Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis

Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration

BACKGROUND

Bacterial infections, especially polymicrobial infections, remain a threat to global health and require advances in diagnostic technologies for timely and accurate identification of all causative species. Digital melt - microfluidic chip-based digital PCR combined with high resolution melt (HRM) - is an emerging method for identification and quantification of polymicrobial bacterial infections. Despite advances in recent years, existing digital melt instrumentation often delivers nonuniform temperatures across digital chips, resulting in nonuniform digital melt curves for individual bacterial species. This nonuniformity can lead to inaccurate species identification and reduce the capacity for differentiating bacterial species with similar digital melt curves.

RESULTS

We introduce herein a new temperature calibration method for digital melt by incorporating an unamplified, synthetic DNA fragment with a known melting temperature as a calibrator. When added at a tuned concentration to an established digital melt assay amplifying the commonly targeted 16S V1 - V6 region, this calibrator produced visible low temperature calibrator melt curves across-chip along with the target bacterial melt curves. This enables alignment of the bacterial melt curves and correction of heating-induced nonuniformities. Using this calibration method, we were able to improve the uniformity of digital melt curves from three causative species of bacteria. Additionally, we assessed calibration's effects on identification accuracy by performing machine learning identification of three polymicrobial mixtures comprised of two bacteria with similar digital melt curves in different ratios. Calibration greatly improved mixture composition prediction.

SIGNIFICANCE

To the best of our knowledge, this work represents the first DNA calibrator-supplemented assay and calibration method for nanoarray digital melt. Our results suggest that this calibration method can be flexibly used to improve identification accuracy and reduce melt curve variabilities across a variety of pathogens and assays. Therefore, this calibration method has the potential to elevate the diagnostic capabilities of digital melt toward polymicrobial bacterial infections and other infectious diseases.

Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes

BACKGROUND

Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes.

METHODS

Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients.

RESULTS

The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections.

CONCLUSIONS

Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.

Aptamer-based DNA-catalyzed amplification strategy for sensitive fluorescence resonance energy transfer detection of Acinetobacter baumannii

Acinetobacter baumannii (A. baumannii) is a common pathogen that causes hospital-acquired infections and is resistant to a wide variety of antibiotics. Consequently, the rapid and highly sensitive detection of A. baumannii is required during the early stages of infection. Therefore, we developed a DNA-catalyzed amplification mechanism based on aptamers, combined with a novel fluorescence resonance energy transfer (FRET) method based on graphene oxide (GO), for the detection of A. baumannii. In the presence of A. baumannii, an aptamer bound to A. baumannii, releasing the template strand, which triggered an entropy-driven catalysis (EDC) reaction. One EDC product was then used as the catalyst for catalytic hairpin assembly (CHA) on a GO nanosheet. Finally, the GO released a huge amount of FAM-labeled DNA duplices, which could be detected with FRET. This strategy circumvented the extraction of nucleic acids and was easy to execute, with a detection time of ≤1.5 h. The detection of A. baumannii with this method ranges from 5 cfu/mL to 1 × 10⁵ cfu/mL, with a detection limit of 1.1 cfu/mL. The method was sufficiently sensitive and specific to detect A. baumannii rapidly in cerebrospinal fluid. In summary, our strategy provides a new option for the early detection and point-of-care testing (POCT) of A. baumannii infections, allowing their earlier and more precise treatment.

High incidence of the virus among respiratory pathogens in children with lower respiratory tract infection in northwestern China

Lower respiratory tract infection (LRTI) is one of the major reasons for childhood mortality that threaten the health of the public. We aimed to investigate the epidemiological pathogens and their infection analysis among children with LRTI. Sputum specimens were collected for polymerase chain reaction detection and microbiological tests to identify the viral infection and bacterial infection. The serological specimens were separated from venous blood using for Mycoplasma pneumoniae and Chlamydia pneumoniae detection. The virus was confirmed in 86.2% of the children. Human rhinovirus (38.3%), respiratory syncytial virus (32.1%), and parainfluenza virus type 3 (27.2%) were the most frequently identified pathogens. Patients with viral and bacterial coinfection showed younger age (p = 0.032), a higher proportion of wheezing rales (p = 0.032), three depressions sign (p = 0.028), and tachypnea (p = 0.038), and more likely associated with severe pneumonia (p = 0.035). Additionally, older children were more susceptible to viral-atypical bacterial coinfection (p = 0.032). Vomiting (p = 0.011) and fever (p = 0.003) were more likely to occur in children with viral-atypical bacterial coinfection. Attention should be paid to the virus infection of LRTI, as viral-bacterial coinfection and viral-atypical bacterial co-infection may have a detrimental impact on the gravity of LTRI.

Traditional Medicinal Plants—A Possible Source of Antibacterial Activity on Respiratory Diseases Induced by Chlamydia pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae and Moraxella catarrhalis

Background. Nowadays, phytotherapy offers viable solutions in managing respiratory infections, disorders known for considerable incidence in both children and adults. In a context in which more and more people are turning to phytotherapy, finding new remedies is a topical goal of researchers in health and related fields. This paper aims to identify those traditional medicinal plants that show potentially antibacterial effects against four Gram-negative germs (Chlamydia pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, and Moraxella catarrhalis), which are considered to have high involvement in respiratory infections. Furthermore, a comparison with Romanian folk medicines was performed. Methods. An extensive review of books and databases was undertaken to identify vegetal species of interest in the context of the topic. Results. Some traditional Romanian species (such as Mentha × piperita, Thymus vulgaris, Pinus sylvestris, Allium sativum, Allium cepa, Ocimum basilicum, and Lavandulaangustifolia) were identified and compared with the plants and preparations confirmed as having antibacterial effects against specific germs. Conclusions. The antibacterial effects of some traditionally used Romanian medicinal plants are poorly investigated, and deserve further attention.

Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol

INTRODUCTION

Lower respiratory tract infection (LRTI) is the most commonly treated infection in critically ill children. Pathogens are infrequently identified on routine respiratory culture, and this is a time-consuming process. A syndromic approach to rapid molecular testing that includes a wide range of bacterial and fungal targets has the potential to aid clinical decision making and reduce unnecessary broad spectrum antimicrobial prescribing. Here, we describe a single-centre prospective cohort study investigating the use of a 52-pathogen TaqMan array card (TAC) for LRTI in the paediatric intensive care unit (PICU).

METHODS AND ANALYSIS

Critically ill children with suspected LRTI will be enrolled to this 100 patient single-centre prospective observational study in a PICU in the East of England. Samples will be obtained via routine non-bronchoscopic bronchoalveolar lavage which will be sent for standard microbiology culture in addition to TAC. A blood draw will be obtained via any existing vascular access device. The primary outcomes of the study will be (1) concordance of TAC result with routine culture and 16S rRNA gene sequencing and (2) time of diagnostic result from TAC versus routine culture. Secondary outcomes will include impact of the test on total antimicrobial prescriptions, a description of the inflammatory profile of the lung and blood in response to pneumonia and a description of the clinical experience of medical and nursing staff using TAC.

ETHICS AND DISSEMINATION

This study has been approved by the Yorkshire and the Humber-Bradford Leeds Research Ethics Committee (REC reference 20/YH/0089). Informed consent will be obtained from all participants. Results will be published in peer-reviewed publications and international conferences.

TRIAL REGISTRATION NUMBER

NCT04233268.

Accuracy of Molecular Amplification Assays for Diagnosis of Staphylococcal Pneumonia: a Systematic Review and Meta-analysis

Rapid and accurate identification of staphylococcal pneumonia is crucial for effective antimicrobial stewardship. We performed a meta-analysis to evaluate the diagnostic value of nucleic acid amplification tests (NAAT) from lower respiratory tract (LRT) samples from suspected pneumonia patients to avoid superfluous empirical methicillin-resistant Staphylococcus aureus (MRSA) treatment. PubMed, Scopus, Embase, Web of Science, and the Cochrane Library Database were searched from inception to 2 September 2020. Data analysis was carried out using a bivariate random-effects model to estimate pooled sensitivity, specificity, positive likelihood ratio (PLR), and negative likelihood ratio (NLR). Of 1,808 citations, 24 publications comprising 32 data sets met our inclusion criteria. Twenty-two studies (n = 4,630) assessed the accuracy of the NAAT for methicillin-sensitive S. aureus (MSSA) detection, while 10 studies (n = 2,996) demonstrated the accuracy of the NAAT for MRSA detection. The pooled NAAT sensitivity and specificity (with 95% confidence interval [CI]) for all MSSA detection were higher (sensitivity of 0.91 [95% CI, 0.89 to 0.94], specificity of 0.94 [95% CI, 0.94 to 0.95]) than those of MRSA (sensitivity of 0.75 [95% CI, 0.69 to 0.80], specificity of 0.88 [95% CI, 0.86 to 0.89]) in lower respiratory tract (LRT) samples. NAAT pooled sensitivities differed marginally among different LRT samples, including sputum, endotracheal aspirate (ETA), and bronchoalveolar lavage (BAL) fluid. Noticeably, NAAT pooled specificity against microbiological culture was consistently ≥88% across various types of LRT samples. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. This meta-analysis has demonstrated that the NAAT can be applied as the preferred initial test for timely diagnosis of staphylococcal pneumonia in LRT samples for successful antimicrobial therapy.