A-298 A Novel DNA Array Technology to Detect and Discriminate Complex Panels of Microbial Pathogens
Authors: Hogan M E , Eggers F , May M , Wen F , Obrien K , Botros I , Tugwell M 
Published: October 2024

Abstract

Background
UTI (Urinary Tract Infection) is a prototype for the field of polymicrobial testing. Current testing standards suggest that UTI testing may require the Detection and Discrimination of a panel of at least (@24) bacteria and fungi (@2) along with a panel of antibiotic resistance gene (ARG) markers (&gt;12). Today, such analysis of UTI’s at the DNA level can be obtained with predicates such as large-panel qPCR reactions, e.g. the Thermo OpenArray qPCR assembly, or by NGS based microbiomics. The necessary complexity of such polymicrobial testing pushes the content limits of qPCR and, although NGS has substantial capacity to resolve complex mixtures, NGS remains relatively low throughput and requires a level of data processing that exceeds what is practical in some laboratories.

Methods
We have developed a new technology for UTI testing, “D3 ArrayTM-UTI”, which obviates most of the present limitations of DNA based polymicrobial testing. The process begins with urine being isolated and purified using standard automated magnetic bead DNA sample prep, already in place in most molecular laboratories, at up to 96 samples in parallel. This is followed by a single multiplex, endpoint PCR reaction on each sample, also at up to 96 samples in parallel, then automated room temperature hybridization of the PCR product in a standard 96 well format, onto a single 21x21 D3 Array at the bottom of each well. Dedicated autonomous software analyzes the hybridization data yielding the complete list of microbial pathogens and ARG’s detected in a urine specimen. The first deployment of the D3 Array-UTI test is now available to support analysis of 96 urine samples in 6hrs. The results of such preliminary testing are presented here.

Results
aLOD analysis has been performed with purified DNA and found to be in the 0.1-10cp/RXN range among the full set of 24 bacterial species and 12 ARG targets. Concordance analysis for bacterial Species Detection and Discrimination has been performed on 235 clinical isolates obtained from collaborators at Mako Medical laboratories (Thermo Openarray as the comparator) which averaged = 97 +/- 5% for all but two species: A urinae (88%) and M morganii (94%). Concordance analysis for Antibiotic Resistance Gene Detection and Discrimination has been performed on 384 clinical isolates also obtained from Mako Medical laboratories (Thermo Openarray as the comparator) which averaged = 98 +/-5% and was found to be &gt;98% for all but one ARG target: gyrA point mutation (88%).

Conclusions
The data provided here demonstrates that the D3 Array-UTI platform can perform complex polymicrobial/ARG testing as a high throughput 96 well plate based assay, with Sensitivity and Specificity that matches or exceeds that of qPCR, using standard automation that can be deployed in any molecular laboratory. The resulting performance is unique in that Species and ARG Discrimination are readily scalable to 3-4 dozen Species per test, performed in triplicate in a single well with completely autonomous, cloud enabled data analysis, at a sample-to-answer throughput &gt;96 samples per shift. Beta testing has been initiated among laboratory partners.