Biofilms ; Biomedical Research ; DNA, Bacterial

Recombinant bacterial vector vaccines have been widely used as carriers for the delivery of protective antigens and nucleic acid vaccines to prevent certain infectious diseases because of their ability to induce mucosal immunity, humoral immunity and cellular immunity. However, protective antigens and nucleic acids recombined into bacterial vector vaccines are difficult to be released into host cells because of the presence of bacterial cell wall. Vaccine strains that are residual in animals or livestock products may also cause environmental contamination and spread of the vaccine strains. The effective solution for these problems is to construct an auto-lysis system that can regulate the vaccine strains to grow normally in vitro while lysis in vivo. The lysis systems that have been applied in germs mainly include: the lysis system based on regulated delayed peptidoglycan synthesis, the lysis system based on the regulation of bacteriophage lysis protein and the lysis system based on the toxin-antitoxin system. In addition, a potential lysis system based on bacterial Type Ⅵ Secretion System (T6SS) is also expected to be a new method for the construction of auto-lysis strains. This review will focus on the regulatory mechanisms of these bacterial lysis systems.
Animals ; Antigens, Bacterial ; Bacterial Vaccines ; Vaccines, Attenuated ; Vaccines, DNA

Early diagnosis of sepsis helps make effective clinical decisions and improve the survival rate of patients with severe infection. However, the timely and accurate diagnosis of sepsis is still a great challenge in clinic. In order to settle the very problem, the scientists in the world have made a lot of exploration and research in the field of rapid molecular identification of pathogens. Nowadays, the nucleic acid detection of sepsis is mainly composed of 3 types of methodological strategies, either based on positive blood culture, single colonies, or directly on blood specimens. This paper presents a comprehensive overview of advances in the research of early detection of bacterial nucleic acid as molecular diagnosis of sepsis.
DNA, Bacterial ; blood ; Humans ; Sepsis ; blood ; diagnosis

The marine genus Marinobacterium was first identified in 1997, and a total of 18 species have been characterized so far, 10 of which have published whole-genome sequencing data. This article summarizes the characteristics of Marinobacterium genus and analyzes the genome sequencing data related to the carbon source utilization, polyhydroxyalkanoate metabolism, and aromatic compounds degradation. The Marinobacterium species possess the complete glycolysis pathway and tricarboxylic acid cycle, yet lack genes involved in xylose utilization. All strains of the Marinobacterium genus contain the genes encoding for the typeⅠand type Ⅲ polyhydroxyalkanoate synthases, suggesting that the genus may have ability of polyhydroxyalkanoate accumulation. The Marinobacterium species contain the degradation pathways of aromatic compounds. Benzene, phenol and benzoic acid can be degraded into catechol via different enzymes, subsequently catechol is converted to 3-ketoadipate through the ortho-cleavage pathway. Alternatively, catechol can be degraded into pyruvate and acetyl-CoA. The analysis of genome sequencing data of the Marinobacterium genus provides in-depth understanding of the metabolic characteristics, indicating that the genus may have certain applications in the synthesis of polyhydroxyalkanoate and the removal of marine aromatic compounds.
Alteromonadaceae ; DNA, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.
Biotechnology ; Chimera ; DNA ; DNA, Single-Stranded* ; Genome, Bacterial* ; Retroelements ; Reverse Transcription ; RNA ; RNA-Directed DNA Polymerase

OBJECTIVETo set up random amplified polymorphic DNAs (RAPD) method in genotyping Neisseria gonorrhoeae on DNA level, and to explore its use to trace the source of infection.

METHODSFour different pretreatments were used to extract the Neisseria gonorrhoeae genomic DNA with its advantages and disadvantages compared. Arbitrary sequence was then used to amplify the genomic DNA of Neisseria gonorrhoeae and RAPD fingerprint maps was applied to distinct the Neisseria gonorrhoeae strains. Finally, RAPD fingerprint of Neisseria gonorrhoeae strain between patient and his/her sexual partner was compared.

RESULTSCetyltrimethylammonium bromide method was classical in extracting genomic DNA, and could get integrated genomic DNA and good fingerprint maps, since main segments were common to all the Neisseria gonorrhoeae but some were different among strains so that the fingerprint of different Neisseria gonorrhoeae were distinctive. However, fingerprint maps of Neisseria gonorrhoeae collected from sex partners were quite similar.

CONCLUSIONBased on genomic levels, effective fingerprint maps could be identified and to classify the Neisseria gonorrhoeae into different genotypes. RAPD fingerprint maps could be used to trace the source of infection.

DNA Fingerprinting ; DNA, Bacterial ; analysis ; Genotype ; Humans ; Neisseria gonorrhoeae ; classification ; genetics ; Random Amplified Polymorphic DNA Technique

Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.
DNA ; DNA, Bacterial/genetics* ; Laboratories ; Metagenomics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA

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

OBJECTIVETo evaluate the application of different variable number tandem repeats (VNTR) locus in genotyping of Mycobacterium tuberculosis (M.tuberculosis) strains isolated from eight provinces in China, and to find the suitable locus-set of VNTR for epidemical strains in China.

METHODSAll 140 M.tuberculosis strains were randomly selected from 2800 M.tuberculosis strains isolated from eight provinces in China, 27 VNTR loci were used for typing all isolates. Discriminatory power (Hunter-Gaston Index, HGI) of every locus and different locus-set were analyzed by BioNumerics software. Meanwhile, Spoligotyping was used to identify Beijing family and non-Beijing family. Then the HGI of different locus-sets in two families was also evaluated.

RESULTSAll 140 isolates were clustered into Beijing kindred (112 strains, 80%) and non-Beijing kindred (28 strains, 20%) by Spoligotyping. The discriminatory power of Spoligotyping in 140 isolates was 0.4589. Every locus showed different polymorphism and HGI were from 0 to 0.809. The number of VNTR loci with HGI higher than 0.5 in all strains, Beijing family and non-Beijing family was 8, 7 and 14 respectively. 27 loci were combined into four groups which included 8, 12, 15 and 24 VNTR loci respectively. Four locus-sets showed different polymorphism, HGI of eight-locus, 12-locus, 15-locus, and 24-locus set in 140 strains was 0.9991, 0.9882, 0.9980 and 0.9986, and their discriminatory power were calculated in Beijing kindred (HGI: 0.9987, 0.9318, 0.9969 and 0.9975) and non-Beijing kindred (HGI: 1, 0.9894, 1 and 1).

CONCLUSIONDifferent VNTR locus and locus-set showed different discriminatory power in the selected M.tuberculosis strains isolated from China. Eight-locus set can be used in molecular epidemiological study of M.tuberculosis in China after standardization.

Bacterial Typing Techniques ; DNA, Bacterial ; genetics ; Mycobacterium tuberculosis ; classification ; genetics ; isolation & purification ; Tandem Repeat Sequences

Bacterial morphology can be altered by various factors, including antibiotics. Unusually shaped, large, swollen organisms were observed in a urine culture obtained from a patient who had no history of antibiotic therapy. The organism was identified as Escherichia coli by the Vitek 2 system and by DNA sequencing of 16S rRNA and gyrB. The patient had no symptoms except fever, which subsided without medication. Microbiology laboratories should be aware of the potential appearance of such bacilli to avoid confusion with fungi and other naturally occurring filamentous organisms.
Anti-Bacterial Agents ; Atypical Bacterial Forms ; Escherichia ; Escherichia coli ; Fever ; Fungi ; Humans ; Sequence Analysis, DNA