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

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.

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

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.

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

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.

scholarly journals Reagentless Bacterial Identification Using a Combination of Multiwavelength Transmission and Angular Scattering Spectroscopy

2016 ◽  
Vol 2016 ◽  
pp. 1-9
Author(s):  
Debra E. Huffman ◽  
Yulia M. Serebrennikova ◽  
Jennifer M. Smith ◽  
Alison Roth ◽  
Jack N. Lindon ◽  
...  
Keyword(s):  
Bacterial Pathogens ◽  
New Technology ◽  
Rapid Identification ◽  
Clinical Isolates ◽  
Identification System ◽  
Bacterial Identification ◽  
E Coli ◽  
Chemical Reagents ◽  
Angular Scattering ◽  
Hospital Systems

Optics based technologies are being advanced by many diagnostic companies around the globe. This resurgence is being driven by several factors including novel materials, enhanced computer power, nonlinear optics, and advances in algorithmic and statistical analysis. This study expands on a previous paper that evaluated the capability of a reagent-free optical profiling platform technology that used multiwavelength transmission spectroscopy to identify bacterial pathogens from pure culture. This study combines multiwavelength angular scattering with transmission based analysis into a single algorithm that will identify bacterial pathogens. Six predominant organisms,S. aureus, E. coli,K. pneumoniaeandP. aeruginosa,E. faecalis,and coagulase negativeStaphylococcus, were analyzed from a total of 753 clinical isolates received from three large community hospital systems. The bacterial identification method used for comparison in this study was the Vitek-2 (bioMerieux) which utilizes a biochemically based identification system. All of the clinical isolates received were blinded as to their identification until completion of the optical analysis. Sensitivities ranged from 87.7 to 94.6% with specificities ranging from 97.2 to 99.9% indicating that optical profiling is a powerful and exciting new technology that could be developed for the rapid identification of pathogens without the use of chemical reagents.

Aetiology of acute pharyngitis: the role of atypical bacteria

2004 ◽  
Vol 53 (7) ◽  
pp. 645-651 ◽  
Author(s):  
Susanna Esposito ◽  
Francesco Blasi ◽  
Samantha Bosis ◽  
Roberta Droghetti ◽  
Nadia Faelli ◽  
...  
Keyword(s):  
Chlamydia Pneumoniae ◽  
Bacterial Pathogens ◽  
Rapid Identification ◽  
Acute Pharyngitis ◽  
Paired Samples ◽  
History Of ◽  
Syncytial Virus ◽  
True Infection ◽  
Atypical Bacteria

In order to establish the role of atypical bacteria and compare characteristics of different infectious agents in acute pharyngitis, 127 patients with acute pharyngitis (66 males; median age, 5.33 years; range, 6 months to 14 years) and 130 healthy subjects of similar sex and age were studied. Serology with paired samples and PCR on nasopharyngeal aspirates and throat cultures were used to identify bacteria and viruses. Viruses were identified in 43 patients (33.8 %) and five controls (3.8 %; P < 0.0001), potential bacterial pathogens in 34 patients (26.8 %) and 26 controls (20 %; P = 0.256) and mixed viral/bacterial pathogens in 26 patients (20.5 %) and none of the controls (P < 0.0001). The main aetiological agents were adenovirus, respiratory syncytial virus (RSV), Mycoplasma pneumoniae, Streptococcus pyogenes and Chlamydia pneumoniae. M. pneumoniae was the agent found most frequently as a single pathogen. A history of recurrent pharyngitis, having older siblings and a negative outcome were significantly more common among patients with acute M. pneumoniae infection than among those with infections due to other pathogens or healthy controls. This study demonstrates that: (i) adenovirus and RSV have a prominent role in acute pharyngitis; (ii) S. pyogenes is found frequently, but it is not possible to distinguish simple carriers from patients with a true infection; (iii) M. pneumoniae appears to be able to cause acute pharyngitis per se; and (iv) C. pneumoniae seems to be mainly a co-pathogen. To avoid the risk of an incorrect therapeutic approach, simple laboratory investigations that allow rapid identification of M. pneumoniae infections are urgently needed.

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

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiuqing Ma ◽  
Yanqin Li ◽  
Yuan Liang ◽  
Yang Liu ◽  
Ling Yu ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Rapid Detection ◽  
Bacterial Pathogens ◽  
Microarray Assay

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

2017 ◽  
Vol 11 (1) ◽  
pp. 330-338 ◽  
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.

Identification of Multiple Pathogenic Bacteria Using a DNA Microarray

2002 ◽  
Author(s):  
Chi-Fang Wu ◽  
James J. Valdes ◽  
Jennifer W. Sekowski ◽  
William E. Bentley
Keyword(s):  
Dna Microarray ◽  
Pathogenic Bacteria
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