Genotypic analysis of clinical and environmental Cryptococcus neoformans isolates from Brazil reveals the presence of VNB isolates and a correlation with biological factors

Abstract

Cryptococcal infections are mainly caused by members of the Cryptococcus neoformans species complex (molecular types VNI, VNII, VNB, VNIV and the AD hybrid VNIII). PCR of the mating type loci and MLST typing using the ISHAM-MLST consensus scheme were used to evaluate the genetic relationship of 102 (63 clinical and 39 environmental) C. neoformans isolates from Uberaba, Brazil and to correlate the obtained genotypes with clinical, antifungal susceptibility and virulence factor data. All isolates were mating type alpha. MLST identified 12 known and five new sequence types (ST). Fourteen STs were identified within the VNI isolates, with ST93 (57/102, 56%) and ST77 (19/102, 19%) being the most prevalent. From the nine VNII isolates previously identify by URA5-RFLP only four (ST40) were confirmed by MLST. The remaining five grouped within the VNB clade in the phylogenetic analysis corresponding to the sequence type ST504. Other two environmental isolates also grouped within VNB clade with the new sequence type ST527. The four VNII/ST40 isolates were isolated from CSF. The two VNIV sequence types (ST11 and ST160) were isolated from blood cultures. Two of six patients evaluated with more than one isolates had mixed infections. Amongst the VNI isolates 4 populations were identified, which showed differences in their susceptibility profiles, clinical outcome and virulence factors. These results reinforce that ST93 is the most prevalent ST in HIV-infected patients in the Southeastern region of Brazil. The finding of the VNB molecular type amongst environmental Brazilian isolates highlights that this genotype is not restricted to the African continent.

Microbiological, Epidemiological, and Clinical Characteristics of Patients With Cryptococcal Meningitis at a Tertiary Hospital in China: A 6-Year Retrospective Analysis

“…For example, in 62 Cryptococcus strains collected from meningitis cases from 2006 to 2010 in Brazil, C. gattii species complex accounted for 21%, tremendously higher than that in mainland China ( Matos et al, 2012 ). In addition, there are several studies in Brazil also showing a high prevalence of C. neoformans species complex ( Andrade-Silva et al, 2018 ; Ponzio et al, 2019 ). Infection due to C. gattii species complex is more prevalent in the Northeast of Brazil ( Matos et al, 2012 ), despite has been described in the Southeast ( Vilas-Boas et al, 2020 ).…”

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

“…This suggests, that these STs may have been suppressed during the postpandemic era. As the response to stressful conditions, including the host immune response, were different for each serotype, survival of these 9 STs may have been affected during the post-HIV era since HIV patients are the major source for cryptococcal isolates [57][58][59]. On the other hand, this might simply have been caused by a sampling bias during the HIV pandemic.…”

Identification of pathogen genomic differences that impact human immune response and disease duringCryptococcus neoformansinfection

“…45). ST93 was similarly the most 388 prevalent among advanced HIV patients in Brazil [25]. By contrast, ST93 isolates were less 389 common than ST5 isolates among immunocompetent patients in Vietnam, and non-ST5 strains 390 were associated with decreased mortality compared to ST5 [55].…”

“…Disease is often due to infection by the fungus Cryptococcus neoformans and involves a 24 complex interaction between the human host and the fungal pathogen. Although previous studies 25 have suggested genetic differences in the pathogen impact human disease, it has proven quite 26 difficult to identify the specific C. neoformans genes that impact the outcome of the human 27 infection. Here, we take advantage of a Ugandan patient cohort infected with closely related C. 28 neoformans strains to examine to role of pathogen genetic variants on several human disease 29 characteristics.…”

“…Strain background can 96 significantly influence human disease, and there is tremendous disparity in strain frequency; 97 some strain groups are much more common than others. ST93 is common in Uganda, but is also 98 5 the most frequently isolated ST strain from HIV-infected patients in Brazil (85% [25,26]) and 99 India (71% [27,28]). Sequence type prevalence also has a clear geographic component as 100 different ST groups are dominant in other well-sampled countries (e.g., China, Thailand, 101 Vietnam, Indonesia, Botswana, France [27-29]).…”