Dried Saliva Spots: A Robust Method for Detecting Streptococcus pneumoniae Carriage by PCR

Use of saliva-based qPCR diagnostics for the accurate, rapid, and inexpensive detection of strep throat

OBJECTIVES

Outpatient health care facilities are essential for quickly diagnosing common infectious diseases such as bacterial and viral pharyngitis. The only form of pharyngitis requiring antibiotics is strep throat (ST); however, antibiotic prescription rates are much higher than ST prevalence, suggesting antibiotics are being inappropriately prescribed. Current rapid ST diagnostics may be contributing to this problem due to the low sensitivity and variable specificity of these tests. It is best practice to verify a negative ST diagnosis with a group A Streptococcus (GAS) culture, but many clinics do not perform this test due to the additional cost and 24-72 h required to obtain results. This indicates there is great need for more accurate rapid diagnostic tools in outpatient facilities. We hypothesized that next generation qPCR technology could be adapted to detect GAS DNA from saliva samples (instead of the traditional throat swab) by creating a simple, fast, and inexpensive protocol.

METHODS

Saliva specimens collected from patients at James Madison University Health Center were used to test the effectiveness of our Chelex 100-based rapid DNA extraction method, followed by a fast protocol developed for the Open qPCR machine to accurately detect ST.

RESULTS

Our final saliva processing and qPCR protocol required no specialized training to perform and was able to detect ST with 100 % sensitivity and 100 % specificity (n=102) in 22-26 min, costing only $1.12 per sample.

CONCLUSIONS

Saliva can be rapidly analyzed via qPCR for the accurate and inexpensive detection of ST.

The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study

The human microbiome contributes to health and disease, but the oral microbiota is understudied relative to the gut microbiota. The salivary microbiota is easily accessible, underexplored, and may provide insight into response to infections. We sought to determine the composition, association with clinical features, and heterogeneity of the salivary microbiota in patients with acute lower respiratory tract infection (LRTI). We conducted a multicenter prospective cohort study of 147 adults with acute LRTI presenting to the emergency department of seven hospitals in three states (Pennsylvania, Michigan, and Ohio) between May 2017 and November 2018. Salivary samples were collected in the emergency department, at days 2-5 if hospitalized, and at day 30, as well as fecal samples if patients were willing. We compared salivary microbiota profiles from patients to those of healthy adult volunteers by sequencing and analyzing bacterial 16-rRNA. Compared to healthy volunteers, the salivary microbiota of patients with LRTI was highly distinct and strongly enriched with intestinal anaerobes such as Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae (e.g., mean 10% relative abundance of Bacteroides vs < 1% in healthy volunteers). Within the LRTI population, COPD exacerbation was associated with altered salivary microbiota composition compared to other LRTI conditions. The largest determinant of microbiota variation within the LRTI population was geography (city in which the hospital was located).

The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

Despite its prominence in early scientific records, the usefulness of saliva as a respiratory specimen has been de-emphasised over the past century. However, due to its low cost and reliance on specific supply chains and the non-invasive nature of its collection, its benefits over swab-based specimens are again becoming increasingly recognised. These benefits were highlighted over the course of the COVID-19 pandemic, where saliva emerged as a more practical, clinically non-inferior sample type for the detection of SARS-CoV-2 and saw numerous saliva-based diagnostic tests approved for clinical use. Looking forward, as saliva uniquely contains both respiratory secretions and immunological components, it has potentially wide applications, ranging from clinical diagnostics to post-vaccine disease burden and immunity surveillance. This Personal View seeks to summarise the existing evidence for the use of saliva in detecting respiratory pathogens, beyond SARS-CoV-2, as well as detailing methodological factors that can influence sample quality and thus, clinical utility.

Potential use of a dried saliva spot (DSS) in therapeutic drug monitoring and disease diagnosis

In recent years, scientific researchers have increasingly become interested in noninvasive sampling methods for therapeutic drug monitoring and disease diagnosis. As a result, dried saliva spot (DSS), which is a sampling technique for collecting dried saliva samples, has been widely used as an alternative matrix to serum for the detection of target molecules. Coupling the DSS method with a highly sensitive detection instrument improves the efficiency of the preparation and analysis of biological samples. Furthermore, dried blood spots, dried plasma spots, and dried matrix spots, which are similar to those of the DSS method, are discussed. Compared with alternative biological fluids used in dried spot methods, including serum, tears, urine, and plasma, saliva has the advantage of convenience in terms of sample collection from children or persons with disabilities. This review aims to provide integral strategies and guidelines for dried spot methods to analyze biological samples by illustrating several dried spot methods. Herein, we summarize recent advancements in DSS methods from June 2014 to March 2021 and discuss the advantages and disadvantages of the key aspects of this method, including sample preparation and method validation. Finally, we outline the challenges and prospects of such methods in practical applications.

Optimization and validation of a procedure using the dried saliva spots approach for the determination of tobacco markers in oral fluid

Exposure to tobacco smoke is one of the most common causes of premature death worldwide and is the cause of 8 million deaths annually. We have developed, optimized, and validated a procedure for the detection of nicotine, cotinine and trans-3-hydroxycotinine (biomarkers of tobacco exposure) in oral fluid using the dried saliva spots sampling approach and gas chromatography coupled to tandem mass spectrometry, thus allowing the distinction between active and passive smokers. For optimization, four parameters were evaluated, namely extraction solvent, extraction solvent volume, extraction time and spots drying time. During method validation, the parameters selectivity, linearity, precision and accuracy, recovery, stability, and dilution factor were assessed. Linearity was obtained for all target analytes in the concentration range of 10-200 ng/mL allowing the quantification of compounds up to 1000 ng/mL considering the dilution factor. The method recoveries ranged from 29.2% to 43.30% for nicotine, 66.60-89.10% for cotinine and 80.30-92.80% for trans-3-hydroxycotinine, while achieving intra-day, inter-day and intermediate precision and accuracy values never higher than 10.37% and ±6.62% respectively for all compounds. The herein described analytical method is the first to allow the determination of tobacco biomarkers in oral fluid using dried saliva spots, which is considered a sensitive, simple and low-cost alternative to conventional methods.

Real-time polymerase chain reaction on filter paper spotted samples: a gateway to molecular diagnosis of invasive bacterial diseases for rural areas in low-income countries

BACKGROUND

Bacterial culture is the gold standard for the diagnosis of invasive bacterial diseases (IBDs) but molecular methods are more specific and sensitive. Fresh liquid samples (FLSs) show patent limitations for shipping and storage. We aimed to evaluate the sensitivity and specificity of real-time polymerase chain reaction (PCR) performed on dried sample spots (DSSs) obtained from different biological fluids compared with real-time PCR or culture performed on FLSs.

METHODS

FLSs positive for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Escherichia coli, Streptococcus pyogenes, Staphylococcus aureus, Bordetella pertussis and/or Pseudomonas aeruginosa were spotted on filter paper. Real-time PCR was performed on both FLSs and DSSs and results were compared. The stability of the DSS results over time was evaluated.

RESULTS

Real-time PCR performed on 114 DSSs showed a specificity of 99.1% and a sensitivity of 91.2% for IBD diagnosis. A positive correlation was found between FLS cycle threshold (Ct) and DSS Ct (r=0.84; r2=0.71) with the Pearson statistical test and Bland-Altman analysis showing that 95% of the specimens were within agreeable limits. Although we observed a trend towards signal reduction over time in the DSSs, there was no statistical evidence of an increase in Ct values. Real-time PCR on DSSs was 2.2 times more sensitive than culture.

CONCLUSIONS

Real-time PCR applied to DSSs may be a useful approach in different situations, such as IBD diagnosis, both for rural areas of low-income countries and family practitioners in various settings.

A convenient sampling and noninvasive dried spot method of uric acid in human saliva: Comparison of serum uric acid value and salivary uric acid in healthy volunteers and hyperuricemia patients

Concentration of uric acid (UA) in serum is one of the markers used to diagnose gout and hyperuricemia. However, serum treatment and storage are cumbersome, and wounds are susceptible to infection. Therefore, a new sampling and analysis method using noninvasive biological samples has been developed, called the dried spot method of UA in human saliva (DSM-UHS). Saliva (5 μL) was dropped on filter paper (a spot with a diameter of 5 mm) containing hypoxanthine (IS) (5 μL) and dried at room temperature for 30 min. The filter paper was immersed in 200 μL of lithium carbonate solution and shaken in a block bath shaker for 5 min at 30 °C. Afterward, the extraction was concentrated and reconstituted with 100 μL of lithium carbonate solution analyzed by HPLC-UV. When comparing the concentration of UA in the human saliva of hyperuricemia patients (HPs) and with that of healthy volunteers (HVs), we observed the concentration of UA was higher in the HPs than in the HVs (p < 0.0001). In addition, the results showed a significant linear relationship between the content of UA in saliva and the content of UA in the serum (r = 0.6243). The content of UA in human saliva could indirectly reflect the content of UA in human serum. Then DSM-UHS could be used to determine the content of UA in the saliva of HVs and HPs. This study provides a new research method and strategy for the determination of human UA content and the clinical prewiring of hyperuricemia.

Spectral fingerprinting to evaluate effects of storage conditions on biomolecular structure of filter-dried saliva samples and recovered DNA

Saliva has been widely recognized as a non-invasive, painless and easy-to-collect bodily fluid, which contains biomarkers that can be used for diagnosis of both oral and systemic diseases. Under ambient conditions, salivary biomarkers are subject to degradation. Therefore, in order to minimize degradation during transport and storage, saliva specimens need to be stabilized. The aim of this study was to investigate the feasibility of preserving saliva samples by drying to provide a shelf-stable source of DNA. Human saliva was dried on filters under ambient conditions using sucrose as lyoprotective agent. Samples were stored under different conditions, i.e. varying relative humidity (RH) and temperature. In addition to assessment of different cell types in saliva and their DNA contents, Fourier transform infrared spectroscopy (FTIR) was used to evaluate the effects of storage on biomolecular structure characteristics of saliva. FTIR analysis showed that saliva dried without a lyoprotectant exhibits a higher content of extended β-sheet protein secondary structures compared to samples that were dried with sucrose. In order to evaluate differences in characteristic bands arising from the DNA backbone among differently stored samples, principal component analysis (PCA) was performed, allowing a clear discrimination between groups with/without sucrose as well as storage durations and conditions. Our results indicated that saliva dried on filters in the presence of sucrose exhibits higher biomolecular stability during storage.

Development and Validation of a Method Using Dried Oral Fluid Spot to Determine Drugs of Abuse

A liquid chromatography-mass spectrometry method using dried oral fluid spots was developed and validated for the simultaneous quantification of cocaine, benzoylecgonine, cocaethylene, amphetamine, and 3,4-methylenedioxymethamphetamine. The oral fluid was applied to a Whatman 903 grade paper and submitted to a drying time of 2.5 h. The extraction procedure was optimized by chemometric approach using simplex centroid design. Spots were extracted with a mixture of acetonitrile, buffer, and methanol. Calibration curves covered a linear concentration range of 40-500 ng/mL. Validation parameters of linearity, precision, accuracy, selectivity, carryover, matrix effects, and stability were evaluated and showed satisfactory results. Spot homogeneity was also satisfactory, with less than 15% of deviation from nominal concentration. Spot volume did not influence accuracy when less than 100 μL of the sample was applied to the spot. The validation of the proposed method suggests a potential application in different scenarios in toxicology.

Role of Streptococcus pneumoniae OM001 operon in capsular polysaccharide production, virulence and survival in human saliva

Streptococcus pneumoniae is the leading cause of community-acquired pneumonia in all ages worldwide, and with ever-increasing antibiotic resistance, the understanding of its pathogenesis and spread is as important as ever. Recently, we reported the presence of a Low Molecular Weight Tyrosine Phosphatase (LMWPTP) Spd1837 in the pneumococcus. This protein is encoded in an operon, OM001 with two other genes, with previous work implicating this operon as important for pneumococcal virulence. Thus, we set out to investigate the role of the individual genes in the operon during pneumococcal pathogenesis. As LMWPTPs play a major role in capsular polysaccharide (CPS) biosynthesis in many bacteria, we tested the effect of mutating spd1837 and its adjacent genes, spd1836 and spd1838 on CPS levels. Our results suggest that individual deletion of the genes, including the LMWPTP, did not modulate CPS levels, in multiple conditions, and in different strain backgrounds. Following in vivo studies, Spd1836 was identified as a novel virulence factor during pneumococcal invasive disease, in both the lungs and blood, with this protein alone responsible for the effects of operon’s role in virulence. We also showed that a deletion in spd1836, spd1838 or the overall OM001 operon reduced survival in human saliva during the conditions that mimic transmission compared to the wildtype strain. With studies suggesting that survival in human saliva may be important for transmission, this study identifies Spd1836 and Spd1838 as transmission factors, potentially facilitating the spread of the pneumococcus from person to person. Overall, this study hopes to further our understanding of the bacterial transmission that precedes disease and outbreaks.