Development of DNA Microarray for Parallel Detection of Community-Acquired Pneumonia Bacterial Pathogens

• Published in: Sovremennye tekhnologii v medit͡s︡ine 2024-01, Vol.16 (2), p.16-26
• Main Authors: Sakharnov, N A, Filatova, E N, Popkova, M I, Slavin, S L, Utkin, O V
• Format: Article
• Language: English
• Subjects: Adolescent; Advanced Researches; Child; Child, Preschool; Community-Acquired Infections - diagnosis; Community-Acquired Infections - microbiology; DNA, Bacterial - analysis; Female; Haemophilus influenzae - genetics; Haemophilus influenzae - isolation & purification; Humans; Infant; Male; Oligonucleotide Array Sequence Analysis - methods; Pneumonia, Bacterial - diagnosis; Pneumonia, Bacterial - microbiology; Sensitivity and Specificity; Streptococcus pneumoniae - genetics; Streptococcus pneumoniae - isolation & purification
• ISSN: 2076-4243; 2309-995X; 2309-995X
• DOI: 10.17691/stm2024.16.2.02

was to develop an experimental version of a DNA microarray for parallel detection of community-acquired pneumonia bacterial pathogens. We studied the samples of the pharyngeal mucosa smears taken from children aged 1-15 years with X-ray confirmed pneumonia. The selection of DNA probes for specific detection of community-acquired pneumonia pathogens ( , , , , and ) and development of the microarray design were carried out using the disprose program. The nucleotide sequences of pathogens were obtained from NCBI Nucleotide database. In the research we used CustomArray microarrays (USA). For a pooled sample containing and DNA, we performed a sequential selection of the best combinations of hybridization parameters: DNA fragment size, DNA amount, hybridization temperature. The selection criteria were: the percentage of effective probes with a standardized hybridization signal (SHS) ≥3 , and the excess of SHS levels of effective specific probes compared to SHS of effective nonspecific probes. We selected the probes to detect of and characterized by an effective hybridization signal under optimal conditions. The developed microarray was tested under the selected conditions on clinical samples containing or DNA. Using ROC analysis there were established threshold values for the signals of specific probes at optimal sensitivity points and the test specificity, the excess of which was interpreted as the evidence of pathogen presence in a sample. A microarray design included 142 DNA probes to detect , , , , and , the probes being synthesized onto slides. Using the example of clinical samples containing and/or DNA, we selected optimal parameters for DNA hybridization on microarrays, which enabled to identify bacterial pathogens of community-acquired pneumonia with sufficient efficiency, specificity and reproducibility: the amount of hybridized DNA was 2 μg, the DNA fragment size: 300 nt, hybridization temperature: 47°C. There was selected a list of probes for specific detection of and characterized by an effective hybridization signal under the identified conditions. We determined the threshold values of standardized probe signals for specific detection of (4.5 ) and (4.9 ) in clinical samples. A DNA microarray was developed and synthesized for parallel indication of bacterial pathogens of community-acquired pneumonia. There were selected the optimal parameters for DNA hybridization on a microarray to identify bacterial pathogens - and , and determined the threshold v