Rapid identification of invasive fungal species using sensitive universal primers-based PCR and restriction endonuclease digestions coupled with high-resolution melting analysis

An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections

BACKGROUND

Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens.

AREAS COVERED

We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS).

EXPERT OPINION

PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.

Identification of cuticle and midgut fungal microflora of phlebotomine sandflies collected in Tunisia

Phlebotomine sand flies (Diptera: Psychodidae) are the proven vectors of Leishmaniases which are widespread parasitosis in many tropical and subtropical countries. The development of infective metacyclic Leishmania (Kinetoplastida: Trypanosomatidae) promastigotes stage is restricted to the vector midgut. Recently, several studies have assessed the influence of the sand fly midgut fungal microflora on the development of invective Leishmania stage. The aim of this study was to identify the fungal microflora from the cuticle and midgut of wild caught sandflies. A total of 50 sandflies were caught in two different leishmaniasis foci of center Tunisia and analyzed using an in vitro isolation of fungi followed by a morphological and molecular identification of fungal isolates. The morphological identification of sandflies specimens revealed five Species: Phlebotomus (P.) papatasi (n = 25), P. perniciosus (n = 15) P. riouxi (n = 6), P. longicuspis (n = 3) and P. sergenti (n = 1). Forty positive fungal cultures were isolated from 34 sand flies (19 males and 15 females) distributed as following: P. papatasi (n = 16), P. perniciosus (n = 11), P. riouxi (n = 4), P. longicuspis (n = 2) and P. sergenti (n = 1). Thirty-five cultures were isolated from the cuticles and five from the guts. A total of 15 fungi genera belonging to 8 families were identified with the predominance of Aspergillus genus followed by Penicillium genus. Among the 15 fungi genera, five were common between males and females specimens. Lecytophora canina and Leishmania major co-infection was detected in the gut of a female P. papatasi. Our preliminary findings highlight the high diversity of fungal microflora from the sand flies midguts.

Environmental Factors Affecting Diversity, Structure, and Temporal Variation of Airborne Fungal Communities in a Research and Teaching Building of Tianjin University, China

Airborne fungi are widely distributed in the environment and may have adverse effects on human health. A 12-month survey on the diversity and concentration of culturable airborne fungi was carried out in a research and teaching building of Tianjin University. Indoor and outdoor environments were analyzed using an HAS-100B air sampler. A total of 667 fungal strains, belonging to 160 species and 73 genera were isolated and identified based on morphological and molecular analysis. The most abundant fungal genera were Alternaria (38.57%), Cladosporium (21.49%), and Aspergillus (5.34%), while the most frequently appearing species was A. alternata (21%), followed by A. tenuissima (12.4%), and C. cladosporioides (9.3%). The concentration of fungi in different environments ranged from 0 to 150 CFU/m3 and was significantly higher outdoor than indoor. Temperature and sampling month were significant factors influencing the whole building fungal community, while relative humidity and wind speed were highly correlated with fungal composition outdoor. Variations in the relative abundance of major airborne fungal taxa at different heights above-ground could lead to different community structures at different floors. Our results may provide valuable information for air quality monitoring and microbial pollution control in university building environments.

Species identification and antifungal susceptibility testing of Aspergillus strains isolated from patients with otomycosis in northern China

BACKGROUND/PURPOSE

There are limited studies on species distribution and susceptibility profiles of Aspergillus strains isolated from patients with otomycosis in China.

METHODS

A total of 69 confirmed Aspergillus species isolates were obtained from ear swabs of patients diagnosed with otomycosis from 2017 to 2018 in northern China. Identification of these Aspergillus isolates at the species level was performed using conventional morphological methods and MALDI-TOF MS in combination with molecular sequencing, and in vitro susceptibility to nine antifungal agents was evaluated using the Sensititre YeastOne system.

RESULTS

The Aspergillus section Nigri had the greatest distribution of Aspergillus isolates. A. welwitschiae (n = 25) was the most predominant isolate in section Nigri, followed by A. tubingensis (n = 12) and A. niger (n = 11). Other Aspergillus species were also isolated, including A. terreus (n = 11), A. flavus/A. oryzae (n = 8), and A. fumigatus (n = 2). Amphotericin B, posaconazole, and echinocandins were highly in vitro active against all the isolates tested. 2.9% (2/69) of the isolates were resistant to azoles in our study, including one A. niger isolate with a high MIC value for itraconazole (ITR) (16 mg/L) and one A. tubingensis isolate cross-resistant to both voriconazole (VOR) (MIC >8 mg/L) and ITR (MIC >16 mg/L). One A. welwitschiae and one A. niger isolate both had increased MIC values of 4 mg/L against VOR.

CONCLUSIONS

A. welwitschiae was the most prevalent Aspergillus species isolated from patients with otomycosis. Our findings also indicated that the azole-resistant Aspergillus section Nigri should be utilized to guide clinical medication for Otomycosis.

A national survey on fungal infection diagnostic capacity in the clinical mycology laboratories of tertiary care hospitals in China

BACKGROUND/PURPOSE

As the incidence of fungal infections in China increases, the demand for rapid and accurate diagnosis of mycoses is growing. Yet, information on current diagnostic capacity is scarce.

METHODS

An online survey was conducted in February 2018 to collect information on mycology testing from tertiary care hospitals across China. Responses from 348 hospitals were analyzed, and a scoring system was designed and employed to assess the overall diagnostic capacity.

RESULTS

Most of the surveyed hospitals did not have separate laboratory space, manpower, or equipment dedicated for fungal testing. Conventional staining methods were widely available (>70%), whereas GMS and fluorescent staining were less common. Fungal identification services were offered mostly with chromogenic medium, morphological characterization or automated identification systems, other than more advanced methods such as MALDI-TOF MS and DNA sequencing. Fungal serology testing was available in 81.1%, with G test being the most often used. Though 91.8% of the respondents had the ability to perform antifungal susceptibility testing for yeasts, less than 13% conducted such testing for molds. The percentage of laboratories participating in External Quality Assessment programs and research was 57.5% and 32.5%, respectively. The average score for the 348 surveyed hospitals was 37.2 (out of a maximum of 89 points), with only 15 hospitals scoring >60, suggesting a general lack of high-quality mycology laboratories.

CONCLUSIONS

The overall clinical testing capacity for fungal infection in China is insufficient. More investment and training efforts are warranted to establish centers of excellence and promote access to high-quality diagnostic services.