EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.

EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera that include pathogens. Here we provide an overview on how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio, and Moraxella, and genotyped those assemblies by core genome Multilocus Sequence Typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping, a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports SNP calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of Yersinia pestis over the last 5,000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3 which presents a novel, global overview of the population structure of all of the species, subspecies and clades within Escherichia.

AIM: Evaluation of the safety and efficacy of pulmonary veins isolation in patients with paroxysmal atrial fibrillation (AF) using two new different technologies, cryoballoon (CB) ablation and radiofrequency ablation with contact force (CF)-sensing catheters. METHODS: Prospective single-center evaluation, carried out from January 2016 to June 2018 in Critical Care Medicine Department – Cairo University, comparing CF radiofrequency (Thermocool® SmartTouch, Biosense Webster, Inc.) (CF group) with CB ablation (Arctic Front Advance 28 mm CB, Medtronic, Inc.) (CB group), in regards to procedural safety and efficacy, as well as recurrence at 12 months. Overall, 50 consecutive patients were enrolled (25 in each group). RESULTS: The characteristics of patients of both the groups were similar (46.9 ± 11.2 years, the proportion of women 36%, mean documented AF duration 3 ± 2.3 years, mean CHA2DS2-VASc score 1.4 ± 1.3, and mean HAS-BLED 1.4 ± 0.6). Duration of the procedure was significantly lower in the CB group (171.7 ± 15.24 vs. 199.3 ± 18.94 min, p = 0.002), with a longer duration of fluoroscopy and X-ray exposure in the CB group than the CF group but statistically non-significant difference (58.60 ± 11.57 vs. 48.7 ± 13.86 min and 6273 ± 4934 cGy cm² vs. 6853 ± 5069 cGy cm², p = 0.1 and p = 0.2, respectively). Overall complication rate was similar in both groups: 2 (8%) in each group. At 12 months, AF recurrence occurred in 7 patients (28%) in the CF group and in 9 patients (36%) in the CB group (log rank p = 0.682). CONCLUSION: Pulmonary vein isolation using CF-guided RF and second-generation CB leads to comparable single-procedure arrhythmia-free survival at up to 12 months with similar overall complication rate.

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

Salmonella is considered to be one of the major poultry bacterial pathogens. The poultry species are one of the main reservoirs for the human types, thus serving as public health hazards. The development of drug resistant genes and multidrug resistant types from Salmonella has increased recently. This current study was undertaken to estimate the correlation between extended spectrum beta-lactamase multidrug resistant (ESβL) Salmonella serovars isolated from broilers and their virulence genes. Two hundred and forty samples were collected from clinically diseased broilers chicks (showed disorders of the intestinal tract) and examined for the presence of Salmonella isolates according to ISO 6579: 2002 and ISO. 6579-3:2014 Fifty Salmonella isolates were isolated with an incidence of 20.8%. Isolates of Salmonella were serotyped as follows: 25 S. Kentucky, 9 S. Infantis, 6 S. Enteritidis, 4 S. Heidelberg, and one isolates per serovars S. Labadie, S. Typhi, S. Agona, S. Pullorum, S. Newport and S. Virginia. AST (antimicrobial susceptibility testing) showed that high percentage of isolates were resistant to all Ampicillin (90%), Nalidixic acid (88%), Sulfamethoxazole + Trimethoprim (82%) and Tetracycline (82%). Approximately 86% of the isolates demonstrated multiple resistance, of which 18.75% and 25% were resistant to three and four antimicrobial types, respectively. Phenotypic detection of ESβLs by using screening test (Cefinase®) and confirmatory test by using combined disk diffusion test revealed that 32% of isolates were positive for both tests with 20% similarity and 12% diversity between the two tests. Molecular characterization of some ESβLs genes (blaTEM, blaCTX, blaOXA, blaCMY and blaSHV) and some virulence genes (invA, avrA, sopB, bcfC, stn (was done using PCR. The results showed that all the ESβLs positive serovars were positive for amplification of all tested virulence genes and noticed that all the isolates were negativefor blaCMY gene. The present study suggests that virulent ESβL Salmonella serovars could infect broilers and should be taken into consideration as an important bacterial pathogen affecting poultry.

Fourteen isolates of Corynebacteruim pseudotuberculosis of them 7 were isolated from sheep with Caseous Lymphadenitis "biotype 1" and 7 isolated from buffaloes with Oedematous Skin Disease "biotype 2". All isolates were identified by standard microbiological techniques and by polymerase chain reaction targeting, 16S rRNA and phospholipase D genes. Synergistic haemolytic titers of all isolates were assayed by plate technique. The presences of phospholipase D gene in supernatants of all isolates were performed by sodium dodecyl sulfate polyacrylamide gel electrophoresis immunoblot technique by using hyperimmune serum raised in rabbit immunized with recombinant phospholipase D gene antigen. The concentration of phospholipase D gene was assayed by scanning the bound phospholipase D gene with specific antibodies that appeared at 31.5 kDa. Results presented that there is no correlation between titer of Synergistic haemolytic activity and the actual phospholipase D genes concentration in culture supernatants. Also results presented that Synergistic haemolytic activity and phospholipase D genes produced by biotype 2 (buffalo isolates) was generally higher than those by biotype 1(sheep isolates).

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