Rapid identification of infectious organisms by the clinical microbiology laboratory is critical for reducing the risk of morbidity and mortality in patients.
“Unfortunately, current methods primarily rely on the rather cumbersome and slow method of culturing specimens and using traditional phenotypic analysis for characterizing pathogens. First-generation molecular diagnostics provided greater speed, but could only assay for one or at best a few pathogens, meaning that diagnosticians often had to guess which pathogen to test for,” noted Garth D. Ehrlich, Ph.D., executive director, center for Genomic Sciences, Allegheny-Singer Research Institute.
Dr. Ehrlich says a new method coupling PCR and mass spectrometry could revolutionize the way clinical labs identify pathogens.
“We have begun using a PCR-based mass spectrometry method known as PCR-electron spray ionization, time-of-flight, mass spectrometry (PCR-ESI-TOF-MS). This technology provides unparalleled sensitivity, accuracy, and breadth within the realm of molecular diagnostics for pathogen detection. It takes advantage of the exquisite sensitivity of both PCR and mass spectrometry.
“Further, global specificity derives from the use of multiple, independent genomic amplification targets. Not only can single assays detect and speciate all members of a taxonomic domain, such as eubacteria, fungi, etc., but they can do so in hours, not days.”
The instrument used by Dr. Ehrlich and colleagues is Abbott Laboratories’ Ibis T-5000 system, predecessor to the current PLEX-ID platform that is being commercialized for clinical diagnostics. He says one doesn’t have to initially guess which pathogen(s) might be causing an infection; rather the system is capable of a broad-based identification of bacteria and fungi. His studies have evaluated samples from numerous infectious and inflammatory conditions including total joint failures, osteoarthritis, chronic nonhealing wounds, and surgical site infections, among others.
“The system can semiquantitatively identify mixed populations of microbes with a readout of genotypic analysis. There are so many advantages of this PCR-mass spec system over the rather archaic method of culturing a sample.
“Use of internal calibrations provides for relative quantitative assessments among co-infecting species. It can work even following antibiotic administration. It simultaneously detects multiple species (even biofilms) and has been shown to have superiority to all other bacterial detection methods. Also, there is no need to develop new assays for each specimen type because the technology is already established and validated.”
Although the costs per tests are not high, they do necessitate the purchase of a dedicated mass spectrometer and software package. “Despite this challenge, this new technological approach has the potential to supplant the foundation of clinical microbiology and, in so doing, save many lives.”