OBJECTIVETo analyze the genetic relations of Shigella isolated from Shenzhen in 2001-2006 and develop primary molecular subtyping surveillance network of Shigella.

METHODSChromosomal DNAs from 55 isolated in agarose were digested with the restriction enzyme Xba I, and then were analyzed by pulsed-field gel electrophoresis. Pulsed-field gel electrophoresis (PFGE) patterns were clustered using BioNumerics software.

RESULTSAll 41 distinctive PFGE patterns were identified among 55 strains. 32 strains belonged to one cluster. Differences were observed in other strains.

CONCLUSIONBoth genetic-related clones and non-related clones of Shigella existed in Shenzhen. The development of PFGE molecular subtyping surveillance network would contribute to the active surveillance, outbreak investigation and source tracking for Shigellosis.

Bacterial Typing Techniques ; China ; Electrophoresis, Gel, Pulsed-Field ; methods ; Feces ; microbiology ; Humans ; Shigella ; classification ; isolation & purification

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

OBJECTIVETo develop a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Acinetobacter pittii typing.

METHODSPolymorphic VNTRs were searched by Tandem Repeats Finder. The distribution and polymorphism of each VNTR locus were analyzed in all the A. pittii genomes deposited in the NCBI genome database by BLAST and were evaluated with a collection of 20 well-characterized clinical A. pittii strains and one reference strain. The MLVA assay was compared with pulsed-field gel electrophoresis (PFGE) for discriminating A. pittii isolates.

RESULTSTen VNTR loci were identified upon bioinformatic screening of A. pittii genomes, but only five of them showed full amplifiability and good polymorphism. Therefore, an MLVA assay composed of five VNTR loci was developed. The typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. Compared with PFGE, the new optimized MLVA typing scheme provided the same and even greater discrimination.

CONCLUSIONCompared with PFGE, MLVA typing is a faster and more standardized alternative for studying the genetic relatedness of A. pittii isolates in disease surveillance and outbreak investigation.

Acinetobacter ; classification ; genetics ; DNA Fingerprinting ; methods ; Electrophoresis, Gel, Pulsed-Field ; Minisatellite Repeats ; Polymerase Chain Reaction

OBJECTIVETo develop fluorescent amplified fragment length polymorphism (AFLP) method and to evaluate the its typing capability with pulsed-field gel electrophoresis (PFGE) in molecular typing of Vibrio cholerae.

METHODSForty-seven strains of V. cholerae, with different PFGE patterns, were selected as the reference group to optimize the selective primers of AFLP analysis. Eighty-three strains including 20 strains from one epidemic episode, isolated from different provinces during 1961 and 2005, were used to compare the typing abilities of AFLP and PFGE. LI-COR4300 DNA sequencing system was used for AFLP electrophoresis. The images were recorded by Saga(MX) software and transferred to BioNumerics for clustering analysis. A standard protocol for V. cholerae from PulseNet was used in PFGE.

RESULTSWhen comparison was made with different selective primers on AFLP based on the 47 strains, results showed that the optimized selective primer pair was EcoR I-G/Mse I-T, and the reproducibility of the tests was 99.2%. Eighty-three isolates showed 52 AFLP patterns and 44 PFGE patterns, with D values as 0.9545 (AFLP) and 0.9251 (PFGE) respectively.

CONCLUSIONThe protocol of fluorescent AFLP on V. cholerae typing was established. AFLP was higher than PFGE in discrimination of V. cholerae which could be used for molecular typing. When combined with PFGE, AFLP became a more insightful tool to identify genome difference of different isolates.

Amplified Fragment Length Polymorphism Analysis ; methods ; Electrophoresis, Gel, Pulsed-Field ; Genotype ; Phylogeny ; Vibrio cholerae ; classification ; genetics

OBJECTIVETo determine the genetic relationships between different Vibrio cholerae isolates in Shenzhen from 1993 to 2002.

METHODSChromosomal DNA from 60 isolates was digested in seakem gold agrose with restriction enzyme Not I and plugs were then analyzed by pulsed-field gel electrophoresis. Pulsed-field gel electrophoresis (PFGE) patterns of V. cholerae isolates were clustered using BioNumerics software.

RESULTS39 distinctive PFGE patterns were identified with each pattern having 20 to 30 bands. Most PFGE patterns were divided into cluster A or cluster B.

CONCLUSIONThe closely related pandemic clone clusters of V. cholerae strains did exist in Shenzhen. PFGE of V. cholerae could be used for active surveillance and tracking for cholerae.

China ; epidemiology ; Cholera ; epidemiology ; microbiology ; Electrophoresis, Gel, Pulsed-Field ; methods ; Humans ; Phylogeny ; Vibrio cholerae ; classification ; genetics

OBJECTIVETo establish and compare the pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and automated ribotyping for subtyping of Citrobacter strains.

METHODSPFGE protocol was optimized in terms of plug preparation procedure, restriction enzymes and configuration of electrophoretic parameters. MLVA method was evaluated by finding variable number tandem repeats in two genomes of Citrobacter strains. The ribotyping was performed by using the automated RiboPrinter system.

RESULTSWe optimized the plug preparation procedure, focused on the cell suspension concentration (turbidity of 2.5 to 3.5), SDS addition (no SDS needed) and lysis time (1 h), and selected the appropriate restriction enzyme (XbaI) and the electrophoretic parameters (1.0 s-20.0 s for 19 h) of PFGE. There was nearly no discriminatory power of MLVA between Citrobacter strains. For 51 Citrobacter strains, automated ribotyping gave a D-value of 0.9945, while PFGE gave a D-value of 0.9969. Both PFGE and automated ribotyping clustered strains from the same sources (with the same species from the same place at the same time identified as the same source) and divided strains from different sources (from different years, places and hosts) into different subtypes.

CONCLUSIONPFGE protocol established in this paper and automated ribotyping are suitable for application in Citrobacter subtyping.

Automation ; Citrobacter ; classification ; genetics ; Electrophoresis, Gel, Pulsed-Field ; methods ; Minisatellite Repeats ; genetics ; Multilocus Sequence Typing ; methods ; Phylogeny ; Ribotyping ; methods

OBJECTIVETo apply pulse-field gel electrophoresis analysis(PFGE) in analysing a case of food poisoning caused by Vibrio parahaemolyticus.

METHODSPFGE using restriction enzyme Not I was employed in molecular subtyping of thirty strains of V. parahaemolyticus isolated from a case of food poisoning in Guangzhou city and PFGE patterns were analyzed by using BioNumerics Version 4.0 software to perform cluster analysis. Pattern profiles were compared by using the Dice coefficient and unweighted pair group method with arithmetic averages (UPGMA).

RESULTSThirty strains were of the same type of pulsotype.

CONCLUSIONSMolecular subtyping by PFGE might disclose the epidemiological relationships of the strains from humans, food and the environment, giving a strong molecular epidemiological evidence and a support for the source-tracking of outbreak events.

Bacterial Typing Techniques ; methods ; China ; Electrophoresis, Gel, Pulsed-Field ; methods ; Foodborne Diseases ; microbiology ; Humans ; Vibrio parahaemolyticus ; classification ; genetics ; isolation & purification

OBJECTIVETo evaluate the feasibility of the application of variable-number tandem repeat (VNTR) loci of Salmonella Enteritidis (S. enteritidis) in subtyping mutiple-locus variable-number tandem repeat analysis (MLVA).

METHODSA total of 16 isolates of S.enteritidis from different place and time in China were preliminarily assessed by choosing 11 reported VNTR loci, the loci with single amplified bands were picked to subtype all 104 S. enteritidis isolates. The isolates were also analyzed by pulse field gel electrophoresis (PFGE) to compare the superiority or inferiority of MLVA method and PFGE method.

RESULTSSeven VNTR loci were selected from the preliminary screening to expand the analysis, and the 7 VNTR loci had grouped 104 of S.enteritidis isolates into either 16 MLVA subtypes or 22 PFGE subtypes, with the D value at 0.7222 and 0.7974, respectively. Comparing with the isolates in MLVA subtypes, the isolates in PFGE showed a stronger resolving power. Meanwhile the results in PFGE showed a more disperse frequency distribution than those in MLVA.

CONCLUSIONThese results indicate that some VNTR locus which have shown a good polymorphism internationally, may fail to show polymorphism in China, thereby, more VNTR loci should be included in MLVA and the wide screening may benefit the unity of global laboratorial methods.

Bacterial Typing Techniques ; methods ; Electrophoresis, Gel, Pulsed-Field ; Minisatellite Repeats ; Multilocus Sequence Typing ; methods ; Salmonella enteritidis ; classification ; genetics

OBJECTIVETo develop a pulsed field gel electrophoresis (PFGE) method for molecular typing of Lactobacillus and Streptococcus thermophilus (S. thermophilus) and to apply it in identification and characterization of both bacteria isolated from yoghurt collected from Beijing supermarket.

METHODSThe five most useful restriction enzymes including Apa I, Not I, Sfi I, Xba I and Sma I were chosen to cut DNA of 52 strains of Lactobacillus, S. thermophilus as well as associated standard bacteria strains. The endonucleases and electrophoresis conditions for PFGE analysis were optimized and applied in molecular typing of Lactobacillus and S.thermophilus isolates. Cluster analysis based on the PFGE data was conducted. The identification results of PFGE were compared with those obtained in biochemical and 16s ribosomal RNA PCR identification tests.

RESULTSNot I was suitable for L. bulgaricus, L. fermentum and L. delbrueckii digestion. While Apa I was an appropriate endonuclease for S. thermophilus, L. acidophilus and L. casei digestion. The results of molecular typing indicated that 24 strains of L.bulgaricus and 15 strains of S. thermophilus were grouped into 8 types by PFGE method, respectively. While 7 strains of L.acidophilus were grouped into 3 types and 2 strains of L. delbrueckii were grouped into 2 different PFGE types.

CONCLUSIONThe results of PFGE analysis are in compliance with those of 16s rRNA PCR and biochemical identification. The PFGE method developed in this study is suitable for molecular characterization of both Lactobacillus and S. thermophilus.

Bacterial Typing Techniques ; methods ; Electrophoresis, Gel, Pulsed-Field ; methods ; Lactobacillus ; classification ; isolation & purification ; Streptococcus thermophilus ; classification ; isolation & purification

OBJECTIVETo analyze the characteristics of Sequence-based Typing (SBT) of the Serotype 1 Legionella pneumophila (Lp1) isolated from environmental water in China, and then create a preliminary database.

METHODSA total of 82 strains of Lp1 isolated from environmental water in 9 provinces of China between 2005 and 2008 were genotyped by SBT method and Pulsed-field Gel Electrophoresis (PFGE) method. The results of the two different typing methods were then compared by cluster analysis, adopting BioNumerics version 5.1 software.

RESULTSBy SBT method, the 82 strains of Lp1 were divided into 22 ST types, of which 17 new types and one new allele was discovered. The dominant type was ST-1 type, found in 8 provinces, accounting for 46.3% (38/82). ST-1, ST-150, ST-154, ST-159, ST-160 and ST-630 types were found in more than 2 isolated-sites; while more than 2 different ST types were found in 5 isolated-sites, as site B4, B5, B6, S3 and S8. In cluster analysis, 15 ST types were grouped into three complexes (ST-1 complex, ST-154 complex and ST-149 complex); and the other 7 ST types were not assigned complex. By PFGE method, 46 banding patterns were observed. As a result of the combination of the two methods, the 82 isolates strains could be divided into 54 molecular types, which showed a reliable accordance in the cluster analysis between the two methods.

CONCLUSIONThe SBT of the Lp1 in environmental water in China was unique. From the study, a preliminary SBT database was set up.

China ; Cluster Analysis ; Electrophoresis, Gel, Pulsed-Field ; Genotype ; Legionella pneumophila ; classification ; genetics ; isolation & purification ; Serotyping ; methods ; Water Pollution