Lab Matters Fall 2024 | Page 58

APHL 2024 POSTER ABSTRACTS

used to generate samples . IDOHL looks to collect additional patient specimens in the 10-25 IU / mL category for reevaluation .

Presenter : Stephanie Sweets , ssweets @ health . in . gov

Extracting SARS-CoV-2 Population-level Viral Load Data From Cycle Threshold Values and Correlation with Prevalence Within a Hospital System

D . Jarem 1 , J . Canchola 1 , E . Pujadas 2 , C . Cordon-Cardo 3 , M . Danieletto 3 , D . Adhimoolam 3 , Roche Molecular Diagnostics 1 , Memorial Sloan Kettering Cancer Center 2 , Icahn School of Medicine at Mount Sinai 3

Aim : Quantification of SARS-CoV-2 RNA is only available in selected labs ; consequently , the widespread inappropriate use of Ct values as ( semi ) quantitative qPCR readout has hampered clinical and epidemiological interpretation of viral load . Evaluation of a subset of results from a quantitative laboratory developed test ( LDT ) was used to train an algorithm to interpret Ct values as viral load ( VL ) from a larger data set obtained with a commercial high-throughput solution .

Methods : VL was initially calculated using the delta Ct method for each of the primers N1 , N2 and N3 from the CDC 2019- nCoV Real-Time RT-PCR Diagnostic Panel . A standard curve was generated by plotting the Ct values against the log quantity of known starting sample for serial dilutions with known viral RNA genome equivalents / uL . A subset of data with paired results between the LDT and cobas ® SARS-CoV-2 assay ( cobas ), a commercial high throughput solution , were trifurcated randomly into three data sets ( training , validation , test ) for the derivation of a conversion algorithm ( using the training data set ). This algorithm was then was applied , utilizing the cobas internal control to correct for variability over reagents / instrument / time to generate viral load for the qualitative test , which was then compared to positivity rate within the hospital system over time .

Results : The final conversion factor for application to the cobas quantitation values was 29.23 gEq / Units . Method comparison of final cobas vs . LDT quantitation ( log10 ) showed excellent linearity via Deming regression ( n = 1207 ; slope = 1.005 with 95 % CI : 0.99 to 1.021 ; intercept = -0.032 with 95 % CI : -0.099 to 0.034 ). Multiple regression showed the log10 VL to be predictive of the logit-transformed percent positivity over time ( p = 0.005 ) within the hospital system , allowing for the prediction of a new wave , with a lead time , prior to peak positivity .

Discussion : Transforming qualitative testing into quantitative VL may assist clinicians in risk-stratifying patients and choosing among available therapies and clinical trials , however , here we suggest that peak VL derived from standard qualitative solutions can be used as a surrogate for impending waves of infection . Earlier notice may allow for better allocation of personnel and resources and possibly curb the extent of the surge by heightening protections earlier .

Presenter : Daniel Jarem , daniel . jarem @ roche . com

Group A Streptococcus Molecular Surveillance - Los Angeles County

J . Garrigues 1 , P . Hemarajata 2 , A . Marutani 1 , B . Dao 1 , T . Burleson 1 , P . Gounder 1 , N . Green 1 , Los Angeles County Public Health 1 , Association of Public Health Laboratories 2

Group A Streptococcus ( GAS ) causes a myriad of disease types , ranging from pharyngitis to invasive disease and post-infectious sequelae associated with significant morbidity and mortality . Although invasive GAS disease ( iGAS ) is relatively rare , Los Angeles County experienced a record preliminary number of 688 reported iGAS cases in 2023 , with seven identified outbreaks in assisted living facilities . The Los Angeles County Department of Public Health requested clinical and commercial reference laboratories in our jurisdiction to submit GAS isolates from pediatric and adult invasive and skin / soft tissue infection ( SSTI ) cases for further characterization . As of January 2024 , our laboratory has characterized 223 GAS isolates received since November 2022 by whole genome sequencing ; of these , 129 were associated with invasive disease , providing almost 20 % coverage of reported iGAS / SSTI cases in Los Angeles County . Most isolates were from wound or bloodstream infections and included a case of invasive reinfection . Results from genomic analyses identified emm types , virulence factors and antimicrobial resistance genes . Most common emm types causing invasive disease in our geographic region included 44 , 12 , 89 , 76 , 92 , 53 and 1 , which differs considerably from the nearest CDC Active Bacterial Core ( ABC ) surveillance catchment area ( San Francisco Bay Area ). Consistent with recent national trends among iGAS , 16 % of isolates displayed molecular evidence of antimicrobial resistance to erythromycin . Phage-related virulence factors identified included deoxyribonucleases and superantigens . These findings suggest the need for continued population-based surveillance of iGAS to better understand changing trends in resistance patterns and emm types within our geographic region .

Presenter : Nicole Green , nicgreen @ ph . lacounty . gov

Identification of a Commensal Neisseria sp . Carrying the Gonococcal Diagnostic Signature DR-9

J . Ayala 1 , J . Hutton 1 , J . Cartee 1 , J . Reimche 1 , S . Joseph 1 , H . Liu 1 , H . LaPoint 2 , L . Cao 2 , T . Baldwin 2 , Y . Gainey 2 , S . St Cyr 1 , M . Schmerer 1 , Centers for Disease Control and Prevention 1 , Texas Department of State Health Services 2

Neisseria gonorrhoeae ( NG ) is the causal agent of the sexually transmitted infection ( STI ) gonorrhea , which is the second most reported bacterial STI in the world . Currently , most clinical microbiology laboratories in the United States have shifted from culture-based diagnostics to nucleic acid amplification tests ( NAAT ). NAAT are sensitive , high-throughput , cost-effective and help to expand gonorrhea testing to prevent chronic infection , but they do have limitations . These may include specificity problems due to cross-reactivity with commensal species of the Neisseria genus , which are closely related to NG . Here we report the identification of a commensal Neisseria sp . isolated from the oropharynx of a patient with a suspected gonococcal treatment failure . The patient was initially diagnosed with gonorrhea using the Cobas CT / NG NAAT test on the Cobas 8800 platform ( Roche ), which is FDA approved for oropharyngeal specimens , resulting in a persistently NG positive oropharynx test after the initial diagnosis and appropriate antibiotic treatment . Therefore , secondary testing was performed using