Recent Trends And Advances In Clinical Microbiology
The field of clinical microbiology is evolving at a rapid pace with the advent of new technologies, rapid evolution of antimicrobial resistance, and discovery of new pathogens. Platforms such as the Phoenix (BD), Vitek (bioMérieux), and MicroScan (Siemens) have significantly replaced the conventional microbiological methods. Direct detection of microorganisms from patient specimens is an area of great interest because of the potential benefits of rapid identification to patient care, antimicrobial stewardship, and healthcare cost. Rapid organism identification clearly impacts therapy. Optimizing antimicrobial therapy may reduce the selective pressures for resistance selection. Electrospray ionization (ESI)-MS, matrix assisted laser desorption ionization-time of flight (MALDI-TOF) MS, and ion trap-based identification technologies recently have been broadly applied to the identification of bacteria and other microorganisms in the clinical microbiology laboratory.
Organism identification by MS technology directly from specimens as well as antibiotic susceptibility (MBT-ASTRA) will impact the turnaround time. Automated specimen handlers can be utilized for automated inoculation of liquid specimens and manual plating of other types of specimens as well as for slide preparation. Semi-automated technologies provide platforms for organism identification and antimicrobial susceptibility testing. Closed-systems are designed to run specific assays which are cleared by regulatory agencies. Open-system platforms are available for real-time and quantitative PCR analysis. There are also automated or sample-to-result open platforms available in the market. There have been exciting developments in recent years in TB diagnostics, including the WHO endorsement of Xpert MTB/RIF, Xpert MTB/RIF Ultra, Xpert MTB/RIF OMNI, loop-mediated isothermal amplification (LAMP), and lateral flow lipoarabinomannan.
PCR could be successfully used for identification of a wide menu of organisms and determining minimum inhibitory concentrations (MICs) of antibiotics. Use of NAATs enables more rapid, accurate identification of the pathogens. There has been recent shift from PCR-based amplification to transcription-mediated amplification (TMA) of a nucleic acid target in molecular diagnostics. Isothermal amplification methods, including LAMP and helicase-dependent amplification (HDA), effectively reduce the cost of instrumentation and enable these tests to be used outside today’s molecular laboratory and closer to the point-of-care (PoC). Systems like the m2000 (Abbott), Cobas AmpliPrep (Roche), Max and BD Viper (BD), Tigris (Hologic Gen-Probe), and Cobas AmpliPrep/Cobas TaqMan (Roche) have greatly reduced manual interventions and simplified the workflow. RT-PCR systems have made multiplex pathogen detection a simple and viable option for molecular diagnostics.
DNA sequencing has undergone significant modifications, culminating in massive parallel or next-generation whole-genome sequencing (WGS) methods. Genomic techniques like amplified fragment length polymorphism (AFLP), pulsed-field gel electrophoresis (PFGE), and multi locus sequence typing (MLST) are used for subtyping of bacteria for epidemiological purposes in many laboratories. Next-generation sequencing (NGS) allows sequencing of the whole genome of numerous pathogens in one sequence run. WGS can precisely and individually determine the required drug combinations and will eventually completely replace the standard drug susceptibility testing methods for tuberculosis as per recent studies.
MALDI typing is a simple, cost-effective, and time-saving method in contrast to the gold standard method, PFGE. It could allow broad and prospective typing of all clinical isolates detected in clinical settings. It can be performed directly on clinical specimens for rapid identification of bacteria, outbreak management, molecular case finding, characterization and surveillance of pathogens, taxonomy, metagenomics approaches on clinical samples, and for the determination of the transmission of zoonotic microorganisms from animals to humans by using a single protocol for all pathogens for both identification and typing applications.
The next decade, and particularly the next few years, should prove intriguing as we strive to further impact clinical decision-making for infectious diseases by advances in clinical microbiology. There is a need for creation of clinical laboratory consortiums or user groups to combine data from multisite investigations of new technology to meet Clinical Laboratory Improvement Act (CLIA) requirements for laboratory-developed test (LDT) method verification.
