Mycobiology.  2023 Dec;51(6):452-462. 10.1080/12298093.2023.2272380.

Determining Potential Link between Environmental and Clinical Isolates of Cryptococcus neoformans/Cryptococcus gattii Species Complexes Using Phenotypic and Genotypic Characterisation

• Kebabonye K
• Jongman M
• Loeto D
• Moyo S
• Choga W
• Kasvosve I

• KMID: 2550774
• DOI: http://doi.org/10.1080/12298093.2023.2272380

Abstract

Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes con tinue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR finger printing and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans x C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n= 3), and 5.3% of C. tetragattii (n = 2) in 38 representa tive isolates that have been characterized. Mating type-specific PCR performed on 38 repre sentative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MATα hybrids, 17 (44.7%) were MATα, and five (13.2%) possessed MATa mating type. We used con ventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.

Keyword

Cryptococcus gattii; Cryptococcus neoformans; genetic diversity; intergenic spacer region; Oxford nanopore sequencing