A Test Combining Multiplex-PCR with Pooled Antibiotic Susceptibility Testing Has High Correlation with Expanded Urine Culture for Detection of Live Bacteria in Urine Samples of Suspected UTI Patients

Festa, Richard A.; Luke, Natalie; Mathur, Mohit; Parnell, Laura; Wang, Dakun; Zhao, Xinhua; Magallón, Jesus; Remedios-Chan, Mariana; Nguyen, Janet; Cho, Tim; Ngo, Annie; Murphy, Maxwell; Baunoch, David

doi:10.2139/ssrn.4345709

Cited by 2 publications

(1 citation statement)

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“…Like other molecular-based studies, BIOTIA-ID showed increased detection of atypical pathogens including Candida, G. vaginalis, Aerococcus spp., anaerobic bacteria (Prevotella spp.) and fastidious bacteria, organisms not reported with culture-based diagnostics (30,(82)(83)(84)(85). Although the rise of molecular based diagnostics and clinical studies using these technologies have revealed that gram-positive, atypical, or fastidious pathogens account for a larger percentage of cUTI infections, more interventional, and clinical utilization studies are needed to understand the pathogenesis and epidemiology of these understudied microbes (19,62,(86)(87)(88).…”

Section: Discussionmentioning

confidence: 99%

Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay

Couto-Rodriguez,

Danko,

Wells

et al. 2024

Preprint

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Culture is currently the gold standard for diagnosis of urinary tract infections (UTIs); however, it has poor sensitivity detecting urogenital pathogens, especially if patients have already initiated antimicrobial therapy, or have an infection from an organism that is not commonly cultured. False negative urine culture results can lead to the inappropriate use of antimicrobial therapies or to the progression to urosepsis in high-risk patients. Though not commonly applied to urine in a clinical setting, Next-generation sequencing (NGS)-based metagenomics offer a solution as a precision diagnostic. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for the detection and identification of pathogens in urine specimens. Remnant clinical urine specimens, and contrived sterile urine spiked with common UTI pathogens, were processed with our end-to-end assay including extraction, metagenomic library preparation and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning (ML) to identify pathogens. Internal controls and other quality control measures were incorporated into the process to provide rigorous and standardized results. The assay was tested on 1,470 urine specimens and achieved 99.92% sensitivity, 99.95% specificity and a limit of detection (LoD) of <25,000 CFU/mL and <5,000 CFU/mL in bacteria and fungi, respectively. Discordant results were reconciled with additional testing by target-specific qPCR or 16S Sanger sequencing; 87% of the NGS results were ultimately determined to be the correct result. Overall, these data demonstrate that BIOTIA-ID is a highly accurate clinical-grade diagnostic tool with notable advantages over current culture-based diagnostics

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Section: Discussionmentioning

confidence: 99%

Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay

Couto-Rodriguez,

Danko,

Wells

et al. 2024

Preprint

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Improving Patient Outcomes While Reducing Empirical Treatment with Multiplex-Polymerase-Chain-Reaction/Pooled-Antibiotic-Susceptibility-Testing Assay for Complicated and Recurrent Urinary Tract Infections

Haley,

Luke,

Korman

et al. 2023

Diagnostics

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This study compared rates of empirical-therapy use and negative patient outcomes between complicated and recurrent urinary tract infection (r/cUTI) cases diagnosed with a multiplex polymerase chain reaction or pooled antibiotic susceptibility testing (M-PCR/P-AST) vs. standard urine culture (SUC). Subjects were 577 symptomatic adults (n = 207 males and n = 370 females) presenting to urology/urogynecology clinics between 03/30/2022 and 05/24/2023. Treatment and outcomes were recorded by the clinician and patient surveys. The M-PCR/P-AST (n = 252) and SUC (n = 146) arms were compared after patient matching for confounding factors. The chi-square and Fisher’s exact tests were used to analyze demographics and clinical outcomes between study arms. Reduced empirical-treatment use (28.7% vs. 66.7%), lower composite negative events (34.5% vs. 46.6%, p = 0.018), and fewer individual negative outcomes of UTI-related medical provider visits and UTI-related visits for hospitalization/an urgent care center/an emergency room (p < 0.05) were observed in the M-PCR/P-AST arm compared with the SUC arm. A reduction in UTI symptom recurrence in patients ≥ 60 years old was observed in the M-PCR/P-AST arm (p < 0.05). Study results indicate that use of the M-PCR/P-AST test reduces empirical antibiotic treatment and negative patient outcomes in r/cUTI cases.

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A Test Combining Multiplex-PCR with Pooled Antibiotic Susceptibility Testing Has High Correlation with Expanded Urine Culture for Detection of Live Bacteria in Urine Samples of Suspected UTI Patients

Cited by 2 publications

References 0 publications

Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay

Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay

Improving Patient Outcomes While Reducing Empirical Treatment with Multiplex-Polymerase-Chain-Reaction/Pooled-Antibiotic-Susceptibility-Testing Assay for Complicated and Recurrent Urinary Tract Infections

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