Modern clinical microbiology: new challenges and solutions

Abstract

In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.

Figure 1. The number of identified microbial species from 1979 to 2012.

The development of new technologies has had a substantial impact on the number of microbial species that are identified each year. PowerPoint slide

Figure 2. Current applications of MALDI–TOF mass spectrometry in the clinical microbiology laboratory.

MALDI–TOF mass spectrometry (MS) allows the identification and antibiotic-susceptibility testing of microbial pathogens in urine samples or cultivated on agar or in blood culture bottles. Alternatively, strain identification can be carried out by PCR–ESI–QTOF MS (PCR followed by electrospray ionization–quadrupole TOF MS) characterization of PCR amplicons from the microbial DNA. PowerPoint slide

Figure 3. Diagnosis of infectious diseases using point-of-care assays.

Specimens referred to the point-of-care (POC) laboratory are tested according to the clinical picture and the physicians' queries. POC tests that will detect the most likely causative pathogen or a pathogen-associated antigen are carried out according to the clinical syndrome and the patient history. BSL3, biosafety level 3. PowerPoint slide

Figure 4. Overview of new methods in the workflow of clinical microbiology laboratories.

The figure describes the processing of specimens from patients who are thought to have an infectious disease. Sampling is carried out using syndrome- and disease-based sampling kits, and the resulting specimens are tested using point-of-care assays, when available. Culturing, strain characterization (phenotypic or molecular identification, and antibiotic-susceptibility testing) and molecular detection in clinical samples are carried out in the core laboratory. Unusual pathogens, conserved by the laboratory, are reported to the physician in charge and possibly to the sanitary authorities, and are further characterized by genome sequencing. MS, mass spectrometry. PowerPoint slide