Molecular Epidemiology and Antifungal Resistance of Cryptococcus neoformans From Human Immunodeficiency Virus-Negative and Human Immunodeficiency Virus-Positive Patients in Eastern China

Abstract

Cryptococcosis is an opportunistic and potentially lethal infection caused by Cryptococcus neoformans and Cryptococcus gattii complex, which affects both immunocompromised and immunocompetent people, and it has become a major public health concern worldwide. In this study, we characterized the molecular epidemiology and antifungal susceptibility of 133 C. neoformans isolates from East China Invasive Fungal Infection Group (ECIFIG), 2017–2020. Isolates were identified to species level by matrix-assisted laser desorption ionization-time of flight mass spectrometry and confirmed by IGS1 sequencing. Whole-genome sequencing (WGS) was conducted on three multidrug-resistant isolates. Among the 133 strains, 61 (45.86%) were isolated from HIV-positive patients and 72 (54.16%) were isolated from HIV-negative patients. In total, C. neoformans var. grubii accounted for 97.74% (130/133), while C. neoformans var. neoformans was rare (2.06%, 3/133). The strains were further classified into nine sequence types (STs) dominated by ST5 (90.23%, 120/133) with low genetic diversity. No association was observed between STs and HIV status. All strains were wild type to voriconazole, while high antifungal minimal inhibitory concentrations (MICs) above the epidemiological cutoff values (ECVs) were observed in C. neoformans strains, and more than half of isolates were non-wild-type to amphotericin B (89.15%, 109/133). Eight isolates were resistant to fluconazole, and eight isolates were non-wild type to 5-fluorocytosine. Furthermore, WGS has verified the novel mutations of FUR1 in 5-fluorocytosine-resistant strains. In one isolate, aneuploidy of chromosome 1 with G484S mutation of ERG11 was observed, inducing high-level resistance (MIC: 32 μg/ml) to fluconazole. In general, our data showed that there was no significant difference between HIV-positive and HIV-negative patients on STs, and we elucidate the resistant mechanisms of C. neoformans from different perspectives. It is important for clinical therapy and drug usage in the future.

Antifungal susceptibility and molecular characteristics of Cryptococcus spp. based on whole-genome sequencing in Zhejiang Province, China

“…Using genome assemblies, Mashtree was used to reconstruct the phylogenetic tree efficiently. Not only can CNSCs and CGSCs be clearly distinguished, but subclusters in the major cluster can also be classified, as reported by Ziyi Zhou et al in 2022 in a study that showed that ST5 has different subtypes based on the detection of single nucleotide polymorphism (SNPs) variants ( Zhou et al, 2022 ), and the ST5 cluster and ST31 cluster can be roughly considered CC5 and CC31 ( Fan et al, 2016 ; Cogliati et al, 2019 ; Thanh et al, 2019 ). Furthermore, the relationship between AD hybrids and other CCs could be clearly distinguished.…”

“…in 2022 in a study that showed that ST5 has different subtypes based on the detection of single nucleotide polymorphism (SNPs) variants (Zhou et al, 2022), and the ST5 cluster and ST31 cluster can be roughly considered CC5 and CC31 (Fan et al, 2016;Cogliati et al, 2019;Thanh et al, 2019). Furthermore, the relationship between AD hybrids and other CCs could be clearly distinguished.…”

“…These results improved the typing methods and revealed the biodiversity of Cryptococcus spp. in China ( Zang et al, 2022 ; Zhou et al, 2022 ).…”

“…neoformans JEC21 and Cryptococcus gattii WM276 are 18.57 Mb and 18.4 Mb, respectively, and include 14 chromosomes ( Loftus et al, 2005 ; D’Souza et al, 2011 ). Previous analysis showed that ST5 has different subtypes, which was observed following the detection of single nucleotide polymorphism (SNPs) variants ( Zhou et al, 2022 ), and WGS can further be used to analyse resistance mechanisms and simultaneously acquire other typing features ( Zang et al, 2022 ; Zhou et al, 2022 ). Considering the complexity of Cryptococcus spp.…”

Temporal trends in antifungal susceptibility of Cryptococcus neoformans isolates from a reference laboratory in the United States, 2011–2021

“…7 Our reported AMB MIC trend has been described in other studies outside the United States. [35][36][37] In one study that evaluated the MIC distribution of different antifungal agents against Cryptococcus isolates collected from clinical and environmental samples from different countries before 1980 (prior to the HIV epidemic), 71.2% of C.…”