[Mission oriented diagnostic real-time PCR]

Application of metagenomic next-generation sequencing in the detection of pathogens in spinal infections

BACKGROUND CONTEXT

The precise diagnosis and treatment of spinal infections (SI) remains challenging for spine surgeons. Identifying the pathogens of SI through metagenomic next-generation sequencing (mNGS) may be a key approach to addressing this challenge.

PURPOSE

To evaluate the accuracy and applicability of mNGS in determining the etiology of SI.

STUDY DESIGN

Diagnostic test study.

PATIENT SAMPLE

Twenty-five patients who had a clinical suspicion of SI and underwent mNGS testing.

OUTCOME MEASURES

The specificity, sensitivity, and time cost of mNGS and bacterial culture were compared. Clinical outcomes were assessed using the numeric rating scale (NRS) score, Oswestry Disability Index (ODI), and the Japanese Orthopedic Association (JOA) score. Demographic data and laboratory results (blood cell count (WBC), erythrocyte sedimentation rate (ESR), neutrophil percentage (NEUT%), and C-reactive protein level (CRP) were also evaluated.

METHODS

In this retrospective study, samples were obtained from 25 eligible patients via surgery or CT-guided puncture and subjected to histopathological examination, bacterial culture, and mNGS. The sensitivity and specificity of the bacterial cultures and mNGS were calculated with respect to the histopathological results as a reference. Postoperative antibiotics or antituberculosis drugs were administered on the basis of mNGS results, combined with clinical manifestations, imaging examination, and histopathology. The changes of clinical outcomes and laboratory results after treatment were observed.

RESULTS

Of the 25 patients, 21 had a positive pathology, of which 10 showed a tuberculous pathology, and the remaining 11 showed a nontuberculous inflammatory pathology. The sensitivity of mNGS was higher than that of the bacterial culture. However, the difference in specificity between bacterial culture and mNGS was not significant. Moreover, the time needed to perform mNGS was significantly lower than that of bacterial culture and pathology. All patients were followed up for more than three months, and CRP and NEUT% significantly decreased by three months after treatment. There was no significant difference in WBC and ESR. The ODI, NRS and JOA scores were significantly improved after treatment.

CONCLUSION

Metagenomic next-generation sequencing technology can play an important role in the detection of pathogens in SI and should be further investigated and applied in future studies.

Raman spectroscopy as a potential tool for detection of Brucella spp. in milk

Detection of Brucella, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible Brucella isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify Brucella from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different Brucella, Escherichia, Ochrobactrum, Pseudomonas, and Yersinia spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for Brucella from medium and 94% for Brucella from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting Brucella. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.