MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil

Ferreira-Paim, Kennio; Andrade-Silva, Leonardo; Fonseca, Fernanda Machado; Ferreira, Thatiana Bragine; Mora, Delio José; Andrade-Silva, Juliana; Khan, Aziza; Dao, Aiken; Reis, Eduardo C.; Almeida, Margarete Teresa Gottardo de; Maltos, André Luiz; Virmondes, R.; Trilles, Luciana; Rickerts, Volker; Chindamporn, Ariya; Sykes, Jane E.; Cogliati, Massimo; Nielsen, Kirsten; Boekhout, Teun; Fisher, Matthew C.; Kwon‐Chung, June; Engelthaler, David M.; Lazéra, Márcia dos Santos; Meyer, Wieland; Silva‐Vergara, Mario León

doi:10.1371/journal.pntd.0005223

Cited by 64 publications

(65 citation statements)

References 95 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…As we have shown here and previously, the ST5 lineage is associated with apparently immunocompetent patients in Vietnam [25,53]. ST93 was the most prevalent sequence type in India, Indonesia, Uganda and Brazil (varying between 48% and 77%) [10,54,55], but accounted for less than 4% of isolates from Vietnam and Laos.…”

Section: Discussionsupporting

confidence: 67%

Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure ofCryptococcus NeoformansVar.Grubiiin Vietnam

Lam

Phan

Rattanavong

et al. 2017

Preprint

View full text Add to dashboard Cite

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 neoformans var. 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) for C. neoformans to define the population structure of clinical isolates of Cryptococcus neoformans var. grubii from 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 of Cryptococcus neoformans var. grubii supported 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 intermediate Cryptococcus neoformans var. grubii population 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 summaryCryptococcus neoformans is 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 of Cryptococcus neoformans var. 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).

show abstract

Section: Discussionsupporting

confidence: 67%

Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure ofCryptococcus NeoformansVar.Grubiiin Vietnam

Lam

Phan

Rattanavong

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, we observed differences in the disease progression/pathogenesis in mice infected with the three low virulence strains. One of the low virulence strains (UgCl223) had high terminal lung CFUs (1X 10 7 ) and very few CFUs in the spleen (10) and brain (10). Histologic examination of lung and brain from 2 additional animals revealed low numbers of cryptococci in the lung with moderate inflammation, and one mouse had small cryptococci infiltrating the meninges, scattered in small areas of necrosis within the neuropil.…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies showed that pathogen-specific characteristics, such as genotype or the degree of antigen shedding, influence immune responses to C. neoformans and the clinical outcome of infected patients (5, 7–9). Multi-locus sequence typing (MLST) of 7 genetic loci has been used previously to identify genetically similar strains (5–10). For example, studies of clinical isolates in both Uganda and Brazil showed higher patient mortality associated with sequence type 93 (ST93) strains (5, 10).…”

Section: Introductionmentioning

confidence: 99%

“…Multi-locus sequence typing (MLST) of 7 genetic loci has been used previously to identify genetically similar strains (5–10). For example, studies of clinical isolates in both Uganda and Brazil showed higher patient mortality associated with sequence type 93 (ST93) strains (5, 10). ST93 strains had increases in type 2 cytokines in ex vivo cytokine release assays, suggesting that these strains may shift the Th1/Th2 immune balance (5).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Closely related Cryptococcus neoformans strains possess differential virulence both in humans and the mouse inhalation model

Mukaremera

McDonald

Nielsen

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

24Cryptococcal meningitis (CM) causes high rates of HIV-related mortality, yet Cryptococcus 25 factors influencing patient outcome are not well understood. Pathogen-specific traits, such as the 26 strain genotype and degree of antigen shedding, are associated with clinical outcome but the 27 underlying biology remains elusive. In this study, we examined factors determining disease 28 outcome in HIV-infected cryptococcal meningitis patients infected with C. neoformans strains 29 with the same multi-locus sequence type. Both patient mortality and survival were observed 30 during infections with the same sequence type. Disease outcome did not correlate with 31 underlying patient immune deficiencies. Patient mortality was associated with higher antigen 32 levels, fungal burden in the CSF, and low CSF fungal clearance. Virulence of a subset of clinical 33 strains with the same sequence type were analyzed using the mouse inhalation model of 34 cryptococcosis. We showed a strong correlation between human and mouse mortality rates, 35 demonstrating the mouse inhalation model recapitulates human infection. Similar to human 36 infection, the ability to multiply in vivo, demonstrated by high fungal burden in the lung and 37 brain tissues, was associated with mouse mortality. Mortality rate was not associated with single 38 C. neoformans virulence factors in vitro or in vivo; rather, a trend in mortality rate correlated 39 with a suite of traits. These observations show that genotype similarities between C. neoformans 40 strains do not necessarily translate into similar virulence either in the mouse model or in human 41 patients. In addition, our results show that in vitro assays do not fully reproduce in vivo 42 conditions that influence C. neoformans virulence. 44Cryptococcus neoformans is a fungal pathogen that causes disease mainly in 45 immunocompromised patients such as individuals living with HIV/AIDS or receiving organ 46 transplants. The availability of antiretroviral therapy has reduced AIDS-related mortality, 47 however deaths due to cryptococcal meningitis (CM) have plateaued with C. neoformans still 48 causing 15 % of all AIDS-related deaths globally (1, 2). Mortality rates due to Cryptococcus 49 infection varies by region from 70% in low-income countries to 20-40% of all infected patients 50 in high-income countries (2). Although differences in mortality rates between high-and low-51 income countries can be linked to sub-optimal antifungal treatments in low-income countries (3), 52 variations in mortality rates between patient groups receiving similar treatments and residing in 53 the same region of the world are observed (1,(4)(5)(6). Mortality is a measure influenced by many 54 intrinsic host and pathogen factors (as well as host-pathogen interaction factors). Thus, we need 55 better proxies to understand C. neoformans pathogenesis in patients and identify factors 56 determining clinical outcome. 57Although C. neoformans pathogenesis in the mouse model of cryptococcosis has been 58 extensively studied, the...

show abstract

“…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]).…”

mentioning

confidence: 99%

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

Gerstein

Jackson

McDonald

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

1 2Patient outcomes during infection are due to a complex interplay between the quality of medical 3 care, host immunity factors, and the infecting pathogen's characteristics. To probe the influence 4 of pathogen genotype on human immune response and disease, we examined Cryptococcus 5 neoformans isolates collected during the Cryptococcal Optimal ART Timing (COAT) trial in 6 Uganda. We measured human participants' immunologic phenotypes, meningitis disease 7 parameters, and survival. We compared this clinical data to whole genome sequences from 38 C. 8 neoformans isolates of the most frequently observed sequence type (ST) ST93 in our Ugandan 9 participant population, and an additional 18 strains from 9 other sequence types representing the 10 known genetic diversity within the Ugandan Cryptococcus clinical isolates. We focused our 11 analyses on 652 polymorphisms that: were variable among the ST93 genomes, were not in 12 centromeres or extreme telomeres, and were predicted to have a fitness effect. Logistic 13 regression and principal component analyses identified 40 candidate Cryptococcus genes and 3 14 hypothetical RNAs associated with human immunologic response or clinical parameters. We 15 infected mice with 17 available KN99α gene deletion strains for these candidate genes and found 16 that 35% (6/17) directly influenced murine survival. Four of the six gene deletions that impacted 17 murine survival were novel. Such bedside-to-bench translational research provides important 18 candidate genes for future studies on virulence-associated traits in human Cryptococcus 19 infections.Even with the best available care, mortality rates in cryptococcal meningitis range from 23 20-60%. 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. Using a pathogen whole genome sequencing approach, we showed that 40 C. 30neoformans genes are associated with human disease. Surprisingly, many of these genes are 31 specific to Cryptococcus and have unknown functions. We also show deletion of these genes 32 alters disease in a mouse model of infection, confirming their role in disease. These findings are 33 particularly important because they are the first to identify C. neoformans genes associated with 34 human cryptococcal meningitis and lay the foundation for future studies that may lead to new 35 treatment strategies aimed at reducing patient mortality. 36 37 38Cryptococcus neoformans is the etiological agent of cryptococcal meningitis, the most 39 common brain infection in Sub-Saharan Africa, which enc...

show abstract

MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil

Cited by 64 publications

References 95 publications

Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure ofCryptococcus NeoformansVar.Grubiiin Vietnam

Multilocus Sequence Typing Reveals A Unique Co-Dominant Population Structure ofCryptococcus NeoformansVar.Grubiiin Vietnam

Closely related Cryptococcus neoformans strains possess differential virulence both in humans and the mouse inhalation model

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

Contact Info

Product

Resources

About