Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin

Abstract

The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year, causing up to a third of all AIDS-related deaths. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly-virulent emerging lineages are changing patterns of human disease both temporally and spatially. Cryptococcus neoformans variety grubii (Cng, serotype A) constitutes the most ubiquitous cause of cryptococcal meningitis worldwide, however patterns of molecular diversity are understudied across some regions experiencing significant burdens of disease. We compared 183 clinical and environmental isolates of Cng from one such region, Thailand, Southeast Asia, against a global MLST database of 77 Cng isolates. Population genetic analyses showed that Thailand isolates from 11 provinces were highly homogenous, consisting of the same genetic background (globally known as VNI) and exhibiting only ten nearly identical sequence types (STs), with three (STs 44, 45 and 46) dominating our sample. This population contains significantly less diversity when compared against the global population of Cng, specifically Africa. Genetic diversity in Cng was significantly subdivided at the continental level with nearly half (47%) of the global STs unique to a genetically diverse and recombining population in Botswana. These patterns of diversity, when combined with evidence from haplotypic networks and coalescent analyses of global populations, are highly suggestive of an expansion of the Cng VNI clade out of Africa, leading to a limited number of genotypes founding the Asian populations. Divergence time testing estimates the time to the most common ancestor between the African and Asian populations to be 6,920 years ago (95% HPD 122.96 - 27,177.76). Further high-density sampling of global Cng STs is now necessary to resolve the temporal sequence underlying the global emergence of this human pathogen.

Determination of Epidemiology of Clinically Isolated Cryptococcus neoformans Strains in Japan by Multilocus Sequence Typing

“…A recent epidemiological study has shown that clinical and environmental isolates in Thailand predominantly consist of 3 STs, ST44, ST45, and ST46, accounting for up to 90z of the total isolates investigated (14), indicating low genetic diversity. In Japan, Mihara et al (15) has reported that 31 of the 35 isolates in Nagasaki, Japan exhibited ST5.…”

“…This discrepancy of ST might be due to the MLST database; http://cneoformans.mlst.net and http://mlst.mycology lab.org are used for this study and the study of Mihara et al, respectively. To compare STs in this study with the large-scale investigation by Simwami et al (14), we adopted the former database. A Chinese epidemiological study has shown that the majority of C. neoformans isolates exhibited the same ST, in which the nucleotide sequences of 5 loci examined (GPD1, IGS1, LAC1, PLB1, and SOD1) are identical to those of ST46 (19).…”

“…AB744719-AB745026). Each unique allelic profile was concatenated and assigned an ST using the archived online C. neoformans database on MLST.net (http://cneofor mans.mlst.net/) (14).…”

“…Based on the ISHAM scheme, 183 clinical and environmental isolates from Thailand and 77 isolates from the global collection of C. neoformans var. grubii were analyzed, and the MLST database was established (14). The majority of Thailand isolates exhibit 3 sequence types (STs): ST44 (33z, n ＝ 70), ST45 (43z, n ＝ 78), and ST46 (14z, n ＝ 26).…”

“…The majority of Thailand isolates exhibit 3 sequence types (STs): ST44 (33z, n ＝ 70), ST45 (43z, n ＝ 78), and ST46 (14z, n ＝ 26). ST44 and ST45 are unique to Thailand, and ST46 has been identified in Thailand and Japan (14). A recent epidemiological report has shown that 31 of the 35 C. neoformans var.…”