Predictive values of methicillin-resistant Staphylococcus aureus nasal swabs for pneumonia in burn ICU patients.

INTRODUCTION/OBJECTIVE: This retrospective cohort study aimed to determine the sensitivity, specificity, and positive (PPV) and negative predictive values (NPV) of MRSA nasal swabs for pneumonia in burn-injured intensive care unit (ICU) patients. METHODS: Patients 18 years or older admitted to the Burn ICU at a tertiary medical center from 2016 to 2021 were included if they had any burns, a pneumonia ICD-10 code, an MRSA nasal swab obtained during admission, and any respiratory cultures associated with at least five consecutive days of antibiotics. RESULTS: There were 267 occurrences of pneumonia across 136 patients. MRSA nasal swabs had an overall sensitivity of 39 %, specificity of 98.7 %, PPV of 84.2 %, and NPV of 89.9 %. MRSA nasal swabs obtained less than seven days from antibiotic initiation had a specificity of 98.6 % and NPV of 98.6 %; meanwhile, swabs obtained at least seven days from antibiotic initiation had a specificity of 98.7 % and NPV of 86.4 %. CONCLUSIONS: The high specificity and NPV indicate that negative MRSA nasal swabs obtained less than seven days from antibiotic initiation may be used to de-escalate anti-MRSA antibiotics in clinically stable burn-injured patients with suspicion of pneumonia. The decrease in NPV suggests that it may be beneficial to obtain a repeat swab periodically.

Impact of swabbing solutions on the recovery of biological material from non-porous surfaces.

Cotton swabs are one of the most effective methods of retrieving biological evidence. The efficiency of swab-based DNA recovery is impacted by many factors, such as the swabbing technique, source of DNA and volume and type of wetting solution used to moisten the swab head. This study aimed to evaluate a series of different swab-moistening solutions. The types of swabbing solutions included buffers, detergent-based solutions, and chelating agents. The DNA deposits, including cell-free DNA, cellular DNA, blood, and saliva, were collected from three non-porous surfaces: plastic, glass, and metal. The difference in the performance of the swab-wetting solutions was heavily influenced by the type of biological fluid, with the chelating agents, EGTA and EDTA, being the most suitable for recovering DNA from saliva and blood samples. Conversely, water and detergent-based solutions were more appropriate for cell-free and cellular DNA material likely to be found in trace DNA deposits.

Integration of surface swab with optical microscopy for detection and quantification of bacterial cells from stainless-steel surfaces.

Swab sampling is a common method for recovering microbes on various environmental surfaces. Its successful application for a specific target depends on the proper swab method and the following detection assay. Herein, we evaluated critical factors influencing surface swab sampling, aiming to achieve the optimal detection and quantification performance of optical detection for bacterial cells on stainless-steel surfaces. Our results showed the recovery rate of Salmonella enterica (SE1045) cells from the 10×10 cm2 stainless-steel surface reached up to 92.71±2.19% when using ammonia bicarbonate-moistened polyurethane foam swabs for gentle collection, followed by ultrasound-assisted release in NH4HCO3 solution. Among the six different foam swabs, the Puritan™ Sterile Large Foam Swab contributed the lowest background noise and highest recovery efficiency when integrated with the optical detection assay. Notably, our method exhibited a strong linear relationship (r2 = 0.9983) between the detected cell numbers and the theoretical number of SE1045 cells seeded on surfaces in the range of 104-107 CFU, with a limit of detection of 7.2×104 CFU 100 cm-2. This integration was completed within 2 hours, exhibiting the applicable potential in various settings.

Influence of Solvent Relative Permittivity in Swab Spray Mass Spectrometry.

The influence of solvent properties on ion generation by swab spray ionization was investigated. The ability of a variety of solvents of different relative permittivity, surface tension, and viscosity to form a stable and reproducible electrospray was examined. It is demonstrated that in swab spray ionization, a crucial balance between solvent composition, applied potential, and the solvent flow fed to the swab head must be maintained. The solvent composition was found to significantly affect the shape of the Taylor cone and the emerging cone jet, which eventually have an impact on the resulting ion yield. The results indicate that the relative permittivity of solvents measured under standard conditions is the main factor governing jet shaping, and consequently, the ionization efficacy. Short jets, which are required for maximum ion yield, were observed for solvents with relative permittivity εr higher than 25. Solvents exhibiting lower relative permittivity required the addition of 20% to 60% methanol to limit the jet length and to avoid the ineffective dripping pulsation. The observed effects were compared to conventional electrospray ionization and paper spray ionization.

Optical detection and enumeration of Escherichia coli and Salmonella enterica using a low-magnification light microscope.

A rapid and cost-effective method for detecting bacterial cells from surfaces is critical to food safety, clinical hygiene, and pharmacy quality. Herein, we established an optical detection method based on a gold chip coating with 3-mercaptophenylboronic acid (3-MPBA) to capture bacterial cells, which allows for the detection and quantification of bacterial cells with a standard light microscope under low-magnification (10×) objective lens. Then, integrate the developed optical detection method with swab sampling to detect bacterial cells loading on stainless-steel surfaces. Using Salmonella enterica (SE1045) and Escherichia coli (E. coli OP50) as model bacterial cells, we achieved a capture efficiency of up to 76.0 ± 2.0 % for SE1045 cells and 81.1 ± 3.3 % for E. coli OP50 cells at 103 CFU/mL upon the optimized conditions, which slightly decreased with the increasing bacterial concentrations. Our assay showed good linear relationships between the concentrations of bacterial cells with the cell counting in images in the range of 103 -107 CFU/mL for SE1045, and 103 -108 CFU/mL for E. coli OP50 cells. The limit of detection (LOD) was 103 CFU/mL for both SE1045 and E. coli OP50 cells. A further increase in sensitivity in detecting E. coli OP50 cells was achieved through a heat treatment, enabling the LOD to be reduced as low as 102 CFU/mL. Furthermore, a preliminary application succeeded in assessing bacterial contamination on stainless-steel surfaces following integration with the approximately 40 % recovery rate, suggesting prospects for evaluating the bacteria from surfaces. The entire process was completed within around 2 h, costing merely a few dollars per sample. Considering the low cost of standard light microscopes, our method holds significant potential for practical industrial applications in bacterial contamination control on surfaces, especially in low-resource settings.

Traumatic CSF rhinorrhea associated with COVID-19 testing: a case series and systematic review.

BACKGROUND: This report analyzes traumatic anterior skull base CSF leaks following nasopharyngeal swab testing for detection of SARS-CoV-2 in the largest case series to date, combined with a systematic literature review. METHODS: Retrospective multi-institutional case-series of traumatic anterior skull base CSF leak with clear antecedent history of COVID-19 swab was completed. A comprehensive search of databases was performed for the systematic literature review. RESULTS: Thirty-four patients with traumatic CSF leak after COVID-19 nasopharyngeal swab testing were identified. Women were more than twice as likely to experience a CSF leak, as compared to men. The majority of patients (58.8%) had no reported predisposing factor in their clinical history. Common defect sites included the cribriform plate (52.9%), sphenoid sinus (29.4%), and ethmoid roof (17.6%). Four patients (11.8%) presented with meningitis. The median time between the traumatic COVID swab and the detection of CSF leak was 4 weeks (IQR 1-9). Patients with meningitis had a median leak duration of 12 weeks (IQR 8-18). The average leak duration was significantly longer in patients with meningitis compared to without meningitis (p = 0.029), with a moderate effect size (r = - 0.68). Most cases (92.9%) managed with endoscopic endonasal surgical repair were successful. CONCLUSIONS: This report clarifies the presentation, risk factors, and management of CSF leaks attributable to diagnostic nasopharynx swabbing procedures in the COVID-19 era. Timely surgical repair is the recommended management option for such leaks.

Impact of Hand Hygiene Interventions on Handwashing Practices and Microbial Risk: A Study in an Orphanage-based School in Pakistan.

BACKGROUND: Orphaned children are often deprived of quality care, making them more susceptible to diseases due to inadequate hand hygiene. OBJECTIVE: The present study aimed to assess the prevalence of hand hygiene practices and detect bacterial loads on children's hands before and after hygiene interventions in an orphanage school. METHOD: The study enrolled all the orphan children registered with the Save Our Souls (SOS) children's orphanage School in Pakistan. The WHO standard checklist for assessing handwashing practices and swab samples from the hand were collected to evaluate the impact of hand-hygiene practices on bacterial load before and after the intervention. The Quantitative Microbial Risk Assessment (QMRA) model was used to predict the health risk. RESULT: The study identified the two most common bacteria: S. aureus and E. coli. Before exposure to the intervention, S. aureus contamination was observed in both groups: intervention (1261 CFU/Hand) and control (1008 CFU/Hand) while E. coli in children's hands were prevalent in the intervention (1042 CFU/Hand) and control (1798 CFU/Hand) groups. The bacterial contamination was significantly reduced after the intervention (S. aureus 166 CFU/ml and E. coli 185 CFU/ml). The higher bacterial ingestion rate was attributed to hand contamination and increased bacteria transfer from hand to mouth. CONCLUSION: The implementation of the multicomponent hand hygiene intervention showed improvement in accessibility to hand hygiene resources and practices. The findings underscore the need for hygiene interventions in orphanage schools to improve health and educational outcomes.

Salivary cortisol and alpha-amylase as stress markers to evaluate an individualized music intervention for people with dementia: feasibility and pilot analyses.

OBJECTIVES: We investigated salivary biomarkers of stress, more specifically, cortisol and alpha-amylase, to evaluate effects of individualized music listening (IML) in people with dementia. METHOD: Participants were N = 64 nursing home residents with dementia (meanage = 83.53 ± 7.71 years, 68.8% female). Participants were randomly assigned to either listening to their favorite music every other day for a period of six weeks (intervention), or standard care (control). Using the Saliva Children`s Swab (SCS), saliva was collected before, after, and 20 min after IML sessions at the beginning and end of the intervention period for the analysis of salivary alpha-amylase and cortisol. RESULTS: Using the SCS was feasible in people with dementia. Nevertheless, there was no effect of IML on salivary stress markers. DISCUSSION: Although using SCS was feasible, active patient engagement is required. Future studies need to corroborate findings in larger samples. TRIAL REGISTRATION: German Clinical Trials Register: DRKS00015641, ISRCTN registry: ISRCTN59052178.

Mediated self-assembled gold nanoclusters with mesoporous silica particles to boost fluorescence for enhanced on-site monitoring of organophosphate pesticides.

Accurate detection of organophosphate pesticides (OPs) is paramount for ensuring food safety. Dendritic mesoporous silica sphere was employed to confine gold nanoclusters (AuNCs@dmSiO2) to ameliorate fluorescent property of AuNCs. A AuNCs@dmSiO2-based fluorescent method was developed for OPs sensing. Identification of Cu2+ by AuNCs quenched AuNCs@dmSiO2 fluorescence. Interaction between Cu2+ and generated thiocholine in catalysis of acetylcholinesterase (AChE) caused fluorescence enhancement. OPs, an inhibitor of AChE, suppressed thiocholine production to cause fluorescence quenching. Based on fluorescent variation, a fluorescent method was proposed for OPs by selecting paraoxon as a model within range of 0.05-25.0 ng/mL with a limit of detection (LOD) of 0.032 ng/mL. Besides, a portable test swab was prepared for on-site monitoring OP paraoxon with a smartphone-based 3D-printing portable device with a LOD of 0.65 ng/mL. This work is highlighted by the inspiration of designing highly fluorescent AuNCs, and the provision of a viable avenue for OPs-related food analysis.

Uncovering the Presentation and Diagnosis of Human Bocavirus in a Patient at a Tertiary Care Center: A Case Report.

A toddler, thriving well, developmentally normal, and fully immunized, presented with fever, cough, and cold for a day, followed by breathing difficulty. Although the child was not ill upon admission, he had a fever and was breathing rapidly. On examination, visible sub-costal retractions and wheezing in both lungs were noted. He required Intensive Care Unit (ICU) management for a brief period, with oxygen supplementation, round-the-clock nebulization, and other supportive care. Initially, he was diagnosed with a wheeze-associated lower respiratory tract infection, as his chest X-ray showed bilateral hyperinflated lung fields. Blood investigations revealed microcytic hypochromic anemia, and his renal function tests, electrolytes, and liver function tests were within normal limits. C-reactive protein (CRP) was positive at 15.1 mg/L (≥10 mg/L considered positive), and the blood culture was sterile. A nasopharyngeal swab on day 2 of admission tested positive for reverse transcription-polymerase chain reaction (RT-PCR) of Human Bocavirus (HBoV). Gradually, the child's condition improved, and he was able to be taken off oxygen support two days after admission. Upon discharge, the child was managed symptomatically with oral medications.

Development and validation of supervised machine learning multivariable prediction models for the diagnosis of Pneumocystis jirovecii pneumonia using nasopharyngeal swab PCR in adults in a low-HIV prevalence setting.

BACKGROUND: The global burden of the opportunistic fungal disease Pneumocystis jirovecii pneumonia (PJP) remains substantial. Polymerase chain reaction (PCR) on nasopharyngeal swabs (NPS) has high specificity and may be a viable alternative to the gold standard diagnostic of PCR on invasively collected lower respiratory tract specimens, but has low sensitivity. Sensitivity may be improved by incorporating NPS PCR results into machine learning models. METHODS: Three supervised multivariable diagnostic models (random forest, logistic regression and extreme gradient boosting) were constructed and validated using a 111-person Australian dataset. The predictors were age, gender, immunosuppression type and NPS PCR result. Model performance metrics such as accuracy, sensitivity, specificity and predictive values were compared to select the best-performing model. RESULTS: The logistic regression model performed best, with 80% accuracy, improving sensitivity to 86% and maintaining acceptable specificity of 70%. Using this model, positive and negative NPS PCR results indicated post-test probabilities of 84% (likely PJP) and 26% (unlikely PJP), respectively. CONCLUSIONS: The logistic regression model should be externally validated in a wider range of settings. As the predictors are simple, routinely collected patient variables, this model may represent a diagnostic advance suitable for settings where collection of lower respiratory tract specimens is difficult but PCR is available.

Our Experience With Intractable Epistaxis After COVID-19 Nasopharyngeal Swab.

INTRODUCTION: Although a COVID-19 nasopharyngeal swab is a safe procedure routinely performed by healthcare providers, it can lead to complications that can be life-threatening. We present seven cases of intractable epistaxis following a nasopharyngeal swab that required sphenopalatine artery ligation. We aim to shed light on this life-threatening condition, emphasizing the importance of recognizing and mitigating such complications. MATERIALS AND METHODS: This retrospective chart review involved cases of intractable epistaxis following a COVID-19 swab from January 2020 to June 2022. The patient's charts were reviewed for the location of the epistaxis and different intranasal and extranasal factors that could have led to it. RESULTS: Seven cases had intractable epistaxis following a nasopharyngeal COVID-19 swab. Six of the seven cases had a deviated nasal septum, and one case had an enlarged inferior turbinate. All patients had bleeding from the ipsilateral nasal structural abnormality. All patients underwent successful sphenopalatine artery ligation. CONCLUSION: Our study highlights the significance of recognizing the potential risk of intractable epistaxis post-COVID-19 swabs and emphasizes the importance of comprehensive training programs to ensure the safe and effective execution of nasopharyngeal swab procedures.

Peptide nucleic acid probe-assisted paper-based electrochemical biosensor for multiplexed detection of respiratory viruses.

The similar transmission patterns and early symptoms of respiratory viral infections, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza (H1N1), and respiratory syncytial virus (RSV), pose substantial challenges in the diagnosis, therapeutic management, and handling of these infectious diseases. Multiplexed point-of-care testing for detection is urgently needed for prompt and efficient disease management. Here, we introduce an electrochemical paper-based analytical device (ePAD) platform for multiplexed and label-free detection of SARS-CoV-2, H1N1, and RSV infection using immobilized pyrrolidinyl peptide nucleic acid probes. Hybridization between the probes and viral nucleic acid targets causes changes in the electrochemical response. The resulting sensor offers high sensitivity and low detection limits of 0.12, 0.35, and 0.36 pM for SARS-CoV-2 (N gene), H1N1, and RSV, respectively, without showing any cross-reactivities. The amplification-free detection of extracted RNA from 42 nasopharyngeal swab samples was successfully demonstrated and validated against reverse-transcription polymerase chain reaction (range of cycle threshold values: 17.43-25.89). The proposed platform showed excellent clinical sensitivity (100 %) and specificity (≥97 %) to achieve excellent agreement (κ ≥ 0.914) with the standard assay, thereby demonstrating its applicability for the screening and diagnosis of these respiratory diseases.

Nanozyme-catalyzed and zwitterion-modified swabs based for the detection of Listeria monocytogenes in complex matrices.

In recent years, nanozymes have been widely used in the field of biosensing and food safety testing due to their advantages of low cost, high stability, easy modification and adjustable catalytic activity. However, how to reduce the signal interference generated by reducing substances, macromolecules and colored substances in the food matrix in nanozymes-based colorimetric sensing is still a major challenge. In this paper, using Listeria monocytogenes as a model analyte, sodium sulfonyl methacrylate (SBMA) polymers were modified onto cotton swabs by photothermal polymerization and combined with Listeria monocytogenes-specific aptamer (Apt1) to prepare swabs that can specifically capture and isolate Listeria monocytogenes from complex matrices (SBMA/Apt1 cotton swab). In addition, in combination with the inhibitory effect of the aptamer (Apt2) on the oxidase activity of Mn3O4 NPs, a colorimetric biosensor based on nanozymes that can quantitatively, sensitively, and specifically identify Listeria monocytogenes in food products was constructed. The results showed that the colorimetric signal of the method was linear with the concentration of Listeria monocytogenes in the range of 2.83-2.83 × 105 CFU/mL, and the limit of detection was 2.64 CFU/mL, which can be used for the detection of Listeria monocytogenes in complex environments and food samples.

A novel metric-based approach of scoring early host immune response from oro-nasopharyngeal swabs predicts COVID-19 outcome.

Unpredictable fatal outcome of COVID-19 is attributed to dysregulated inflammation. Impaired early adaptive immune response leads to late-stage inflammatory outcome. The purpose of this study was to develop biomarkers for early detection of host immune impairment at first diagnosis from leftover RNA samples, which may in turn identify high risk patients. Leftover RNA samples of COVID-19 patients at first diagnosis were stored. Following prospective follow-up, the samples were shorted and categorized into outcome groups. Impaired adaptive T cell response (severity score) and Impaired IL-10 response (undetectable IL-10 in the presence of high expression of a representative interferon response gene) were determined by RT-PCR based assay. We demonstrate that a T cell response based 'severity score' comprising rational combination of Ct values of a target genes' signature can predict high risk noncomorbid potentially critical COVID-19 patients with a sensitivity of 91% (95% CI 58.7-99.8) and specificity of 92.6% (95% CI 75.7-99) (AUC:0.88). Although inclusion of comorbid patients reduced sensitivity to 77% (95% CI 54.6-92.2), the specificity was still 94% (95% CI 79.8-99.3) (AUC:0.82). The same for 'impaired IL-10 response' were little lower to predict high risk noncomorbid patients 64.2% (95% CI 35.1-87.2) and 82% (95% CI 65.5-93.2) respectively. Inclusion of comorbid patients drastically reduce sensitivity and specificity51.6% (95% CI 33.1-69.8) and 80.5% (95% CI 64.0-91.8) respectively. As best of our knowledge this is the first demonstration of a metric-based approach showing the 'severity score' as an indicator of early adoptive immune response, could be used as predictor of severe COVID-19 outcome at the time of first diagnosis using the same leftover swab RNA. The work flow could reduce expenditure and reporting time of the prognostic test for an earliest clinical decision ensuring possibility of early rational management.

Report of SARS-CoV-2 JN.1 variant in Morocco.

In this study, we report the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) JN.1 variant and the quasi-complete genomic sequencing of four clinical samples in Morocco. Nasopharyngeal swabs were obtained from four patients (one female, three males). The Illumina COVIDSeq Test was used for comprehensive genomic analysis.

Spleen Swabs for Sensitive and High-Throughput Detection of African Swine Fever Virus by Real-Time PCR.

African swine fever (ASF) continues to spread in Africa, Europe, Asia and the island of Hispaniola, increasing the need to develop more streamlined and highly efficient surveillance and diagnostic capabilities. One way to achieve this is by further optimization of already established standard operating procedures to remove bottlenecks for high-throughput screening. Real-time polymerase chain reaction (real-time PCR) is the most sensitive and specific assay available for the early detection of the ASF virus (ASFV) genome, but it requires high-quality nucleic acid extracted from the samples. Whole blood from live pigs and spleen tissue from dead pigs are the preferred samples for real-time PCR. Whole blood can be used as is in nucleic acid extractions, but spleen tissues require an additional homogenization step. In this study, we compared the homogenates and swabs prepared from 52 spleen samples collected from pigs experimentally inoculated with highly and moderately virulent ASF virus strains. The results show that not only are the spleen swabs more sensitive when executed with a low-cell-count nucleic acid extraction procedure followed by real-time PCR assays but they also increase the ability to isolate ASFV from positive spleen samples. Swabbing is a convenient, simpler and less time-consuming alternative to tissue homogenization. Hence, we recommend spleen swabs over tissue homogenates for high-throughput detection of ASFV by real-time PCR.

Reliability of superficial swab culture results compared with deep wound culture results in Fournier's gangrene: A retrospective study.

OBJECTIVES: To compare isolates from deep wound and superficial swab cultures to evaluate the detectability of pathogens by each culture in Fournier's gangrene; and evaluate the association between microorganisms isolated from deep wounds and those isolated from blood or urine. METHODS: Patients with Fournier's gangrene who underwent debridement between October 2006 and January 2023 were retrospectively reviewed. In addition to comparing the isolates from deep wound cultures at initial debridement with those from superficial swab, blood, and urine cultures, the relationship between the traits of the organisms from deep wounds and patient disease severity and prognosis was examined. RESULTS: Among 25 patients, deep wound and superficial swab cultures were obtained from 25 to 18 patients, respectively. The frequency of anaerobic isolates was significantly lower in the superficial cultures than in the deep wound cultures (31/76 versus 13/56, p = 0.034). Bacteria not isolated from deep wounds were isolated from superficial cultures in 55.6 % of the patients; the concordance rate between deep and superficial cultures was 27.8 % (5/18). The positive rates of blood and urine cultures were 20.8 % and 35.7 %, respectively; all isolates from the urine and blood cultures reflected the results of the deep wound culture. No significant association was observed between the severity or mortality and the type of causative bacteria. CONCLUSIONS: Superficial swab cultures cannot be substituted for deep wound cultures in Fournier's gangrene. Although the positivity rates for blood and urine cultures were not high, they were helpful in determining antibiotic de-escalation.

Dry Swabs and Dried Saliva as Alternative Samples for SARS-CoV-2 Detection in Remote Areas in Lao PDR.

Background: Surveillance of SARS-CoV-2 circulation is mainly based on real-time reverse transcription-polymerase chain reaction, which requires laboratory facilities and cold chain for sample transportation. This is difficult to achieve in remote rural areas of resource-limited settings. The use of dried blood spots shipped at room temperature has shown good efficiency for the detection of arboviral RNA. Using a similar approach, we conducted a study at 3 provincial hospitals in Laos to compare the detection of SARS-CoV-2 from neat and dried spot samples. Methods: Between January 2022 and March 2023, patients with respiratory symptoms were recruited. Nasopharyngeal/oropharyngeal swabs in virus transport medium (VTM), dry swabs, saliva, and dried saliva spotted on filter paper were collected. All samples were tested by SARS-CoV-2 real-time reverse transcription-polymerase chain reaction. Results: In total, 479 participants were included. The VTM samples tested positive for 288 (60.1%). High positive percent agreements were observed for dry swab (84.8%; 95% CI, 80.2%-88.8%) and saliva (89.2%; 95% CI, 85.1%-92.6%) as compared with VTM. There was a loss of sensitivity when saliva was dried on filter paper (73.6%; 95% CI, 68.1%-78.6%) as compared with saliva. SARS-CoV-2 variant (Delta or Omicron) had no significant impact on the performance of the different sample types. Conclusions: Our findings suggest that dry swabs could be a good alternative for sample collection and permit easy shipping at ambient temperature for subsequent viral SARS-CoV-2 RNA purification and molecular investigation. This is a useful tool to consider for a rapid implementation of large-scale surveillance of SARS-CoV-2 in remote areas, which could be extrapolated to other respiratory targets during routine surveillance or in the case of a novel emerging pandemic.