OBJECTIVETo provide further pathogenic evidence of Granulocytic ehrlichia infection in China.

METHODSSpecific primers derived from 444-Epank gene were used to amplify Granulocytic ehrlichia DNA from specimens of ticks, animals and human blood. PCR products of ticks were cloned and sequenced.

RESULTS444 bp specific DNA fragments were amplified from 2 of 62 pools of Ixodes persulcatus collected from Heilongjiang province and 1 of 129 blood specimens from forest workers in Inner Mongolia. Eight animal specimens were negative. PCR products from ticks were then cloned and sequenced. It differed at 23 positions in comparison to American strain (AF047897) with 94.9% homology. The homology of deduced ammonia was 88.44%.

CONCLUSIONOur findings further confirmed that Granulocytic ehrlichia infection did exist in China.

DNA, Bacterial ; analysis ; Ehrlichia ; classification ; genetics ; isolation & purification ; Ehrlichiosis ; microbiology ; Genes, Bacterial ; Humans ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA

Animals ; Borrelia burgdorferi ; genetics ; China ; DNA, Bacterial ; genetics ; isolation & purification ; Rodentia ; microbiology ; Sequence Analysis, DNA

The application potential of rep-PCR in typing beer-spoilage isolates was studied. The effects of different factors, including DNA templates and primers, on the quality and reproducibility of fingerprints were investigated. The CTAB protocol was shown to be the feasible method for DNA extraction. Primers BOXA1R and (GTG)5 were used in rep-PCR, and the PCR products were sequenced to identify strains isolated from two breweries. Rep-PCR fingerprint profiles were obtained by using GelCompar II software. Cluster analysis showed that the isolates belonging to Lactobacillus brevis, L. buchneri, L. casei/paracasei, L. plantarum are divided into 2 or 3 subgroups. In addition, the two rep-PCR fingerprint profiles complemented with each other in typing these isolates. Combining the similarity coefficient cut-off (SCC) of species, 9 unknown isolates were identified rapidly by using both fingerprint databases. The results indicate that rep-PCR is a simple, reliable and promising method for rapid identification of beer-spoilager.
Beer ; microbiology ; Cluster Analysis ; DNA Fingerprinting ; methods ; DNA, Bacterial ; genetics ; isolation & purification ; Databases, Genetic ; Lactobacillus ; genetics ; isolation & purification ; physiology ; Polymerase Chain Reaction ; methods ; Sequence Analysis, DNA ; Time Factors

The aim of this study was to establish a fast and accurate method for developing specific DNA sequences and PCR primers for the detection of Staphylococcus aureus. An automatic C++ program for genomic comparison was used to identify specific DNA sequences from the genome of S. aureus MRSA 252. Four primer pairs were obtained from 9 specific target sequences by comparison of 2656 coding sequences with our local genome database, and 2 pairs of primers were confirmed to be specific to S. aureus by PCR evaluation against 137 bacterial strains, including 11 species of Staphylococcus. Furthermore, the DNA detection sensitivity of primer SA3 was 13.7 fg/microL and the cell sensitivity for this primer was 9.25 x 10(2) CFU/mL. This method has overcome the limitations of specific target mining in conventional assays, and it could be easily and widely used for other foodborne pathogens.
DNA Primers ; DNA, Bacterial ; analysis ; genetics ; Genome, Bacterial ; genetics ; Genomics ; methods ; Polymerase Chain Reaction ; methods ; Sequence Analysis, DNA ; methods ; Software ; Staphylococcus aureus ; genetics ; isolation & purification

OBJECTIVETo explore the feasibility of using gene chip method to identify pathogens in blood cultures.

METHODSClinical blood samples were obtained and cultured using an automated blood culture system. A gene chip diagnostic kit was used to detect the pathogenic bacteria in these blood cultures following the procedures of target gene extraction and amplification, hybridization and result analysis. The conventional method was also used to isolate and identify the bacteria from the clinical blood cultures, and the results of the two methods were compared.

RESULTSIn the 86 clinical blood samples, 74 were positive and 12 negative according to the conventional method, while 48 were positive and 38 negative as found by the gene chip method, showing significant differences in the results (P<0.05). The two methods only had a concordance rate of 69.77%.

CONCLUSIONThe gene chip diagnostic kit has low concordance rate with the conventional method for detecting pathogens in clinical blood cultures and awaits further improvement.

Bacteria ; genetics ; growth & development ; isolation & purification ; Bacterial Typing Techniques ; methods ; Blood ; microbiology ; DNA, Bacterial ; analysis ; genetics ; isolation & purification ; Humans ; Oligonucleotide Array Sequence Analysis ; methods ; RNA, Ribosomal, 16S ; genetics

OBJECTIVETo develop a rapid and definite diagnostic test of bacterial enteritis caused by pathogenic enterobacteria, the most frequent etiologic agent of infectious enteritis in the world.

METHODSA set of conventional PCR assays were applied to detect and identify salmonella, shigella, and E. coli O157:H7 directly from pure culture and fecal samples. The general primers of pathogenic enterobacteria were located on the uidA gene, which were found not only in E. coli nuclear acid, but also in shigella and salmonella genes. Shigella primer was from ipaH gene whose coded invasive plasmid relative antigen existed both in plasmid and in genome. The primers of salmonella were designed from the 16SrRNA sequence. The primer of E. coli O157:H7 was taken from eaeA gene. Five random primers were selected for RAPD. The detection system included common PCR, semi-nested PCR and RAPD.

RESULTSThis method was more sensitive, specific and efficient and its processing was rapid and simple. For example, the method could be used to specifically detect and identify salmonella, shigella, and E. coli O157:H7, and its sensitivity ranged from 3 to 50 CFU, and its detection time was 4 hours.

CONCLUSIONThis PCR method, therefore, can serve as a routine and practical protocol for detecting and identifying pathogenic microorganisms from clinical samples.

DNA Primers ; DNA, Bacterial ; analysis ; Escherichia coli O157 ; isolation & purification ; Feces ; microbiology ; Humans ; Polymerase Chain Reaction ; Salmonella typhi ; isolation & purification ; Sensitivity and Specificity ; Shigella flexneri ; isolation & purification

OBJECTIVETo identify the relationship between amino acid mutations in Neisseria gonorrhoeae isolates and their antibiotic resistance.

METHODSPI gene fragments of Neisseria gonorrhoeae from 17 clinical isolates were obtained with PCR amplification. They were cloned into the PCR cloning vector pBS-T to form pBS-T-PI and sequenced. The sequences of PI genes were analyzed. At the same time, minimum inhibitory concentration (MIC) of penicillin and tetracycline to these 17 isolates were measured and contrasted with the corresponding PI sequence.

RESULTSThe recombinants of PI gene from 17 clinical isolates of Neisseria gonorrhoeae were successfully constructed and sequenced. They were divided into PIA and PIB subtypes according to the results from blastn software by comparing the sequences with the GenBank. Mutations were found at the sites of 120 and 121. There were only some of the sequences having an aspartic acid (D) mutation on 120 and 121 sites, which was not the same as reported. On the other hand,there were two PI sequences,5-9 and 6-1, whose mutations on No. 120 were lysine, similar to those documented.

CONCLUSIONSome relationship between PI amino acids mutations at sites 120 and 121 in Neisseria gonorrhoeae isolates from Chengdu, China and their resistance to penicillin and tetracycline were found. However,further studies need to be done in the future to confirm this hypothesis.

Amino Acid Sequence ; Anti-Bacterial Agents ; pharmacology ; DNA Mutational Analysis ; DNA, Bacterial ; Drug Resistance, Bacterial ; Mutation ; Neisseria gonorrhoeae ; drug effects ; genetics ; isolation & purification ; Polymerase Chain Reaction

BACKGROUND: The aims of this study were to compare several DNA extraction methods and 16S rDNA primers and to evaluate the clinical utility of broad-range PCR in continuous ambulatory peritoneal dialysis (CAPD) culture fluids. METHODS: Six type strains were used as model organisms in dilutions from 10(8) to 100 colony-forming units (CFU)/mL for the evaluation of 5 DNA extraction methods and 5 PCR primer pairs. Broad-range PCR was applied to 100 CAPD culture fluids, and the results were compared with conventional culture results. RESULTS: There were some differences between the various DNA extraction methods and primer sets with regard to the detection limits. The InstaGene Matrix (Bio-Rad Laboratories, USA) and Exgene Clinic SV kits (GeneAll Biotechnology Co. Ltd, Korea) seem to have higher sensitivities than the others. The results of broad-range PCR were concordant with the results from culture in 97% of all cases (97/100). Two culture-positive cases that were broad-range PCR-negative were identified as Candida albicans, and 1 PCR-positive but culture-negative sample was identified as Bacillus circulans by sequencing. Two samples among 54 broad-range PCR-positive products could not be sequenced. CONCLUSIONS: There were differences in the analytical sensitivity of various DNA extraction methods and primers for broad-range PCR. The broad-range PCR assay can be used to detect bacterial pathogens in CAPD culture fluid as a supplement to culture methods.
Bacillus/genetics/isolation & purification ; Bacteria/genetics/*isolation & purification ; Candida albicans/genetics/isolation & purification ; DNA Primers/genetics ; DNA, Bacterial/*analysis/isolation & purification ; *Genetic Techniques/standards ; Humans ; Peritoneal Dialysis, Continuous Ambulatory ; Peritonitis/*microbiology ; Polymerase Chain Reaction ; Reagent Kits, Diagnostic ; Sequence Analysis, DNA

OBJECTIVETo study the resistance phenotype and homology of Klebsiella pneumoniae (KPN) in burn patients with infection.

METHODSFifty-four strains of KPN were isolated from wound excretion, blood, sputum, venous catheter, feces, and oral cavity of patients hospitalized in Institute of Burn Research of Southwest Hospital (briefly called our institute) from January 2007 to June 2011. Drug resistance of the 54 strains of KPN to 18 antibiotics commonly used in clinic, including ampicillin, ticarcillin, etc, was tested by K-B paper disk diffusion method after being identified. Extended-spectrum β-lactamase (ESBL)-producing KPN was screened based on the drug resistance result. The positive rates of drug-resistant genes SHV, TEM, and CTX-M of the ESBL-producing KPN were detected by polymerase chain reaction. The homology of the ESBL-producing KPN was analyzed by pulse field gel electrophoresis and clustering methodology. The homology of ESBL-producing KPN isolated in each year was analyzed too.

RESULTS(1) The sensitive rate of the 54 strains of KPN to imipenem, meropenem, and ertapenem was respectively 96.30%, 92.59%, and 81.48%, that of these strains to cefotetan and cefoxitin was respectively 70.37% and 64.81%, and that of these strains to ceftazidime was 57.41%. The sensitive rates of the 54 strains of KPN to the other antibiotics were all lower than 40.00%. (2) Twenty-six ESBL-producing KPN strains were screened and the positive rate of SHV, TEM, and CTX-M was 96.15% (25/26), 76.92% (20/26), and 57.69% (15/26), respectively. Detection rate of ESBL-producing KPN strains carrying three genes at the same time was 42.31% (11/26), that of these strains carrying both SHV and TEM was 34.62% (9/26), and those of these strains carrying only a single gene were all less than 10.00%. (3) The twenty-six ESBL-producing KPN were classified into 9 gene types, with 30.77% (8/26) in type A, 19.23% (5/26) in type B, 15.38% (4/26) in type C, 11.54% (3/26) in type D, 7.69% (2/26) in type E, and the rest four strains respectively in type F, G, H, I [3.85% (1/26)]. (4) The major gene type of ESBL-producing KPN in the year of 2007 and 2010 was type A, respectively accounting for 2/3 and 1/2, while that in the year of 2009 was type B, accounting for 1/2. The three strains in 2008 was respectively in type C, E, and F. The four strains in 2011 was respectively in type A, D, H, I.

CONCLUSIONSKPN in burn patients with infection in our institute are highly resistant to commonly used antibiotics in clinic, but carbapenems antibiotics can be used for the treatment. Most of the ESBL-producing KPN strains carry two or three drug-resistant genes, and the main gene type of them is type A.

Anti-Bacterial Agents ; pharmacology ; Burns ; microbiology ; Carbapenems ; pharmacology ; DNA, Bacterial ; analysis ; Drug Resistance, Bacterial ; genetics ; Genes, Bacterial ; Humans ; Klebsiella pneumoniae ; genetics ; isolation & purification ; Microbial Sensitivity Tests ; Sequence Homology

OBJECTIVETo analyze the genetic differences of Orientia tsutsugamushi (Ot) Sta56 gene between Shandong isolates and other strains deposited in GenBank.

METHODSPCR and restriction fragment length polymorphism (RFLP) were used to amplify the complete sequence of Ot-Sta56 gene. RFLP profiles of Ot were predicted by a computer program according to their complete sequences of Ot-Sta56 gene. PCR amplicon from XDM2 strain was sequenced and analyzed by Clustal X (1.8) and PHYLIP software.

RESULTSThe complete sequences (about 1.6 kbp) of Ot-Sta56 gene were amplified from B16 strain (isolated from patients), FXS2 strain (isolated from A. agrarius) and XDM2 strain. Four species of restriction endonucleases (Hha I, Hinf I, Hae III, Pst I) were used to digest the PCR amplicons from the 3 isolates. When comparing with the RFLP profiles of prototype Ot, the RFLP profiles of PCR amplicons from the 3 isolates were similar to those of Japan Kawasaki strain, but were quite different from the international reference strains Gilliam, Karp, Kato. Results from DNA sequence analysis showed that the complete sequence of Ot-Sta56 gene homology to Japan Kawasaki strain of XDM2 strain was 97%, and deduced amino acid sequence was 92%.

CONCLUSIONData from the complete sequence of Sta56 gene indicated that the genotypes of Ot isolates in Shandong province were similar, but with distinction from the Kawasaki strain.

Amplified Fragment Length Polymorphism Analysis ; Antigens, Bacterial ; genetics ; Bacterial Proteins ; genetics ; Bacterial Typing Techniques ; classification ; DNA, Bacterial ; genetics ; Genes, Bacterial ; Membrane Proteins ; genetics ; Orientia tsutsugamushi ; genetics ; isolation & purification ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA