PhD theses : Medical Laboratory Sciencehttps://repository.sustech.edu/handle/123456789/13262024-03-29T13:16:06Z2024-03-29T13:16:06ZMolecular Characterization of Helicobacter pylori Virulence Genes and Antimicrobial Resistance Genes in Gastric Biopsies among Symptomatic Patients, Khartoum State-SudanAli, Maram Mustafa MohammedSupervisor, - Yousif Fadalla HamedelnilCo-Supervisor, - Hisham Nouraldayem Altaybhttps://repository.sustech.edu/handle/123456789/277642022-11-09T06:55:57Z2022-01-01T00:00:00ZMolecular Characterization of Helicobacter pylori Virulence Genes and Antimicrobial Resistance Genes in Gastric Biopsies among Symptomatic Patients, Khartoum State-Sudan
Ali, Maram Mustafa Mohammed; Supervisor, - Yousif Fadalla Hamedelnil; Co-Supervisor, - Hisham Nouraldayem Altayb
Helicobacter pylori is a gastrointestinal bacterium that causes peptic ulcer and stomach cancer in about half of the world's population. The outcome of H. pylori-related disorders is influenced by many virulence factors. Clarithromycin- resistant H. pylori strains represent a worldwide health problem. This is descriptive cross sectional study aimed to detect the frequency of H. pylori, the virulence factors of H. pylori, and clarithromycin resistant associated mutations in Sudanese patients with gastritis symptoms. Also to study molecular characterization of H. pylori virulence genes and antimicrobial resistance genes by PCR and sequencing.
Gastric biopsies were obtained from 384 patients with gastritis symptoms from different hospitals in Khartoum State from December 2018 to January 2021, their ages ranged from 14 to 88 years and mean age of 43 years. Out of them, 209 (54.4%) were males, while 175 (45.6%) were females. All gastric biopsies were subjected to polymerase chain reaction (PCR) to detect H. pylori 16S rRNA gene, virulence genes (cagA, cagE, vacA, iceA1, and dupA), and Clarithromycin resistance genes. Allele-specific PCR and DNA sequencing were used to screen for the presence of A2142G and A2143G point mutations.
From 384 patients, two hundred sixty-nine (70.0%) patients were diagnosed with gastritis which was found to be the most common endoscopic findings, thirty-eight (9.9%) as a gastric ulcer, twenty-eight (7.3%) as a duodenal ulcer, sixteen (4.2%) as esophagitis and thirty-three (8.6%) were of normal mucosa.
H. pylori was detected in 28.4% (109/384) specimens by PCR using specific H. pylori 16S rRNA, there was no significant association between the presence of H. pylori, socio-demographic data (gender, age groups, and geographical distribution), and clinical outcome among study population.
The positive specimens were genotyped using PCR targeting cagA, cagE, vacA, dupA, and iceA1 genes. All of strains were vacA positive 100% (109/109) followed by dupA 44.0% (48/109), cagA 38.5% (42/109), cagE gene 37.6% (41/109), and iceA1 gene was detected in only 18.3% (20/109). The vacA s1/m1 70% (77/109) was the most prevalent vacA subtype. There was no significant difference between the presence of H. pylori virulence genes in regards to gender with different age groups. Although there was no significant association of H. pylori cagA, cagE, iceA1, and vacA s/m status according to endoscopic findings, the dupA gene was significantly associated with the clinical outcome (p. value of 0.016).
Allele-specific PCR detected the variant A2142G in the 9/53 (~ 17%) specimen, while A2143G mutation was not found in any specimen. The DNA sequencing revealed the presence of mutations associated with clarithromycin-resistance in 36% (9/25) of samples; the A2142G was present in one sample, A2143G in 5 samples, and T2182C in 4 samples. Additionally, another point mutation (C2195T) was detected in 3 samples.
The study conclude H. pylori virulence genes were extremely prevalent and diverse among Sudanese gastritis patients. H. pylori dupA gene was associated with the clinical outcome. A high frequency of mutations associated with clarithromycin resistance using DNA sequencing of the 23S rRNA gene’s V domain. This information should be taken into consideration to avoid eradication therapy failure.
Thesis
2022-01-01T00:00:00ZAssociation of Osteopontin, Interleukin10 and Interleukin17 Levels with Liver Function Tests in Sudanese Patients with Rheumatoid ArthritisEltahir, Mohamed AbdelrhmanSupervisor, - Amar Mohamed IsmailCo-Supervisor, - Kawthar Abdelgaleil Mohammedsalihhttps://repository.sustech.edu/handle/123456789/269132021-12-29T11:37:24Z2021-08-09T00:00:00ZAssociation of Osteopontin, Interleukin10 and Interleukin17 Levels with Liver Function Tests in Sudanese Patients with Rheumatoid Arthritis
Eltahir, Mohamed Abdelrhman; Supervisor, - Amar Mohamed Ismail; Co-Supervisor, - Kawthar Abdelgaleil Mohammedsalih
Background: rheumatoid arthritis (RA) is worldwide prevalent autoimmune disease. Associated with abnormal liver functions, and the medications used for RA are often hepatotoxic. Furthermore non treated RA patients also have liver problem. Therefore, this study aimed to investigate the association between pro-inflammatory and anti-inflammatory cytokines and liver function tests in RA patients.
Materials and methods: this is a case-control hospital-based study conducted from December 2017 to August 2020 in Khartoum State in Sudan. Eighty eight Sudanese patients diagnosed with rheumatoid arthritis according to American Criteria for Rheumatology (ACR) at three different hospitals (Alamal, Military and Zain hospitals), patients with age range 28-90 years old were enrolled, 84 of them were women and 4 men. And 88 apparently health control matched (age and sex). Osteopontin (OPN), interleukin17 (IL-17) and interleukin10 (IL-10) were measured using the ELISA technique. Aspartate transaminase (AST), alanine transaminase (ALT), gammaglutamyl transferase (GGT), alkaline phosphatase (ALP), total protein and albumin were estimated using full automation Mindray analyzer. Data were analyzed by using SPSS version 14 and bioinformatics tools.
Results: The frequency of RA was higher among adults aged >41 years 72 (81.8%) than young adults aged ≤41 years 16 (18.2%). RA was more common in women 84 (95.5%) than in men 4 (4.5%) – approximately 21:1-fold. Mean age was (41±11.7) years old. As well as 59 (67%) were anti-CCP positive and other 29 (33%) were negative. There were significant increases in mean level of OPN and IL-10 (38.3±29.6 ng/mL and 45.9±42.9 pg/mL) when compared to control (10.1±10.6 ng/mL and 8.48±7.36 pg/mL), with (p-value 0.000 and p-value 0.000) respectively, while IL-17 exhibited insignificant difference (6.55±1.17 pg/mL), in comparing to control (10.3±8.04 pg/mL); with (p-value 0.123). As well as mean liver enzymes activities (AST, ALT and GGT) were significantly increased in RA patients (16.6±6.98 U/L, 5.62±2.59 U/L and 27.3±23.1 U/L) than control group (7.86±7.86 U/L, 2.76±3.15 U/L and 20.9±13.4 U/L) with (p-value 0.000, p-value 0.000 and p-value 0.026) respectively. Whereas ALP showed insignificant difference (70.6±21.6 U/L) compared to control (66.8±19.6 U/L) with (p-value 0.225). Total protein and albumin were significantly decreased in RA patients (6.68±0.61 g/dL and 3.91±0.40 g/dL), than control group (7.18±0.695 g/dL and 4.22±0.460 g/dL) with (p-value 0.000 and p-value 0.000) respectively. Young adults had higher abnormal IL-10 than adult RA patients (OR = 3.72, p-value 0.044). Abnormal IL-17 (OR = 5.67, p-value 0.034) was found to be increased in young-adult RA patients. No association was observed between age and OPN, and between the duration of disease and IL-10, IL-17, and OPN. Similarly, no association was noted between the types of treatment and IL-10, IL-17, and OPN, nor between IL-10, IL-17, OPN and liver parameters (AST, ALT, ALP, ALB, TP, and GGT).
Conclusion: Liver enzymes are higher in RA patients, while liver proteins are lower than control. RA patients had higher OPN and IL-10. No association are observed between Pro-inflammatory, anti-inflammatory cytokines and liver function parameters in RA patients.
Thesis
2021-08-09T00:00:00ZAssessment of Fat Mass and Obesity-Associated Gene (rs9939609) Single Nucleotide Polymorphism in Susceptibility to Metabolic SyndromeTibin, Khansa Ibrahim MusaSupervisor, - Amar Mohamed IsmailCo-Supervisor, - Mariam Abbas IbrahimCo-Supervisor, - Mai Abdul Rahman Mohammed Masrihttps://repository.sustech.edu/handle/123456789/265792021-09-29T07:33:20Z2021-03-01T00:00:00ZAssessment of Fat Mass and Obesity-Associated Gene (rs9939609) Single Nucleotide Polymorphism in Susceptibility to Metabolic Syndrome
Tibin, Khansa Ibrahim Musa; Supervisor, - Amar Mohamed Ismail; Co-Supervisor, - Mariam Abbas Ibrahim; Co-Supervisor, - Mai Abdul Rahman Mohammed Masri
This study is a case-control hospital-based study conducted from December 2016 to November 2020 in Khartoum State in Sudan.
This study aimed to assessment of fat mass and obesity-associated gene (rs9939609) single nucleotide polymorphism in susceptibility to metabolic syndrome in Sudanese patients.
Two hundred fifteen Sudanese patients diagnosed with metabolic syndrome according to international diabetes federation (IDF) criteria at three different hospitals (Zinam Diabetic Centre, Gaber-Aboeliz, and Rebate Teaching Hospital), age range 37-84 years old. And two hundred fifteen healthy individuals were considered as a control group, age and sex were matched in both groups.
Ethical approval for this study was obtained by Ethical Committee of Ministry of Health, after approving from Scientific Committee of the College of Medical Laboratory Science at Sudan University of Science and Technology, written informed consent was obtained from all study subjects.
Waist circumference, BMI, and blood pressure were measured. Blood samples were analyzed for sd-LDL using the ELISA technique, lipids and fasting blood glucose were measured by Mindray automation, blood genomic DNA was extracted using kits, and genotyped for single nucleotide polymorphisms (rs 9939609) of FTO gene by polymerase chain reaction (PCR-RFLP) analysis. Whole DNA sequencing was done by using HiSeq Macrogen Company (Korea).
Data were computed and analyzed by using SPSS version 21 and bioinformatics tools.
The results of the study showed that there were significantly increased Waist circumference, total cholesterol, triglyceride, LDL-C, fasting blood glucose, Systolic, Diastolic blood pressure, and decreased HDL-C in
patients compared to control with P-value (0.000). An insignificant difference was found in sd-LDL in the case compared to control with P-value (0.209).
The heterozygous and homozygous mutants a risk factor for metabolic syndrome in our population, with P- value (0.000, 0.017) and OR (5.191, 2.297) receptively. The result also showed significantly increased distribution of mutant A allele in metabolic syndrome patients compared to the T allele in healthy individuals.
The FTO (rs9939609) gene polymorphism showed an insignificant association between FTO gene polymorphism and study variable (age, sex, dietary habits, and physical activity), moreover, a significant association was found between the FTO gene and BMI with P-value (0.017), on the other hand, significantly increased total cholesterol and dietary intake in AT/AA Genotypes compared to TT genotype.
Insignificant difference in metabolic syndrome components between males and females except in BMI significantly increased in females compared to males with P-value (0.016).
In conclusion, the FTO (rs 9939609) gene is considered as a risk factor for metabolic syndrome in Sudanese patients.
Thesis
2021-03-01T00:00:00ZGenetic Polymorphisms of Glutathione- S-Transferase and N-Acetyltransferase-2 among Sudanese Patients with Acute Lymphoblastic LeukemiaAli, Amna Elsadig ElsafiSupervisor, - Babiker Ahmed MohamedCo-Supervisor, - Nazik Elmalaika Obaid Seid Ahmedhttps://repository.sustech.edu/handle/123456789/255272020-12-02T09:44:03Z2020-01-01T00:00:00ZGenetic Polymorphisms of Glutathione- S-Transferase and N-Acetyltransferase-2 among Sudanese Patients with Acute Lymphoblastic Leukemia
Ali, Amna Elsadig Elsafi; Supervisor, - Babiker Ahmed Mohamed; Co-Supervisor, - Nazik Elmalaika Obaid Seid Ahmed
Leukaemia represents the second type of the ten top most common cancers in Sudan, and acute lymphoblastic leukaemia (ALL) is the first malignancy of childhood cancer in Sudan. This study aimed to study the genetic plymrphism of N-acetyltransferase-2 (NAT2) {TagG590A (rs1799930), Dde A803 (rs1208), BamH1 G857A (rs1801279) and Kpn1C481T (rs1799929)} and glutathione S-transferases (GSTT1, M1 and P1). And to investigate the haematological picture and to determine the frequency of ALL phenotypes. Has been associated with acute lymphocytic leukemia (ALL) in the different regions of the Sudan. The blood samples are collected from 300, people of whom 150 were patients arriving to Khartoum Oncology Hospital (KOH) and the remaining 150 were healthy matched volunteered controls. Were genotyped for GSTs and NAT2 in the study from 2015 to 2018. Sequence technique to PCR product for 55 (NAT2/547bp) patients and controls samples and also 11(GSTP1) patients samples by Sanger Sequencing (BGI TECH SOLU TIONS (HONGKONG), CO. China). Bioinformatics has done using various publicly available soft ware's (Sift, PolyPhen-2 I Mutant 3.0, and Chimera)the effect of each SNP was predicted.
The mean age of all subjects was 13.6 years. Their sex (63.8%) males and female (36.2%). The incidence of ALL among the adolescent group (7-18 years of age) was slightly higher (41.2%) than that registered among children group (1-6 years) (32.2%) and elderly group (>18 years of age) (22.6%). The majority of ALL patients showed ‘B’ immune- phenotype (75.5%). Afro-Asiatic linguistic ethnic was the most popular group (72%). According to residence, the high frequencies were reported in Khartoum (22%), Kordofan (17%), AL-Jazira and Darfur (~12% each). A significant association between affected tribes and disease frequency at states (P=0.000) was reported. The mean of the complete blood count parameters of ALL patients after treatment (Hb=10±1g/dl, RBC=4±1x106/ml, HCT34±1%, PLT 269± 125x109/L) was signific- antly lower (p =0.00) than that in controls (Hb= 12±1g/dl, RBC=5± 5.2 106 / ml, HCT36±3%, PLT 353±8x109/L) and the other parameters (WBC=19±51x103/ml, MCV=84±12fl, MCH=28±2pg, Blast= 8±21%) was significantly higher (p=0.00) than that in control (WBC=7.6 ±2x103/ml, MCV =81±3fl, MCH=27±1pg, Blast=0.00%). Regarding genetic analysis, the risk of ALL in patients with GSTT1 null genotype was not significant (OR=1.23, 95% CI=0.74 -2.0, P-0.44). The GSTM1 null genotype was significantly higher in the ALL group (79, 60.3 %) compared to controls (52, 39.78%) and increased the risk to ALL by about two folds (OR= 1.72, 95% CI=1.1-2.7, p=0.03). The frequency of GSTP1 genotypes was also significantly different between the two groups (P=0.000). AG, GG and AG+GG genotypes were found to increase the risk of ALL by more than three times (P<0.000) compared to the AA genotype. Allele frequencies were also significantly different (P= 0.001, OR= 1.79, CI= 1.247-2.58). In bioinformatics results for GSTP1, (Ile/Val 105; rs1695) SNP was deleterious and probably damaging by using SIFT and Polphen-2 software, respectively. The protein of GSTP1 changed from isoleucine to valine at codon 105 by the Chimera prediction software.
The NAT2-Tag G590A (rs1799930) genotype was significantly different between the two groups (p=0.01). The AA and AA+AG genotypes were found to increase the risk of ALL by about two folds (P=0.01, 0.03, respectively) compared to the GG genotype. Allele frequencies were also significantly different (P=0.00) between ALL cases and controls. The Dde A803G (rs1208) genotype was significantly different between the two groups (p=0.02). GG genotype was found to increase the risk of ALL by more than two times (p=0.02) compared to the AA genotype. Allele frequencies were also significantly different (OR=1.16, 95% CI=0.77-1.74, P=0.01).The BamH1 G857A (rs1801279) genotype was significantly different between the two groups (p=0.00). The AA and AA+AG genotypes were found to increase the risk of ALL by about three times (P=0.01), compared to the GG genotype. Allele frequencies were also significantly different (P=0.00, OR=1.9, 95% CI= 1.3-2.84). Regarding Kpn1 C481T (rs1799929) genotype and allele frequencies, they were insignificant different between the two groups. The additive model exposed that SNPs with a significant association with ALL were Tag G590A (rs1799930) and BamH1 G857A (rs1801279) (OR=1.5, p=0.01). Sequence analysis (Multiple Alignment) shows changes of nucleotide from C to T at Kpn1 C481T (rs1799929) SNP and from G to A at Tag G590A (rs17 99930) and BamH1G857A (rs1801279). In bioinformatics analysis, the Tag G590A (rs179 9930) and BamH1 G857A(rs1801279)ware predicted as deleterious, probably damaging and decrease protein stability using the Sift, Poly- Phen-2 and I Mutant 3.0 soft wares respectively. Project HOPE showed that the three-dimensional structure of proteins was changed by homology modelling server from arginine (R) to glutamine (Q) at position 197 (rs1799930) and 64 (rs1 80 1279). Regarding the two other SNPs, they have no deleterious effect with the same software. The study concludes that, ALL among Sudanese children shows male predominance, with significant different males in haematological parameters than unaffected children. The more affected age group with ALL is 7-18 years, and B-phenotype represented high-frequency rate. This study indicates that GST (M1 and P1) and NAT2 (Tag (G590A), Dde (A803G) and BamH1 (G857A) mutant genotype exhibit significant association with the risk of developing ALL among Sudanese patients. The Western and Central Sudan recorded the highest rates of ALL. Most of ALL patients are from the Afro-Asiatic ethnic group.
Thesis
2020-01-01T00:00:00Z