ abbott . com

Alinity m You-Create Lab-developed Tests for Lymphogranuloma venereum and Treponema pallidum Using Commercially Available Reagents

M . Sasaki , X . Wang , D . Lucic , Abbott Molecular

Introduction : Laboratory developed tests ( LDTs ) play an important role in the realm of infectious diseases . Current molecular diagnostic platforms offer fully automated high-throughput performance capable of running LDTs . The Alinity m platform enables users to run LDTs concurrently with other FDA cleared or approved IVD assays with its Alinity m You-Create feature . Here , we investigated the performance of two LDT assays targeting Lymphogranuloma venereum ( LGV ) and Treponema pallidum , using commercially available reagents .

Methods : Commercially available PCR buffers including 10x TAQ Polymerase Buffer ( ThermoFisher , Cat : 18067017 ), 5x Platinum II TAQ Polymerase buffer ( ThermoFisher , Cat : 14966005 ), 10x GeneAMP II buffer ( ThermoFisher , Cat : 4379878 ), 10x GeneAMP Gold buffer ( ThermoFisher , Cat : 4379874 ), or Tris- HCl ( ThermoFisher , Cat : J22638 . K2 ) ranging from 10 to 100mM were used to evaluate a PCR reaction containing Platinum II TAQ polymerase ( ThermoFisher , Cat : 14966005 ), dNTP ( ThermoFisher , Cat : 18427088 ) and 6 mM MgCl2 ( Sigma-Aldrich , Cat : 46878- U ). Panels were prepared in Alinity m Transport Buffer ( LGV and T . pallidum ) and UTM ( T . pallidum ) using frozen aliquots of LGVII ( Zeptometrix , Buffalo , NY ), or a positive clinical specimen for T . pallidum . Samples extraction utilized Alinity m Sample Prep Kit 1 or 2 .

Results : Alinity m You-Create for LGV had 100 % detection as low as 1 IFU / mL for all PCR buffers tested . Alinity m You-Create for T . pallidum had 100 % detection as low as 10 IFU / mL . Alinity m Sample Prep Kit 1 resulted in earlier target CT for LGV and T . pallidum .

Conclusion : This study demonstrated successful implementation of LDTs for LGV and T . pallidum on the Alinity m platform using the Alinity m You-Create feature using commercially available PCR reagents . The Alinity m You-Create feature for LGV and T . pallidum has not been approved by FDA for use in the detection or diagnosis for LGV and T . pallidum and its safety and effectiveness has not been established .

Presenter : Mark Sasaki , mark . sasaki @ abbott . com

Bayes Inference for Disease Transmission . Case : COVID-19 Transmission Model with Simulated Data

O . Linares-Perodmo 1 , K . Oakeson 2 , Utah DHHS-Utah Public Health Laboratory ( Unified State Laboratory ) 1 , Utah Public Health

Laboratory 2

Materials and methods : A Bayesian generative model approach for simulation and inference for disease transmission was derived and coded using R and STAN . To model the data a negative-binomial distribution was probability distribution selected and to estimate the posterior distribution of model parameters the Markov Chain Monte Carlo ( MCMC ) was used . The simulation-based calibration method ( SBC ) was used to validate the model inferences .

Results : The results presented on this preliminary study comes from simulate data . The main purpose was to analyze the model behavior and the inference of the algorithm . Future study will be using real COVID-19 data .

Discussion : There is an increase interest in the uses of Bayes theorem for model and inference in many fields for its capacity of adaptation as more information becomes available for model parameters estimation , make new predictions and quantify uncertainty . The general problem is the quantification of the prior ( s ) when using exact analytical solutions that are often intractable . This study used the MCMC for the quantification of the prior ( s ) in a disease transmission model coded in R / stan . This Bayesian model can be adapted to analyze other types of data such as influenza or wastewater-data .

Conclusion : We developed a Bayesian approach for disease transmission using R and STAN with different probabilities distribution to analyze the model parameters and the inference behavior .

Presenter : Olinto Linares-Perdomo , olinares-perdomo @ utah . gov