Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies

Abstract

SUMMARY Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.

Considerations for diagnostic COVID-19 tests

“…Whereas the UK government centralized all testing in a number of reference laboratories 100 , Germany relied on a clinical laboratory network that enabled the detection of the virus in collected samples within 2.5 hours 101 . Either way, by combining different levels of expertise, consolidated laboratories not only processed large volumes of samples but also supported surveillance systems 102 . Although the best surveillance system still needs to be defined, the setting up of networks of regional sequencing centres hosted in academic institutions and/or public health agencies provided a close-to-real-time sequencing facility that enabled genomic data to be interpreted and used locally for epidemiological monitoring 103 .…”

“…In the case of a positive COVID-19 test result, the routine implementation of further tests to assess cardiac and respiratory risk factors, which might define the potential gravity of the COVID-19 progression, will be of high medical value for patient management and treatment decisions. Given the rapid accrual of high volumes of clinical data, artificial intelligence (AI) and machine learning approaches that integrate clinical and laboratory data will need to be developed 102 , 127 , with a particular emphasis on high-risk patient groups 128 , 129 . The integration of tests that would allow the monitoring of the dynamics of the patients’ global microbial flora and/or the identification of new markers into the laboratory workflow through AI is key 130 , 131 .…”

Development and potential usefulness of the COVID-19 Ag Respi-Strip® diagnostic assay in a pandemic context

“…If a 24/7/365 work organization is proposed by the lab, the rapid result for positive cases in 30 minutes after reception of the specimen, would help to take immediate measures to prevent further spread of the most infectious cases. In a multi-site consolidated clinical microbiology laboratory model such as in the LHUB-ULB (22), a 24-h COVID-19 diagnostic service is provided by dedicated clinical microbiology technologists located in the central lab, while in satellite labs the COVID-19 Ag Respi-Strip is handled 24 hours a day by technologists from chemistry or haematology after cross-training to competently perform and interpret the results of the rapid test. Samples with a negative ICT result are transferred to the central laboratory for molecular diagnosis.…”

Healthcare Transformation in the Post-Coronavirus Pandemic Era

“…However, the continuing rationalization of public health costs has led to the consolidation of a number of clinical microbiology laboratories involving a shift toward laboratory amalgamation. Through this consolidation activity, an operational model emerged with large centralized clinical laboratories performing on one central platform and one or several distal laboratories dealing locally only with urgent analyses (29,30). It would be informative to see if this reduction in the number of small clinical laboratories and the aggregation of the remaining ones conditioned or not the ability to detect epidemiological changes in the context of COVID-19.…”