Laboratory Diagnostics for Fungal Infections: A Review of Current and Future Diagnostic Assays

Molecular detection, not extended culture incubation, contributes to diagnosis of fungal infection

Background

Despite its low sensitivity, fungal culture remains one of the key methods for diagnosis and treatment of fungal infections, as it identifies the etiology at the genus and species level and affords the opportunity for susceptibility testing. The Manual of Clinical Microbiology recommends that fungal culture screening for all pathogens should routinely be held for 4 weeks to maximize the recovery of slow-growing species. Information on the optimal fungal culture time in this era of expansion of immunocompromised populations and availability of molecular diagnostics is lacking. We reviewed our experience with fungal culture to determine the optimal culture incubation time. In addition, our experience of broad-range ITS PCR for diagnosis of culture-negative fungal infections was also reviewed.

Methods

Fungal culture and ITS PCR results from January 1, 2013, to December 31, 2017, were reviewed.

Results

This study included 4234 non-duplicated positive cultures. Ninety-six percent (4058) of the positive cultures were detected in the first 7 days of incubation. During the second week of incubation, 111 (2.8%) positives were detected from day 8 to day 10, and 71 (1.7%) were detected from day 11 to day 14. Only 6 (0.1%) positive cultures were detected in the third week of incubation, and no positive culture was detected in the fourth week of incubation. No clinically significant fungal isolates were recovered after 14 days. Clinically significant pathogens were detected in 16 (0.2%) culture-negative samples by ITS PCR.

Conclusion

Extending culture incubation beyond 2 weeks did not generate clinically relevant results. When culture failed to make a laboratory diagnosis, broad-range internal transcribed spacer (ITS) rRNA gene PCR followed by sequencing produced clinically significant results.

Fungal Genomics in Respiratory Medicine: What, How and When?

Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.

Molecular Diagnostic Advances in Transplant Infectious Diseases

PURPOSE OF REVIEW

The infectious complications of transplantation can have devastating consequences for patients. Early and accurate diagnosis is essential to good outcomes. This review describes recent advances in pathogen-directed diagnostic testing and discusses the role of new methods for transplant infectious diseases.

RECENT FINDINGS

Several molecular assays have been introduced into clinical practice in recent years. When the results of rapid testing are linked to patient-specific interventions, improved outcomes can be realized. Syndromic testing along with metagenomic next-generation sequencing (mNGS) represents novel approaches to infection diagnosis. However, the optimal use of these tests for transplant patients along with an overall assessment of cost-effectiveness demands further study. Molecular diagnostics are revolutionizing transplant care. Clinicians need to be aware of the current diagnostic landscape and have a working knowledge of the nuances related to test performance, result interpretation, and cost.

Recent trends in the epidemiology, diagnosis, treatment, and mechanisms of resistance in clinical Aspergillus species: A general review with a special focus on the Middle Eastern and North African region

Globally, more than billion people suffer from fungal infections each year. The early diagnosis of aspergillosis is mandatory for successful treatment outcome. As careful testing takes time, epidemiological surveillance is crucial to guide individual patient therapy and to promote a high standard of health care. In this paper, we first present current trends in the epidemiology and antifungal susceptibility patterns of Aspergillus spp. in Middle Eastern and North African (MENA) countries in order to support infectious disease specialists and health workforces in this geographic area to treat adequately patients with aspergillosis. Then we discuss the existing literature data regarding the available diagnostic tools and antifungal resistance mechanisms of Aspergillus spp. Although a limited number of studies were reviewed here, the currently available data show that Aspergillus infections are not negligible in the MENA region, and that the emergence of antifungal resistance is a growing health issue, especially among immunocompromised patients.