No abstract available.
Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Cefotaxime/analogs & derivatives/therapeutic use ; Cholangiopancreatography, Endoscopic Retrograde ; Gallstones/surgery ; Gram-Negative Anaerobic Bacteria/drug effects/genetics/*isolation & purification ; Gram-Negative Bacterial Infections/*diagnosis/drug therapy/microbiology ; Humans ; Male ; Metronidazole/therapeutic use ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Tomography, X-Ray Computed

Bacterial Proteins ; chemistry ; genetics ; metabolism ; DNA, Bacterial ; chemistry ; genetics ; metabolism ; Gene Expression Regulation, Bacterial ; physiology ; Glutathione ; metabolism ; Listeria monocytogenes ; chemistry ; genetics ; metabolism ; Peptide Termination Factors ; chemistry ; genetics ; metabolism

BACKGROUND: Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. METHODS: In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. RESULTS: ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). CONCLUSIONS: Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
Area Under Curve ; Bacteria/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Candida/*genetics/isolation & purification ; Female ; Fungal Proteins/genetics ; Gardnerella vaginalis/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; ROC Curve ; Sequence Analysis, DNA ; Trichomonas vaginalis/genetics/isolation & purification ; Vagina/*microbiology ; Vaginitis/*diagnosis/microbiology

No abstract available.
Animals ; Anti-Bacterial Agents/pharmacology ; Bites and Stings ; Disk Diffusion Antimicrobial Tests ; Dogs ; Female ; Humans ; Middle Aged ; Pasteurella/drug effects/genetics/*isolation & purification ; Pasteurella Infections/*diagnosis/microbiology ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Republic of Korea ; Sequence Analysis, DNA ; Soft Tissue Infections/*diagnosis/microbiology

No abstract available.
Aged ; Aneurysm/surgery ; Anti-Bacterial Agents/pharmacology ; Brain Diseases/surgery ; Craniotomy/adverse effects ; DNA, Bacterial/chemistry/genetics/metabolism ; Female ; Flavobacteriaceae Infections/etiology/microbiology ; Flavobacterium/classification/drug effects/*isolation & purification ; Humans ; Meningitis/*diagnosis/microbiology ; Microbial Sensitivity Tests ; Phylogeny ; Postoperative Complications ; Sequence Analysis, DNA

No abstract available.
Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/chemistry/genetics/metabolism ; Drug Resistance, Bacterial ; Integrons/*genetics ; Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/*enzymology/isolation & purification ; Sequence Analysis, DNA ; beta-Lactamases/*genetics

No abstract available.
Adult ; Anti-Bacterial Agents/therapeutic use ; Bacterial Proteins/chemistry/genetics/metabolism ; Brucella melitensis/classification/genetics/*isolation & purification ; Brucellosis/*diagnosis/drug therapy/microbiology ; Doxycycline/therapeutic use ; Humans ; Magnetic Resonance Imaging ; Male ; Phylogeny ; Polymerase Chain Reaction ; Republic of Korea ; Rifampin/therapeutic use ; Sequence Analysis, DNA ; Spondylitis/diagnostic imaging

BACKGROUND: We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool. METHODS: A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively. RESULTS: The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes. CONCLUSIONS: By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.
Acinetobacter Infections/*drug therapy/microbiology ; Acinetobacter baumannii/drug effects/*genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Bacterial Proteins/genetics ; Carbapenems/*therapeutic use ; DNA, Bacterial/chemistry/*genetics/metabolism ; Drug Resistance, Bacterial ; Genomic Islands/genetics ; Humans ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Plasmids/genetics/metabolism ; Polymerase Chain Reaction ; Sequence Analysis, DNA

In order to develop a rapid and reliable method for B. cereus genotyping, factors influencing PFGE results, including preparation of bacterial cells embedded in agarose, lysis of embedded cells, enzymatic digestion of intact genomic DNA, and electrophoresis parameters allowing for reproducible and meaningful DNA fragment separation, were controlled. Optimal cellular growth (Luria-Bertani agar plates for 12-18 h) and lysis conditions (4 h incubation with 500 µg/mL lysozyme) produced sharp bands on the gel. Restriction enzyme NotI was chosen as the most suitable. Twenty-two isolates were analyzed by NotI digestion, using three electrophoretic parameters (EPs). The EP-a was optimal for distinguishing between isolates. The optimized protocol could be completed within 40 h which is a significant improvement over the previous methods.
Bacillus cereus ; genetics ; isolation & purification ; Bacteriological Techniques ; DNA, Bacterial ; chemistry ; genetics ; Electrophoresis, Gel, Pulsed-Field ; methods

The objective of this study was to investigate the prevalence of tick-borne pathogens in the Korean water deer (Hydropotes inermis argyropus). Pathogens were identified using PCR which included Anaplasma, Ehrlichia, Rickettsia, and Theileria. Rickettsia was not detected, whereas Anaplasma, Ehrlichia, and Theileria infections were detected in 4, 2, and 8 animals, respectively. The most prevalent pathogen was Theileria. Of the 8 Theileria-positive animals, 2 were mixed-infected with 3 pathogens (Anaplasma, Ehrlichia, and Theileria) and another 2 animals showed mixed-infection with 2 pathogens (Anaplasma and Theileria). Sequencing analysis was used to verify the PCR results. The pathogens found in this study were identified as Anaplasma phagocytophilum, Ehrlichia canis, and Theileria sp. To the best of our knowledge, this is the first report identifying these 3 pathogens in the Korean water deer. Our results suggest that the Korean water deer may serve as a major reservoir for these tick-borne pathogens, leading to spread of tick-borne diseases to domestic animals, livestock, and humans. Further studies are needed to investigate their roles in this respect.
Anaplasma/isolation & purification ; Animals ; Bacterial Infections/epidemiology/microbiology/*veterinary ; Cluster Analysis ; Coinfection/epidemiology/microbiology/veterinary ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Ehrlichia/*isolation & purification ; Korea/epidemiology ; Molecular Sequence Data ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Rickettsia/*isolation & purification ; Ruminants/*microbiology ; Sequence Analysis, DNA ; Theileria/*isolation & purification