Comparison of Multi-locus Genotypes Detected in Aspergillus fumigatus Isolated from COVID Associated Pulmonary Aspergillosis (CAPA) and from Other Clinical and Environmental Sources

Abstract

Background: Aspergillus fumigatus is a saprophytic fungus, ubiquitous in the environment and responsible for causing infections, some of them severe invasive infections. The high morbidity and mortality, together with the increasing burden of triazole-resistant isolates and the emergence of new risk groups, namely COVID-19 patients, have raised a crescent awareness of the need to better comprehend the dynamics of this fungus. The understanding of the epidemiology of this fungus, especially of CAPA isolates, allows a better understanding of the interactions of the fungus in the environment and the human body. Methods: In the present study, the M3 markers of the STRAf assay were used as a robust typing technique to understand the connection between CAPA isolates and isolates from different sources (environmental and clinical-human and animal). Results: Of 100 viable isolates that were analyzed, 85 genotypes were found, 77 of which were unique. Some isolates from different sources presented the same genotype. Microsatellite genotypes obtained from A. fumigatus isolates from COVID+ patients were all unique, not being found in any other isolates of the present study or even in other isolates deposited in a worldwide database; these same isolates were heterogeneously distributed among the other isolates. Conclusions: Isolates from CAPA patients revealed high heterogeneity of multi-locus genotypes. A genotype more commonly associated with COVID-19 infections does not appear to exist.

Genomic Epidemiology Identifies Azole Resistance Due to TR34/L98H in European Aspergillus fumigatus Causing COVID-19-Associated Pulmonary Aspergillosis

“…This finding was replicated in one Spanish and one Portuguese study using tandem repeats within the exons of surface proteins and erg coding genes (TRESPERG), and microsatellite methods, respectively, to compare isolates obtained from CAPA patients and the environment [22,25]. The authors identified that the CAPA isolates were from a diverse genetic pool [22,23,25]. However, compared to WGS, TRESPERG and microsatellite methods are limited in their power to provide an in-depth analysis of the genetic structure and diversity within a population [57,58], due to only utilising a small proportion of the whole genome [58].…”

“…A larger multicentre study using microsatellite methods to genotype isolates identified that the genotypes obtained were genetically distinct from one another [23]. This finding was replicated in one Spanish and one Portuguese study using tandem repeats within the exons of surface proteins and erg coding genes (TRESPERG), and microsatellite methods, respectively, to compare isolates obtained from CAPA patients and the environment [22,25]. The authors identified that the CAPA isolates were from a diverse genetic pool [22,23,25].…”

“…The genotypes from the 21 CAPA isolates showed genetic overlapping with the A. fumigatus genotypes isolated from the patients with IA, and those obtained from other patients and the environment. In the five previous genomic epidemiological studies of CAPA, the genotypes from the CAPA isolates were only compared with non-CAPA clinical isolates or COVID-19 patients who were colonised with A. fumigatus and had no active IA [21][22][23][24][25]. The results of Steenwyk et al suggest that overall, the CAPA genotypes are drawn from the wider clinical population of A. fumigatus isolates, despite observing some genetic clustering [24].…”

“…Using the Clinical and Laboratory Standards Institute (CLSI) method, a second German study (n = 4) did not find any resistant isolates [24]. Finally, a Portuguese study reported a high prevalence of ARAf of 45.5% (n = 5/11 [25].…”

“…In A. fumigatus, genomic epidemiological methods have begun to unravel the genetics of environmental and clinical antifungal resistance and the potential mechanisms of dispersion [1,13,16,32]. To date, there are only five genomic epidemiologic studies of CAPA using multiple methods [21][22][23][24][25]. The results of these analyses were inconclusive on the genetic and epidemiological relatedness of A. fumigatus causing CAPA.…”