Bioinformatics in Clinical Microbiology:

Emerging infectious diseases (including community-, hospital- and bioterrorism-acquired infections), emerging resistance to antimicrobial agents and increased social demand are increasing the volume and altering the nature of the activities required from clinical microbiology laboratories. Centralization, an increase in automation and advances in bioinformatics allow clinical microbiology laboratories to keep up with these ever-increasing demands. Technologies and techniques that are progressing at the moment include rapid molecular detection, identification and genotyping of bacteria; antimicrobial-resistance determination; rapid immunological detection of pathogens; easy-to-use electron microscopy; and data digitalization and the secure online exchange of information. The future evolution of clinical microbiology might include the spread of 'at-doctor' tests and bedside tests at the same time as specialized diagnoses are centralized in reference laboratories that are connected on national and international scales. Centralization should allow the development of p3/p4 laboratories, molecular-biology platforms, including mass spectrometry, and serology platforms, including antigenic microarrays for serodiagnosis.Sampling strategies might evolve towards pathology-based sampling kits in accordance with the development of multiplex platforms. In addition, data reporting could be based solely on digitalized figures and could include data interpretation and the addition of electronic links to up-to-date literature, which can be exchanged in a timely manner through the internet. Large clinical microbiology laboratories could engage in the regular reporting of epidemiological trends for pathogens, pathogen subtypes and antimicrobial resistance.

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