Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems

Background: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. Methods: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMerieux, Marcy l'Etoile, France), and ASTA MicrolDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com ). Results: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. Conclusions: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.

Changes in activity and isozyme patterns of peroxidase and chitinase in kiwifruit pollen

In this study, changes in activity and isozyme patterns of peroxidase (POD) and chitinase in kiwifruit (Actinidia chinensis) pollen were investigated under different storage conditions. Although residual activity was detected in heat-treated pollen, changes in POD activity were observed due to difference in storage conditions as revealed by preliminary studies in which pollen germination varied with different storage conditions. POD activity of kiwifruit pollen increased as proportions of viable pollen increased, indicating a positive correlation (R2=0.993) between pollen viability and POD activity. There was a detectable difference in the relative activity of POD enzyme between heat-treated and viable pollen. Decoloration of Congo Red was observed in germination medium which fresh pollen was cultured. The activity of individual chitinase isozymes present in kiwifruit pollen differed depending on storage conditions, which had a direct impact on pollen vigor. Although direct evidence showing that chitinase isozymes are implicated in pollen vigor is still uncertain, distinction of isozymes may facilitate more precise identification of viable pollen which possesses germination potential from non-viable pollen. Taken together, these results suggest that monitoring the activity of POD and chitinase can be an attractive alternative to evaluate pollen vigor in kiwifruit

Down-regulation of phospholipase D during differentiation of mouse F9 teratocarcinoma cells

AbstractPhospholipase D has been recognized as playing an important role in signal transduction in many types of cells. We investigated the expression of phospholipase D during the differentiation of F9 embryonal teratocarcinoma cells. The ADP ribosylation factor-dependent phospholipase D activity, as measured by an in vitro assay, and H2O2-induced phospholipase D activity and phospholipase D protein content in whole cells were decreased during the differentiation of F9 cells induced by a combination of dibutyryl cyclic AMP and all-trans retinoic acid. In contrast, these changes were not observed when cells were induced by retinoic acid. These results suggest that down-regulation of phospholipase D protein is associated with differentiation of F9 cells to a parietal endoderm lineage

Comparative Genomic Analysis of the 2016 Vibrio cholerae Outbreak in South Korea

In August 2016, South Korea experienced a cholera outbreak that caused acute watery diarrhea in three patients. This outbreak was the first time in 15 years that an outbreak was not linked to an overseas source. To identify the cause and to study the epidemiological implications of this outbreak, we sequenced the whole genome of Vibrio cholerae isolates; three from each patient and one from a seawater sample. Herein we present comparative genomic data which reveals that the genome sequences of these four isolates are very similar. Interestingly, these isolates form a monophyletic Glade with V. cholerae strains that caused an outbreak in the Philippines in 2011. The V. cholerae strains responsible for the Korean and Philippines outbreaks have almost identical genomes in which two unique genomic islands are shared, and they both lack SXT elements. Furthermore, we confirm that seawater is the likely source of this outbreak, which suggests the necessity for future routine surveillance of South Korea's seashore.

Impact of the Metabolic Syndrome on the Clinical Outcome of Patients with Acute ST-Elevation Myocardial Infarction

We sought to determine the prevalence of metabolic syndrome (MS) in patients with acute myocardial infarction and its effect on clinical outcomes. Employing data from the Korea Acute Myocardial Infarction Registry, a total of 1,990 patients suffered from acute ST-elevation myocardial infarction (STEMI) between November 2005 and December 2006 were categorized according to the National Cholesterol Education Program-Adult Treatment Panel III criteria of MS. Primary study outcomes included major adverse cardiac events (MACE) during one-year follow-up. Patients were grouped based on existence of MS: group I: MS (n=1,182, 777 men, 62.8±12.3 yr); group II: Non-MS (n=808, 675 men, 64.2±13.1 yr). Group I showed lower left ventricular ejection fraction (LVEF) (P=0.005). There were no differences between two groups in the coronary angiographic findings except for multivessel involvement (P=0.01). The incidence of in-hospital death was higher in group I than in group II (P=0.047), but the rates of composite MACE during one-year clinical follow-up showed no significant differences. Multivariate analysis showed that low LVEF, old age, MS, low high density lipoprotein cholesterol and multivessel involvement were associated with high in-hospital death rate. In conclusion, MS is an important predictor for in-hospital death in patients with STEMI

Impact on environment, ecosystem, diversity and health from culturing and using GMOs as feed and food

Modern agriculture provides the potential for sustainable feeding of the world's increasing population. Up to the present moment, genetically modified (GM) products have enabled increased yields and reduced pesticide usage. Nevertheless, GM products are controversial amongst policy makers, scientists and the consumers, regarding their possible environmental, ecological, and health risks. Scientific-and-political debates can even influence legislation and prospective risk assessment procedure. Currently, the scientifically-assessed direct hazardous impacts of GM food and feed on fauna and flora are conflicting; indeed, a review of literature available data provides some evidence of GM environmental and health risks. Although the consequences of gene flow and risks to biodiversity are debatable. Risks to the environment and ecosystems can exist, such as the evolution of weed herbicide resistance during GM cultivation. A matter of high importance is to provide precise knowledge and adequate current information to regulatory agencies, governments, policy makers, researchers, and commercial GMO-releasing companies to enable them to thoroughly investigate the possible risks

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.

A Newly Developed Pericardial Tuberculoma During Antituberculous Therapy

Tuberculosis generally affects the respiratory tract. In developing nations, the pericardium is the most common location of extrapulmonary tuberculosis; however, tuberculous pericarditis rarely appears as a localized mass or tuberculoma. We present here a case of a 62-year-old woman with pericardial tuberculoma. She had a history of effusive tuberculous pericarditis and drainage. Because she had taken regular medication over a period of six months, the pericardial mass with an adjacent lung nodule newly detected on the chest radiogram was initially suspected of being invasive lung cancer. Prior to pathologic confirmation, precise information from imaging tests, including computed tomography, magnetic resonance imaging, and positron emission tomography-computed tomography are helpful when making decisions regarding which methods should be used for surgical approach and treatment. Through imaging, our case showed typical features of pericardial tuberculoma and a favorable clinical course after two months with a change in antituberculous therapy