Medical Laboratory science علوم المختبرات الطبية
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- ItemDetection of Carbapenem- Resistant Genes in Klebsiella pneumoniae from Varios Clinical Samples.(Al-Quds University, 2025-08-09) Aseel Khaled Jamal ALSharif; اسيل خالد جمال الشريفBackground: Klebsiella pneumoniae (K. pneumoniae) is a significant cause of hospital-acquired infections. Penicillin, cephalosporins, and carbapenems are the β-lactam antibiotics that most frequently prescribed to treat this type of infection. However, this bacterium has become multidrug-resistant (MDR), and it is clear that rise resistance around the world lead to threaten public health on global scale. Carbapenem is often considered the last effective treatment option for multidrug-resistant gram-negative bacteria. Unfortunately, K. pneumoniae has developed resistance to the last effective beta-lactam antibiotic which is carbapenem. This resistance primarily results from the production of carbapenemases, such as K. pneumoniae Carbapenemase, KPC; Verona Integron Metallo Beta-lactamase, VIM; New Delhi Metallo-β-Lactamase-Mediated Carbapenem, NDM; and Oxacillin-Hydrolyzing Carbapenemases, OXA-48, which can be acquired in both hospital and community settings. Aims: K. pneumoniae strains resistant to carbapenem (CR-Kp) are major health care-associated pathogens found globally. This study aimed to reveal the antibiotic resistance of clinical CR-Kp isolates and to find out whether carbapenemase genes, such as bla KPC, bla VIM, bla NDM, and bla OXA-48, are present, using multiplex PCR techniques. Methodology: A total of 100 bacterial isolates were collected from Prince Alia Governmental Hospital in Hebron, Palestine. The isolates were identified as K. pneumoniae based on their colony morphology and subsequently confirmed using the VITEK 2 Compact system. Antibiotic susceptibility testing (AST) was determined using the same system. The ESBL was conducted by the double disk synergy test (DDTS). The screening for carbapenem resistance was carried out using meropenem (MEM) disks, followed by multiplex PCR to detect the presence of the carbapenemase genes bla KPC, bla VIM, bla NDM, and bla OXA-48 Result: Out of the 100 K. pneumoniae isolates included in this study, analysis indicated that 77 of the isolates (77%) showed extended-spectrum beta-lactamase (ESBL). Out of 100 isolates 35 representing (35%) were carbapenem resistant (CR). All of the 35 isolates were tested for the presence of carbapenemase genes. The results for the genes of carbapenemase were as follows: The bla OXA-48 gene was found in 32 of the 35 samples (91.4%); the bla NDM gene was in 29 of the 35 samples (82.8%); and the bla KPC gene was in 2 of the 35 samples (5.7%). However, the bla VIM gene was not found in any of the samples (0.0%). The co-occurrence of both bla NDM and bla OXA was observed in 26 out of 30 samples (74%). Conversely, the co-occurrence of bla KPC and bla OXA was found in only one isolate (28%). Additionally, fifteen isolates that tested positive for extended-spectrum beta-lactamases (ESBL) but were sensitive to the meropenem (MEM) disk (carbapenem sensitive) were randomly chosen to be checked for carbapenemase genes. Out of the 15 isolates, blaVIM was found in 7 out of 15 samples (46.6%); while the bla OXA-48 gene was found in 4 out of 15 samples (26.6%). In contrast, the bla NDM gene was detected in only one sample (6.7%). Conversely, the co-occurrence of bla VIM and bla OXA was found in 4 out of 15 samples (26.6%). Conclusion: The study findings clearly indicated that the rate of carbapenem-resistant Enterobacteriaceae (CRE) produced by K. pneumoniae isolates was high, making it a significant cause of healthcare-associated infections. Resistance to carbapenems is not limited to carbapenem-resistant isolates; some strains exhibiting this resistance can also be found among extended-spectrum beta-lactamase (ESBL) isolates. To ensure effective treatment, it is important to keep track of the local molecular epidemiology of CRE-resistant genes, and/or another reliable assay. Keywords: K.pneumoniae, Carbapenemases gene, multiplex PCR, Antibiotic susceptibility. blaKPC, blaVIM, blaNDM, and bla OXA-48.
- ItemCytokines Analysis Combined with Machine Learning for Determining the Etiology of Inaccessible Infection(Al-Quds University, 2025-05-10) Amal Mazen Aref Dofesh; امل مازن عارف دوفشAccurate diagnosis of viral and bacterial infections in patients with fever is crucial in clinical diagnosis to ensure appropriate treatment. It requires obtaining a high-quality sample from the patient for laboratory testing. In some cases, obtaining a sample from the patient is difficult, especially in cases of inaccessible infections which may require invasive procedures. Routine laboratory tests, such as complete blood cell (CBC) count, C-reactive protein (CRP), etc. lack the high sensitivity to identify the primary cause of the infection associated with fever. This can lead to misdiagnosis in some cases which can impact patients’ health. The goal of this study is to combine cytokine results with machine learning models to develop a unique diagnostic tool that can separate and differentiate between types of infections. We focused on three cytokine indicators (IP-10, IL-6, and TRAIL) and combined them with advanced machine learning techniques such as Principal Component Analysis, Linear Discriminant Analysis, and Support Vector Machine (SVM). Our study included 268 pediatric patients, 245 of them met the inclusion criteria. Blood samples were drawn from the participants after obtaining ethical approval. 97 samples were selected for testing, based on our capabilities. 22 cases were confirmed as having a bacterial infection in the diagnostic microbiological laboratory, 55 were diagnosed with a viral infection (using PCR), 10 were diagnosed with fever of unknown origin, and 10 were diagnosed with an inaccessible infection. 87 controls participated in the study. Cytokine tests were performed using ELISA technique. We initially found the cut-off values for cytokine measurements, but the cut-off values failed to differentiate between bacterial and viral samples due to the high overlap between the results. This finding prompted us to move from using cytokine biomarkers alone to correlating cytokine values with more advanced techniques. PCA and LDA demonstrated the ability of cytokines to separate different infection groups, achieving success rates of up to 90%. However, when WBC and CRP variables were added to the cytokine biomarkers, our results showed lower success rates, dropping to 65%, and the accuracy of the model was reduced. Despite the high success rates of the PCA and LDA models, our data was abnormally distributed. For this reason, we turned to use a more advanced classification technique based on machine learning algorithms. The results of the three cytokines were integrated with the Support Vector Machine (SVM) technique, showing a sensitivity of 87.5% and a specificity of 73.6%, with an AUC of 0.94 for classifying viral infections from bacterial infections. In conclusion, our study demonstrates that using cytokines combined with machine learning algorithms is a faster, newer, and less painful tool for detecting the cause of infection. Thus, directly treating the patient with the correct treatment, as well as improving clinical diagnosis and reducing the excessive consumption of unnecessary antibiotics, which reduces the spread of antibiotic-resistant strains of bacteria and promote effective antibiotic stewardship.
- Item“Evaluation of antibody titers and serotypes in COVID-19 vaccinated human being”(Al-Quds University, 2025-01-04) Ahmad Ziyad Khalil Abdelkader; أحمد زياد خليل عبد القادرIntroduction: SARS-CoV-2 is a novel coronavirus that emerged in 2019 and is now classified in the genus Coronavirus with closely related SARS-CoV. Due to the high pathogenicity of this virus in humans, It is classified as biosafety level 3 (BSL-3) pathogen, which makes manipulating it relatively difficult due to its infectious nature that killed high number of people. Methods: To assessment immune system and antibodies titer the serum samples collected from 85 hospitalized vaccinated patients against COVID-19 disease or were previously infected patients and from normal non vaccinated negative donors. To evaluation of antibody titers an Enzyme-linked immunosorbent assay (ELISA) technology performed in laboratories, and evaluation the virus infection, and proteins M and S spike proteins of SARS-CoV-2 evaluated and determined for detection of spikebinding neutralizing antibody titers in sera from hospitalized COVID-19 vaccinated patients by using commercial enzyme and ELISA technology. Furthermore, to measure SARS-CoV-2 neutralizing antibodies under BSL conditions, an ELISA for SARS-CoV-2 was developed. Recording the results of laboratory analyzes and saving them in a database using a computer. Result: An analysis and assessment the antibodies titer was conducted and obtain results about the Corona virus, its spread and its effect on people, where the immunological and microbiological results of the people were analyzed and then enter this data as input into the laboratory database, and it was found from this study that there is a clear discrepancy between the data of vaccinated and healthy people, as it appeared that the vaccinated show higher titer than unvaccinated normal individuals. In conclusion, this study aimed to evaluate the long-term effectiveness of COVID-19 vaccination in Palestine people by analyzing they response to the vaccine after two years, based on anti-SARS-CoV-2 protein S and M antibody titer levels. This study demonstrates the importance of knowing the impact of the Corona virus on people, efficacy of vaccines and presence of neutralizing antibodies against Covid19. To evaluate an immune system throw examination by assessment antibody titer and serotypes specially using high specificity and sensitivity ELISA technology to COVID-19 system, which easily can be implemented and performed within a biosafety level laboratory (BSL) for evaluating the occurrence of neutralizing antibodies against SARS-CoV-2 and assessment of both S and M antigens to control and limit the transmission of the COVID 19 in order to find an appropriate treatment for this virus and improve new vaccination in Palestine
- ItemEvaluating Peripheral Blood Smear Testing in Palestine: A Step Towards Quality Assurance and Diagnostic Excellence(Al-Quds University, 2025-05-10) Wisam Abdallah Ahmad Alshalash; وسام عبدالله أحمد الشلشPeripheral blood smear (PBS) test is a critical diagnostic tool in hematology for identifying various blood disorders and malignancies. The absence of a national external quality assurance scheme (EQAS) for PBS testing in Palestine suggests a significant gap in ensuring test quality and standardization. This study aimed to evaluate laboratory technicians’ knowledge and practices regarding PBS preparation, staining, and examination, and evaluate laboratory performance regarding PBS examination, and contribute to the establishment of an EQAS program for PBS testing in Palestine. Methods: A mixed-methods approach was utilized, consisting of two parts: (1) assessment of laboratory technicians' knowledge and practice about PBS test through a structured questionnaire targeting laboratory technicians across Palestine, with a total of 235 participants, and (2) evaluation of laboratory performance in PBS examination using three pre-stained PBS smears distributed to 39 laboratories that performed both PBS preparation and examination, identified through a preliminary screening survey. Participants were evaluated based on Z-scores for inter-laboratory agreement and the coefficient of variation (CV%) for intra- and inter-laboratory precision. Results: Knowledge assessment revealed high performance in smear preparation (92.5%±11.3) but marked deficiencies in staining process (56.7%±21.3), examination methods (60.7%±18.4), and blood cell morphology (64.1%±21.0), with an overall score of 65.9%±14.4. Higher qualifications and active PBS involvement correlated with improved knowledge outcomes. Practical inconsistencies were found in staining process, fixation, drying, and microscope usage. Performance evaluation showed acceptable Z-scores in most parameters (94.3% in WBC counts, 97.1% in lymphocyte differentials, and 100% in platelet counts), yet CV% analysis revealed high intra- and inter-laboratory variability. Morphological agreement with experts was notably low, especially for identifying microcytosis (11.4%), spherocytes (8.6%), and ovalocytes (11.4%). Conclusion: The findings highlight significant deficiencies in laboratory technicians’ knowledge and substantial variability in PBS-related practices and examination of PBS across clinical laboratories in Palestine. These findings highlight the urgent need for standardized protocols, targeted training, and the establishment of a national EQAS program for PBS examination to enhance diagnostic accuracy and ensure consistent testing quality.
- ItemAntibiotic Resistance Patterns and Molecular Typing of Acinetobacter baumannii Clinical Isolates and Hospital Environment at Alia Governmental Hospital, Palestine(Al-Quds University, 2024-05-28) Donia Mohammad Mosbah Khderat; دنيا محمد مصباح خضيراتBackground:In recent years, Acinetobacter baumanniireceived increasing attention;due to theircabability of acquiring multi-resistance to antibiotics and their potential to cause disease in humans. It is also known for its intrinsic antimicrobial resistance mechanisms: several studies documentedthe increase in the percentage of resistance to antimicrobial agents in four majorantimicrobialclasses: Fluoroquinolones,aminoglycosides, β-lactams including Carbapenems. The increase in Carbapenems resistance is of important concern, as thisclass of antibiotics isusually considered the last choice in treating resistant A.baumannii.This opportunistic pathogen able to survive in the environment under unfavorable conditions for prolonged periods,this contributes to its increased virulance. Thus, the hospital environment may serve asa reservoir for the resistantA. baumannii strainsallowing easily spread in hospital,serve as a nosocomial infections in patients, healthcare personnel, and visitors. Aims: This study aimed at characterization of A. baumanniiisolates from inpatients and hospital environments.To find out their antimicrobial resistance pattern, detect Carbapenems resistant A.baumannii(CRAB), and to find out genetic relatedness between isolates using random amplification of polymorphic DNA (RAPD) typing technique. Methodology: In this study, a total of 24 clinical isolates obtained from various clinical specimenssuch as wounds, blood, urine, earswabs and sputumduring the period April1, 2023, and December 31, 2023fromAlia Governmental Hospital, Hebron,Palestine. The Vitek2 system was used for identification and antibiotic susceptibility testing. Concurrently a total of 126 specimen were collected from different environments of the hospital identified as A. baumanniiusing conventional identification methodsand CHROMagar Acinetobacterselective medium. The isolates then tested for antibiotic susceptibility testing using disk diffusion methods.All isolates (both clinical and v environmental) were tested for the presence ofblaOXA-51 gene using PCR. And finally, the genetic relatedness between isolates was determined using RAPDtyping technique. Results:Twenty fourclinical isolates and 29 environmental isolates were identified as A. baumannii. All isolates were confirmed to be A. baumanniiby detecting blaOXA-51-like gene.Among the environmental isolates patient’s beds were the most contaminated site (20.6%, 6/29),while the largest number of clinical isolates were obtained from wounds (10 isolates: 41.7%). The majority of clinical and environmental isolates were collected from intensive care unit (ICU).Multidrug resistant A.baumannii (MDRAB) was detected in approximately 74% of clinical isolates and in 100% of environmental isolates.Co-trimoxazole (COT) was the most effective antibiotic against both clinical and environmentalA.baumannii isolates. For other antibiotics, clinical and environmentalA.baumanniiisolates showed high resistance rates:86.2% and 96.6% of environmentalisolates were resistant to imipenem (IM) and meropenem (MEM) respectively,while clinical isolates had a resistant rate of 72.7% and 77.3% to IM and MEM, respectively.Using the RAPD-PCR typing technique, four clusters grouped A-D had more than one isolateand the remaining isolates each had unique pattern. Some RAPD clusters were seen with environmental as well as clinical isolates. Conclusion and recomendations:Thisstudy clearly suggests that the rate of MDRAB and CRAB are increasing and considered an important cause of nosocomial infections.The relatednessbetween clinical and environmental isolates and the detection of high rate of antimicrobial-resistant A.baumanniiin various hospital environments suggested the potential role of the hospital environments through various clinical activities in the cross contamination of A.baumanniiinfections, particularly in the ICU. These findings highlight the importance of identifying A.baumannii infections early and implementing very strict infection control strategies.It is recommended that hospital wards must be vigorously sanitized and disinfected periodically.