Digital Repository for Department of Biochemistry and Molecular Biology

The detection of somatic mutations in tumours is essential for the understanding of cancer development and targeting therapy. The screening for BRAF V600E mutation is employed in clinical practice in Libya for its prognostic and potentially predictive role in patients with metastatic colorectal carcinoma (mCRC). Using of BRAF mutant DNA and wild type DNA targets, we found that the sensitivity of allelic discrimination-Real Time PCR was applicable. The Real Time PCR assay displayed increased analytical sensitivity in detecting the BRAF V600E mutation. The association of BRAF mutations with clinical and pathological features was assessed using Real Time PCR assay. Qiagen Real Time PCR Platform was utilised using a set of primers. forward 5-GAC. CTC. ACA. GTA. AAA. ATA. GGT. G 3, reverse 5-TCC. AGA. CAA. CTG. TTC. AAA. CTG. A. 3. Our study indicates that Real Time PCR-based assays is convenient to detect the BRAF V600E mutation in CRC and that BRAF mutations screening should not be restricted to selected patients on the basis of the clinicalpathological characteristics. arabic 9 English 63
Abdul M Gbaj, Abdulla Bashein(1-2018)

Acinetobacter baumannii is an opportunistic pathogen causing various nosocomial infections. The aim of this study was to characterize the molecular support of carbapenem-resistant A. baumannii clinical isolates recovered from four hospitals in Tripoli, Libya. Bacterial isolates were identified and antibiotic susceptibility testing was per-formed using automated system. Carbapenem resistance determinants were studied phenotypically using two dif-ferent techniques: E-test; chromogenic culture media. Polymerase chain reaction (PCR) amplification was used to determine the presence of bla OXA23 and blaOXA51 genes among isolates. A total of 119 isolates were characterized, overall the resistance prevalence was extremely high for aminoglycosides (79-96.6%), fluoroquinolones (94-96%), cephalosporins (96.6-100%) and carbapenemes (93.2-100%), all isolates were susceptible to colistin. In addition, 97.5% of isolates were identified as multidrug resistance (MDR). Varying degree of phenotypic detection of car-bapenemes was determined; highest levels of carbapenemes were detected using chromogenic media (76.5%) com-pared with E-test (45.4 %). The carbapenem resistance-encoding genes detected were blaOXA23 (84%) and blaOXA51 (73.1%); the highest occurrence of blaOXA23 was demonstrated in Tripoli’s Central Hospital (5/5; 100%) then in Tripoli Medical Center (44/51; 86.27%). The co-occurrence of these genes was demonstrated in (75/119; 63%) showing dissemination of carbapenemes resistance MDR A. baumannii in hospitals. This study shows that the high prevalence of OXA-23 contribute to antibiotic resistance in … arabic 14 English 113
Nada Elgrew, Abdulla Bashein(1-2016)

Background: Phenylketonuria (PKU) is one of the most common inborn errors of amino acids metabolism. It is an autosomal recessive disease that is caused by mutations in phenylalanine hydroxylase (PAH) gene. In the North Africa and Eastern Mediterranean region, E280K missense mutation and c.1055del.G frameshift mutation in PAH gene are one of the most common pathogenic mutations seen in PKU patients. Materials and Methods: In this study, we developed molecular protocols for rapid screening of the PKU patients for these two mutations. These protocols are based on hydrolysis probe real-time polymerase chain reaction technique using allele-specific probes labeled with 6-carboxyfluorescein (FAM) for wild-type (WT) and hexachloro-6-carboxyfluorescein (HEX) for mutant genotypes and Black Hole Quencher 1 as a quencher and high-resolution melting analysis using EvaGreen saturating dye. Results: There was complete accordance between the developed protocols in differentiating genotypes and they proved to be rapid, sensitive, and efficient for the detection and differentiation between WT, mutant, and heterozygous genotypes of the E280K and c.1055del.G mutations. Conclusions: These protocols allow easy molecular screening of the mutations studied among the families of affected people, especially for premarital screening. arabic 27 English 170
Abdulla Bashein(1-2017)

Abstract Introduction: Extended-spectrum β-lactamases (ESBLs), AmpC type, carbapenem resistant Enterobacteriaceae (CRE), are important mechanisms of resistance among Enterobacteriaceae. The aim of this study was to investigate the prevalence of ESBL, AmpC and CRE among Enterobacteriaceae isolates recovered from pediatric patients in Tripoli, Libya. Methods: This cross-sectional study was carried out in Tripoli Children Hospital (TCH), a total of 915 Gram negative bacteria isolates were evaluated for susceptibility to a panel of antimicrobials and were analyzed phenotypically for the ESBL, AmpC type and CRE using chromagen media, E-test and combination disc test. Results: The predominant organisms were Escherichia coli (56.8%) and Klebsiella spp. (21.4%). The overall prevalence of ESBL producing Enterobacteriaceae was 24.5% (224/915). Out of 224, Enterobacteriaceae proved ESBL producer, Klebsiella spp. (54%) and E. coli (34.4%) were the leading ESBL producers. ESBL-producers were more often resistant to major classes of antibiotics compared with non-ESBL producers, significantly high resistance rates (P < 0.001) were observed for ceftriaxone, cefepime, and ceftazidime (87.5 - 95.9%) among ESBL producers compared to non-ESBL producers (7.2 - 13.5%). MDR was documented for 50/224 (22.3%) of ESBL producers and was significantly higher (P < 0.0001) among ESBLs compared with non-ESBL producer isolates. Phenotypic detection of AmpC revealed 60/915 (6.6%) isolates as potential AmpC β-lactamase producers, E. coli exhibited a lower level of AmpC (8.3%) compared with Klebsiella spp. (56.6%). The overall prevalence of CRE was 9% (83/915). Carbapenemase-producing organisms in this study were as follows: Klebsiella spp. (44.6%); Acinetobacter spp. (24%); Pseudomonas spp. (9.6%). Conclusion: This study revealed that the prevalence of ESBL, AmpC, CRE and MDR Enterobacteriaceae isolates in Children hospital was within acceptable frequency. arabic 11 English 91
Abdulaziz Zorgani, Abdulla Bashein, (1-2017)

Objectives Multidrug resistance (MDR) and emergence of extended-spectrum β-lactamases (ESBLs) among uropathogenic Escherichia coli have been reported worldwide, but there was no information on the detection of blaCTX-M-15 in major teaching hospitals in Libya. The aim of the study was to investigate the occurrence of CTX-M-15 β-lactamases producers isolated from five teaching hospitals in Tripoli, Libya. Methods A total of 346 urine samples were collected from hospitalized patients in five teaching hospitals with a diagnosis of urinary tract infection (UTI). Phenotypic confirmation of ESBLs was confirmed by E-test strip; all ESBL-producing E. coli isolates were screened for the blaCTX-M-15 gene. Results The distribution of ESBL-producing E. coli varied among the five hospitals. The highest proportion was identified in Tripoli Medical Centre (67.6%). There were extremely high proportions of isolates resistant to ceftriaxone, cefepime, and ceftazidime (93.0–100.0%) among ESBL producers compared to non-ESBL producers (2.2–4.7%). MDR was detected in 22.2% of isolates. The majority of isolates (85.9%) in which blaCTX-M-15 was identified were ESBL producers. There was a correlation (p < 0.001) between expression of CTX-M-15 and resistance to ceftazidime. Conclusions The isolation of MDR ESBL-producing uropathogens expressing the CTX-M-15 gene will limit the choices clinicians have to treat their patients with UTIs. Continued surveillance and implementation of efficient infection control measures are required. arabic 17 English 94
Abdulaziz Zorgani, Abdulla Bashein(1-2017)

Introduction: Extended-spectrum β-lactamases (ESBLs), including the AmpC type, are important mechanisms of resistance among Klebsiella pneumoniae and Escherichia coli isolates. Objective: The aim of the study was to investigate the occurrence of AmpC-type β-lactamase producers isolated from two hospitals in Tripoli, Libya. Methods: All clinical isolates (76 K. pneumoniae and 75 E. coli) collected over two years (2013-2014) were evaluated for susceptibility to a panel of antimicrobials and were analyzed phenotypically for the ESBL and AmpC phenotype using E-test and ESBL and AmpC screen disc test. Both ESBL and AmpC-positive isolates were then screened for the presence of genes encoding plasmid-mediated AmpC β-lactamases by polymerase chain reaction (PCR). Results: Of the K. pneumoniae and E. coli tested, 75% and 16% were resistant to gentamicin, 74% and 1.3% to imipenem, 71% and 12% to cefoxitin, 80% and 12% to cefepime, 69% and 22.6% to ciprofloxacin, respectively. None of the E. coli isolates were multidrug resistant compared with K. pneumoniae (65.8%). K. pneumoniae ESBL producers were significantly higher (85.5%) compared with (17.3%) E. coli isolates (P
Abdulaziz Zorgani, Abdulla Bashein(1-2017)

Despite the relative abundance of sunny weather, surprisingly, there is increasing evidence that vitamin D deficiency is extremely prevalent in females of reproductive age in Middle East countries. There is also increasing interest in the non-classical roles of vitamin in health and disease including its relation to incidence of gestational diabetes, its impact on glycaemic control in diabetes mellitus, and its association with some complications of pregnancy like preeclampsia. The objective of this study was to estimate the prevalence of Vitamin D deficiency in pregnant diabetic patients in west Libya and analyse potential links to socioeconomic and cultural factors. This is a cross sectional observational study. Random plasma was collected form expected mothers attending the Antenatal Diabetes Clinic at Tripoli’s Main Maternity Hospital. Demographics and socioeconomic and cultural factors were recorded at the same time. Samples were analysed for vitamin D level and biochemical screening panel. Vitamin D level was obtained from 160 patients (mean age 35 years). Over all 95 % of the study population had vitamin D levels below normal (defined as vitamin D level of < 20 ng/mL). Results were subcategorised into severe deficiency ( 30 ng/ml, only 1.3%, 2 patients). All patients were taking daily vitamin D Supplements at a dose of 400 IU as per hospital policy. Vitamin D deficiency is extremely prevalent in pregnant diabetic patients in Libya. There is no clear association with socioeconomic risk factors like employment, type of accommodation or geographic distribution. However, most of the study population had life style characterized by minimal exposure to direct sun arabic 11 English 70
G Murad, A Bashein(1-2019)

Background and Aims: Despite the well‑known association between human papillomavirus (HPV) and cervical cancer, yet there are no available data concerning the prevalence of HPV and its type distribution among Libyan women. The aim of this study was to investigate the prevalence of the most common high‑risk HPV types 16 and 18 among Libyan women in Tripoli and to compare it with the cytological findings of the cervix. Methods: A total of 132 cervical samples were collected from women who sought medical attention at the gynecology outpatient clinic of the Tripoli University Hospital and other gynecology private clinics in Tripoli region. Cervical cytological status was classified according to the Bethesda System 2014. Quantitative polymerase chain reaction was used to facilitate the specific detection of HPV types 16 and/or 18. Results: The cytopathological examination showed that 92.4% of women had normal cervical cytology (n = 122/132) and 7.5% (n = 10/132) of them had cervical lesions. The overall prevalence of the most common oncogenic HPV types was 4.5%, as only six samples (n = 6/132) were confirmed of harboring HPV‑DNA. Concerning the cytological status of the cervix, HPV‑DNA was not found (0%) in women with a normal cervix, and it was present in 60% of women with cervical lesions. The high‑risk HPV type 16 was the exclusive type among our all positive samples, with no detection of HPV type 18 among all our recruited subjects. Conclusion: Even though our findings showed a low overall prevalence of high‑risk HPV types among Libyan women, the burden of HPV 16 among women with cervical lesions highlights the need to raise attention toward expanding research about HPV and adopt measures to prevent cervical cancer by vaccination and national screening program. The introduction of HPV‑DNA testing in cervical cancer management will greatly benefit early‑stage HPV detection and help prevent cervical lesions from progression to cancer. arabic 15 English 81
H Alzaquzi, A Bashein(1-2019)