Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls - an update.

INTRODUCTION: Multiplex nucleic acid diagnostics for blood-borne pathogens have moved closer to clinical application in the two years since we first reviewed this topic. Areas covered: A new emphasis on detecting pathogens directly in a blood sample without culture, coupling PCR amplification to microfluidic devices and higher multiplexing in isothermal amplification are some of the advances. A wholly new approach of correlating host gene expression response with specific infectious agents opens another opportunity for multiplex detection. Established microarrays, which had been the highest multiplicity platform, are being displaced by Next Generation Sequencing (NGS) having potentially no limit to the number of pathogens that it can identify. Greater accessibility of sequencing devices, standardization of bioinformatic analysis pathways and increased acceptance from regulatory authorities are driving this technology. Expert commentary: The landscape of traditional diagnostics for detection of blood-borne pathogens has changed in the last 5 years. There is no doubt that NSG is recognized as a disruptive technology with a growing repertoire of tools, such as subtyping, resistome analysis, etc., available for clinical microbiology. Increasing acceptance indicates the dominating position of NGS as the future of multiplex molecular diagnostics for blood-borne pathogens.

Comparison of multiplex PCR hybridization-based and singleplex real-time PCR-based assays for detection of low prevalence pathogens in spiked samples.

Molecular diagnostic devices are increasingly finding utility in clinical laboratories. Demonstration of the effectiveness of these devices is dependent upon comparing results from clinical samples tested with the new device to an alternative testing method. The preparation of mock clinical specimens will be necessary for the validation of molecular diagnostic devices when a sufficient number of clinical specimens is unobtainable. Examples include rare pathogens, some of which are pathogens posing a biological weapon threat. Here we describe standardized steps for developers to follow for the culture and quantification of three organisms used to spike human whole blood to create mock specimens. The three organisms chosen for this study were the Live Vaccine Strain (LVS) of Francisella tularensis, surrogate for a potential biothreat pathogen, Escherichia coli, a representative Gram-negative bacterium and Babesia microti (Franca) Reichenow Peabody strain, representing a protozoan parasite. Mock specimens were prepared with blood from both healthy donors and donors with nonspecific symptoms including fever, malaise, and flu-like symptoms. There was no significant difference in detection results between the two groups for any pathogen. Testing of the mock samples was compared on two platforms, Target Enriched Multiplex-PCR (TEM-PCR™) and singleplex real-time PCR (RT-PCR). Results were reproducible on both platforms. The reproducibility demonstrated by obtaining the same results between two testing methods and between healthy and symptomatic mock specimens, indicates the standardized methods described for creating the mock specimens are valid and effective for evaluating diagnostic devices.