Limits...
Geographically structured populations of Cryptococcus neoformans Variety grubii in Asia correlate with HIV status and show a clonal population structure.

Khayhan K, Hagen F, Pan W, Simwami S, Fisher MC, Wahyuningsih R, Chakrabarti A, Chowdhary A, Ikeda R, Taj-Aldeen SJ, Khan Z, Ip M, Imran D, Sjam R, Sriburee P, Liao W, Chaicumpar K, Vuddhakul V, Meyer W, Trilles L, van Iersel LJ, Meis JF, Klaassen CH, Boekhout T - PLoS ONE (2013)

Bottom Line: HIV-status, sequence types and geography were found to be confounded.However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates.Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand ; CBS-KNAW Fungal Biodiversity Centre, Department of Yeast and Basidiomycete Research, Utrecht, The Netherlands ; Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.

ABSTRACT
Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

Show MeSH

Related in: MedlinePlus

Diagram showing DNA polymorphisms of C.neoformans var. grubii from different Asian regions.(A) DNA polymorphism, genetic differentiation and gene flow; (B) same as A, but comparing African, American, Asian and European populations.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3760895&req=5

pone-0072222-g004: Diagram showing DNA polymorphisms of C.neoformans var. grubii from different Asian regions.(A) DNA polymorphism, genetic differentiation and gene flow; (B) same as A, but comparing African, American, Asian and European populations.

Mentions: The number of polymorphisms of the concatenated sequences of C. neoformans var. grubii isolates obtained from the East Asian region, including China, Hong Kong and Japan, were lower than those from South/Southeast Asian isolates (i.e. India, Indonesia and Thailand), and those from the Middle East (i.e. Kuwait and Qatar) (Figure 4A and Table E in Supplementary Tables S1). The highest nucleotide diversity (π = 0.002), the highest average number of nucleotide differences per sequence (k = 7.962), and the highest haplotype diversity (Hd = 0.924) were found in C. neoformans isolates from Kuwait and Qatar. C. neoformans isolates from South/Southeast Asia had 75 polymorphic site (S) and 21 different haplotypes (h), and a high mutation rate per sequence (θs = 11.816). Within the South/Southeast region, haplotype diversity (Hd) of each population was almost similar, while other nucleotide polymorphism estimation values of each population, such as number of polymorphic sites (S), nucleotide diversity (π), mutation rate (θ) and the average number of nucleotide differences per sequence (k), were different (Figure 4A, Table E in Supplementary Tables S1). A significant signal of purifying selection was observed in two C. neoformans populations, namely the one from East Asia (i.e. the Japanese population) and the South/Southeast Asian one (i.e. the Indian population), whereas evidence of a balancing selection or expansion of rare polymorphisms was found in the Indonesian population (Table E in Supplementary Tables S1).


Geographically structured populations of Cryptococcus neoformans Variety grubii in Asia correlate with HIV status and show a clonal population structure.

Khayhan K, Hagen F, Pan W, Simwami S, Fisher MC, Wahyuningsih R, Chakrabarti A, Chowdhary A, Ikeda R, Taj-Aldeen SJ, Khan Z, Ip M, Imran D, Sjam R, Sriburee P, Liao W, Chaicumpar K, Vuddhakul V, Meyer W, Trilles L, van Iersel LJ, Meis JF, Klaassen CH, Boekhout T - PLoS ONE (2013)

Diagram showing DNA polymorphisms of C.neoformans var. grubii from different Asian regions.(A) DNA polymorphism, genetic differentiation and gene flow; (B) same as A, but comparing African, American, Asian and European populations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3760895&req=5

pone-0072222-g004: Diagram showing DNA polymorphisms of C.neoformans var. grubii from different Asian regions.(A) DNA polymorphism, genetic differentiation and gene flow; (B) same as A, but comparing African, American, Asian and European populations.
Mentions: The number of polymorphisms of the concatenated sequences of C. neoformans var. grubii isolates obtained from the East Asian region, including China, Hong Kong and Japan, were lower than those from South/Southeast Asian isolates (i.e. India, Indonesia and Thailand), and those from the Middle East (i.e. Kuwait and Qatar) (Figure 4A and Table E in Supplementary Tables S1). The highest nucleotide diversity (π = 0.002), the highest average number of nucleotide differences per sequence (k = 7.962), and the highest haplotype diversity (Hd = 0.924) were found in C. neoformans isolates from Kuwait and Qatar. C. neoformans isolates from South/Southeast Asia had 75 polymorphic site (S) and 21 different haplotypes (h), and a high mutation rate per sequence (θs = 11.816). Within the South/Southeast region, haplotype diversity (Hd) of each population was almost similar, while other nucleotide polymorphism estimation values of each population, such as number of polymorphic sites (S), nucleotide diversity (π), mutation rate (θ) and the average number of nucleotide differences per sequence (k), were different (Figure 4A, Table E in Supplementary Tables S1). A significant signal of purifying selection was observed in two C. neoformans populations, namely the one from East Asia (i.e. the Japanese population) and the South/Southeast Asian one (i.e. the Indian population), whereas evidence of a balancing selection or expansion of rare polymorphisms was found in the Indonesian population (Table E in Supplementary Tables S1).

Bottom Line: HIV-status, sequence types and geography were found to be confounded.However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates.Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand ; CBS-KNAW Fungal Biodiversity Centre, Department of Yeast and Basidiomycete Research, Utrecht, The Netherlands ; Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.

ABSTRACT
Cryptococcosis is an important fungal disease in Asia with an estimated 140,000 new infections annually the majority of which occurs in patients suffering from HIV/AIDS. Cryptococcus neoformans variety grubii (serotype A) is the major causative agent of this disease. In the present study, multilocus sequence typing (MLST) using the ISHAM MLST consensus scheme for the C. neoformans/C. gattii species complex was used to analyse nucleotide polymorphisms among 476 isolates of this pathogen obtained from 8 Asian countries. Population genetic analysis showed that the Asian C. neoformans var. grubii population shows limited genetic diversity and demonstrates a largely clonal mode of reproduction when compared with the global MLST dataset. HIV-status, sequence types and geography were found to be confounded. However, a correlation between sequence types and isolates from HIV-negative patients was observed among the Asian isolates. Observations of high gene flow between the Middle Eastern and the Southeastern Asian populations suggest that immigrant workers in the Middle East were originally infected in Southeastern Asia.

Show MeSH
Related in: MedlinePlus