Panfungal DNA sequencing assay for invasive fungal infections shows good sensitivity (97%) and specificity (98%)

Submitted by BethBradshaw on 27 November 2017

Invasive fungal infections are best treated by giving the right antifungal for that strain as quickly as possible. This is challenging because clinical symptoms and radiological signs are often non-specific, and growth on culture is slow and can lack sensitivity. In the past 10 years, nucleic acid amplification tests (NAATs) have emerged as a favourable alternative, but more large-scale studies are required to test their performance in a routine clinical setting.

Gomez et al recently described a large-scale study using a DNA sequencing assay on clinical samples from the Stanford Health Care Clinical Microbiology laboratory (California). They looked retrospectively over 7 years at 233 samples (fresh tissue, FFPE embedded tissues, BAL and sterile body fluids) taken from patients with known and suspected invasive fungal infections.

In this assay, PCR was used to amplify a section of DNA from each of two regions (ITS2 and D2) that are universally present in all fungi (‘panfungal’). These were then sequenced and compared against a sequence database to identify the genus and species present.The most common fungi detected were Aspergillus (30%), Mucorales (23%) and Candida (15%).

The test performed well, with an overall specificity of 98% and a sensitivity of 97%. In comparison, the galactomannan assay for Aspergillus only had a sensitivity of 44% in this group. Testing worked best when a large amount of material was taken from an open biopsy, rather than from the smaller amounts recovered from a needle biopsy.