Molecular Screening of Carbapenem-Resistant K. pneumoniae (CRKP) Clinical Isolates for Concomitant Occurrence of Beta-Lactam Genes (CTX-M, TEM, and SHV) in the Kingdom of Bahrain.

The emergence of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae, including CRKP infections, has resulted in significant morbidity and mortality worldwide. We aimed to explore the presence of bla genes (CTX-M, TEM, and SHV) in CRKP isolates. A total of 24 CRKP isolates were randomly selected from the Salmaniya Medical Complex Microbiology Laboratory. These isolates, which were positive for carbapenemases, were further explored for CTX-M, TEM, and SHV genes using PCR. All the CTX-M PCR amplicons were sent for sequencing. To determine genetic relatedness, molecular typing by ERIC-PCR was performed. The bla gene testing demonstrated that a significant proportion of these isolates harbored SHV, CTX-M, and TEM genes (100%, 91.6%, and 45.8%), respectively. Bioinformatic analyses confirmed CTX-M-15 in these isolates. ERIC-PCR analysis showed three clusters demonstrating genetic relatedness. The study findings reveal the concomitant carriage of the SHV and CTX-M-15 and a comparatively lower carriage of TEM genes in CRKP isolates. Our findings highlight the significance of routinely reporting the presence of antibiotic resistance genes along with regular antibiotic sensitivity reports, as this will aid clinicians in prescribing appropriate antibiotics.

Reduction of Panton-Valentine Leukocidin Production in the Staphylococcal Strain USA300 After In Vitro Ascorbic Acid and Nicotinamide Treatment.

Background Panton-Valentine leukocidin (PVL) is one of the most important determinants of virulence in Staphylococcus aureus. It is associated with a propensity for complicating skin and soft tissue infections and necrotizing pneumonia. This study aims to quantitively examine the effect of ascorbic acid and nicotinamide on PVL production in the reference strain USA300. Methodology Sandwich enzyme-linked immunosorbent assay (ELISA) was used to quantitively measure the production of PVL via the commercial LukS sandwich ELISA kit (IBT Bio-services, MD, USA). Results Incubating USA300 with subinhibitory concentrations of antioxidants resulted in a statistically significant eight-fold reduction in PVL production at 1.25 mg/mL and 30 mg/mL for ascorbic acid and nicotinamide, respectively. Although the mechanism by which antioxidants inhibit PVL production is yet to be elucidated, we suggest that it can be due to interrupting PVL gene expression. Conclusions Ascorbic acid and nicotinamide have the potential to be toxin-suppressing agents that may be effective in supporting the bactericidal effect of antibiotics to improve the outcome of PVL-associated infections; however, further extensive research is required.

Effect of HMGB1 and HBD-3 levels in the diagnosis of sepsis- A comparative descriptive study.

Sepsis is a life-threatening condition characterized by a dysregulated host response to infection. Early and accurate diagnosis of sepsis is crucial for timely intervention and improved patient outcomes. In recent years, there has been growing interest in identifying reliable biomarkers to aid in the diagnosis of sepsis. This study aims to evaluate the levels of two potential biomarkers, high-mobility group box 1 (HMGB1) and human ß-defensin 3 (HBD-3), and compare their diagnostic efficacy in sepsis. We aimed to assess HMGB-1 and HBD-3 levels in sepsis and assess the combined diagnostic validity of HMGB-1 and HBD-3. In this case-control study, the plasma concentration of HMGB-1 and HBD-3 was measured using an enzyme-linked immunosorbent assay (ELISA). Two groups, totaling 144 people, were formed; 66 patients treated in the ICU for sepsis were included in the patient group. 78 Blood donors from the Salmaniya Medical Complex Blood Bank who had no prior infection or inflammatory disease made up the Control group. The statistical computations were performed using the STATA 8® statistical software tool (StataCorp LP, College Station, TX, USA). In patients' mean HMGB-1 levels were 2.1442 ng/ml, compared to 0.62141 ng/ml in the control group. The mean HBD-3 level was 1068.453 ng/ml in sepsis patients versus 589.935 ng/ml in controls. A significant difference between the two groups has been observed in both biomarkers (P < 0.05). The sensitivity of HMGB-1 was 75.8% and 41.3%, respectively. The sensitivity and specificity of HBD-3 were 63.6% and 93.5%, respectively. The levels of HMGB-1 and HBD-3 between healthy and septic subjects varied significantly. HMGB-1 and HBD-3 levels in the blood tested together might accurately identify sepsis. These findings contribute to the growing body of evidence supporting the utility of biomarkers in sepsis diagnosis, and may ultimately aid in the development of more effective diagnostic strategies for sepsis management.

Prevalence of Carbapenemases in Carbapenem-Resistant Acinetobacter baumannii Isolates from the Kingdom of Bahrain.

BACKGROUND: Acinetobacter baumannii is regarded as a significant cause of death in hospitals. The WHO recently added carbapenem-resistant Acinetobacter baumannii (CRAB) to its global pathogen priority list. There is a dearth of information on CRAB from our region. METHODS: Fifty CRAB isolates were collected from four main hospitals in Bahrain for this study. Bacterial identification and antibiotic susceptibility tests were carried out using the BD PhoenixTM and VITEK-2 compact, respectively. Using conventional PCR, these isolates were further screened for carbapenem resistance markers (blaOXA-51, blaOXA-23, blaOXA-24, blaOXA-40, blaIMP, blaNDM, blaVIM, and blaKPC). RESULTS: All of the isolates were resistant to imipenem (100%), meropenem (98%), and cephalosporins (96-98%), followed by other commonly used antibiotics. All these isolates were least resistant to gentamicin (64%). The detection of resistance determinants showed that the majority harbored blaOXA-51 (100%) and blaIMP (94%), followed by blaOXA-23 (82%), blaOXA-24 (46%), blaOXA-40 (14%), blaNDM (6%), blaVIM (2%), and blaKPC (2%). CONCLUSION: The study isolates showed a high level of antibiotic resistance. Class D carbapenemases were more prevalent in our CRAB isolate collection. The resistance genes were found in various combinations. This study emphasizes the importance of strengthening surveillance and stringent infection control measures in clinical settings to prevent the emergence and further spread of such isolates.

Multidrug-Resistant Staphylococcus aureus Isolates in a Tertiary Care Hospital, Kingdom of Bahrain.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a ubiquitous pathogen associated with a wide spectrum of human infections. In recent decades, MRSA infections have been increasingly reported in individuals without established risk factors, infecting immunocompetent members of the community. This emergence is attributed to the production of various virulence factors, notably Panton-Valentine leukocidin (PVL). OBJECTIVE: The aim of this study was to better understand the prevalence, antibiotic resistance profiles, and molecular characteristics of S. aureus and MRSA in a tertiary care hospital in the Kingdom of Bahrain. MATERIALS AND METHODS: This cross-sectional study was carried out in a tertiary hospital for a one-year period, from December 2020 to December 2021. A total of 161 consecutive S. aureus isolates were collected. Antibiotic susceptibility was tested using BD Phoenix™ automated identification and susceptibility testing system. Molecular analysis was conducted via conventional PCR and conventional multiplex PCR for SCCmec typing. RESULTS: In this study, 161 S. aureus isolates were investigated, 60% (n=97) were characterized as MRSA, of which, 12% (n=12) were healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) while 88% (n=85) were community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). No statistically significant difference (P>0.05) in antibiotic resistance trends between HA-MRSA and CA-MRSA was detected. Multidrug resistance (MDR) amounted to 19% (n=30) of all S. aureus isolates, 14% (n=9) of methicillin-susceptible Staphylococcus aureus (MSSA) isolates, and 22% (n=21) of MRSA isolates. SCCmec typing demonstrated a high prevalence of type IV (61%, n=59), followed by type V (32%, n=31), then type II (4%, n=4), and type III (3%, n=3). The PVL prevalence was 39% (n=25) in MSSA and 62% (n=60) in MRSA, 33% (n=4) in HA-MRSA, and 66% (n=56) in CA-MRSA. CONCLUSION: This study demonstrated the emergence of PVL-producing CA-MRSA in a tertiary care hospital, as well as the detection of PVL-producing MDR strains. This development prompts serious measures to be taken in order to sustain a healthy clinical environment.

Synergistic antimicrobial effect of ascorbic acid and nicotinamide with rifampicin and vancomycin against SCCmec type IV methicillin-resistant Staphylococcus aureus (MRSA).

Background. Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogenic bacteria involved in a wide spectrum of human diseases. Many virulence factors promote this widespread propagation. One important factor is acquiring antibiotic resistance genes, which leads to a reduction in the availability and efficacy of therapy options. Recently, research has suggested that the remarkable antimicrobial effect of antioxidants against superbugs such as MRSA shows synergistic effects when accompanied by antimicrobial therapy. This paper aims to examine the synergistic effects of ascorbic acid and nicotinamide with a panel of antibiotics used in antimicrobial therapy against MRSA. Material and Methods. Two SCCmec type IV MRSA reference strains (EMRSA-15 and USA300) and 10 MRSA clinical isolates feature in this paper. SCCmec typing was conducted on the 10 clinical isolates via multiplex PCR after identification. Synergy experiments on antioxidants and antibiotics were evaluated via checkerboard assay. The minimum inhibitory concentration (MIC) of each agent was determined in accordance with the Clinical and Laboratory Standards Institute (CLSI) M100 guidelines through twofold microdilution assay. Results and Discussion. Synergy (FIC <0.5) was demonstrated for ascorbic acid (1/2 to 1/4 MIC) with rifampicin (1/2 to 1/8 MIC), and also ascorbic acid (1/2 to 1/16 MIC) when associated with vancomycin (1/2 MIC). Similarly, nicotinamide (1/2 to 1/16 MIC) showed a synergistic effect when paired with low concentrations of rifampicin (1/2 to 1/16 MIC), and also (at 1/4 to 1/16 MIC) with vancomycin (1/2 MIC). All reduced MICs due to synergistic combinations demonstrated statistical significance (P<0.05). Conclusion. The synergistic activity demonstrated in associating antioxidants with antibiotics shows promise in managing superbugs. However, more research is required to better understand the mechanism of the synergy and for utilization in clinical care.

The Effect of Ascorbic Acid and Nicotinamide on Panton-Valentine Leukocidin Cytotoxicity: An Ex Vivo Study.

Background: Panton−Valentine Leukocidin sustains a strong cytotoxic activity, targeting immune cells and, consequently, perforating the plasma membrane and inducing cell death. The present study is aimed to examine the individual effect of ascorbic acid and nicotinamide on PVL cytotoxicity ex vivo, as well as their effect on granulocytes viability when treated with PVL. Materials and Methods: The PVL cytotoxicity assay was performed in triplicates using the commercial Cytotoxicity Detection Kit PLUS (LDH). LDH release was measured to determine cell damage and cell viability was measured via flow cytometry. Results and discussion: A clear reduction in PVL cytotoxicity was demonstrated (p < 0.001). Treatment with ascorbic acid at 5 mg/mL has shown a 3-fold reduction in PVL cytotoxicity; likewise, nicotinamide illustrated a 4-fold reduction in PVL cytotoxicity. Moreover, granulocytes' viability after PVL treatment was maintained when incubated with 5 mg/mL of ascorbic acid and nicotinamide. Conclusions: our findings illustrated that ascorbic acid and nicotinamide exhibit an inhibitory effect on PVL cytotoxicity and promote cell viability, as the cytotoxic effect of the toxin is postulated to be neutralized by antioxidant incubation. Further investigations are needed to assess whether these antioxidants may be viable options in PVL cytotoxicity attenuation in PVL-associated diseases.

Clinical carbapenem-resistant Klebsiella pneumoniae isolates simultaneously harboring bla NDM-1, bla OXA types and qnrS genes from the Kingdom of Bahrain: Resistance profile and genetic environment.

The prevalence of Carbapenem-resistant Klebsiella pneumoniae (CRKP) is currently increasing worldwide, prompting WHO to classify it as an urgent public health threat. CRKP is considered a difficult to treat organism owing to limited therapeutic options. In this study, a total of 24 CRKP clinical isolates were randomly collected from Salmaniya Medical Complex, Bahrain. Bacterial identification and antibiotic susceptibility testing were performed, on MALDI-TOF and VITEK-2 compact, respectively. The isolates were screened for carbapenem resistance markers (bla NDM, bla OXA-23, bla OXA-48 and bla OXA-51) and plasmid-mediated quinolone resistance genes (qnrA, qnrB, and qnrS) by monoplex PCR. On the other hand, only colistin-resistant isolates (n=12) were screened for MCR-1, MCR-2 and MCR-3 genes by monoplex PCR. Moreover, the Genetic environment of bla NDM, integrons analysis, and molecular characterization of plasmids was also performed. Antibiotic susceptibility revealed that all the isolates (100%) were resistant to ceftolozane/tazobactam, piperacillin/tazobactam, 96% resistant to ceftazidime, trimethoprim/sulfamethoxazole, 92% resistant to meropenem, gentamicin and cefepime, 88% resistant to ciprofloxacin, imipenem, and 37% resistant to amikacin. Ceftazidime/avibactam showed the least resistance (12%). 75% (n=12/16) were resistant to colistin and 44% (n=7/16) showed intermediate susceptibility to tigecycline. The detection of resistant determinants showed that the majority (95.8%) of CRKP harbored bla NDM-1, followed by bla OXA-48 (91.6%) bla OXA-51 (45.8%), and bla OXA-23 (41.6%). Sequencing of the bla NDM amplicons revealed the presence of bla NDM-1. Alarmingly, 100% of isolates showed the presence of qnrS. These predominant genes were distributed in various combinations wherein the majority were bla NDM-1 + bla OXA-51+ qnrS + bla OXA-48 (n =10, 41.7%), bla NDM-1 + bla OXA-23+ qnrS + bla OXA-48 (n=8, 33.3%), among others. In conclusion, the resistance rate to most antibiotics is very high in our region, including colistin and tigecycline, and the genetic environment of CRKP is complex with the carriage of multiple resistance markers. Resistance to ceftazidime/avibactam is uncommon and hence can be used as a valuable option for empirical therapy. Molecular data on resistance markers and the genetic environment of CRKP is lacking from this geographical region; this would be the first report addressing the subject matter. Surveillance and strict infection control strategies should be reinforced in clinical settings to curb the emergence and spread of such isolates.

Trends in methicillin-resistant Staphylococcus aureus in the Gulf Cooperation Council countries: antibiotic resistance, virulence factors and emerging strains.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a ubiquitous pathogen that is increasing in Gulf Cooperation Council (GCC) countries. It is implicated in a wide range of infections, from superficial skin infections to lifethreatening syndromes. MRSA has moved beyond healthcare facilities, affecting individuals in the community without substantial risk factors. Aims: To review the prevalence and molecular characterization of MRSA in GCC countries during 2011-2021. Methods: We comprehensively searched PubMed using the following keywords: MRSA, Staphylococcus aureus, GCC, Kuwait, Saudi Arabia, Bahrain, Oman, Qatar, UAE, prevalence, and molecular characterization for articles published after 2011. Results: Thirty-nine of 111 articles examined, fulfilled the purpose of this review. Most studies were in Kuwait (44%), Saudi Arabia (28%) and United Arab Emirates (10%). Studies from other GCC countries were sporadic. Several studies demonstrated a clear emergence in antibiotic resistance especially against fusidic acid, ciprofloxacin and clindamycin. Regional prevalence of MRSA is reported as 25-35%, with clear dominance of community-acquired (CA)-MRSA. Panton- Valentine leucocidin (PVL)-producing strains accounted for 35-45%, with clear association with CA-MRSA emergence, but there were some sporadic reports of incorporation of PVL in healthcare-associated (HA)-MRSA. The reported dominant strains included EUST80, USA1100 and WA-MRSA-51. Novel strains are more likely to produce PVL and show fusidic acid resistance. Conclusion: There is a need for national and regional MRSA surveillance programmes, especially with the emergence of strains that require no underlying risk factors to cause illness, as well as the propagation of chimeric resistance elements in both HA-MRSA and CA-MRSA.

Perception of online and face to face microbiology laboratory sessions among medical students and faculty at Arabian Gulf University: a mixed method study.

BACKGROUND: The COVID-19 pandemic has impacted all spheres of society including medical education and healthcare systems. In response to the pandemic, there has been a transition in medical education practice from traditional forms of teaching to online instruction delivery and virtual learning. Effective clinical microbiology education involves a combination of 'hands-on' practical learning and instructional delivery of scientific knowledge. Microbiology practical laboratories are critical learning environments offering 'hands-on' learning experiences that cannot be replicated through online learning. We conducted a mixed-methods study to understand the perception of online and face-to-face microbiology laboratory sessions among the medical students and microbiology faculty at Arabian Gulf University (AGU). METHODS: The study participants were third and fourth-year undergraduate medical students and faculty involved in delivering microbiology labs at AGU. The questionnaire consisted of questions ranging from perceived learning style to attitude towards online delivery of microbiology curriculum. After the questionnaire administration (google form), focus group discussion (FGD) was conducted for students and microbiology faculty separately. RESULTS: Among 168 students, 50.6% preferred face-to-face lab sessions as compared to 30.4% who preferred online labs, and 51.8% considered online labs to be an essential addition to face-to-face labs. Among the faculty, 85.7% preferred the face-to-face mode of teaching. All the faculty (100%) disagreed that all the microbiology labs teaching should be online. 57.2% considered online labs to be an essential addition to traditional face-to-face labs. Both faculty and students hold that a blended mode of instructional delivery is vital and indispensable for the transfer of skills and knowledge for microbiology students. CONCLUSION: The blended mode of delivering microbiology laboratory sessions in medical school is successful and well-received by both students and faculty. Students take the responsibility for furthering their own learning and understanding of concepts. Instructors have also noticed that blending learning strategies also successfully enhances the development of cognitive skills and problem-solving abilities in students. A review of the microbiology lab curriculum is necessary to identify content areas that can be delivered effectively through online, face-to-face lab sessions, or both, supported with appropriate tools and infrastructure.

Antibiotic-Resistance Genes in E. coli strains in GCC Countries: A Meta-Analysis.

Background: Antimicrobial resistance (AMR) in Escherichia coli is an alarming issue worldwide, including in the Gulf Cooperation Council (GCC) countries, yet the prevailing gene patterns have not recently been reviewed. This study was conducted to determine and report on the dominant E. coli antimicrobial resistant gene patterns in GCC countries. Method: A scoping review identified the predominant AMR genes in GCC countries: CTX M, TEM, SHV, NDM, OXA, and VIM genes. For the systematic review, two authors independently searched Scopus, PubMed, Google Scholar, Science Direct, and Web of Science for interventional, clinical, or observational studies on the chosen AMR-conferring genes in E. coli published from GCC countries between January 2013 and June 2019, when the last search was carried out. The search strategy followed the PRISMA guidelines. The risk of bias was assessed using a 6-item standardized checklist. Random-effects modeling was used for all analyses. Results: A total 32 studies were included in the final synthesis of evidence. Overall, CTX-M (53.8%) was the most prevalent gene in the region followed TEM (40.6%), NDM-1 (28.4%), OXA (24.3%), VIM (8.5%), and SHV (7.8%). Most included studies were from Saudi Arabia: CTX-M was again most common with a prevalence of 46.8% from 5442 isolates. Conclusion: The risk of bias analysis showed a mean quality score of 4.25 ± 0.75, indicating high-quality in studies included in this meta-analysis. This review found that CTX-M gene is the most common AMR-conferring gene in E. coli strains from most GCC countries.

Reported Adverse Effects and Attitudes among Arab Populations Following COVID-19 Vaccination: A Large-Scale Multinational Study Implementing Machine Learning Tools in Predicting Post-Vaccination Adverse Effects Based on Predisposing Factors.

Background: The unprecedented global spread of coronavirus disease 2019 (COVID-19) has imposed huge challenges on the healthcare facilities, and impacted every aspect of life. This has led to the development of several vaccines against COVID-19 within one year. This study aimed to assess the attitudes and the side effects among Arab communities after receiving a COVID-19 vaccine and use of machine learning (ML) tools to predict post-vaccination side effects based on predisposing factors. Methods: An online-based multinational survey was carried out via social media platforms from 14 June to 31 August 2021, targeting individuals who received at least one dose of a COVID-19 vaccine from 22 Arab countries. Descriptive statistics, correlation, and chi-square tests were used to analyze the data. Moreover, extensive ML tools were utilized to predict 30 post vaccination adverse effects and their severity based on 15 predisposing factors. The importance of distinct predisposing factors in predicting particular side effects was determined using global feature importance employing gradient boost as AutoML. Results: A total of 10,064 participants from 19 Arab countries were included in this study. Around 56% were female and 59% were aged from 20 to 39 years old. A high rate of vaccine hesitancy (51%) was reported among participants. Almost 88% of the participants were vaccinated with one of three COVID-19 vaccines, including Pfizer-BioNTech (52.8%), AstraZeneca (20.7%), and Sinopharm (14.2%). About 72% of participants experienced post-vaccination side effects. This study reports statistically significant associations (p < 0.01) between various predisposing factors and post-vaccinations side effects. In terms of predicting post-vaccination side effects, gradient boost, random forest, and XGBoost outperformed other ML methods. The most important predisposing factors for predicting certain side effects (i.e., tiredness, fever, headache, injection site pain and swelling, myalgia, and sleepiness and laziness) were revealed to be the number of doses, gender, type of vaccine, age, and hesitancy to receive a COVID-19 vaccine. Conclusions: The reported side effects following COVID-19 vaccination among Arab populations are usually non-life-threatening; flu-like symptoms and injection site pain. Certain predisposing factors have greater weight and importance as input data in predicting post-vaccination side effects. Based on the most significant input data, ML can also be used to predict these side effects; people with certain predicted side effects may require additional medical attention, or possibly hospitalization.

Evaluation of Two Phenotypic Methods for the Detection of Plasmid-Mediated AmpC ß-Lactamases among Enterobacteriaceae Isolates.

Objectives AmpC ß-lactamases are cephalosporinases that confer resistance to cephalothin, cefazolin, cefoxitin, penicillin, and ß-lactamase inhibitor-ß-lactam combinations. Even though the AmpC resistance is reported, but the accurate occurrence of AmpC ß-lactamases in Enterobacteriaceae members is still unknown. Techniques to identify AmpC producers are still evolving but not yet optimized for the clinical laboratory. Here we aimed to compare the test performance of two different phenotypic methods, that is inhibitor-based assay using boronic acid and disk approximation test for AmpC detection in Enterobacteriaceae isolates from a tertiary hospital microbiology laboratory. Materials and Methods The study includes 137 nonrepeat Enterobacteriaceae strains. Bacterial isolates, that yielded a zone diameter of less than 18 mm for cefoxitin by disk diffusion method were considered potential AmpC producers and further confirmed by phenotype methods-inhibitor-based assay using boronic acid and disk approximation test. A multiplex polymerase chain reaction was used to detect the most common plasmid-mediated AmpC genes: ACC, FOX, MOX, DHA, CIT, and EBC. Results Of the 137 clinical isolates, 58 (42.33%) were cefoxitin resistant, while 53.4 and 18.9% of the cefoxitin-resistant isolates were positive by inhibitor-based assay and disk approximation test. Multiplex PCR detected 42 (30.6%) isolates with AmpC genes. Of the 42 isolates, the inhibitor-based assay detected 25 (59.5%) isolates, while the disk approximation test detected nine (21.4%) isolates. Conclusion Our findings suggest that inhibitor-based assay using boronic acid can be used for the detection of the isolates that harbor AmpC ß-lactamases. This method is cost-effective, simple to perform, and easy to interpret. Thus AmpC detection as a routine in clinical laboratories can help in appropriate therapeutic intervention and improved infection control.

Molecular detection of plasmid-derived AmpC ß-lactamase among clinical strains of Enterobacteriaceae in Bahrain.

BACKGROUND: Enterobacteriaceae with AmpC ß-lactamase are multidrug-resistant organisms and represent a significant challenge to patient care. This study aims to determine the prevalence of plasmid-derived AmpC ß-lactamase among extended spectrum ß-lactamases (ESBL)-producing Enterobacteriaceae strains in Bahrain. METHODS: It was a cross-sectional study. A total of 185 ESBL-producing Enterobacteriaceae isolates were recovered from clinically significant specimens from January 2018 to December 2019. The samples underwent initial screen for cefoxitin resistance by disc diffusion test and subsequent phenotypic confirmation of AmpC production with phenyl boronic acid assays as well as genotypic analysis by multiplex polymerase chain reactions for AmpC subtypes. Drug-resistant features of these clinical isolates were also examined. RESULTS: Twenty-nine ESBL-producing Enterobacteriaceae isolates were cefoxitin resistant. Phenotypic and genotypic analyses confirmed that 8 and 12 cefoxitin-resistant isolates are AmpC positive, respectively. These AmpC producers are multidrug resistant, and Escherichia coli is the dominant strain among them. CONCLUSIONS: Plasmid-mediated spread of AmpC is present in clinically relevant Enterobacteriaceae species in Bahrain. Rational antimicrobial therapy against these multidrug-resistant organisms and continued surveillance of antimicrobial resistance mechanisms among the clinical isolates are recommended for optimal patient care.

Dysregulation of human beta-defensin-3 expression in the peripheral blood of patients with sepsis.

OBJECTIVES: Sepsis is a serious medical condition caused by the body's systemic inflammatory response to infections. The antimicrobial peptides, human beta-defensins, play a key role in modulating host immune responses, and aberrant expression of human beta-defensins has been implicated in many infections and inflammatory diseases. However, little is known about the expression of human beta-defensin-3 in systemic infectious diseases. METHODS: We investigated the gene expression and protein level of human beta-defensin-3 in peripheral whole blood from 107 participants-67 patients with sepsis and 40 healthy controls-and evaluated the feasibility of human beta-defensin-3 as an indicator for sepsis. Total RNA was extracted from peripheral blood samples, and relative mRNA expression of human beta-defensin-3 was determined by reverse transcription-quantitative polymerase chain reaction. Plasma concentration of human beta-defensin-3 was measured by enzyme-linked immunosorbent assay. Pearson's correlation analysis was performed to assess the relationship between human beta-defensin-3 mRNA and protein levels. Receiver operating characteristic analysis was performed to evaluate the value of human beta-defensin-3 as a biomarker for sepsis. RESULTS: Human beta-defensin-3 mRNA expression was significantly downregulated in sepsis patients compared to controls (p = 0.001). The mean fold change of mRNA expression (±standard error) was 0.82 ± 0.63 in sepsis patients and 1.39 ± 1.09 in controls. Plasma concentration of human beta-defensin-3 (pg/mL) was significantly lower in sepsis patients compared to healthy controls (p = 0.039). The mean protein concentration (±standard error) was 539.6 ± 39.4 in sepsis patients and 715.5 ± 53 in controls. There was a significant correlation between human beta-defensin-3 mRNA expression and the corresponding protein level in sepsis patients (r = 0.358, p = 0.04), but not in healthy controls (r = 0.124, p = 0.51). For discriminating sepsis patients from healthy controls, the area under the receiver operating characteristic curve was 0.722 (95% confidence interval: 0.597-0.847, p = 0.002) for human beta-defensin-3 mRNA and 0.689 (95% confidence interval: 0.557-0.827, p = 0.009) for human beta-defensin-3 protein. CONCLUSION: This is the first study to show the downregulation of human beta-defensin-3 gene expression and protein level in sepsis, which may contribute to the complex immunological imbalance in sepsis. The significant correlation between human beta-defensin-3 mRNA expression and protein concentration suggests that mRNA expression could be used to predict protein level. Our study also showed a potential role of human beta-defensin-3 as a blood-based biomarker for sepsis. More studies on the clinical significance of human beta-defensin-3 in sepsis could further support a biomarker development.

Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain.

The challenges imposed by the ongoing outbreak of severe acute respiratory syndrome coronavirus-2 affects every aspect of our modern world, ranging from our health to our socio-economic needs. Our existence highly depends on the vaccine's availability, which demands in-depth research of the available strains and their mutations. In this work, we have analyzed all the available SARS-COV2 genomes isolated from the Kingdom of Bahrain in terms of their variance and origin analysis. We have predicted various known and unique mutations in the SARS-COV2 isolated from Bahrain. The complexity of the phylogenetic tree and dot plot representation of the strains mentioned above with other isolates of Asia indicates the versatility and multiple origins of Bahrain's SARS-COV2 isolates. We have also identified two high impact spike mutations from these strains which increase the virulence of SARS-COV2. Our research could have a high impact on vaccine development and distinguishes the source of SARS-COV2 in the Kingdom of Bahrain.

Variant analysis of SARS-CoV-2 genomes in the Middle East.

BACKGROUND: Coronavirus (COVID-19) was introduced into society in late 2019 and has now reached over 88 million cases and 1.9 million deaths. The Middle East has a death toll of ~80,000 and over 35000 of these are in Iran, which has over 1.2 million confirmed cases. We expect that Iranian cases caused outbreaks in the neighbouring countries and that variant mapping and phylogenetic analysis can be used to prove this. We also aim to analyse the variants of severe acute respiratory syndrome coronavirus-2 (SARS -CoV-2) to characterise the common genome variants and provide useful data in the global effort to prevent further spread of COVID-19. METHODS: The approach uses bioinformatics approaches including multiple sequence alignment, variant calling and annotation and phylogenetic analysis to identify the genomic variants found in the region. The approach uses 122 samples from the 13 countries of the Middle East sourced from the Global Initiative on Sharing All Influenza Data (GISAID). FINDINGS: We identified 2200 distinct genome variants including 129 downstream gene variants, 298 frame shift variants, 789 missense variants, 1 start lost, 13 start gained, 1 stop lost, 249 synonymous variants and 720 upstream gene variants. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. These high impact variant ultimately results in 36 number of mutations on spike glycoprotein. Variant alignment and phylogenetic tree generation indicates that samples from Iran likely introduced COVID-19 to the rest of the Middle East. INTERPRETATION: The phylogenetic and variant analysis provides unique insight into mutation types in genomes. Initial introduction of COVID-19 was most likely due to Iranian transmission. Some countries show evidence of novel mutations and unique strains. Increased time in small populations is likely to contribute to more unique genomes. This study provides more in depth analysis of the variants affecting in the region than any other study.

Student Perception of Microbiology Laboratory Skills Learning Through a Problem-Based Learning Curriculum: Arabian Gulf University Experience.

INTRODUCTION: The curriculum at medical school at Arabian Gulf University is centered on small group learning and real-life problems provided to students and guiding students to learn actively. In microbiology, laboratory skills are taught in an innovative manner using mini cases and different lab sessions and are integrated with other basic sciences. This article describes the format and pattern of laboratory skills sessions conducted using PBL methods at Arabian Gulf University and discusses the perception of students towards PBL in laboratory skill learning and way forward for the same. METHODS: The study sample size was 110. The students' perception of the laboratory skills teaching methods was assessed through an exit survey at the end of each session. A semi-structured self-administered survey instrument was prepared, and the questions were arranged in two sessions and focused on identifying the relevance, timing, strengths, and weaknesses of the teaching method and recommendations to improve the same. RESULTS: We observed that more than 50% of the participants agreed or strongly agreed that the time given for PBL was adequate, topics discussed were relevant, presentations were clear, pre-session briefing and Case-Based Studies (team-based learning (TBL)) helped in their learning. The participants identified the demonstration of experiments and hands-on experience provided in the laboratory were most helpful. When enquired about the difficulty, among 48% of the participants, 80% observed that the slides used in the learning/teaching were lengthy. CONCLUSION: The use of PBL in a lab setting promotes active learning. In the heart of PBL, TBL is a powerful tool in the educational process offering the students deep comprehension and allowing them to gain practical and intellectual skills.

Outcomes of COVID-19 in the Eastern Mediterranean Region in the first 4 months of the pandemic.

OBJECTIVES: To summarize the outcomes of the coronavirus disease 2019 infections in the Eastern Mediterranean Region (EMR) in the first 4 months of the pandemic. METHODS: A meta-analysis approach was used in this context. We used the aggregate data from the World Health Organization Regional Office for the EMRO (until 26 May 2020) to generate this report. RESULTS: An analysis of official data from all 22 countries and territories in the Middle East, North Africa, the Horn of Africa, and Central Asia K=22 (a total of 438,717 cases) was performed. The total number of cases, recovered cases were 438,717,228,986,  and deaths was 11,290 in the EMR. Meta-analytic pooling of the point estimates of recovery rate per country in the EMR was 52.5% (95% CI 52.3% - 52.6%). The lowest recovery rates were in Somalia (4.3%), and the highest rates were in Tunisia (87.4%). Meta-analytic pooling of the point estimates of death rate per country in the EMR yielded 3.85% [95% CI 3.80% - 3.9%]. Meta-analytic pooling of the point estimates of recovery rate per country in the Gulf Cooperation Council countries was 46.1% (95% CI 45.8% - 46.3%). Meta-analytic pooling of the point estimates of death rate per country in the Gulf Cooperation Council countries was 0.6% (95% CI 0.50% - 0.65%). CONCLUSION: Wide variability was found between EMR countries in recovery and mortality, implying the possible impact of resource availability, and genetic and environmental factors on the morality and recovery of the COVID-19.

The Curriculum at the College of Medicine and Medical Sciences at Arabian Gulf University: A Way Forward to Meet the Future Medical Education Needs.

Arabian Gulf University (AGU) follows a curriculum based on Problem Based Learning (PBL). PBL is a learner-centered approach that empowers students for life-long learning. Students are taught through problems that are designed based on global health problems customized to the local needs. The classroom teaching is complemented through adjunct programs like community health activities and professional skills program. Medical education aims to meet the changing needs of society. Demographics, disease epidemiology and healthcare needs of the gulf countries have changed over 38 years since the inception of AGU. To keep pace with the changing demands, it is imperative that the curriculum is reviewed in the light of advances in technology and newer techniques of medical education.In the present article the curriculum at AGU is reviewed based on the predictors for future medical education and alternative teaching methods that can be integrated to optimize the student outputs are explored.