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Clostridium* ; Molecular Typing*

Animals ; Clostridium difficile ; classification ; genetics ; Humans ; Molecular Typing ; Ribotyping

Bacterial Typing Techniques ; Molecular Biology ; Mycobacterium tuberculosis ; classification ; genetics

BACKGROUND: In the year 1996, there were some outbreaks of Salmonella typhi infection in Pusan and therefore, the incidence of S. typhi infection was markedly increased in comparison with the previous year. To differentiate the isolates epidemiologically, a random amplified polymorphic DNA(RAPD) fingerprinting method has been developed. METHODS: A total of 9 arbitrary primers were screened with S. typhi strains isolated in Pusan, 1996. This allowed selection of a panel of primers capable of detecting DNA polymorphisms among S. typhi isolates. This panel was used to examine 54 strains of S. typhi, which had been isolated in Pusan including the cases of outbreaks that was previously characterized by phage typing. RESULTS: Four single primers and one combination of two primers were selected to discriminate the S. typhi isolates. RAPD analysis resolved the 54 strains into 20 different subtypes. At least two outbreaks were found by RAPD analysis. The isolates of E1 phage type, which are the most common in Korea, were perfectly differentiated with each other, except the strains isolated within the outbreaks. CONCLUSION: The RAPD approach is the useful epidemiologic tool to S. typhi subtyping, which is providing high discriminatory power. There were at least two outbreaks when the epidemic Salmonella infections of Pusan in 1996 had been occurred. The primers or their comb ination capable to discriminate the S. typhi isolates were described.
Animals ; Bacteriophage Typing ; Bacteriophages ; Busan ; Comb and Wattles ; Dermatoglyphics ; Disease Outbreaks ; DNA* ; Incidence ; Korea ; Molecular Typing* ; Salmonella Infections ; Salmonella typhi* ; Salmonella*

OBJECTIVETo identify and characterize the Brucella strains from Guizhou province in 2010-2013.

METHODSA total of 12 strains of Brucella suspicious bacteria were isolated in Guizhou province from 2010 to 2013. Four strains (GZLL3, GZLL4, GZLL11 and SH2) were isolated from goat blood samples and eight strains (SH4, GZZY, GZSQ, GZZA, BR13001, BR13004, BR13005 and BR13006) were isolated from blood samples of patient 12 Brucella suspicious strains were identified and characterized using conventional methods. Brucella genus specific gene BCSP31-based PCR (BCSP31-PCR) was used to identify the genus of Brucella and IS711 insert sequence-based PCR (AMOS-PCR) was applied to identify the species of Brucella strains. Goats and patients originated Brucella strains were comparatively analysed using Pulse-field Gel Electrophoresis (PFGE).

RESULTSBoth of conventional methods and PCR identified the 12 Brucella suspicious strains as B. melitensis biotype 3. BCSP31-PCR identification results showed that a specific DNA bands (223 bp) were detected in all the 12 strains and positive control samples with no DNA band in negative samples. AMOS-PCR amplified a 731 bp-DNA bands in all the 12 strains, with 731 bp, 498 bp and 275 bp in M5, S2 and A19 strains, respectively, and no DNA band was detected in the negative control samples. PFGE analysis showed that 12 Brucella isolates from patients and goats showed consistent PFGE patterns with the digestion of restriction enzyme Xba I.

CONCLUSIONThe epidemic species/type of Brucella in both human and animal in Guizhou province was B. melitensis biotype 3 and goat was the main animal source of infection of brucellosis in Guizhou province.

Animals ; Bacterial Typing Techniques ; Brucella ; classification ; Brucellosis ; epidemiology ; China ; epidemiology ; DNA, Bacterial ; Goats ; Humans ; Molecular Typing ; Polymerase Chain Reaction

Traditional identification of fungi is based on their gross morphology and microscopic findings. It takes a long time and needs experience and sometimes it is difficult because their morphology may change. Nucleic acid detection methods such as PCR have become a common tool for microbial identification and diagnosis. Molecular typing techniques provide information to detect their infection routes. They are fast, sensitive, and reproducible. Pure DNA, the targets, and methods are important for good results. There are lots of techniques like sequencing, RFLP, RAPD, and hybridization. Each method has its advantage and limitation, and proper selection is essential. In clinical application, careful consideration will reduce errors. There is a limited number of reports about cutaneous fungal infection. We review the molecular methods for fungal identification and typing, and discuss the advantages and limitations of the methods.
Diagnosis ; DNA ; DNA, Ribosomal ; Fungi ; Molecular Biology* ; Molecular Typing ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length

Acute Disease ; Adenovirus Infections, Human ; Child ; Humans ; Molecular Epidemiology ; Molecular Typing ; Respiratory Tract Infections

The molecular genetics of colorectal cancers (CRCs) is among the best understood of common human cancers. It is difficult to predict the prognosis and/or to predict chemoresponding in CRC patients. At present, prognosis is based predominantly on the tumor stage and pathological examination of the disease. Molecular classification of CRCs, based on genomics and transcriptomics, proposed that CRCs can be classified into at least three-to-six subtypes, depending on the gene expression pattern, and groups of marker genes representing to each subtype have also been reported. Gene expression-based subtyping is now widely accepted as a relevant source of disease stratification. We reviewed the previous studies on CRC subtyping, international consortium dedicated to large-scale data sharing and analytics recently established four consensus molecular subtypes with distinguishing features. Predictive markers identified in these studies are under investigation and large-scale clinical evaluations of molecular markers are currently in progress.
Classification* ; Colonic Neoplasms ; Colorectal Neoplasms* ; Consensus ; Gene Expression ; Genomics ; Humans ; Information Dissemination ; Molecular Biology ; Molecular Medicine ; Molecular Typing ; Prognosis

BACKGROUND: Vancomycin-resistant enterococci (VRE) have been increasingly reported worldwide. The understanding of VRE dissemination in the hospital requires a molecular typing of the strains. VRE appeared recently in Chonnam University Hospital. The purpose of this study is to analyse the strains for their genetic relatedness. METHODS: Nine vancomycin-resistant E. faecium isolates, collected from six patients during 1995-1996 in Chonnam University Hospital, were typed using plasmid DNA and RAPD analyses. The plasmid DNA of the isolates was obtained by a alkaline lysis method. For RAPD, eight random primers were used. The cluster analysis was performed by NTSYS-pc (numerical taxonomy system and multivariate analysis system, version 1.50, Applied Biostatistics Inc., CA). RESULTS: Nine VRE isolates were separated into two different molecular types (group A and B) by the plasmid DNA patterns, which were agreed with the RAPD results: the isolates of each group showed the same plasmid DNA patterns and high similarity values in the RAPD analysis. Group A was consisted of two strains isolated from two patients who were admitted at the same room in May 1995. Seven strains of group B were isolated from four patients in the different wards during June 1995 to June 1996. CONCLUSIONS: Nine VRE isolates from six patients were typed to two groups by plasmid DNA or RAPD analysis. These results suggested the intrahospital spread of two clonal strains of vancomycin-resistant E. faecium.
Biostatistics ; Classification ; DNA* ; Enterococcus faecium* ; Enterococcus* ; Humans ; Jeollanam-do ; Molecular Typing ; Multivariate Analysis ; Plasmids*

Acinetobacter species encounters frequently with clinical specimens and now accounts for a substantial proportion of endemic nosocomial infections in Korea. Recent trends indicate that the antimicrobial resistant strains of Acinetobacter species are increasing. Sixty-one strains were isolated from specimens of patients suspected of nosocomial infections during 1991 to 1996. At present, phenotypic identification of Acinetobacter using biochemical test may not be reliable and resulted in the difficulty to clarify the source of infections and epidemiological study of hospital-acquired infections. Aware of the importance of rational taxonomic proposal for these isolates, correct species identification of these organisms by molecular typing method was carried out. A total of fifty-four strains of A. calcoaceticus-A. baumannii complex species which were identified to genospecies 2 and 13 by biochemical characteristics was subjected to identify by ribotyping using restriction endonuclease EcoRI, ClaI, and SalI. Of fifty-four strains, twenty-five strains were identified as A. baumannii (genospecies 2) and twenty-one strains as genospecies 13, and six strains changed to genospecies 3, and the rest two strains were confirmed as A. haemolyticus (genospecies 4). This result suggests that the ribotyping may be of value for identification of genospecies and epidemiological information of Acinetobacter strains.
Acinetobacter baumannii* ; Acinetobacter calcoaceticus* ; Acinetobacter* ; Cross Infection ; DNA Restriction Enzymes ; Humans ; Korea ; Molecular Typing ; Ribotyping*