Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients

Abstract

Fungal infections are common complications of respiratory viral infections and are associated with the increased need for intensive care and elevated mortality. Data regarding microbiological and molecular characteristics of such infections in COVID-19 patients are scarce. Here, we performed a comprehensive analysis, including species identification, antifungal susceptibility testing, molecular resistance determinants analysis, typing, and retrospective clinical data review, of fungal isolates recovered from 19 COVID-19 patients, who were hospitalized at the Hackensack University Medical Center (HUMC) in Hackensack, New Jersey, USA, in the initial phase of the pandemic from April–May 2020. In total, 17 Candida albicans, two C. parapsilosis, and two Aspergillus fumigatus were analyzed. All Candida spp. isolates were susceptible to micafungin and azole drugs (fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole). A. fumigatus isolates were susceptible to micafungin and all triazole drugs except fluconazole (intrinsic resistance). Multilocus sequence typing (MLST) of C. albicans isolates revealed 15 different sequence types (STs), which clustered below the clade-defining limit of p-distance < 0.04. Pulsed-field gel electrophoresis (PFGE) karyotyping revealed no chromosomal rearrangements in these isolates. A. fumigatus isolates were of different, non-related genotypes. We speculate that virus- and drug-induced immunosuppression (94.7% of the patients received corticosteroids), together with prolonged hospital stay (median duration of 29 days) and mechanical ventilation (median duration of 24 days) likely increased the susceptibility to secondary respiratory and bloodstream infections in the studied patient population. The presence of fungi in blood or respiratory tract fluid was a prognosticator for poor clinical outcome, which presented as an 89.5% 30-day mortality in our patient cohort.

Incidence of Candidemia Is Higher in COVID-19 versus Non-COVID-19 Patients, but Not Driven by Intrahospital Transmission

“…Further to this, ours is the first study in which isolates causing candidemia during the COVID-19 pandemic have been genotyped to gain more insight about patient-to-patient transmission not only in patients with COVID-19 but also in patients with candidemia and non-COVID-19. Previous studies in which Candida genotyping was carried out are limited by the fact that the number of isolates was low, they were sourced exclusively from patients with COVID-19, and they were not designed to address the question of clonal spreading as a driver of higher candidemia incidence in COVID-19 patients [ 30 , 31 ]. As a whole, comparison of this population with patients without COVID-19 provides valuable and thorough information not previously described, since comparisons of candidemia episodes including patients with and without COVID-19 have been only occasionally carried out [ 14 , 18 , 19 , 20 , 21 ].…”

Emerging Status of Multidrug-Resistant Bacteria and Fungi in the Arabian Peninsula

“…Various detection methods are used to identify MDR organisms: the disc diffusion method [ 300 , 330 ], Kirby and Bauer method [ 335 ], microdilution process [ 161 ], PCR with specific primers [ 336 ], real-time PCR tests with temperature melting analysis [ 49 ], MDR-TB detection [ 125 ], E-test for antimicrobial resistance [ 4 , 148 ], automated identification and susceptibility system [ 330 ], Growth Indicator Tube system [ 337 ] automated Phoenix method [ 221 ], matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) [ 4 ], GeneXpert assay [ 338 ], AcrAB–TolC efflux pump system [ 36 ], multiplex PCR for confirming isolates [ 300 , 317 ], multilocus sequence typing [ 300 ], sequences of 18S rRNA gene and ITS region for MDR fungi [ 24 ], 16S rRNA gene sequencing [ 317 ], toxin genes multiplex PCR [ 317 ], multiplex real-time quantitative PCR [ 339 ], DNA Microarray Detection [ 84 ] and whole-genome sequencing [ 21 ].…”

“…Candida auris is an emerging fungal pathogen with multidrug resistance, causing nosocomial infections and invasive deaths [ 336 ]. A trustworthy diagnostic approach, such as using the 18S rRNA gene and ITS region against MDR fungi, is urgently needed [ 24 ].…”

“…A trustworthy diagnostic approach, such as using the 18S rRNA gene and ITS region against MDR fungi, is urgently needed [ 24 ]. C. auris is often mistaken for numerous other yeast species by phenotypic identification platforms [ 336 ]. In this work, PCR and real-time PCR tests were used for identifying C. auris and related species: Candida duobushaemulonii, Candida haemulonii and Candida lusitaniae .…”

“…In this work, PCR and real-time PCR tests were used for identifying C. auris and related species: Candida duobushaemulonii, Candida haemulonii and Candida lusitaniae . Targeted rDNA nucleotide region sequences, C. auris -specific, primers-based PCR or real-time PCR experiments followed by electrophoresis or temperature melting analysis, respectively, were performed using a panel of 140 clinical fungus isolates [ 336 ]. The findings of the tests completely corroborated the findings of the DNA sequencing.…”