Molecular detection of Nocardia: development and application of a real-time PCR assay in sputum and bronchoalveolar lavage fluid samples

Nucleic acid-functionalized nanoscale porous carbon-based electrochemical genosensor for detection of Nocardia spp. in real samples

In this study, a porous carbon derived from a metal-organic framework (PCMOF) as a target-responsive material functionalized with Nocardia particular antisense ssDNA oligonucleotide (ssDNA capture probe) was developed to construct a simple genosensor based on biogatekeeper strategy for sensitive detection of Nocardia in complex biological samples. The PCMOF with suitable pores volume was used to encapsulate electroactive dye methylene blue (MB), and the ssDNA capture probe was used as a gatekeeper to cap PCMOF. Without the presence of Nocardia target, the electrochemical signal of trapped MB was high. Upon adding the target, the hybridization of ssDNA capture probe and target led to the formation of a probe-target double-stranded (dsDNA) structure which dissociated from PCMOF and allowed MB molecules to be released. Therefore, the electrochemical signal of the genosensor decreased. The detection of Nocardia was accomplished by observing variations in the MB peak current intensity in a dose-dependent manner. For this genosensor, a linearity range from 10-18 to 10-7 M for synthetic ssDNA target and 10 to 108 copies/mL for two standard isolates, Nocardia farcinica PTCC 1309 and Nocardia brasiliensis ATCC 19296 as well as for clinical isolates (identified as Nocardia otitidiscaviarum) was observed, respectively. The detection limit (DL) values were 0.54 aM for synthetic ssDNA target and 5, 7, and 4 copies/mL for N. farcinica, N. brasiliensis, and N. otitidiscaviarum, respectively. This genosensor was also characterized by good specificity, reproducibility, and stability.

Development and Validation of a Novel Multiplex Real-Time PCR Assay for Rapid Detection of Carbapenemase Genes in Carbapenem-Resistant Enterobacterales Isolates and Clinical Samples

Purpose

Carbapenem-resistant Enterobacterales (CRE) infection is an urgent threat to human health. This study aimed to develop and validate a novel multiplex real-time PCR (multi-qPCR) assay for the detection of the blaKPC, blaNDM, blaIMP, blaOXA-48-like, and blaVIM genes in CRE isolates and clinical samples, as well as to compare it with three phenotypic methods.

Methods

The reliability and limit of detection (LOD) of the multi-qPCR assay were evaluated. PCR and DNA sequencing were used as the reference methods to identify carbapenemase genes in CRE isolates and clinical samples. The accuracy of the multi-qPCR assay, modified carbapenem inactivation and EDTA-modified carbapenem inactivation method (mCIMandeCIM), carbapenemase inhibitor-based combined disk test (CDT), and colloidal gold-based immunochromatographic test was compared with the reference methods with 182 isolates of CRE. Furthermore, 112 clinical samples were collected to validate the efficacy of this multi-qPCR assay.

Results

The standard deviations (CVs) of intra-assay and inter-assay of the multi-qPCR assay were ≤ 0.53% and ≤ 2.04% for detecting the five major carbapenemase genes, respectively; while the LOD ranged from 2×102 copies/mL to 8×102 copies/mL. PCR and DNA sequencing confirmed 168 out of 182 CRE isolates producing carbapenemase(s): KPC (n = 93), NDM (n = 46), IMP (n = 8), OXA-48-like (n = 14), VIM (n = 1), KPC&NDM (n = 5), and KPC&NDM&IMP (n = 1). The accuracy of mCIMandeCIM, CDT, Colloidal Gold, and the multi-qPCR assay was 96.2%, 89.6%, 100%, and 100% respectively for detecting carbapenemase(s) producers. Moreover, the sensitivity and specificity of the multi-qPCR assay were all 100% for the detection of each carbapenemase gene in clinical samples, compared with PCR and sequencing.

Conclusion

For clinical isolate detection, the multi-qPCR assay is comparable to Colloidal Gold, and superior to mCIMandeCIM and CDT; while for clinical samples detection, it also shows excellent performance. Therefore, the multi-qPCR assay has great potential for clinical diagnosis.

Clinical screening of Nocardia in sputum smears based on neural networks

Objective

Nocardia is clinically rare but highly pathogenic in clinical practice. Due to the lack of Nocardia screening methods, Nocardia is often missed in diagnosis, leading to worsening the condition. Therefore, this paper proposes a Nocardia screening method based on neural networks, aiming at quick Nocardia detection in sputum specimens with low costs and thereby reducing the missed diagnosis rate.

Methods

Firstly, sputum specimens were collected from patients who were infected with Nocardia, and a part of the specimens were mixed with new sputum specimens from patients without Nocardia infection to enhance the data diversity. Secondly, the specimens were converted into smears with Gram staining. Images were captured under a microscope and subsequently annotated by experts, creating two datasets. Thirdly, each dataset was divided into three subsets: the training set, the validation set and the test set. The training and validation sets were used for training networks, while the test set was used for evaluating the effeteness of the trained networks. Finally, a neural network model was trained on this dataset, with an image of Gram-stained sputum smear as input, this model determines the presence and locations of Nocardia instances within the image.

Results

After training, the detection network was evaluated on two datasets, resulting in classification accuracies of 97.3% and 98.3%, respectively. This network can identify Nocardia instances in about 24 milliseconds per image on a personal computer. The detection metrics of mAP50 on both datasets were 0.780 and 0.841, respectively.

Conclusion

The Nocardia screening method can accurately and efficiently determine whether Nocardia exists in the images of Gram-stained sputum smears. Additionally, it can precisely locate the Nocardia instances, assisting doctors in confirming the presence of Nocardia.