Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

Abstract

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Aspergillus fumigatusand aspergillosis: From basics to clinics

“…The lowering costs and continuing developments in high-throughput sequencing have recently allowed zooming into the specific genomes of particular strains, revealing how genomic and phenotypic plasticity are connected. In addition, our ability to access full genomic sequences in a timely and cost-effective manner are opening new avenues for clinical applications such as species identification and diagnosis of resistance potential ( Consortium & Gabaldón 2019 ). Currently, three major sequencing platforms exist that differ in their functionalities and suitability for different purposes ( Table 6 ).…”

Diagnostic Mycology: Xtreme Challenges

“…MALDI-TOF MS, conversely, may be more feasible, as it currently has been used to explore resistance and identification in C. albicans and C. glabrata (34). However, studies have focused mainly on comparing spectra produced when yeast cultures are grown in different levels of antifungal (35), which could be costly or time-consuming.…”

Comparison of Two Commercial Colorimetric Broth Microdilution Tests for Candida Susceptibility Testing: Sensititre YeastOne versus MICRONAUT-AM

“…These opportunistic pathogens can cause a wide range of infections ranging from mild dermatosis to serious systemic infections. Candida species are the most common cause of invasive fungal infections [ 1 , 2 ]. Candidemia is an important cause of morbidity and mortality in high-risk patient groups.…”

“…The prevalence of Candida infections is high in immunocompromised patients, transplant patients, patients with cancer and patients with a prolonged stay at the intensive care unit. Other common risk factors include use of broad-spectrum antibiotics, abdominal surgery, indwelling central venous and urinary catheters, total parenteral nutrition and hemodialysis [ 1 , 3 ]. Compared to antibiotics, the number of antifungal agents is rather limited [ 4 ].…”