Table 1.

Overview of the top ten innovations in clinical microbiology over the past decade, highlighting their applications, key benefits, and associated challenges

	Innovation area	Applications	Key benefits	Challenges/Limitations
Preanalytic	Clinical decision support tools	Best-practice alerts Guidelines and algorithms Indication selection using guided test ordering Change in order sets	Drive appropriate test selection Prevent overutilization of tests in low-impact situations	Decreased testing when actually indicated Alert fatigue leading to clinicians overriding alerts Provider and IT pushback
	Host Pathogen Response	Inflammatory markers (Procalcitonin) Urinalysis Reflex to Culture	Antibiotic discontinuation Diagnostic stewardship	Specificity and Reproducibility Utilization management Integration with microbiology
Analytic	Sequencing	Broad range PCR, targeted NGS Metagenomic sequencing Whole genome sequencing	Identification of organisms directly from clinical specimens, even when culture negative High species level resolution for organism identification Determine strain relatedness for epidemiological purposes	Sensitivity and specificity dependent on preanalytic factors Results can be difficult to interpret when commensal organisms or contaminants are identified Unknown how to report and act upon WGS data in real-time Does not provide phenotypic susceptibility data
	Multiplex panels	Syndromic-based testing	Antibiotic stewardship Avoid decision fatigue	Positive results not always clinically relevant Expense
	Rapid susceptibility testing	Novel methods of rapid susceptibility testing	Guides early selection and use of optimal antibiotics	Requires adjudication of discrepancies between rapid AST and finalized traditional AST results
	MALDI TOF MS	Bacterial, fungal identification from isolates	Improved accuracy Shorter turnaround time	Capital costs Over-reporting
	Home testing	Rapid home-based antigen tests	Convenience Privacy Access	Test performance and result interpretation Potential cost per test Quality control of the testing components Linkage to care and inclusion in the EMR Tracking of any results that are of concern for public health
Post analytic	Clinician-lab interface	Framing Cascade reporting Selective reporting Result review and feedback	Guides appropriate decision-making following test results Automates stewardship interventions and education	Limiting clinician’s input leading to missed diagnosis
Other	Laboratory consolidation	Acquisition by commercial laboratories Centralized/localized testing within a health system Total laboratory automation	Increased cost savings and efficiency Concentration of resources/expertise/ technology within a network to provide access to highest quality across the system Uniform adherence to stewardship best practices and guidelines	Increased turnaround time for results to remote sites Logistical challenges, such as specimen stability Risk for financial considerations to drive decisions at the expense of patient safety or quality