Gray, R. A. | Search bioRxiv

bioRxiv2025

Rapid Detection of Carbapenemase-Producing Organisms Using a Luminescent Biosensor

Carbapenemase-producing organisms (CPOs) pose an urgent global health threat due to their ability to inactivate carbapenems, a group of last resort antibiotics. Infections caused by these pathogens are associated with poor patient outcomes, high mortality rates, and added burden to infection prevention and control programs, making early detection vital to ensure optimal antimicrobial therapy and appropriate implementation of infection control practices. In this study, we report the application of a luminescent whole-cell biosensor for the rapid detection of CPOs. This biosensor provides positive test results within 2.5 hours, inclusive of setup time, and has been validated with a panel of laboratory and clinical isolates producing a diverse range of carbapenemases (KPC, NDM, IMP, VIM and OXA-48-like). The assay successfully identified all CPO isolates tested with a sensitivity of 100%, including strains producing weak OXA-48-like carbapenemases which are sometimes missed by currently used detection methods. The assay also demonstrated a specificity of 100 %, with all non-CPO clinical isolates testing negative under the optimized assay conditions. Due to the rapid time-to-positivity, minimal setup requirements, and high sensitivity, this test could serve as an attractive alternative to CPO detection methods currently employed by clinical microbiology labs, and could also facilitate CPO screening in other settings (e.g., environmental, agricultural).

microbiology↗

bioRxiv2021

Design and execution of a Verification, Validation, and Uncertainty Quantification plan for a numerical model of left ventricular flow after LVAD implantation

Backgroundleft ventricular assist devices (LVADs) are implantable pumps that act as a life support therapy for patients with severe heart failure. Despite improving the survival rate, LVAD therapy can carry major complications. Particularly, the flow distortion introduced by the LVAD in the left ventricle (LV) may induce thrombus formation. While previous works have used numerical models to study the impact of multiple variables in the intra-LV stagnation regions, a comprehensive validation analysis has never been executed. The main goal of this work is to present a model of the LV-LVAD system and to design and follow a verification, validation and uncertainty quantification (VVUQ) plan based on the ASME V&V40 and V&V20 standards to ensure credible predictions. MethodsThe experiment used to validate the simulation is the SDSU cardiac simulator, a bench mock-up of the cardiovascular system that allows mimicking multiple operation conditions for the heart-LVAD system. The numerical model is based on Alya, the BSCs in-house platform for numerical modelling. Alya solves the Navier-Stokes equation with an Arbitrarian Lagrangian-Eulerian (ALE) formulation in a deformable ventricle and includes pressure-driven valves, a 0D Windkessel model for the arterial output and a LVAD boundary condition modeled through a dynamic pressure-flow performance curve. The designed VVUQ plan involves: (a) a risk analysis and the associated credibility goals; (b) a verification stage to ensure correctness in the numerical solution procedure; (c) a sensitivity analysis to quantify the impact of the inputs on the four quantities of interest (QoIs) (average aortic root flow [Formula], maximum aortic root flow [Formula], average LVAD flow [Formula], and maximum LVAD flow [Formula]); (d) an uncertainty quantification using six validation experiments that include extreme operating conditions. ResultsNumerical code verification tests ensured correctness of the solution procedure and numerical calculation verification showed small numerical errors. The total Sobol indices obtained during the sensitivity analysis demonstrated that the ejection fraction, the heart rate, and the pump performance curve coefficients are the most impactful inputs for the analysed QoIs. The Minkowski norm is used as validation metric for the uncertainty quantification. It shows that the midpoint cases have more accurate results when compared to the extreme cases. The total computational cost of the simulations was above 100 [core-years] executed in around three weeks time span in Marenostrum IV supercomputer. ConclusionsThis work details a novel numerical model for the LV-LVAD system, that is supported by the design and execution of a VVUQ plan created following recognised international standards. We present a methodology demonstrating that stringent VVUQ according to ASME standards is feasible but computationally expensive.

bioengineering↗