Browsing by Author "Ramsuran, Veron."

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Case report: mechanisms of HIV elite control in two African women.
(BioMed Central., 2018) Moosa, Yumna.; Tanko, Ramla F.; Ramsuran, Veron.; Singh, Ravesh.; Madzivhandila, Mashudu.; Yende-Zuma, Fortunate Nonhlanhla.; Abrahams, Melissa-Rose.; Selhorst, Philippe.; Gounder, Kamini.; Moore, Penelope L.; Williamson, Carolyn.; Abdool Karim, Salim Safurdeen.; Garrett, Nigel Joel.; Burgers, Wendy A.
Abstract available in pdf.
Characterisation of antibiotic resistance in Streptococcus, Enterococcus and Staphylococcus using a bioinformatics approach.
(2005) Ramsuran, Veron.; Beukes, Mervyn.
The rate at which bacterial pathogens are becoming resistant to antibiotics is quite alarming, and therefore much attention has been focussed on this area. The mechanism whereby the bacterial cells acquire resistance is studied in order to determine how this process works as well as to determine if any future resistance mechanisms can be circumvented. In this study three different genera and the antibiotics that are resistant to them were used, namely, penicillin resistant Streptococcus, vancomycin resistant Enterococcus and methicillin resistant Staphylococcus. The results prove that the active sites SXXK, SXN and KT(S) G in the penicillin resistance Streptococcus plays a major role in resistance. It is seen in this study that the SXXK active site is found in all the resistant and most of the intermediate strains, therefore proving to be an important component of the cell wall resistance. It was subsequently noticed the greater the number of mutations found in the sequences the higher the resistance. Three dimensional structures showed the actives sites and their binding pockets. The results also show the change in conformation with a mutation in the active site. The results also proved that the Penicillin Binding Protein (PBP) genes essential for resistance are PBP Ia, PBP 2b and PBP 2x. The results obtained, for the vancomycin resistance in Enterococcus study, proved that the VanC and VanE cluster are very much alike and VanE could have evolved from VanC. There is also close similarity between the different ligase genes. The VanX 3D structure shows the position of the critical amino acids responsible for the breakdown of the D-Ala-D-Ala precursors, and the VanA ligase 3D structure shows the amino acids responsible the ligation of the D-Ala-D-Lac precursors. The analysis performed on the methicillin resistance in Staphylococcus study showed that the genes used to confer resistance are very similar between different strains as well as different species.
Duffy-Null–Associated Low Neutrophil Counts Influence HIV-1 Susceptibility in High-Risk South African Black Women.
(Oxford University Press., 2010) Ramsuran, Veron.; Kulkarni, Hemant.; He, Weijing.; Mlisana, Koleka Patience.; Wright, Edwina J.; Werner, Lise.; Castiblanco, John.; Dhanda, Rahul.; Le, Tuan.; Dolan, Matthew J.; Guan, Weihua.; Weiss, Robin A.; Clark, Robert A.; Abdool Karim, Salim Safurdeen.; Ahuja, Sunil K.; Ndung'u, Peter Thumbi.
Background. The Duffy-null trait and ethnic netropenia are both highly prevalent in Africa. The influence of pre-seroconversion levels of peripheral blood cell counts (PBCs) on the risk of acquiring human immunodeficiency virus (HIV)–1 infection among Africans is unknown. Methods. The triangular relationship among pre-seroconversion PBC counts, host genotypes, and risk of HIV acquisition was determined in a prospective cohort of black South African high-risk female sex workers. Twenty seven women had seroconversion during follow-up, and 115 remained HIV negative for 2 years, despite engaging in high-risk activity. Results. Pre-seroconversion neutrophil counts in women who subsequently had seroconversion were significantly lower, whereas platelet counts were higher, compared with those who remained HIV negative. Comprising 27% of the cohort, subjects with pre-seroconversion neutrophil counts of <2500 cells/mm3 had a ~3-fold greater risk of acquiring HIV infection. In a genome-wide association analyses, an African-specific polymorphism (rs2814778) in the promoter of Duffy Antigen Receptor for Chemokines (DARC -46T>C) was significantly associated with neutrophil counts (P = 7.9 x10-11). DARC -46C/C results in loss of DARC expression on erthyrocytes (Duffy-null) and resistance to Plasmodium vivax malaria, and in our cohort, only subjects with this genotype had pre-seroconversion neutrophil counts of <2500 cells/mm3. The risk of acquiring HIV infection was ~3-fold greater in those with the trait of Duffy-null–associated low neutrophil counts, compared with all other study participants. Conclusions. Pre-seroconversion neutrophil and platelet counts influence risk of HIV infection. The trait of Duffy-null–associated low neutrophil counts influences HIV susceptibility. Because of the high prevalence of this trait among persons of African ancestry, it may contribute to the dynamics of the HIV epidemic in Africa.
Epidemiology and alternative approaches for SARS-CoV-2 testing within limited resources settings=Isifundo ngembangela nokusabalala kwezifo i-epidemiology nezindlela ezahlukile zokuhlolwa kwe-SARS-CoV-2 esimeni sokwesweleka kwezinsiza.
(2023) Duma, Zamathombeni.; Mkhize-Kwitshana, Zilungile Lynette.; Chuturgoon, Anil Amichund.; Ramsuran, Veron.
Background: In the context of the global battle to contain the rapidly mutating SARS-CoV-2, diagnostic testing for SARS-CoV-2 infection remains a challenge, particularly in low-middleincome countries (LMICs) due to low socioeconomic backgrounds. Concerningly, because less attention is paid to asymptomatic cases, particularly in LMICs with limited resources for SARSCoV- 2 testing, the virus is spreading silently in communities, and the majority of these individuals could be contributing to the resurgence of SARS-CoV-2 infection. This study aimed to determine the epidemiology and alternative approaches for SARS-CoV-2 testing within limited resources settings. Methods: A total sample size of 1335 residual patient samples from the Global Health Innovation (GHI) laboratory was used for the epidemiology study and methods comparison. Results and Discussion: Literature review showed that high income countries (HICs) test more frequently for SARS-CoV-2 infection, with a range of 113% to 146% higher than LMICs (1% to 43%). The present study demonstrated a higher proportion of asymptomatic cases (68%) among SARS-CoV-2 infected patients. Regarding the methods comparison for the detection of SARSCoV- 2, the evaluated alternative methods [three RNA extraction (Lucigen QuickExtract™ RNA Extraction Kit, Bosphore EX-Tract Dry Swab RNA Solution, Sonicator method and four commercial SARS-CoV-2 RT-PCR assay kits (Nucleic Acid COVID-19 Test Kit (SARS-CoV-2), abTESTM COVID-19 qPCR I Kit, PCL COVID19 Speedy RT-PCR Kit, and PCLMD nCoV One- Step RT-PCR Kit)] were found to be cheaper and faster. Conclusion: Notably LMICs are undertesting for SARS-CoV-2 infection compared to HICs, and there was a higher proportion of asymptomatic cases among SARS-CoV-2 infected patients in South Africa. This study suggests that using the above-mentioned cost-effective, quick, and accurate evaluated alternative methods for mass SARS-CoV-2 testing in routine diagnostic laboratories with limited resources can help to increase testing capacity for SARS-CoV-2 infection in LMICs. This means that the sooner SARSCoV- 2 infection control and prevention measures can be implemented to reduce community transmission. IQOQA Isendlalelo: Esimeni somzabalazo womhlaba jikelele wokuvimba i-SARS-CoV-2 eguquguquka ngokushesha, uvivinyo oluhlolayo lokutheleleka nge-SARS-CoV-2 luselokhu luyinselelo, ikakhulu emazweni anemiholo ephansi kuya kwephakathi nendawo (low-middle income countries - MICs) ngenxa yesizinda senhlalomnotho ephansi. Ngokuxakayo-ke, ngenxa yokunganakwa kokutheleleka okungenazimpawu, ikakhulu ama-LMIC anezinsiza zokuhlolela i-SARSCoV-2, igciwane liyanda buthule emiphakathini, futhi iningi lalaba bantu lingase libe nomthelela yokuvembuka kabusha kokuthelelana nge-SARSCoV-2. Lolu cwaningo lwaluhlose ukuthola imbangela nokusabalala kwezifo i-epidemiology nezinye izindlela zokuhlola i-SARSCoV-2 esimeni sokwesweleka kwezinsiza. Izindlela: Kwasetshenziswa isampula eliphelele lamasampula eziguli ezisilele eziyi-1332 avela emalaborethri akwaGlobal Health Innovation (GHI) ngokocwaningo lwe-ephidemiyoloji nokuqhathaniswa kwezindlela. Imiphumela nengxoxo: Imibhalo eyabuyekezwa yakhombisa ukuthi amazwe anemiholo ephezulu (high income countries - HICs) ahlolela ukutheleleka kwe-SARS-CoV-2 kaningana ngokwebanga eliyi-113% kuya kweliyi-146% ngaphezu kwama-LMICs (1% kuya kuma-43%). Lolu cwaningo lwakhombisa isibalo esiphezulu lotho olungenazimpawu (68%) phakathi kweziguli ezitheleleke nge-SARS-CoV-2. Mayelana nezindlela zoqhathaniso lokuhlolwa kwe-SARS-CoV-2, izindlela ezahlukile ezihloliwe zokukhishwa kokuthathu (Lucigen QuickExtract™ RNA Extraction Kit, Bosphore EX-Tract Dry Swab RNA Solution, nendlela iSonicator) nezinsiza ze-assayi i-SARS-CoV-2 RT-PCR (Nucleic Acid COVID-19 Test Kit (SARS-CoV-2), abTESTM COVID-19 qPCR I Kit, PCL COVID19 Speedy RT-PCR Kit, ne-PCLMD nCoV OneStep RT-PCR Kit)] okwatholwa kushibhile futhi kushesha. Isiphetho: Ngokuqaphelekayo ama-LMIC akuhlolela kancane ukutheleleka nge-SARS-CoV-2 uma kuqhathaniswa nama-HIC, futhi kwakunesibalo esiphezulu sotho olungenazimpawu phakathi kweziguli ezitheleleke nge-SARS-CoV-2 eSouth Africa. Lolu cwaningo lukhomba ukuthi ukusebenzisa izindlela ezibalwe ngenhla ezishibhile, ezisheshayo, futhi ezinembayo nezihloliwe futhi ezingezinye izindlela zokuhlola isisindo se-SARS-CoV-2 engukuhlola okwejwayelekile emalabhorethri anezinsiza ezingeziningi kungasiza ekukhuliseni ukukwazi ukuhlola kokutheleleka nge-SARS-CoV-2 ema-LMIC. Lokhu kuchaza ukuthi uma kungashesha ukulawulwa kokutheleleka nge-SARS-CoV-2 nezinyathelo zokuvikeleka kungenziwa ukunciphisa ukuthelelana emphakathini.
Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor.
(United States National Academy of Sciences., 2015) Gornalusse, German G.; Mummidi, Srinivas.; Gaitan, Alvaro A.; Jimenez, Fabio.; Ramsuran, Veron.; Picton, Anabela.; Rogers, Kristen.; Manoharan, Muthu Saravanan.; Avadhanam, Nymisha.; Murthy, Krishna K.; Martinez, Hernan.; Murillo, Angela Molano.; Chykarenko, Zoya A.; Hutt, Richard.; Daskalakis, Demetre.; Shostakovich-Koretskaya, Ludmila.; Abdool Karim, Salim Safurdeen.; Martin, Jeffrey N.; Deeks, Steven G.; Hecht, Frederick M.; Sinclair, Elizabeth.; Clark, Robert A.; Okulicz, Jason.; Valentine, Fred T.; Martinson, Neil.; Tiemessen, Caroline Tanya.; Ndung'u, Peter Thumbi.; Hunt, Peter W.; He, Weijing.; Ahuja, Sunil K.
Abstract available in pdf.
Genetic/epigenetic determinants in chemokines and chemokine receptor genes that influence HIV susceptibility in a cohort of high-risk women from South Africa.
(2010) Ramsuran, Veron.; Ndung'u, Peter Thumbi.; Ahuja, Sunil K.; Kormuth, Emil.
No abstract available.
Genotypic and phenotypic analysis of Neisseria gonorrhoeae for the identification of resistance to various antibiotics in pregnant women attending antenatal care at the King Edward VIII Hospital in Durban, KwaZulu-Natal, South Africa.
(2021) Oree, Glynis.; Abbai, Nathlee Samantha.; Ramsuran, Veron.
Introduction: Worldwide antimicrobial resistance (AMR) is making the clinical management of sexually transmitted infections (STIs) increasingly challenging with a particular emphasis on the emergence of antibiotic resistant strains of Neisseria gonorrhoeae (N. gonorrhoeae). In the current study, the detection and emerging patterns of drug resistant clinical isolates of N. gonorrhoeae to previous and current antibiotics to treat cervicitis pathogens as per syndromic management guidelines was investigated. Methodology: This cross-sectional study was conducted at King Edward VIII Hospital and included 307 antenatal attendees. Two endocervical swabs were collected from each enrolled woman. Each enrolled women also provided data on socio-demographic, behavioural and clinical factors. The first swab was placed in Amies Charcoal media immediately after collection. This swab was used to confirm the identification of N. gonorrhoeae clinical isolates using culture based assays. Culture confirmed isolates were grown in Mueller Hinton Broth and were each adjusted to have a bacterial suspension turbidity of a 0.5 McFarland Standard. These isolates were then subjected to antibiotic susceptibility testing to ceftriaxone, tetracycline, spectinomycin, azithromycin, ciprofloxacin, penicillin G and cefixime using the Etest™ method. The second swab was processed for molecular based assays. Extracted DNA from the second swab was subjected to the TaqMan quantitative Polymerase Chain Reaction (qPCR) assay, an in-house 16S ribosomal RNA (rRNA) PCR and PCR detection of the opacity (opa) gene. DNA extracted from the endocervical swabs and cultured isolates were used for the detection of specific targets (genes/plasmids/mutations) associated with resistance to penicillin, tetracycline, ciprofloxacin, spectinomycin, cefixime, azithromycin and ceftriaxone. All statistical analysis performed in this study was conducted in RS Studio. Results: The prevalence of N. gonorrhoeae was 7.8% (24/307) when detected by the TaqMan qPCR assay and 1.9% (6/307) by culture. When compared to culture, PCR for the opa gene and PCR for the 16S rRNA, the TaqMan qPCR assay was a more superior assay demonstrating a diagnostic accuracy of 94.5%. Susceptibility testing of the six isolates obtained after culturing showed resistant phenotypes for penicillin G (12 - 64 mg/L), tetracycline (1.9 - 32 mg/L) and ciprofloxacin (1.16 - 3 mg/L). Isolates displayed either dual or triple resistance to these 3 antibiotics. However, all isolates showed susceptibility to spectinomycin (>64mg/L), azithromycin (1mg/L), ceftriaxone (>0.125 mg/L) and cefixime (>0.125 mg/L). This study also detected the resistance determinants associated with penicillin, tetracycline, ciprofloxacin, spectinomycin, cefixime, ceftriaxone and azithromycin from the molecular level using the primary endocervical swab sample. Gene mutations and plasmids associated with resistance to tetracycline (tetM gene carried on a plasmid), penicillin G (penicillinase producing plasmid) and ciprofloxacin (Ser-91 mutation) were detected confirming the results obtained with the susceptibility assays. Resistance mutations associated with the remaining antibiotics were not detected. There was a 100% correlation of cultured isolates and endocervical swabs for detecting the specific AMR determinants conferring resistance to tetracycline, penicillin G, and ciprofloxacin. Conclusion: The TaqMan qPCR assay has the ability to serve as a future diagnostic assay for the detection of N. gonorrhoeae. Despite the lack of resistance to spectinomycin, cephalosporins and azithromycin in our study population, continuous surveillance for emerging patterns of resistance to these antibiotics is still required since they form part of the current South African treatment guidelines. The detection of resistance determinants from the molecular level without the need for culture may prove to be more feasible for future epidemiological investigations focused on tracking antimicrobial susceptibility or resistance patterns in N. gonorrhoeae.
Identifying novel transcriptional regulatory elements of HLA-A alleles through the evaluation of the 5’ un-translated region sequences.
(2020) Singh, Saiyuri.; Ramsuran, Veron.
Sub-Saharan Africa holds approximately half the population living with human immunodeficiency virus (HIV) in the world (~19.6 million), of which around 7.2 million cases are found in South Africa. Although antiretroviral therapy can suppress viral loads to below detectable levels in most cases, drug resistance is a growing problem. Therefore, identifying novel treatment strategies are warranted against HIV. The strongest human genetic associations with HIV disease have been found within the human leukocyte antigen (HLA) region. The expression levels of various HLA genes have been associated with HIV disease outcomes. Increased HLA-A mRNA expression results in poor HIV outcomes due to the inhibition of natural killer (NK) cells since high mRNA expression of HLA-A results in high protein expression of HLA-E which serves as an inhibitory receptor for NK cells. Identifying factors that regulate the expression of HLA-A has the potential to serve as an avenue for HIV drug target sites. DNA methylation has previously been identified as one of the factors responsible for HLA-A expression regulation. In this study, we aimed to identify additional regulatory mechanisms for the HLA-A gene. The identification of a putative CCCTC-binding factor (CTCF) binding site upstream of HLA-A suggested that CTCF may play a role in regulation of HLA-A. Sequence alignments about 2 kilobases (2KB) upstream of the transcriptional start site (TSS) were analysed for polymorphisms that associate with HLA-A expression. Six HLA-A promoter variants (rs9260084, rs9260086, rs9260092, rs9260101, rs9260116 and rs41560714) were observed to significantly associate with HLA-A mRNA expression. However, only one single nucleotide polymorphism (SNP), rs9260084 (-993G>A), was predicted to disrupt a CTCF binding site. Despite the predicted disrupted binding site, using a chromatin immunoprecipitation (ChIP) assay, we did not detect any difference in CTCF binding across the -993 G>A variants. Additional transcriptional regulators, Nuclear Factor 1 (NF1), Ras related protein (RAP1) and glucocorticoid receptor (GR), were predicted to have differential binding to -993G>A, -226G>A and -885C>G, respectively. The results provided here serve as a basis for further studies exploring the role HLA-A promoter variants have in regulating HLA-A expression. These variants may serve as potential target sites for future therapeutic intervention against HIV.
Influence of variations in CCL3L1 and CCR5 on tuberculosis in a northwestern Colombian population.
(Oxford University Press on behalf of The Infectious Diseases Society of America., 2010) Mamtani, Manju.; Mummidi, Srinivas.; Ramsuran, Veron.; Pham, Minh-Hieu.; Maldonado, Robert.; Begum, Kazi.; Valera, Maria Soledad.; Sanchez, Racquel.; Castiblanco, John.; Kulkarni, Hemant.; Ndung'u, Peter Thumbi.; He, Weijing.; Anaya, Juan Manuel.; Ahuja, Sunil K.
We investigated the association of polymorphisms in CCR5, the major human immunodeficiency virus (HIV)–1 coreceptor, and copy number of its potent ligand CCL3L1 with tuberculosis in 298 individuals from Colombia. The CCR5-HHD haplotype, a known genetic determinant of increased susceptibility to HIV-AIDS, and a high copy number of CCL3L1, a known genetic determinant of enhanced CCL3/CCL3L1 chemokine expression, each associated with presence of tuberculosis. Furthermore, CCR5-HHD was associated with higher CCR5 gene and surface expression. These results substantiate the strong link between the pro-inflammatory effects of CCR5 and its ligands with active tuberculosis and suggest that chemokine-chemokine receptor genetic determinants may influence tuberculosis in addition to HIV/AIDS.
Measuring HLA-B allele expression across differential cell types.
(2018) Ramphal, Upasana.; Ramsuran, Veron.
Background: The human leukocyte antigen (HLA) region has shown to have the strongest disease associations and recent studies have shown that expression levels of these HLA molecules play a major role in the clinical course of diseases. Differences in the expression levels of these molecules have been found to have a major effect on their ability to present specific peptide antigens. HLA molecules are critical to the interaction between diseases and components of the immune system. Expression of such molecules, namely HLA-C and HLA-A, have been shown to associate with HIV disease outcomes. An increase in expression of HLA-C leads to protection against HIV whereas an increase in HLA-A expression leads to rapid HIV progression. Furthermore, studies have shown the region with the strongest genetic effect falls within the HLA-B gene, as determined by genome wide association studies. However, limited information is available for HLA-B allelic expression levels and the variation across differential cell types. Materials and Methods: Allelic expression levels of HLA-B were measured using cryopreserved PBMC samples from HIV negative and positive cohorts with HLA typing. Antibodies specific to the HLA-B protein were identified. The affinity of the antibodies relative to class-I alleles were determined. Based on these affinities, donors with specific alleles were selected for HLA-B cell surface measurement using the flow cytometer. mRNA levels were measured across HLA-A, -B, -C and -E genes within the following cell types T-cells, B-cells, Monocytes and NK cells. These levels and a comparison of HIV infected and uninfected mRNA levels from the same donor were measured using droplet digital PCR (ddPCR). Conclusions: Contrary to HLA-B mRNA expression levels, we find cell surface expression levels vary in an allele-specific manner. We further observed differential mRNA expression patterns for HLA-A, HLA-B, HLA-C and HLA-E across cell types. We also observed no mRNA expression variation across pre- and post- HIV samples. When comparing HLA-B mRNA and surface expression across alleles and donors no significant correlation was found. However, at an donor level, some alleles may be differentially regulated at the cell surface. This study built existing knowledge and fills in some of the gaps in knowledge surrounding HLA-B expression. We also report, for the first-time, variation in allele specific expression, variation in expression across differential cell types and lack of expression variation across pre- and post- HIV infection at the mRNA level. ”