Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure ofCryptococcus NeoformansVar.Grubiiin Vietnam
Authors: Tuan Thanh Lam , Hai Trieu Phan , Rattanavong Sayaphet , Nguyen Trinh Mai , Van Anh Duong , Dacon Cherrelle , Nha Thu Hoang , Nguyen Lan Phu Huong , Tran Chau Thi Hong , Davong Viengmon , Nguyen Chau Van Vinh , Thwaites Guy E. , Boni Maciej F. , Dance David , Ashton Philip M. , Day Jeremy N. 
Published: September 2017

Cryptococcosis is amongst the most important invasive fungal infections globally, with cryptococcal meningitis causing an estimated 180,000 deaths each year in HIV infected patients alone. Patients with other forms of immunosuppression are also at risk, and disease is increasingly recognized in apparently immunocompetent individuals.Cryptococcus neoformansvar.grubii(serotype A, molecular type VNI) has a global distribution and is responsible for the majority of cases. Here, we used the consensus ISHAM Multilocus Sequence Typing (MLST) forC. neoformansto define the population structure of clinical isolates ofCryptococcus neoformansvar.grubiifrom Vietnam (n=136) and Laos (n=81). We placed these isolates into the global context using published MLST data from 8 other countries (total N = 669). We observed a phylo-geographical relationship in which Laos was similar to its Southeast Asian neighbor Thailand in being dominated (83%) by Sequence Type (ST) 4 and its Single Locus Variant ST6. On the other hand, Vietnam was uniquely intermediate between Southeast Asia and East Asia having both ST4/ST6 (35%) and ST5 (48%) which causes the majority of cases in East Asia. Analysis of genetic distance (Fst) between different populations ofCryptococcus neoformansvar.grubiisupported the intermediate nature of the population from Vietnam. A strong association between ST5 and infection in apparently immunocompetent, HIV-uninfected patients was observed in Vietnam (OR: 7.97, [95%CI: 3.18-19.97],p< 0.0001). Our study emphasizes that Vietnam, with its intermediateCryptococcus neoformansvar.grubiipopulation structure, provides the strongest epidemiological evidence of the relationship between ST5 and infection of HIV-uninfected patients. Human population genetic distances within the region suggest these differences in CNVG population across Southeast Asia are driven by ecological factors rather than host factors.

Author summary

Cryptococcus neoformansis a yeast that causes meningitis in people, usually with damaged immune systems. There are >180,000 deaths in HIV-infected patients each year, most occurring where there are the highest HIV/AIDS disease burdens. Vietnam and Laos have contributed significantly to clinical trials aiming to improve the treatment of cryptococcal meningitis, but the relationship of isolates from these countries to the global population is not yet described. Here, we address this knowledge gap by using Multilocus Sequence Typing to study the population ofCryptococcus neoformansvar.grubii(CNVG) in Laos and Vietnam, with the specific aim of incorporating these populations into the wider global context. We found that, in most countries, a single lineage (family) of strains was responsible for most disease. The Vietnamese CNVG population was unusual in that 2 main lineages circulated at the same time. The Vietnamese CNVG population occupies a middle ground between Thailand/Laos in the west and China in the east. The differences in population structure moving from West to East are probably due to ecological differences. Disease in HIV uninfected patients was almost always due to members of a single family of strains (ST5).