Objective:To explore the hypothesis of "pathogen storage pool" by analyzing the local microbial community of adenoids. Methods:Under the guidance of a 70° nasal endoscope, sterile swabs were used to collect secretions from the adenoid crypts of the subjects. The samples were sent to the laboratory for DNA extraction and standard bacterial 16S full-length sequencing analysis. Results:At the species level, the top three microbial communities in adenoid crypts were Bacillus subtilis（18.78%）, Fusobacterium pyogenes（11.42%）, and Streptococcus pneumoniae（9.38%）. Conclusion:The local microbial community of adenoids exhibits a high degree of diversity, including microbial communities from the oral cavity and gastrointestinal tract. Our research results support the hypothesis that adenoids act as a " pathogen reservoir".
Humans ; Adenoids/microbiology* ; RNA, Ribosomal, 16S/genetics* ; Microbiota/genetics* ; Streptococcus pneumoniae/isolation & purification* ; Bacillus subtilis/genetics* ; DNA, Bacterial/analysis*

Adolescent ; Adult ; Aged ; Aged, 80 and over ; Air Microbiology ; Bacteria/isolation & purification* ; Child ; Child, Preschool ; China/epidemiology* ; DNA, Bacterial/analysis* ; DNA, Ribosomal/analysis* ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Pneumonia, Bacterial/microbiology* ; Risk Assessment/methods* ; Young Adult

Objective: To evaluate multidrug resistant loop-mediated isothermal amplification (MDR-LAMP) assay for the early diagnosis of multidrug-resistant tuberculosis and to compare the mutation patterns associated with the Methods: MDR-LAMP assay was evaluated using 100 Results: The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MDR-LAMP were 85.5%, 93.6%, 96.7%, and 74.4% for the detection of resistance to isoniazid and rifampicin, respectively, and 80.5%, 92.3%, 98.6%, and 41.4% for the detection of Conclusion MDR-LAMP is a rapid and accessible assay for the laboratory identification of rifampicin and isoniazid resistance of
Antitubercular Agents ; Bacterial Proteins/genetics* ; Catalase/genetics* ; DNA, Bacterial/analysis* ; DNA-Directed RNA Polymerases/genetics* ; Drug Resistance, Multiple, Bacterial/genetics* ; Isoniazid ; Molecular Diagnostic Techniques/methods* ; Mutation ; Mycobacterium tuberculosis/isolation & purification* ; Nucleic Acid Amplification Techniques/methods* ; Oxidoreductases/genetics* ; Phenotype ; Rifampin ; Whole Genome Sequencing

Objective: To analyze the effect of the identification and evaluation of Escherichia (E.) coli and Shigella, based on the upstream flanking sequences of CRISPR1. Methods: Both CRISPR and cas sequences were obtained through the BLAST with repeating sequences against the publicly complete genome in GenBank that related to E. coli and Shigella. Clustal X was used to perform multi-sequences alignment of the flanking sequences. PCR method was used to amplify the upstream flanking sequences of CRISPR1 in order to appraise the effect of identification and evaluation of upstream flanking sequences on E. coli and Shigella, which were based on the upstream flanking sequences of CRISPR1. Results: The results showed that 73.4% of the strains containing the I-E CRISPR/Cas that belonged to the phylogroups A, B1, D while 8.4% strains carried the I-F CRISPR/Cas. Another 17.2% of the strains owned CRISPR3-4 (non-CRISPR/Cas) only belonged to the phylogroups B2. All the Shigella strains carried I-E CRISPR/Cas. More than 99% of similarity the CRISPR1 upstream-flanking sequences was seen in E. coli (except B2) and Shigella and E. coli (B2). Both sensitivity and specificity were greater than 91% after PCR amplification in the region to identify the E.coli and Shigella. Conclusion: The upstream of CRISPR1 could achieve a preliminary identification effect on E.coli and Shigella.
Clustered Regularly Interspaced Short Palindromic Repeats/genetics* ; DNA, Bacterial/genetics* ; Escherichia coli/isolation & purification* ; Genotype ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA ; Shigella/isolation & purification*

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

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

PURPOSE: The detection of high-level tetracycline-resistant strains of Neisseria gonorrhoeae (TRNG) can make important epidemiological contributions that are relevant to controlling infections from this pathogen. In this study, we aimed to determine the incidence of TRNG isolates over time and also to investigate the characteristics and genetic epidemiology of these TRNG isolates in Korea. MATERIALS AND METHODS: The antimicrobial susceptibilities of 601 isolates of N. gonorrhoeae from 2004 to 2011 were tested by standard Clinical and Laboratory Standards Institute methods. To determine the molecular epidemiological relatedness, N. gonorrhoeae multi-antigen sequence typing was performed. RESULTS: The incidence of TRNG increased from 2% in 2004 to 21% in 2011. The minimum inhibitory concentration distributions of ceftriaxone and susceptibility of ciprofloxacin in TRNG were different from non-TRNG and varied according to the year of isolation. Most of the TRNG isolates collected from 2004 to 2007 exhibited genetic relatedness, with sequence type (ST) 1798 being the most common. From 2008 to 2011, the STs of the isolates became more variable and introduction of genetically unrelated TRNG were noted. CONCLUSION: The increased incidence of TRNG strains until 2007 appears to be due, at least in part, to clonal spread. However, we propose that the emergence of various STs since 2008 could be associated with foreign import.
Anti-Bacterial Agents/*pharmacology ; Ceftriaxone/pharmacology ; Ciprofloxacin/pharmacology ; DNA, Bacterial/analysis ; Drug Resistance, Multiple, Bacterial/*genetics ; Gonorrhea/drug therapy/epidemiology/microbiology ; Humans ; Incidence ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Neisseria gonorrhoeae/*drug effects/*genetics/isolation & purification ; Republic of Korea/epidemiology ; Sequence Analysis, DNA ; Tetracycline/pharmacology ; Tetracyclines/*pharmacology

PURPOSE: Diagnosis of extrapulmonary tuberculosis (EPTB) poses serious challenges. A careful selection of appropriate gene targets is essential for designing a multiplex-polymerase chain reaction (M-PCR) assay. MATERIALS AND METHODS: We compared several gene targets of Mycobacterium tuberculosis, including IS6110, devR, and genes encoding MPB-64 (mpb64), 38kDa (pstS1), 65kDa (hsp65), 30kDa (fbpB), ESAT-6 (esat6), and CFP-10 (cfp10) proteins, using PCR assays on 105 EPTB specimens. From these data, we chose the two best gene targets to design an M-PCR. RESULTS: Among all gene targets tested, mpb64 showed the highest sensitivity (84% in confirmed cases and 77.5% in clinically suspected cases), followed by IS6110, hsp65, 38kDa, 30kDa, esat6, cfp10, and devR. We used mpb64+IS6110 for designing an M-PCR assay. Our M-PCR assay demonstrated a high sensitivity of 96% in confirmed EPTB cases and 88.75% in clinically suspected EPTB cases with a high specificity of 100%, taking clinical diagnosis as the gold standard. CONCLUSION: These M-PCR results along with the clinical findings may facilitate an early diagnosis of EPTB patients and clinical management of disease.
Bacteriological Techniques/methods ; DNA Transposable Elements/genetics ; DNA, Bacterial/analysis/genetics ; Early Diagnosis ; Female ; Gene Amplification ; Humans ; Male ; Multiplex Polymerase Chain Reaction/*methods ; Mycobacterium tuberculosis/genetics/*isolation & purification ; Polymerase Chain Reaction/*methods/standards ; Sensitivity and Specificity ; Tuberculosis/*diagnosis

No abstract available.
Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteremia/blood/*diagnosis/microbiology ; C-Reactive Protein/analysis ; Cholecystitis/blood/cerebrospinal fluid/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/drug effects/isolation & purification/metabolism ; Humans ; Male ; Microbial Sensitivity Tests ; Microscopy, Electron, Scanning ; Ochrobactrum/drug effects/isolation & purification/*metabolism ; RNA, Ribosomal, 16S/analysis/genetics/metabolism ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

No abstract available.
Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; Ceftriaxone/pharmacology/therapeutic use ; Ciprofloxacin/pharmacology/therapeutic use ; DNA, Bacterial/analysis/metabolism ; Disk Diffusion Antimicrobial Tests ; *Drug Resistance, Bacterial ; Female ; Humans ; Neisseria meningitidis/drug effects/genetics/*isolation & purification ; Polymerase Chain Reaction ; Sepsis/*diagnosis/drug therapy/microbiology ; Transcription Factors/genetics ; Young Adult