The roles of clinical microbiologists include the identify- cation of bacterial, viral, fungal and parasitic agents that cause human disease, providing diagnostic and therapeutic support for the clinical management of patients, and preventing the transmission of infectious diseases in both the health care system and the community. Developments in sampling: he conventional diagnosis of infectious diseases usually relies on a step- wise approach in which the physician examines the patient, diagnoses a clinical syndrome and then tests for pathogens that are potentially responsible for that syndrome, until a diagnosis is made. However, the growing number of emerging pathogens makes it difficult for physicians to memorize the actual list of pathogens for each infectious disease and thus prescribe all the appropriate diagnostic microbiology tests.
Identification and resistance testing of pathogens:
Identification of bacteria, fungi and viruses. Phenotypic identification of bacterial isolates has long relied on a combination of biochemical properties such as oxygen requirement, Gram staining, carbohydrate metabolism and the presence of specific enzymes. However, phenotypic identification systems, such as miniaturized strips, are costly and time-consuming.
Direct microbial identification in specimens:
Mass spectrometry. In 2009, for the first time, MALDI–TOF MS was reported to efficiently identify bacteria directly from blood collected in culture bottles, with results obtained less than 2 hours after the blood culture vial was determined to bepositive, and with a 97.5% success rate. However, the accuracy of bacterial identification might be influenced by unstandardized sample preparation, differences in bacterial concentrations, pre-incubation, prolonged incubation and the blood culture system used.
Sequencing of microbial genomes:
Genomic sequence information from cultivated micro- organisms is widely used for epidemiological studies (TABLE 1). In clinical microbiology, applications of genome sequencing include the development of detection, identification and genotyping tools, the design of culture media and the assessment of antibiotic resistance or virulence repertoires
With the introduction of omics technologies (genomics, proteomics, culturomics, transcriptomics and metabolomics), CMLs face new challenges, such as obtaining a diagnosis at the time of care (FIG. 4). For example, until recently, the usefulness of blood cultures in the emergency room was limited, as the results of identification and antibiotic-susceptibility testing were only available 72 hours after sampling. Under these conditions, either the empirically prescribed antibiotic treatment was effective, or it had to be changed to another treatment, the worst-case scenario being the patient’s death before the diagnosis was established. Clearly, CMLs can only have a major impact on early patient management when diagnostic speed enables the appropriate medical decisions to be made rapidly. In terms of treatment, rapid pathogen identification combined with knowledge about where the patient contracted the infection (for example, whether it was hospital acquired or community acquired) enables the presumptive deduction of antimicrobial susceptibility, and such antibiotic stewardship based on rapid diagnostics can reduce hospitalization costs.
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