Alhusain J. Alzahrani

Simultaneous detection of hepatitis C virus core antigen and antibodies in Saudi drug users using a novel assay

Drug users and particularly, injecting drug users, are at increased risk for infection with hepatitis C virus (HCV). The aims of the study were to simultaneously detect HCV core antigen and specific antibodies in sera from Saudi drug users using the new HCV combination assay and to compare this data with HCV core antigen, anti‐HCV antibodies and HCV RNA data from the same patients. A total of 297 patients who are followed up or admitted to a drug rehabilitation hospital over a period of 3 years were included in this study. Samples were analyzed using the new HCV Ag/Ab combination assay (Meurex), HCV core Ag assay, HCV antibodies and with the HCV RNA assay. Out of the 297 samples from Saudi drug users, 111 samples (37.4%) have detectable HCV core Ag, 112 samples (37.7%) have detectable HCV antibodies, 118 have detectable HCV RNA, and 116 samples were positive by the HCV Ag/Ab combination assay (39.1%). Out of the 116 samples, HCV core Ag was detected in 110 samples (94.8%), HCV antibodies were detected in 111 (95.7%) samples and HCV RNA was detected in 114 samples (98.3%). In the control group (n = 305), only 2 (0.66%) blood donor were positive by HCV antibodies assay, HCV RNA assay as well as HCV Ag/Ab combination assay. The new HCV Ag/Ab combination assay may well improve the overall quality of diagnosis of HCV infection especially in high risk population such as drug users that necessitates rigorous testing. J. Med. Virol. 80:603–606, 2008.

Morphology and antifungal effect of nano-ZnO and nano-Pd-doped nano-ZnO against Aspergillus and Candida

The present work was aimed to study the activity of nano-particulated ZnO and nano Pd doped nano-ZnO against Aspergillus and Candida species, commonly contaminating the water supply systems. Micro-ZnO was purchased from the market (Aldrich, USA) while nano ZnO were synthesized using sole gel and precipitation methods and their morphology was determined using XRD and TEM techniques. The average grain size of nano-ZnO estimated by these techniques was 30 nm and 20 nm, respectively. The doping of nano-ZnO with 5 % Pd was achieved by a thermal decomposition method and its morphology; as characterized by XRD, TEM and FESEM techniques; gave an average grain size of 35 nm. Serial dilutions of nano-ZnO doped with 5 % Pd, pure nano-ZnO and micro-ZnO (as a control) were prepared from 10 mg/mL stock solution of each in dermasel agar (OXOID), inoculated with standard strains of Candida albicans and Aspergillus niger and incubated at 37°C for 24 and 48 hours, respectively. Their antimicrobial effect was compared by the minimal inhibitory concentration (MIC), determined as the dilution giving a negligible growth of microorganism. Nano-ZnO doped with 5 % nano-Pd, pure nano-ZnO and micro-ZnO, showed antifungal activity against Aspergilus niger with an MIC of 1.25, 2.5 and 5mg/mL, respectively. However, Candida albicans yeasts were relatively resistant to these compounds, with an MIC of 2.5, 5 and 10 mg/mL for Pd doped nano-ZnO, nano-ZnO and micro-ZnO, respectively. Thus nano-ZnO was twice as potent in killing Aspergillus, as compared to its non-nano-counterpart and loading of nano-ZnO with 5 % nano-Pd further increased its activity, four times that of micro-ZnO. Further investigations are needed to confirm the potential use of nano-ZnO and its doping with nano-Pd in the treatment of water supply systems and food preservation.

Molecular detection of hepatitis B, hepatitis C, and torque teno viruses in drug users in Saudi Arabia.

Injecting drug users are at increased risk of infection with hepatitis viruses and blood‐borne pathogens. The aim of this study was to examine HBV, HCV, HDV, and TTV infections in Saudi drug users (N = 344). Extraction of nucleic acid from serum, reverse‐transcription, amplification of viral nucleic acids, and HBV and HCV genotyping were done using established techniques. Of the analyzed samples, 41 (12%) contained detectable HBV DNA, 131 (38%) contained detectable HCV RNA, and 174 (51%) had detectable TTV DNA. The predominant HBV genotype was found to be genotype D and the predominant HCV genotype was found to be genotype 1b. All the samples were negative for HDV. Twelve samples (3.5%) were found to contain mixed HBV and HCV genomes, 24 samples (7%) were found to contain mixed HBV and TTV genomes, 82 samples (24%) were found to contain mixed HCV and TTV genomes, and 9 samples (2.6%) were found to contain mixed HBV, HCV, and TTV genomes. Identification of various infections in drug users will help the control of these infections in this group as well as in the community. J. Med. Virol. 81:1343–1347, 2009.

Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

BackgroundIn addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation.MethodsWe describe here the design and implementation of a customized genome-wide genotyping array, the ‘TxArray’, comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios.ResultsWe show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms.ConclusionsWe have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

Detection of extended spectrum beta-lactamases-producing isolates and effect of AmpC overlapping.

INTRODUCTION Few reports about the prevalence and genetic basis of extended spectrum beta-lactamases (ESBLs) are available from Saudi Arabia. We sought to determine the prevalence of ESBL-producing Enterobacteriaceae in a university hospital in eastern Saudi Arabia and to characterize the ESBLs produced by these isolates at the molecular level. METHODOLOGY All clinical isolates of Escherichia coli, Klebsiella spp., and Proteus spp. collected over two years were evaluated for susceptibility to a panel of antimicrobials and were analyzed for the ESBL phenotype using screening and confirmatory tests. ESBL-positive isolates were then screened for the presence of genes encoding CTX-M, SHV, and TEM beta-lactamases by PCR. RESULTS AND CONCLUSIONS The overall prevalence of ESBL-producing isolates was 4.8% (253/5256). Most isolates (80%) were from the inpatient department. The ESBL phenotype was more frequently detected in K. pneumonia. CTX-M genes were the most prevalent ESBL genes, detected in 82% of the studied isolates. The ESBL producers demonstrated a high multidrug resistance rate (96.6%). In transconjugation assay, the same ESBL gene pattern was transmitted from 29.7% of K. pneumoniae donors to the recipient strain, and the latter exhibited concomitant decreased aminoglycosides and co-trimoxazole susceptibility. We observed the presence of ESBL screen-positive but confirmatory-negative isolates (8.9%). Phenotypic tests for the production of AmpC β-lactamase tested positive in 52% of these isolates. Further studies are needed for appropriate detection of concomitant ESBL and AmpC enzyme production among such isolates. Continued surveillance and judicious antibiotic usage together with the implementation of efficient infection control measures are absolutely required.

The anticancer gene ORCTL3 targets stearoyl-CoA desaturase-1 for tumour-specific apoptosis

ORCTL3 is a member of a group of genes, the so-called anticancer genes, that cause tumour-specific cell death. We show that this activity is triggered in isogenic renal cells upon their transformation independently of the cells’ proliferation status. For its cell death effect ORCTL3 targets the enzyme stearoyl-CoA desaturase-1 (SCD1) in fatty acid metabolism. This is caused by transmembrane domains 3 and 4, which are more efficacious in vitro than a low molecular weight drug against SCD1, and critically depend on their expression level. SCD1 is found upregulated upon renal cell transformation indicating that its activity, while not impacting proliferation, represents a critical bottleneck for tumourigenesis. An adenovirus expressing ORCTL3 leads to growth inhibition of renal tumours in vivo and to substantial destruction of patients’ kidney tumour cells ex vivo. Our results indicate fatty acid metabolism as a target for tumour-specific apoptosis in renal tumours and suggest ORCTL3 as a means to accomplish this.

Existence of HbF Enhancer Haplotypes at HBS1L-MYB Intergenic Region in Transfusion-Dependent Saudi β-Thalassemia Patients

Background and Objectives. β-Thalassemia and sickle cell disease are genetic disorders characterized by reduced and abnormal β-globin chain production, respectively. The elevation of fetal hemoglobin (HbF) can ameliorate the severity of these disorders. In sickle cell disease patients, the HbF level elevation is associated with three quantitative trait loci (QTLs), BCL11A, HBG2 promoter, and HBS1L-MYB intergenic region. This study elucidates the existence of the variants in these three QTLs to determine their association with HbF levels of transfusion-dependent Saudi β-thalassemia patients. Materials and Methods. A total of 174 transfusion-dependent β-thalassemia patients and 164 healthy controls from Eastern Province of Saudi Arabia were genotyped for fourteen single nucleotide polymorphisms (SNPs) from the three QTL regions using TaqMan assay on real-time PCR. Results. Genotype analysis revealed that six alleles of HBS1L-MYB QTL (rs9376090C p = 0.0009, rs9399137C p = 0.008, rs4895441G p = 0.004, rs9389269C p = 0.008, rs9402686A p = 0.008, and rs9494142C p = 0.002) were predominantly associated with β-thalassemia. In addition, haplotype analysis revealed that haplotypes of HBS1L-MYB (GCCGCAC p = 0.022) and HBG2 (GTT p = 0.009) were also predominantly associated with β-thalassemia. Furthermore, the HBS1L-MYB region also exhibited association with the high HbF cohort. Conclusion. The stimulation of HbF gene expression may provide alternative therapies for the amelioration of the disease severity of β-thalassemia.

Exome-Wide Association Analysis of Coronary Artery Disease in the Kingdom of Saudi Arabia Population.

Coronary Artery Disease (CAD) remains the leading cause of mortality worldwide. Mortality rates associated with CAD have shown an exceptional increase particularly in fast developing economies like the Kingdom of Saudi Arabia (KSA). Over the past twenty years, CAD has become the leading cause of death in KSA and has reached epidemic proportions. This rise is undoubtedly caused by fast urbanization that is associated with a life-style that promotes CAD. However, the question remains whether genetics play a significant role and whether genetic susceptibility is increased in KSA compared to the well-studied Western European populations. Therefore, we performed an Exome-wide association study (EWAS) in 832 patients and 1,076 controls of Saudi Arabian origin to test whether population specific, strong genetic risk factors for CAD exist, or whether the polygenic risk score for known genetic risk factors for CAD, lipids, and Type 2 Diabetes show evidence for an enriched genetic burden. Our results do not show significant associations for a single genetic locus. However, the heritability estimate for CAD for this population was high (h2 = 0.53, S.E. = 0.1, p = 4e-12) and we observed a significant association of the polygenic risk score for CAD that demonstrates that the population of KSA, at least in part, shares the genetic risk associated to CAD in Western populations.

A prospective evaluation of synergistic effect of sulbactam and tazobactam combination with meropenem or colistin against multidrug resistant Acinetobacter baumannii

The present study evaluates the synergistic effect of sulbactam/tazobactam in combination with meropenem or colistin against multidrug resistant (MDR) Acinetobacter baumannii isolated from hospitalized patients from a tertiary care hospital in Saudi Arabia. During the study period, 54 multidrug and carbapenem-resistant isolates of A. baumannii isolates were collected from blood and respiratory samples of patients with ventilator-associated pneumonia or bacteremia. Microbroth checkerboard assay (CBA) and E-test were performed to look for synergistic interface of sulbactam and tazobactam with meropenem or colistin. All 54 MDR isolates of A. baumannii were resistant to carbapenem. Minimum inhibitory concentration [50/90] value against sulbactam, tazobactam, meropenem, colistin was found to be 64/128, 64/128, 64/256, and 0.5/1.0 respectively. Synergy was detected in more isolates with CBA compared to E-test. All four combinations showed significant synergistic bactericidal activity. However, the combination with colistin showed greater synergistic effect than combination with meropenem. Antagonism was not detected with any of the combinations and any method, but indifference was seen in tazobactam and colistin combination alone. A significant bactericidal effect was seen with sulbactam combination with meropenem or colistin in both methods. A combination therapy can be a choice of treatment. As colistin is known to exhibit nephrotoxicity, the combination of sulbactam and meropenem might be considered as an alternative antibiotic treatment for such multi- and extremely resistant bacteria. Yet, sample size is small in our study, so further well-designed in vitro and clinical studies on large scale should confirm our findings.

Clinical description of human bocavirus viremia in children with LRTI, Eastern Province, Saudi Arabia

Human bocavirus (HBoV) is a major etiology of lower respiratory tract infection (LRTI) in young children. We tested 149 patients admitted to King Fahd Hospital of the University with diagnosis of LRTI. Viremia caused by the different studied viruses was detected in 31.5% of the total cases by Real-time Polymerase chain reaction. We report five patients who were positive for HBoV in serum samples. Clinical presentation ranged from mild to severe disease as one of them required admission to intensive care unit. Wheezing was a striking feature in most of our patients, but fever was not a consistent finding.