Genetic relationships of Aspergillus fumigatus in hospital settings during COVID-19

ABSTRACT The transmission pathways and risks of COVID-19-associated pulmonary aspergillosis (CAPA) remain unclear. This study investigated the genetic relationships of Aspergillus fumigatus isolates from patients with and without COVID-19 and environmental air samples to suggest possible transmission patterns. We conducted a prospective study from March 2020 to December 2022, collecting clinical and environmental isolates from a tertiary hospital. Isolates from patients with and without COVID-19 were compared with those from air samples at four hospital locations. The genetic analysis included internal transcribed spacer and β-tubulin A sequencing, with azole resistance assessed via cyp51A gene analysis. Multiple locus variable-number tandem repeat analysis was performed to elucidate genetic relationships. A total of 155 isolates (19 from COVID-19 patients, 104 from non-COVID-19 patients, and 32 from environmental samples) were identified and genotyped, revealing 131 sequence types (Simpson Diversity Index 0.9972). Four CAPA clinical strains genetically related to environmental strains were isolated from the COVID-19 intensive care unit (ICU), while two CAPA clinical strains sharing multiple locus variable-number tandem repeat sequence types and azole-resistant mutations were isolated in the same COVID-19 ICU 4 months apart. All but one of these strains were isolated from patients requiring mechanical ventilation. The observed genetic similarities between strains from critically ill patients with COVID-19 and those from the environment, as well as within the same ICU, raise the possibility of nosocomial acquisition via contaminated air or environmental sources. These findings highlight the risks of CAPA associated with negative pressure rooms and the need for enhanced environmental infection control measures.IMPORTANCEThis study reveals genetic links between Aspergillus fumigatus in patients with COVID-19 and environmental sources, suggesting nosocomial transmission and urging a reevaluation of universal negative pressure isolation practices in hospitals, especially for critically ill patients.