Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area

Abstract

A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style.

Population diversity and virulence characteristics of Cryptococcus neoformans/C. gattii species complexes isolated during the pre-HIV-pandemic era

“…Our findings is also similar to what has been reported for Vietnam (83.7%) [ 47 ] and Laos (25%) [ 53 ]. Three other common genotypes—namely, ST2/VNI (13.2%), ST63/VNI (9.8%), and ST40/VNII (9.8%)—were reported in Asia, Africa, Europe, and the United States [ 4 , 10 , 11 , 23 , 54 ]. Interestingly, the most common genotype among the environmental isolates, ST4/VNI (25%), was also the most common (32.6%) sequence type isolated from HIV patients outside of the East Asian countries [ 52 ].…”

First Autochthonous Case of Cryptococcal Meningitis in an Immunocompetent Host Due to Cryptococcus gattii VGIin Northern Italy

“…This was confirmed by molecular typing of the fungal isolate which showed it belonged to genotype ST156. This genotype is the most common C. gattii VGI genotype present in Europe [16] and in Italy and was previously identified in Apulia region from Eucalyptus and olive tree samples, and from a series of samples collected in the cages of exotic animals living in a zoo [17]. The only clinical isolate belonging to this genotype was responsible of disseminated cryptococcosis in an HIV patient living in Bari, in the same Italian region [10] (Table 1).…”

“…Comparison with MLST profiles of global isolates (Fig. 2) showed that the C. gattii VGI isolate here described was identical to several strains recovered from clinical and environmental sources in southern Italy and Spain [16] and was included in an endemic European cluster.…”

Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan

“…4). Few population level genetic analyses are available for non-model fungal species, with most of the literature focusing on species of public interest such as phytopathogens (Benne tt et al 2019), human pathogens (Cogliati et al 2019), insect pathogens (Tsui et al 2019), and mycorrhiza (Savary et al 2018). As a result, comparisons are difficult to obtain.…”