Application of microarray technology for the detection of intracranial bacterial infection

Identification of microbes in wounds using near-infrared spectroscopy

BACKGROUND

Rapid diagnosis of microbes in the burn wound is a big challenge in the medical field. Traditional biochemical detection techniques take hours or days to identify the species of contaminating and drug-resistant microbes. Near-infrared spectroscopy (NIRS) is evaluated to address the need for a fast and sensitive method for the detection of bacterial contamination in liquids.

METHODS

Herin, we developed a novel technique which by using NIRS together with supporting vector machine (SVM), to identify the microbial species and drug-resistant microbes in LB medium, and to diagnose the wound colonization and wound infection models of pigs.

RESULTS

The device could recognize 100% of seven kinds of microbes and 99.47% of the multi-drug resistant Staphylococcus aureus (S. aureus), with a concentration of 10⁹ cfu ml^-1 in LB medium. The accuracy of the microbial identification in colonized and infected wounds in-situ was 100%. The detection limit of NIRS with SVM for the detection of S. aureus and Escherichia coli (E. coli) was 10¹ cfu ml^-1 in LB medium. Identification time was less than 5 s.

CONCLUSION

Our findings validate for the first time a novel technique aimed at the rapid, noncontacted, highly sensitive, and specific recognition of several microbial species including drug-resistant ones. This technique could represent a promising approach to identify diverse microbial species and a potential bedside device to rapidly diagnose infected wounds.

The preparation and clinical application of diagnostic DNA microarray for the detection of pathogens in intracranial bacterial and fungal infections

The present study prepared 2 types of DNA diagnostic chips based on 16S ribosomal DNA (rDNA) and 18S-28S rDNA, and evaluated their values in the detection of pathogens in intracranial bacterial/fungal infections. A total of 14 probes of bacteria (Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Haemophilus influenza, Stenotrophomonas maltophilia, Neisseria meningitidis, Enterobacter spp., Enterococcus faecalis, Enterococcus faecium, Listeria monocytogenes, Staphylococcus aureus, Streptococcus pneumonia and coagulase negative staphylococcus) and 4 probes of fungi (Candida albicans, Candida tropicalis, Candida glabrata and Cryptococcus neoformans), determined frequently in cerebrospinal fluid (CSF), were designed and used for preparation of microarrays. CSF samples from 88 patients with clinically suspected intracranial infection and standard strains were used to evaluate the chips. The same samples were also analyzed by culture and sequencing. The results demonstrated that the sensitivity, specificity and false-positive rate of the microarray assay compared with culture method were 100 vs. 68.3% (P<0.05), 97.1 vs. 100%, and 2.9 vs. 0%, respectively. The minimum concentration of detection with the chips was 10 cfu ml^-1 for bacteria and 100 cfu ml^-1 for fungi. The specificity of the probes was confirmed, and no cross-reaction was detected in the present study. Furthermore, 13 cases were positive in the microarray and negative in culture. However, 4 cases were not identified as clear pathogens and only positive in the 16S probe sites. The diagnostic DNA microarray for intracranial infections has proven to be more rapid and sensitive, and it may be a better option for clinical application than culture methods.

Analysis of microbial community composition and diversity in postoperative intracranial infection using high‑throughput sequencing

Intracranial infection is one of the most serious complications following neurosurgery. It is well acknowledged that bacteria and fungi are the main pathogens responsible for postoperative intracranial infection. However, the microbial community structure, including composition, abundance and diversity, in postoperative intracranial infection is not fully understood, which greatly compromises our understanding of the necessity and effectiveness of postoperative antibiotic treatment. The present study collected eight cerebrospinal fluid (CSF) samples from patients with intracranial infection following neurosurgical procedures. High‑throughput amplicon sequencing for 16S rDNA and internal transcribed spacer (ITS) was performed using the Illumina MiSeq platform to investigate the microbial community composition and diversity between treated and untreated patients. Bioinformatics analysis revealed that the microbial composition and diversity in each patient group (that is, with or without antibiotic treatment) was similar; however, the group receiving antibiotic treatment had a comparatively lower species abundance and diversity compared with untreated patients. At the genus level, Acinetobacter and Staphylococcus were widely distributed in CSF samples from patients with postoperative intracranial infection; in particular, Acinetobacter was detected in all CSF samples. In addition, five ITS fungal libraries were constructed, and Candida was detected in three out of four patients not receiving antibiotic treatment, indicating that the fungal infection should be given more attention. In summary, 16S and ITS high‑throughput amplicon sequencing were practical methods to identify pathogens in the different periods of treatment in patients with postoperative intracranial infection. There was a notable difference in microbial composition and diversity between the treated and untreated patients. Alterations in the microbial community structure may provide a signal whether antibiotic treatment worked in postoperative intracranial infection and may assist surgeons to better control the progression of infection.

Separation of cordycepin from Cordyceps militaris fermentation supernatant using preparative HPLC and evaluation of its antibacterial activity as an NAD+-dependent DNA ligase inhibitor

Cordycepin exhibits various bio-activities, including anticancer, antibacterial, antiviral and immune regulation activities, and is a significant focus of research. However, the preparation of high-purity cordycepin remains challenging. Also, the molecular target with which cordycepin interacts to cause an antibacterial effect remains unknown. In the present study, cordycepin was prepared by preparative high-performance liquid chromatography (prep-HPLC) and the purity obtained was 99.6%, indicating that this technique may be useful for the large-scale isolation of cordycepin in the future. The results of computational molecular docking analysis indicated that the interaction energy between cordycepin and NAD+-dependent DNA ligase (LigA) was lower than that between cordycepin and other common antibacterial targets. The highly pure cordycepin obtained by prep-HPLC demonstrated inhibitory activity against LigA from various bacteria in vitro. In conclusion, cordycepin may be useful as a broad-spectrum antibiotic targeting LigA in various bacteria.