Whole-Genome Analysis of Cryptococcus gattii, Southeastern United States

Molecular type distribution and fluconazole susceptibility of clinical Cryptococcus gattii isolates from South African laboratory-based surveillance, 2005–2013

As is the case globally, Cryptococcus gattii is a less frequent cause of cryptococcosis than Cryptococcus neoformans in South Africa. We performed multilocus sequence typing (MLST) and fluconazole susceptibility testing of 146 isolates randomly selected from 750 South African patients with C. gattii disease identified through enhanced laboratory surveillance, 2005 to 2013. The dominant molecular type was VGIV (101/146, 70%), followed by VGI (40/146, 27%), VGII (3/146, 2%) and VGIII (2/146, 1%). Among the 146 C. gattii isolates, 99 different sequence types (STs) were identified, with ST294 (14/146, 10%) and ST155 (10/146, 7%) being most commonly observed. The fluconazole MIC₅₀ and MIC₉₀ values of 105 (of 146) randomly selected C. gattii isolates were 4 μg/ml and 16 μg/ml, respectively. VGIV isolates had a lower MIC₅₀ value compared to non-VGIV isolates, but these values were within one double-dilution of each other. HIV-seropositive patients had a ten-fold increased adjusted odds of a VGIV infection compared to HIV-seronegative patients, though with small numbers (99/136; 73% vs. 2/10; 20%), the confidence interval (CI) was wide (95% CI: 1.93–55.31, p = 0.006). Whole genome phylogeny of 98 isolates of South Africa’s most prevalent molecular type, VGIV, identified that this molecular type is highly diverse, with two interesting clusters of ten and six closely related isolates being identified, respectively. One of these clusters consisted only of patients from the Mpumalanga Province in South Africa, suggesting a similar environmental source. This study contributed new insights into the global population structure of this important human pathogen.

Cryptococcus is the most common cause of meningitis among adults in South Africa. Most human disease is caused by the members of two species complexes within the genus, Cryptococcus neoformans and Cryptococcus gattii. The environmental range of these species complexes, both found in soil, overlaps in southern Africa though C. gattii is a less common human pathogen. C. gattii is divided into six molecular types: VGI, VGII, VGIII, VGIV, VGV and VGVI. In earlier molecular epidemiology studies including relatively few isolates, most southern African isolates were confirmed as molecular type VGIV. We aimed to determine the molecular diversity of C. gattii in South Africa by genotyping patient isolates obtained through laboratory surveillance, 2005–2013. We confirmed that VGIV was the dominant molecular type and that HIV-seropositive patients were more likely to be infected with VGIV compared to those HIV-seronegative. Analysis of the genomes of South African VGIV isolates revealed that they spanned the whole VGIV clade and confirmed that most isolates did not cluster specifically. However, we observed two interesting clusters of closely related isolates, consisting of patients from three neighbouring provinces in South Africa, suggesting a similar environmental source. Further studies of clinical and environmental African C. gattii isolates are needed to gain a better understanding of this pathogen.

Donor-derived Cryptococcus gattii sensu stricto infection in two kidney transplant recipients, southeastern United States

Cryptococcus gattii infection is a rare cause of severe pulmonary disease and meningoencephalitis that has only recently been detected in the southeastern United States. We describe an organ transplant-associated outbreak of C. gattii infection involving an HIV-negative immunosuppressed donor in this region who died following new-onset headache and seizure of unknown cause. Retrospective cryptococcal antigen (CrAg) testing of donor serum was positive. Two of the three transplant recipients developed severe C. gattii infection 11 and 12 weeks following transplantation. One recipient died from severe pulmonary infection, identified on autopsy, and the other ill recipient survived following treatment for cryptococcal meningitis. This outbreak underscores the importance of considering cryptococcosis in patients with clinical findings suggestive of subacute meningitis or other central nervous system (CNS) pathology, and the potential benefit of routine pre-transplant donor CrAg screening using lateral flow assay to guide recipient antifungal prophylaxis. The case also adds to emerging evidence that C. gattii is a potential threat in the southeastern United States.

Cryptococcus neoformans and Other Opportunistic Cryptococcus Species in Pigeon Dropping in Saudi Arabia: Identification and Characterization by DNA Sequencing

The prevalent variants of Cryptococcus neoformans, and other Cryptococcus species in pigeon excreta in Western Region of Saudi Arabia were studied. Ninety pigeon dropping samples were plated directly on Niger seed agar, and suspected colonies were sequenced using Illumina MiSeq. Species identification was determined using sequence read mapping to reference genomes of the two C. neoformans variants. In addition, sequence reads were identified using the KmerFinder tool. internal transcribed spacer 2 in the rDNA was also used for fungal barcoding of none of the C. neoformans species using two fungal identification databases. Phylogeny was studied using CSI Phylogeny (Center for Genomic Epidemiology, Denmark). The C. neoformans var. grubii mitochondrion and chromosome 1 reference sequences (accession numbers NC_004336.1 and CP022321.1, respectively) were used for sequence comparison and variant calling. Fifteen Cryptococcus isolates were isolated, 11 were identified as C. neoformans var. grubii, and 4 were found to be other opportunistic Cryptococcus species. Phylogeny analysis of C. neoformans var. grubii isolates showed a high degree of similarity between the C. neoformans isolates especially at the mitochondrial genome level. This study supports the fact that pathogenic and opportunistic Cryptococcus species are prevalent in domestic bird excreta which is an easy source of infection in the susceptible population.

A case of Cryptococcus gattii infection in South Carolina: A possible challenge to known endemicity

In the United States, C. gattii is considered to be endemic to the Pacific Northwest and although uncommon, additional cases have been documented in other regions including the Southeastern United States. While it has been hypothesized in the past that C. gattii may be endemic to the Southeastern United States, there remains a paucity of evidence. Here, we present a patient with no history of HIV/AIDS and no organ transplant and document the course of his disease and presentation. There were no adverse long-term neurological outcomes in this patient and the combination of steroid use, antifungal agents, and cerebrospinal fluid drainage resulted in his discharge from the hospital after 12 days. This patient’s subacute presentation with vague neurological symptoms highlights the importance of understanding the treatment of rare causes of meningitis.

Molecular typing of clinical and environmental isolates of Cryptococcus gattii species complex from southern California, United States

BACKGROUND

Two species complexes (SC) cause the majority of human Cryptococcus infections: Cryptococcus neoformans SC and Cryptococcus gattii SC. Infection is typically thought to be acquired following environmental exposure. In an urban setting, parks and other public spaces are a likely source of contact with C. gattii SC.

OBJECTIVES

The goals of this study were to describe the genetic diversity of C. gattii SC in the California environment, to determine the extent of environmental exposure in publicly accessed areas and to correlate the genotypes of environmental C. gattii SC isolates with those from patients in southern California.

METHODS

Specimens from trees and soil from 13 parks and public areas of seven California counties were examined for C. gattii SC isolates. Isolates were sequence typed and compared to sequence types from human clinical isolates from the same area.

RESULTS

Multilocus sequence typing identified C. gattii sensu stricto (VGI molecular type) as well as Cryptococcus bacillisporus (VGIII molecular type). Several C. bacillisporus but none of the C. gattii sensu stricto isolates shared sequence types with human clinical isolates from southern California.

CONCLUSIONS

C. gattii SC colonies exist in some California public parks. The presence of identical STs in environmental and human isolates of C. bacillisporus is suggestive of an arboreal origin of human infections. Two new tree species were documented as hosts for C. gattii SC in California, adding to the four species previously identified.

Cryptococcus gattii Complex Infections in HIV-Infected Patients, Southeastern United States

Increased awareness of C. gattii infections in these patients is critical for improving diagnosis, treatment, and outcomes.

Cryptococcus gattii traditionally infects immunocompetent hosts and causes devastating pulmonary or central nervous system disease. However, this infection rarely occurs in patients infected with HIV. We report 3 cases of HIV-associated C. gattii complex infections in the southeastern United States. Detection of C. gattii in HIV-infected patients in this region warrants increased awareness of this threat to ensure appropriate diagnosis and treatment to optimize patient outcomes.

Timing the Origin of Cryptococcus gattii sensu stricto, Southeastern United States

We conducted molecular clock analysis of whole-genome sequences from a set of autochthonous isolates of Cryptococcus gattii sensu stricto from the southeastern United States. Our analysis indicates that C. gattii arrived in the southeastern United States approximately 9,000–19,000 years ago, long before its arrival in the Pacific Northwest.

Recovery of Cryptococcus gattii from an Infected Ventriculo-Peritoneal Shunt, Illinois, USA

Cryptococcus gattii is a fungal pathogen endemic in tropical and subtropical regions. Isolated cases and outbreaks have been reported in areas of North America and Europe, expanding the distribution pattern beyond warmer regions. We describe a case of ventriculo-peritoneal shunt infection by C. gattii in an immunocompetent person in Illinois.

Dating the Cryptococcus gattii Dispersal to the North American Pacific Northwest

The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events.

The emergence of Cryptococcus gattii, previously regarded as a predominantly tropical pathogen, in the temperate climate of the North American Pacific Northwest (PNW) in 1999 prompted several questions. The most prevalent among these was the timing of the introduction of this pathogen to this novel environment. Here, we infer tip-dated timing estimates for the three clonal C. gattii populations observed in the PNW, VGIIa, VGIIb, and VGIIc, based on whole-genome sequencing of 134 C. gattii isolates and using Bayesian evolutionary analysis by sampling trees (BEAST). We estimated the nucleotide substitution rate for each lineage (1.59 × 10⁻⁸, 1.59 × 10⁻⁸, and 2.70 × 10⁻⁸, respectively) to be an order of magnitude higher than common neutral fungal mutation rates (2.0 × 10⁻⁹), indicating a microevolutionary rate (e.g., successive clonal generations in a laboratory) in comparison to a species’ slower, macroevolutionary rate (e.g., when using fossil records). The clonal nature of the PNW C. gattii emergence over a narrow number of years would therefore possibly explain our higher mutation rates. Our results suggest that the mean time to most recent common ancestor for all three sublineages occurred within the last 60 to 100 years. While the cause of C. gattii dispersal to the PNW is still unclear, our research estimates that the arrival is neither ancient nor very recent (i.e., <25 years ago), making a strong case for an anthropogenic introduction.

IMPORTANCE The recent emergence of the pathogenic fungus Cryptococcus gattii in the Pacific Northwest (PNW) resulted in numerous investigations into the epidemiological and enzootic impacts, as well as multiple genomic explorations of the three primary molecular subtypes of the fungus that were discovered. These studies lead to the general conclusion that the subtypes identified likely emerged out of Brazil. Here, we conducted genomic dating analyses to determine the ages of the various lineages seen in the PNW and propose hypothetical causes for the dispersal events. Bayesian evolutionary analysis strongly suggests that these independent fungal populations in the PNW are all 60 to 100 years old, providing a timing that is subsequent to the opening of the Panama Canal, which allowed for more direct shipping between Brazil and the western North American coastline, a possible driving event for these fungal translocation events.