Current challenges and future perspective of diagnostic microbiology laboratories

The Omics revolution, which primarily focuses on genomics, proteomics, degradomics, and metabolomics, has evolved into the current main drivers of the bench-to-bedside passage of omics without limiting the numerous other omics that opened up new and intriguing perspectives in laboratory medicine and translational medicine (such as transcriptomics, mirnomics, epigenomics, interactomics, etc.).

Therefore, new approaches to diagnosis, the discovery of novel diagnostic and/or prognostic biomarkers, the development of novel target-specific therapies, the design and construction of controlled clinical trials on novel drugs, the creation of novel guidelines (such as those already used in the field of cardiovascular, hematological, and oncological disease) will all be possible through the various omics branches of clinical laboratory medicine. The use of omics in laboratory medicine investigations on the benefits of physical activity Tis one example of how all of these important factors are becoming more closely related to the idea of wellbeing.

Current challenges
Processing of clinical samples

• Direct examination. Gram staining is still a crucial step in identifying pathogens and directing empirical antibiotic therapy, even though the adoption of MALDI-TOF MS to identify cultured colonies would limit its use. Gram staining is typically employed for the direct inspection of uncultured clinical samples. Gram staining can, however, be automated. For example, the PREVI Color Gram (BioMérieux) robot can stain up to 300 slides each hour while posing less of a chemical hazard to workers.
• Infrastructure, equipment, logistics, quality assurance, and human resources. These are the five main issues that clinical microbiology laboratories continue to encounter. The equipment must be tropicalized, as it has sometimes been stated, in order to survive the difficult climatic conditions of high humidity, high temperature, and/or sand. The equipment must also be able to operate predictably, while preferably requiring low maintenance and lesser energy. Examples of recent designs that have considered these factors include, for instance, battery-driven centrifuges that can recharge their batteries using solar energy. These typically deal with individual equipment-specific solutions rather than complete laboratories. In addition to the equipment, consumables must be made with a long shelf life and little waste in mind.
• AMR response. The Global Action Plan acknowledges the significance of linking information on AMR from three key sectors (humans, food chain, and environment), for example, collecting data on the use of antibiotics in human and animal populations. AMR is a typical One Health issue because it is interconnected between humans, animals, and the environment. Within this timeframe, GLASS began a One Health AMR surveillance program, known as the tricycle protocol with the goal of identifying the prevalence of a single universal indicator of AMR, extended-spectrum beta-lactamase-producing Escherichia coli (ESBL), in humans (both in the general population and in clinical E. coli isolates), animals (chicken), and the environment (wastewater and surface water). This protocol’s ease of use enables the identification of national trends as well as inter- and intra-regional comparisons of ESBL E. coli prevalence and provides information for decision makers in the medical, animal, and environmental fields.

Future direction
Clinical diagnostic testing advancements today may offer laboratory teams opportunity to modernize, embrace new technology, and offer new services. However, in addition to lowering costs, greater automation and the consolidation of various analytic systems will boost productivity, shorten turnaround times (TAT), improve the caliber of testing, and free up laboratory staff members to concentrate on more difficult duties.