Browsing by Subject "genotyping"

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    Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.
    (Mol Ecol, 2015-07) Chen, Yuan; Litvintseva, Anastasia P; Frazzitta, Aubrey E; Haverkamp, Miriam R; Wang, Liuyang; Fang, Charles; Muthoga, Charles; Mitchell, Thomas G; Perfect, John R
    Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating-type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.
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    Screening for Cervical Cancer in HIV Positive Kenyan Women: the Role of HPV Genotyping
    (2013) Dainty, Erin E.

    Problem: Among HIV positive women in Kenya, cervical cancer has the highest incidence of any malignancy. In order to create effective screening strategies for both the primary and secondary prevention of cervical cancer in HIV-infected women, an understanding of the natural history of human papillomavirus (HPV) and HIV co infection is critical.

    Objectives: To describe the prevalence of HPV genotypes in HIV infected women with mild dysplasia and those with biopsy-confirmed severe dysplasia and invasive cervical cancer in Eldoret, Kenya. To determine how CD4 count, as a marker of immunocompetence, relates to HPV genotype distribution in patients with compared to those with severe dysplasia and invasive cervical cancer.

    Methodology: This was a cross-sectional study recruiting from two groups: women who have invasive cervical cancer and women who have mild dysplasia. Cervical swabs were collected for genotyping, along with a recent CD4 count and relevant sociodemographic and medical data. HPV genotyping for types 6, 11, 16, 18, 26, 31, 33, 35, 39, 43, 44, 45, 51, 52, 53, 54, 56, 58, 66, 68, 69, 70, 71, 73, 74, and 82 was performing using the INNO-LiPA HPV genotyping assay, SPF10 system version 1 (Innogenetics, Ghent, Belgium). Crude and covariate-adjusted prevalence odds ratios were calculated using logistic regression analysis, and were performed separately for each HPV-type. In addition, modification of HPV-type prevalence ratios by CD4 count was analyzed. All data analysis was performed using Stata 12.1 (College Station, TX).

    Results: HPV 52 had a significantly higher prevalence in this population than HPV 16 or 18. Neither HPV genotype nor CD4 count had changed the prevalence odds of severe dysplasia and invasive cervical cancer. Participant age, history of syphilis, anemia, vaginal bleeding, and greater than five pregnancies increased the prevalence odds of severe dysplasia and invasive cervical cancer, compared to mild dysplasia.

    Conclusions: These findings suggest that duration of HPV infection and host response to infection, rather than HPV genotype or CD4 count, are primarily responsible in the oncogenic transformation of infected cervical tissue. The overwhelming predominance of HPV 52 has implications regarding the efficacy of vaccination against HPV 16 and 18 in the primary prevention of cervical cancer in HIV infected women in Western Kenya.