Isolation of the Bacillus thuringiensis plasmid carrying Bacthuricin F4 coding genes and evidence of its conjugative transfer

INTRODUCTION: Conjugation is an excellent natural mode of DNA transfer in vivo between bacteria, particularly when these conjugative elements carry technological traits such as bacteriocin encoding genes. In the present work, the bacteriocinogenic plasmid pIBF4 from Bacillus thuringiensis responsible of Bacthuricin F4 synthesis was isolated and characterized. METHODOLOGY: To isolate pIBF4, the total plasmid DNA from a non-bacteriocin transposant carrying the mini-Tn10 spectinomycin selective marker was extracted and used to transform Escherichia coli strain Top10. PIBF4 was extracted from the obtained transformant and then subjected to restriction enzyme analysis. Plasmid curing experiments were conducted to test the stability of pIBF4 at a stringent temperature of 42°C. Conjugative behavior of pIBF4 was assessed by mating experiments using the non-bacteriocin transposant mutant as a donor strain and several Bacillus thuringiensis strains as recipients. RESULTS: The pIBF4 plasmid was isolated and had a molecular weight of 19.1 kb. Ninety-five percent of cells retained the pIBF4 plasmid after 200 generations, demonstrating its high stability. PIBF4 was successfully transferred to Bacillus thuringiensis HD1CryB strain with a transfer frequency of 1x10(-8) transconjugants per donor cell. The study of the recipient host range revealed that pIBF4 is specifically transferable to Bacillus thuringiensis strains with variable transfer frequencies depending on the recipient host strain. CONCLUSION: Our results show that pIBF4 is a 19.1 kb highly stable plasmid transferable by conjugation to Bacillus thuringiensis strains with deferent transfer frequencies.Tunisian Ministry of Higher Education, Scientific Research, and Technolog

034 Creatinine clearance and adverse hospital outcomes in patients with myocardial infarction

IntroductionNormal renal function has been Shown in epidemiological studies and clinical trials to be an independent predictor of survival.ObjectiveTo determine whether creatinine clearance at the time of hospital admission is an independent predictor of hospital mortality and adverse outcomes in patients with ST-segment elevation myocardial infarction (STEMI).Patients231 patients hospitalized with STEMI in our institution between January 2005 to December 2006.In-hospital outcomes were compared for patients with creatinine clearance rates of > 60ml/min (normal renal function) and ≤60ml/min (moderate and severe Baseline Renal Dysfunction, BRD).ResultsPatients with BRD were older, were more likely to be women, and presented to with more comorbidites.Patients with BRD had presented more ischemic atrial fibrillation (p = 0.033).A greater number of patients with BRD had impaired left ventricle systolic performance, so this patients had more presented acute heart failure (p = 0.008), and cardiogenic shock (p = 0.017).Patients with worsened renal function had presented more mechanical complications:-free wall rupture and apical ventricular septal defect, in two separate cases, following anterior myocardial infarction, leading to immediate death of these two patients.-ischemic mitral regurgitation in one caseThe in hospital death rate of BRD patients was 6.6%, compared with 0.9% for non BRD patients.In comparison with patients with normal or minimally impaired renal function, patients with moderate renal dysfunction were seven times more likely to die (odds ratio 7, 09, 95% confidence interval 0.7 to 68) after adjustment for other potentially confounding Variables.The risk of bleeding episodes was increased in patients with worsened renal functionOnly one patient, with moderate renal dysfunction, had an ischemic stroke.ConclusionIn patients with ACS, creatinine clearance is an important independent predictor of hospital death

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

Background: In 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. Methods: We 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. Results: We 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. Conclusions: We 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. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0211-x) contains supplementary material, which is available to authorized users

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Improvement of Bacillus thuringiensis bioinsecticide production by sporeless and sporulating strains using response surface methodology

Statistical experimental designs, involving a Plackett-Burman design followed by a rotatable central composite design were used to optimize the culture medium constituents for Bacillus thuringiensis bioinsecticide production. This was carried out by using firstly an asporogenic strain and extrapolated to some sporeless and sporulating strains. Initial screening of production parameters was performed and the variables with statistically significant effects on delta-endotoxin production were identified: glucose, glycerol, yeast extract and MnSO(4). These variables were selected for further optimization by response surface methodology. The obtained results revealed that the optimum culture medium for delta-endotoxin production consists of 22.5 g/l of glucose, 4.8g/l of glycerol, 5.8 g/l of yeast extract and 0.008 g/l of MnSO(4). Under these conditions, delta-endotoxin production was 2,130 and 2,260 mg/l into 250 and 1,000 ml flask respectively, which represent more than 38% improvement in toxin production over the basal medium (1,636 mg/l). Such medium composition was shown to be suitable for overproducing delta-endotoxins by sporeless and sporulating strains.Tunisian Ministry of Higher Education, Scientific Research and Technolog

Venous thromboembolism risk and prophylaxis in the acute hospital care setting-results of the Endorse study in Tunisia

BACKGROUND: There are not information about the risk of venous thromboembolism (VTE) and its prophylaxis in Tunisia. AIM: To report the Tunisian results of a multinational crosssectional study, designed to assess the prevalence of VTE risk in the acute hospital care setting and to determine the proportion of at risk patients who receive effective prophylaxis. METHODS: All hospital inpatients aged 40 years or over admitted to a medical ward or these aged 18 years or over admitted to surgical ward, in 5 Tunisian hospitals were assessed for risk of VTE on the basis of hospital chart review. The 2004 American College of chest physicians (ACCP) evidence based consensus guidelines were used to assess VTE risk and to determine whether patients were received recommended prophylaxis. RESULTS: 885 were enrolled, 212 (24%) were surgical and 673 (76%) were medical. 408 (44, 9%) judged to be at risk, 95 (44, 8%) are surgical and 313 (46, 5%) are medical. LWMH are the most used. Mechanical prophylaxis was never used. CONCLUSION: The percentage of at risk patient in Tunisia is comparable to these of other countries. The majority of at risk patient are medical. The prophylaxis was under used. Hospital strategies to assess patient VTE risk and implementation of prophylaxis protocols are needed