Identification of Multiple Pathogenic Bacteria Using a DNA Microarray

DNA microarrays represent the latest advance in molecular technology. In combination with bioinformatics, they provide unparalleled opportunities for simultaneous detection of thousands of genes or target DNA sequences and offer tremendous potential for studying food-borne microorganisms. This review provides an up-to-date look at the application of DNA microarray technology to detect food-borne pathogenic bacteria, viruses, and parasites. In addition, it covers the advantages of using microarray technology to further characterize microorganisms by providing information for specific identification of isolates, to understand the pathogenesis based on the presence of virulence genes, and to indicate how new pathogenic strains evolved epidemiologically and phylogenetically.Key words: DNA microarrays, food-borne pathogens, detection.

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High-Throughput DNA Microarray Detection of Pathogenic Bacteria in Shallow Well Groundwater in the Kathmandu Valley, Nepal

Current Microbiology ◽

10.1007/s00284-014-0681-x ◽

2014 ◽

Vol 70 (1) ◽

pp. 43-50 ◽

Cited By ~ 12

Author(s):

Daisuke Inoue ◽

Takuji Hinoura ◽

Noriko Suzuki ◽

Junqin Pang ◽

Rabin Malla ◽

...

Keyword(s):

Dna Microarray ◽

High Throughput ◽

Pathogenic Bacteria ◽

Kathmandu Valley ◽

Microarray Detection

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Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

10.21203/rs.2.24314/v3 ◽

2020 ◽

Author(s):

Xiuqing Ma ◽

Yanqin Li ◽

Yuan Liang ◽

Yang Liu ◽

Ling Yu ◽

...

Keyword(s):

Dna Microarray ◽

Legionella Pneumophila ◽

Burkholderia Cepacia ◽

Pathogenic Bacteria ◽

Chlamydia Pneumoniae ◽

Bacterial Pathogens ◽

Bacterial Species ◽

Simultaneous Detection ◽

Clinical Isolates ◽

Microarray Assay

Abstract Background: The rapid identification of pathogenic bacteria is important for determining an appropriate antimicrobial therapy for pneumonia, but traditional bacterial culture is time-consuming and labourious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneous detection of fifteen bacterial species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA genes and other specific genes of each pathogen were chosen as the amplification targets, amplified via multiplex polymerase chain reaction (PCR), and hybridized to oligonucleotide probes in a microarray.Results: The DNA microarray detection limit was 103 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray, and 3 nontarget species from 4 clinical isolates were not detected. Additionally, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results for 99.4% (156/157) of clinical specimens were the same as those from a conventional assay.Conclusions: We developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labour and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

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Pathogenic bacteria identification by diagnostic DNA microarray

Journal of Biotechnology ◽

10.1016/j.jbiotec.2008.07.1834 ◽

2008 ◽

Vol 136 ◽

pp. S194

Author(s):

Seung Min Yoo ◽

Kyung-Hee Chang ◽

Nae Choon Yoo ◽

Ki Chang Keum ◽

Won Min Yoo ◽

...

Keyword(s):

Dna Microarray ◽

Pathogenic Bacteria ◽

Bacteria Identification

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DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab

The Open Microbiology Journal ◽

10.2174/1874285801711010330 ◽

2017 ◽

Vol 11 (1) ◽

pp. 330-338 ◽

Cited By ~ 10

Author(s):

Reza Ranjbar ◽

Payam Behzadi ◽

Ali Najafi ◽

Raheleh Roudi

Keyword(s):

Dna Microarray ◽

Legionella Pneumophila ◽

Rapid Detection ◽

Pathogenic Bacteria ◽

Microarray Chip ◽

Dna Labeling ◽

Detection And Identification ◽

Oligo Microarray ◽

Wet Lab

Background:A rapid, accurate, flexible and reliable diagnostic method may significantly decrease the costs of diagnosis and treatment. Designing an appropriate microarray chip reduces noises and probable biases in the final result.Objective:The aim of this study was to design and construct a DNA Microarray Chip for a rapid detection and identification of 10 important bacterial agents.Method:In the present survey, 10 unique genomic regions relating to 10 pathogenic bacterial agents includingEscherichia coli (E.coli), Shigella boydii, Sh.dysenteriae, Sh.flexneri, Sh.sonnei, Salmonella typhi, S.typhimurium, Brucella sp., Legionella pneumophila,andVibrio cholerawere selected for designing specific long oligo microarray probes. For this reason, the in-silico operations including utilization of the NCBI RefSeq database, Servers of PanSeq and Gview, AlleleID 7.7 and Oligo Analyzer 3.1 was done. On the other hand, thein-vitropart of the study comprised stages of robotic microarray chip probe spotting, bacterial DNAs extraction and DNA labeling, hybridization and microarray chip scanning. In wet lab section, different tools and apparatus such as Nexterion® Slide E, Qarrayminispotter, NimbleGen kit, TrayMixTMS4, and Innoscan 710 were used.Results:A DNA microarray chip including 10 long oligo microarray probes was designed and constructed for detection and identification of 10 pathogenic bacteria.Conclusion:The DNA microarray chip was capable to identify all 10 bacterial agents tested simultaneously. The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes.

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Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

10.21203/rs.2.24314/v1 ◽

2020 ◽

Author(s):

Xiuqing Ma ◽

Yanqin Li ◽

Yuan Liang ◽

Yang Liu ◽

Ling Yu ◽

...

Keyword(s):

Dna Microarray ◽

Legionella Pneumophila ◽

Burkholderia Cepacia ◽

Pathogenic Bacteria ◽

Chlamydia Pneumoniae ◽

Bacterial Pathogens ◽

Positive Control ◽

Negative Control ◽

Clinical Isolates ◽

Microarray Assay

Abstract Background: Rapid identification of pathogenic bacteria is important for appropriate antimicrobial therapy of pneumonia, but traditional bacteria culture is time-consuming and laborious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneously detection of fifteen bacteria species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA and specific genes of each pathogen were chosen as the amplification target, amplified with multiplex polymerase chain reaction (PCR), and hybridized to the oligonucleotide probes on the microarray. Results: The DNA microarray can reach a detection limit of 10 3 copies/μL. Nineteen standard strains, 119 positive control clinical isolates and 4 negative control clinical isolates were correctly detected with our microarray. Meanwhile, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results of 99.4% (156/157) clinical specimens were the same to that from the conventional assay. Conclusions: we developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labor and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

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Development of a DNA microarray assay for rapid detection of fifteen bacterial pathogens in pneumonia

10.21203/rs.2.24314/v2 ◽

2020 ◽

Author(s):

Xiuqing Ma ◽

Yanqin Li ◽

Yuan Liang ◽

Yang Liu ◽

Ling Yu ◽

...

Keyword(s):

Dna Microarray ◽

Legionella Pneumophila ◽

Burkholderia Cepacia ◽

Pathogenic Bacteria ◽

Chlamydia Pneumoniae ◽

Bacterial Pathogens ◽

Rapid Identification ◽

Clinical Isolates ◽

Microarray Assay ◽

Bacteria Culture

Abstract Background: Rapid identification of pathogenic bacteria is important for appropriate antimicrobial therapy of pneumonia, but traditional bacteria culture is time-consuming and laborious. The aim of this study was to develop and evaluate a DNA microarray assay for the simultaneously detection of fifteen bacteria species directly from respiratory tract specimens in patients with pneumonia. These species included Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Mycoplasma pneumoniae, Enterococcus faecalis, Enterococcus faecium, Enterobacter cloacae, Stenotrophomonas maltophilia, Burkholderia cepacia, Legionella pneumophila and Chlamydia pneumoniae. The 16S rDNA and specific genes of each pathogen were chosen as the amplification target, amplified with multiplex polymerase chain reaction (PCR), and hybridized to the oligonucleotide probes on the microarray. Results: The DNA microarray can reach a detection limit of 10 3 copies/μL. Nineteen standard strains and 119 clinical isolates were correctly detected with our microarray and 3 non-target species from 4 clinical isolates were not detected. Meanwhile, bacterial pathogens were accurately identified when two or three bacterial targets were mixed together. Furthermore, the results of 99.4% (156/157) clinical specimens were the same to that from the conventional assay. Conclusions: we developed a DNA microarray that could simultaneously detect various bacterial pathogens in pneumonia. The method described here has the potential to provide considerable labor and time savings due to its ability to screen for 15 bacterial pathogens simultaneously.

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