Mycological testing in Australasian clinical mycology laboratories: survey of the current state and access to testing

Access to mycological diagnostics varies across clinical laboratories. This study aimed to assess the availability of key fungal diagnostic methods in Australia and New Zealand. A survey was distributed to infectious disease physicians, clinical microbiologists (including trainees), and laboratory scientists across Australia and New Zealand. It covered institutional characteristics, perceived common fungal pathogens, and access to various diagnostic methods (microscopy, culture, fungal identification, antibody/antigen testing, molecular assays, therapeutic drug monitoring, and antifungal resistance surveillance). There were 38 responses, mostly from tertiary public hospitals (58%) or public laboratories (18%). Onsite microbiology laboratories were present in 82% of cases, but only 29% performed all mycological procedures. Species-level identification of moulds was widely available (95%). DNA sequencing for fungal identification or direct detection in specimens was accessible in 97% and 92% of responses, respectively, although usually offsite (79%). Whole-genome sequencing was available onsite for 23%. Whilst all had access to antifungal susceptibility testing, onsite testing was less common for moulds (35%) than for yeasts (65%). Aspergillus galactomannan and polymerase chain reaction were available to 97% and 84%, respectively, but only 22-30% had onsite capacity. β-D-glucan testing was available at just one site. Drug resistance surveillance was infrequent (53%). The survey revealed that key non-culture diagnostics are often performed offsite, reflecting centralisation that may delay results. Limited β-D-glucan access and surveillance for resistant fungi are major gaps in regional diagnostic capability.