Precision over Presumption: GeneXpert MTB/RIF Ultra Assay Implementation for Airborne Deisolation of Suspected Pediatric Tuberculosis Patients at The Hospital for Sick Children
This is a TRP Capstone research project. View more projects in our directory.
At The Hospital for Sick Children (SickKids), suspected pediatric tuberculosis (TB) patients remain in airborne infection isolation (AII) for prolonged periods due to delayed microbiologic confirmation. Current practice relies on three negative acid-fast bacilli smears, with turnaround times of 2–6 days, extending isolation unnecessarily. This strains clinical decision-making, hospital resources, and impacts patient and family well-being. Although the GeneXpert MTB/RIF Ultra assay offers faster and more sensitive TB detection, it has not been implemented on-site due to cost and workflow concerns. This project addresses the need for timely, efficient, and cost-effective TB testing to safely reduce isolation duration.
Background
Delayed microbiologic confirmation of pediatric pulmonary tuberculosis (TB) at The Hospital for Sick Children (SickKids) prolongs airborne infection isolation (AII) and strains institutional resources. Current Ontario practice typically requires three negative respiratory acid-fast bacilli (AFB) smears performed offsite at Public Health Ontario before discontinuing isolation, with turnaround times averaging 2–6 days. During this period, patients occupy private rooms and require enhanced infection control precautions, contributing to increased hospital costs, reduced bed availability, and potential delays in care. Prolonged isolation also negatively affects children and families by limiting mobility, procedures, and direct interaction with care teams.
Molecular diagnostics, specifically the GeneXpert MTB/RIF Ultra assay, provide a rapid and highly sensitive compared to smear microscopy, with sensitivity estimated to be 300–600 times greater. The National Tuberculosis Controllers Association and the Association of Public Health Laboratories recommend that two negative GeneXpert MTB/RIF Ultra results from sputum samples collected at least eight hours apart can guide safe deisolation. Despite these recommendations and demonstrated benefits internationally, adoption in Canadian pediatric hospitals has been limited due to concerns regarding upfront costs, laboratory workflow integration, and validation across diverse pediatric specimen types.
This quality improvement project aimed to implement on-site GeneXpert MTB/RIF Ultra testing at SickKids to reduce diagnostic turnaround time, shorten AII duration, and optimize resource utilization. A hospital-perspective micro-costing approach was conducted using institutional financial data and published literature. Costs included diagnostic testing, personal protective equipment (PPE), and daily hospitalization expenses. A cost-benefit analysis compared two on-site GeneXpert tests (≥8 hours apart) with the standard workflow of three early morning negative smears. A scenario analysis further examined cost savings among patients who remained hospitalized after isolation discontinuation.
Implementation required extensive stakeholder engagement. Informal interviews with infectious diseases physicians and participation in TB clinic rounds demonstrated strong clinical support for rapid molecular diagnostics to improve decision-making. Presentations to departmental leadership and Infection Prevention and Control teams highlighted projected operational and financial benefits, facilitating discussion of potential policy updates aligned with national recommendations. Cost analysis and stakeholder feedback directly supported administrative approval for implementation.
Performance verification and formal validation are planned for Health Canada–approved sputum specimens and will later extend to gastric aspirates, stool, and bronchoalveolar lavage samples to evaluate accuracy, precision, limit of detection, and potential interference in pediatric populations.
Overall, on-site GeneXpert MTB/RIF Ultra implementation will improve rapid clinical decision-making, reduces isolation duration, and produces meaningful cost savings. Beyond financial benefits, earlier deisolation enhances patient and family experience, improves access to procedures, and supports more effective care delivery. This project will establish a practical implementation framework and barriers that will inform adoption at other Canadian hospitals, with adaptation to local workflows and laboratory capacity.