Detection Of Respiratory Pathogens Research Articles

A fully automated microfluidic PCR-array system for rapid detection of multiple respiratory tract infection pathogens

Rapid and accurate identification of respiratory tract infection pathogens is of utmost importance for clinical diagnosis and treatment, as well as prevention of pathogen transmission. To meet this demand, a microfluidic chip-based PCR-array system, Onestart, was developed. The Onestart system uses a microfluidic chip packaged with all the reagents required, and the waste liquid is also collected and stored on the chip. This ready-to-use system can complete the detection of 21 pathogens in a fully integrated manner, with sample lysis, nucleic acid extraction/purification, and real-time PCR sequentially implemented on the same chip. The entire analysis process is completed within 1.5 h, and the system automatically generates a test report. The lower limit-of-detection (LOD) of the Onestart assay was determined to be 1.0 × 103 copies·mL−1. The inter-batch variation of cycle threshold (Ct) values ranged from 0.08% to 0.69%, and the intra-batch variation ranged from 0.9% to 2.66%. Analytical results of the reference sample mix showed a 100% specificity of the Onestart assay. The analysis of batched clinical samples showed consistency of the Onestart assay with real-time PCR. With its ability to provide rapid, sensitive, and specific detection of respiratory tract infection pathogens, application of the Onestart system will facilitate timely clinical management of respiratory tract infections and effective prevention of pathogen transmission.Graphical abstract Onestart, a ready-to-use system, can detect 21 pathogens in a fully integrated manner on a microchip within 1.5 h. Supplementary InformationThe online version contains supplementary material available at 10.1007/s00216-021-03171-4.

The epidemiology of community-acquired respiratory viruses during the SARS-CoV-2 pandemic.

In regions of high COVID‐19 endemicity, the incidence of other respiratory viral illnesses is depressed, which may reflect biologic displacement of other pathogens or the impact of preventive strategies to reduce transmission of SARS‐CoV‐2.

Respiratory Pathogen Detection in Pediatric Patients Intubated for Presumed Infection.

Respiratory syncytial virus (RSV) in pediatric patients has been associated with low risk of concomitant bacterial infection. However, in children with severe disease, it occurs in 22% to 50% of patients. As viral testing becomes routine, bacterial codetections are increasingly identified in patients with non-RSV viruses. We hypothesized, among patients intubated for respiratory failure secondary to suspected infection, there are similar rates of codetection between RSV and non-RSV viral detections. This retrospective chart review, conducted over a 5-year period, included all patients younger than 2 years who required intubation secondary to respiratory failure from an infectious etiology in a single pediatric emergency department. Patients intubated for noninfectious causes were excluded. We reviewed 274 patients, of which 181 had positive viral testing. Of these, 48% were RSV-positive and 52% were positive for viruses other than RSV. Codetection of bacteria was found in 76% (n = 65; 95% confidence interval [CI], 66%, 84%) of RSV-positive patients and 66% (n = 63, 95% CI: 57%, 76%) of patients positive with non-RSV viruses. Among patients with negative viral testing, 33% had bacterial growth on lower respiratory culture. Male sex was the only patient-related factor associated with increased odds of codetection (odds ratio [OR], 2.2; 95% CI, 1.08-4.38). The odds of codetection between RSV-positive patients and non-RSV viruses were not significantly different (OR, 1.3; 95% CI, 0.62-2.71). Bacterial codetection is common and not associated with anticipated patient-related factors or with a specific virus. These results suggest consideration of empiric antibiotics in infants with respiratory illness requiring intubation.

Detection of Respiratory Pathogens Does Not Predict Risks After Outpatient Adenotonsillectomy.

Objectives/HypothesisTo determine whether the presence of detectable upper respiratory infections (URIs) at the time of adenoidectomy/adenotonsillectomy is associated with increased morbidity, complications, and unexpected admissions.Study DesignProspective double‐blinded cohort.MethodsIn this prospective cohort study, nasopharyngeal swabs were obtained intraoperatively from 164 pediatric patients undergoing outpatient adenoidectomy/tonsillectomy with or without pressure equalization tubes (PETs) and were analyzed with PCR for the presence of 22 known URIs, including SARS‐CoV‐2. Surgeons and families were blinded to the results. At the conclusion of the study, rates of detectable infection were determined and intraoperative and postoperative events (unexpected admissions, length of PACU stay, rates of laryngospasm/bronchospasm, oxygen desaturation, bradycardia, and postoperative presentation to an emergency department) were compared between infected and uninfected patients.ResultsOf the 164 patients (50% male, 50% female, ages 8 mo‐18 y), 136 patients (82.9%) tested positive for one or more URI at the time of surgery. Forty one patients (25.0%) tested positive for three or more URIs concurrently, and 11 (6.7%) tested positive for five or more URIs concurrently. There were no significant differences in admission rates, length of PACU stay, rates of laryngospasm/bronchospasm, oxygen desaturation, bradycardia, or postoperative presentation to an emergency department between positive and negative patients. No patients tested positive for SARS‐CoV‐2.ConclusionsA recent positive URI test does not confer any additional intraoperative or postoperative risk in the setting of outpatient adenoidectomy/tonsillectomy in healthy patients. There is no utility in preoperative URI testing, and delaying surgery due to a recent positive URI test is not warranted in this population.Level of Evidence3 Laryngoscope, 131:E2074–E2079, 2021

Clinical features of rhinovirus infection in hospitalized adult patients during the epidemic season 2017–2018

Purpose. Rhinovirus infection has in the past been perceived as a disease capable of causing mild respiratory symptoms in most cases in children. Modern clinical and epidemiological studies have shown that rhinovirus infection in adults and children and has a moderate and severe course. The aim of this study was to conduct a clinical and laboratory analysis of cases of rhinovirus infection in adult hospitalized patients and evaluate the etiological role of rinoviruses in the epidemic season of 2017/18.Materials and methods. 1013 case histories of patients admitted to the hospital with a diagnosis of SARS were studied. These patients were taken nasopharyngeal swabs were investigated by PCR for the detection of respiratory pathogens. A positive result was obtained with rhinovirus infection of 51 patients.Results. Of the examined patients, 41,6% had influenza, 45,8% had no viruses and 12,6% had other viral infections, of which 40% were due to rhinovirus infection. Among them, young patients prevailed: the median age for men was 31,0 years, for women-27,5 years. The disease occurred in a moderate form – 78,8%, severe course was observed in 5,3% of patients and was accompanied by infectious and toxic shock. Most often the disease occurred with complications acute bronchitis – 22,1%, pneumonia joined in 15,7% of cases.Conclusion. rhinovirus infection ranks first (40%) among non-influenza causes of viral respiratory tract infection in the examined patients. It was registered mainly in young people. In most cases, it proceeded in a moderate form and had a complicated course, including pneumonia.

Clinical features of 17 patients with 2019-nCoV.

This study aims to discuss the unique clinical features of patients with 2019-nCoV in Zhengzhou City to provide references for clinical diagnosis and treatment. Seventeen patients with 2019-nCoV in Zhengzhou People's Hospital from February to March 2020 were collected. Their epidemiology, clinical symptoms, laboratory examinations, and chest CT images were reviewed. All 17 patients were aged between 12-83 years, with an average age of 47 years, and consisted of 10 males (58.8%) and 7 females (41.2%). Two patients had histories of living or traveling in Wuhan, and 9 patients were attacked locally. The 6 remaining patients were unknown about incidence reasons. The average incubation period was 10 days, and the average time of the course of the disease was 9 days. Among the participants, 12 patients had fever as the first symptoms and 5 patients had normal body temperature. One patient was symptom-free carrier, and one patient had serious symptoms. One patient developed from mild symptoms to severe symptoms, and 14 patients had mild symptoms. Moreover, 7 patients had complications of cardiovascular and cerebrovascular diseases and hypertension, 1 patient was in the advanced stage of squamous cell lung carcinoma, and 1 patient had diabetes mellitus, renal failure, and late-stage uremia. According to novel coronavirus nucleic acid test, 8 patients were positive, accounting for 47.1%. All patients were negative in the novel coronavirus IgM antibody test and negative in other common respiratory pathogen detection. All 17 patients had ground glass-like high-density shadow or stripped high-density shadow on lung CT images, accompanied with many affected lesions on two lungs. The average stay in hospital was 10 days, and the average time of the course of the disease was 9 days. After hospitalization, 15 patients were discharged from the hospital upon recovery, 1 patient was transferred to superior hospital for continuous treatment, and 1 patient died. Patients with 2019-nCoV in Zhengzhou People's Hospital were mainly attacked in local areas, and most of them had mild symptoms. The positive rate of the nucleic acid test was 47.1%. The main clinical characteristics are increased neutrophil granulocytes, increased C-reactive proteins, decreased lymphocytes, ground glass-like or stripped lesions on lung CT image, common complications of cardiovascular and cerebrovascular diseases, and favorable prognosis.

Common respiratory viral infections: Bilateral versus unilateral bronchoalveolar lavage versus endotracheal aspiration.

Data about the diagnostic efficiency of bilateral bronchoalveolar lavage (BAL) samples and endotracheal aspirates (EA) testing for common viral respiratory infections are scarce. We analyzed data from 167 cases, where bilateral BAL samples were tested, and from 101 cases, where BAL samples and EA were tested. Multiplex polymerase chain reaction (PCR) was performed with the fast track diagnostics viral respiratory panel, producing data on the adenovirus, coronavirus, enterovirus, human metapneumovirus, bocavirus, influenza virus, parainfluenza virus, rhinovirus, and respiratory syncytial virus status of patients with respiratory disease symptoms. In the bilateral BAL cohort, 46 (27.5%) cases were positive for at least one of the viruses mentioned above in both samples. Discrepant results (virus not detected on one side) were seen in six (3.6%) cases. In the BAL versus EA cohort, 12 (11.9%) cases were positive in both materials, discrepant results (only one material being positive) were observed in 11 (10.9%) cases, with seven (63.6%) BAL samples, and four (36.4%) EA being positive. Bilateral sampling does not significantly improve the diagnostic efficiency of BAL for the detection of common respiratory viral pathogens via PCR. The diagnostic quality of EA and BAL samples for the detection of common viral respiratory pathogens is comparable.

How sure are you? A web-based application to confront imperfect detection of respiratory pathogens in bighorn sheep.

The relationships between host-pathogen population dynamics in wildlife are poorly understood. An impediment to progress in understanding these relationships is imperfect detection of diagnostic tests used to detect pathogens. If ignored, imperfect detection precludes accurate assessment of pathogen presence and prevalence, foundational parameters for deciphering host-pathogen dynamics and disease etiology. Respiratory disease in bighorn sheep (Ovis canadensis) is a significant impediment to their conservation and restoration, and effective management requires a better understanding of the structure of the pathogen communities. Our primary objective was to develop an easy-to-use and accessible web-based Shiny application that estimates the probability (with associated uncertainty) that a respiratory pathogen is present in a herd and its prevalence given imperfect detection. Our application combines the best-available information on the probabilities of detection for various respiratory pathogen diagnostic protocols with a hierarchical Bayesian model of pathogen prevalence. We demonstrated this application using four examples of diagnostic tests from three herds of bighorn sheep in Montana. For instance, one population with no detections of Mycoplasma ovipneumoniae (PCR assay) still had an 6% probability of the pathogen being present in the herd. Similarly, the apparent prevalence (0.32) of M. ovipneumoniae in another herd was a substantial underestimate of estimated true prevalence (0.46: 95% CI = [0.25, 0.71]). The negative bias of naïve prevalence increased as the probability of detection of testing protocols worsened such that the apparent prevalence of Mannheimia haemolytica (culture assay) in a herd (0.24) was less than one third that of estimated true prevalence (0.78: 95% CI = [0.43, 0.99]). We found a small difference in the estimates of the probability that Mannheimia spp. (culture assay) was present in one herd between the binomial sampling approach (0.24) and the hypergeometric approach (0.22). Ignoring the implications of imperfect detection and sampling variation for assessing pathogen communities in bighorn sheep can result in spurious inference on pathogen presence and prevalence, and potentially poorly informed management decisions. Our Shiny application makes the rigorous assessment of pathogen presence, prevalence and uncertainty straightforward, and we suggest it should be incorporated into a new paradigm of disease monitoring.

Mechanical properties of 3-D printed polyvinyl alcohol matrix for detection of respiratory pathogens

Polyvinyl alcohol is used to 3D print (fused deposition modelling) sampling matrices for bacterial detection. A specific configuration was designed using Computer-Aided Design software. The mechanical properties of the printed samples were studied using uniaxial tensile testing, and compared to those of the original Polyvinyl alcohol filament, with and without heat treatment. The effects of different factors such as UV treatment, printing speed, infill density and printing direction on the mechanical properties of the printed samples including strength, strain and modulus of elasticity were studied. The results show that the effect of the fused deposition modelling process on the mechanical properties of the printed Polyvinyl alcohol cannot be explained by its exposure to heat. UV treatment reduced the strength, characteristic strains and Young's modulus. It makes Polyvinyl alcohol samples brittle. The effects of printing speed and the infill density on the mechanical properties of printed samples can be no linear. An unexpected relation between printing direction and mechanical properties was demonstrated by the studied specimens that needs further theoretical understanding. There is a huge scatter in strength of PVA samples compared with typical engineering materials, and in the fracture strain of original PVA filament, the 3D printing process can reduce the scatter but only by a limited extent. To summarise, there is a sophisticated relation between printing parameters and the mechanical properties of the printed Polyvinyl alcohol.

3-D printed polyvinyl alcohol matrix for detection of airborne pathogens in respiratory bacterial infections

Novel sampling matrices were manufactured using 3D printing for the detection of respiratory pathogens in expired air. A specific configuration of the matrices was designed using Computer-Aided Design software. Polyvinyl alcohol (PVA) was printed using fused deposition modelling to create a multilayer matrix to enhance the capture of bacteria. The performance of these matrices was compared with gelatine filters that have been used for this work to date. PVA matrices (60 mm diameter) were contaminated with bacteria either by direct inoculation, or by aerosol exposure using an Omron A3 nebuliser. Rough and smooth morphotypes of Mycobacterium abscessus, M. smegmatis and M. bovis BCG, were used in this study to contaminate the matrices. PVA matrices and gelatine sampling filters were contaminated to compare recovery rates for quantitative analyses. These were dissolved in water, bacteria pelleted and DNA extracted followed by a Mycobacterium-specific quantitative Polymerase Chain Reaction (qPCR).The results showed that 3D printed PVA matrices are very effective to capture the bacteria. 3D printed PVA matrix and gelatine filters yielded results of the same order of magnitude for mycobacterial analyses, however, PVA matrix offers several advantages over the latter material. 3D printed PVA is considered as an economic and time-effective matrix as it is cheaper than gelatine filters. PVA is sufficiently robust to be handled and loaded into the surgical masks for sampling, compared to the brittle gelatine filters that required supportive frames. PVA is a synthetic material and it is suitable for DNA-based analyses, whilst gelatine is derived from animal collagen, and carries a high bacterial DNA background that interferes with the target DNA analysis. Furthermore, PVA dissolves in distilled water without requiring chemicals or enzymes, such as the case for gelatine hydrolysis. To summarise, 3D printed PVA sampling matrix is considered a promising tool used for microbiological diagnostic purposes.

Cepheid Xpert® Flu/RSV and Seegene Allplex™ RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice

BackgroundMolecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert® Flu/RSV vs Allplex™ RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice.MethodsWe retrospectively identified 914 patient encounters where testing with both Xpert® Flu/RSV and Allplex™ RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa.ResultsThe positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV.ConclusionsThe Xpert® Flu/RSV and Allplex™ RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.

Guidance for the management of adult patients with coronavirus disease 2019.

In December 2019, a novel coronavirus was identified in Wuhan City, Hubei Province, China and later the disease was named coronavirus disease 2019 (COVID-19). On March 11, 2020, the World Health Organization (WHO) officially announced that COVID-19 had reached global pandemic status. This article summarized the understanding of the etiology, pathogenesis, epidemiology, clinical characteristics, diagnosis, treatment, rehabilitation, and prevention and control measures of COVID-19 based on the available data and anti-epidemic experience in China.

Determining a sampling regime for PCR detection of respiratory tract viral infection at coronial post-mortem examinations

Death due to respiratory infection is commonly encountered at autopsy. With only one opportunity to obtain samples for identification of a causative agent, it is important to ensure that sampling regimes are optimized to provide the greatest detection, without the expense and redundancy that can arise from over-sampling. This study was performed retrospectively using data from Coronial autopsies over the period 2012–2019 from which swabs from the nasopharyngeal region, trachea and lung parenchyma, in addition to samples of lung tissue, had been submitted for multiplex PCR detection of respiratory pathogens. From 97 cases with all four samples, there were 24 with at least one positive result for viral infection. Some cases had multiple positive results and a total of 27 respiratory tract viruses were identified, of which rhinovirus, influenza A virus and respiratory syncytial virus were the most common. Seventeen of the 27 viral infections (63%) were identified in all four samples. However, in nearly all cases (96%) the nasopharyngeal swab detected the infective agent when the multiplex PCR panel had detected infection in any of the four sample types. A nasopharyngeal swab is considered to be an optimal sample for detection of respiratory tract viral infection. As the samples analyzed were acquired before the appearance of the COVID-19 virus, the applicability of this finding for COVID-19 screening is not established.

Investigation of the Shedding of Selected Respiratory Pathogens in Healthy Horses Presented for Routine Dental Care.

The main objective of the study was to determine the frequency of detection of selected infectious respiratory viruses and bacteria in healthy horses presented over a 12-month period for routine dental care at 2 veterinary hospitals. Nasal secretions were collected from 579 horses and tested for equine herpesviruses (EHV-1, EHV-2, EHV-4, EHV-5), equine influenza virus (EIV), equine rhinitis A and B viruses (ERAV, ERBV), Streptococcus equi subspecies equi (S equi), S equi subspecies zooepidemicus (S zooepidemicus), and methicillin-resistant Staphylococcus aureus (MRSA) using routine diagnostic quantitative polymerase chain reaction assays. True respiratory pathogens (EHV-1, EHV-4, EIV, ERBV, and MRSA) were detected in 129 (22%) of the horses. Commensal respiratory pathogens (EHV-2, EHV-5, and S zooepidemicus) were detected in 515 (89%) of the study horses. ERAVand S equi were not detected in any of the study horses. The horses showed statistical differences between the 2 veterinary hospitals in regard to breed, age, presence of nasal discharge, rectal temperature, and detection of true and commensal respiratory pathogens. The data generated from the present study supports the risk for the transmission of true and commensal respiratory pathogens from subclinical shedders to susceptible horses. Equine veterinarians performing routine dental care should engage in routine biosecurity practices, with the goal to reduce disease spread.

Effectiveness of rapid multiplex polymerase chain reaction for early diagnosis and treatment of pertussis.

BackgroundPertussis, is an infectious respiratory disease caused by Bordetella pertussis. The incidence of pertussis has been increasing in South Korea to due to waning vaccine-induced immunity. Culture has a low sensitivity and a long turnaround time (TAT). Recently, a rapid multi-polymerase chain reaction (mPCR) test with a TAT of about 1 h was developed for the detection of respiratory pathogens (17 viruses and three bacteria), including B. pertussis. This study aimed to investigate the effectiveness of mPCR for early diagnosis and treatment of pertussis.MethodsWe performed a retrospective study of patients with pertussis diagnosed from May 2017 to June 2019 at a university hospital in South Korea. Nasopharyngeal swab specimens were tested using mPCR. Data were extracted from medical records.ResultsA total of 27 patients with a median age of 48.9 years (range: 3.3–82.2 years) were diagnosed with pertussis, of whom 9 (33.3%) were male. Eleven (40.7%) had fever, 12 (44.4%) had dyspnea, three (11.1%) had paroxysmal cough, and nine (33.3%) had inspiratory whooping. The median interval from symptom onset to diagnosis was 9.0 days (range: 1–31 days). Twenty-four patients (81.5%) were diagnosed within 2 weeks from symptom onset. All but one patient was prescribed macrolide antibiotics. Twenty-two patients (81.5%) required hospitalization, including three (11.1%) who required intensive care unit care for ventilation.ConclusionTesting patients with respiratory symptoms using mPCR can improve early diagnosis of pertussis, ensure proper treatment, and may help with outbreak control.

Multicenter Evaluation of QIAstat-Dx Respiratory Panel V2 for Detection of Viral and Bacterial Respiratory Pathogens.

QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these discordant targets were considered to represent true positives after discrepancy testing by a third method. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems, including the ePlex RPP assay, is the ability to generate cycle threshold (CT ) values, which could help with the interpretation of results. Taking the data together, this study showed good performance of the QIAstat-Dx RP assay in comparison to the ePlex RPP assay for the detection of respiratory pathogens. The QIAstat-Dx RP assay offers a new, rapid, and accurate sample-to-answer multiplex panel for the detection of the most common viral and bacterial respiratory pathogens and therefore has the potential to direct appropriate therapy and infection control precautions.

Analysis of adenovirus infection in acute respiratory tract infection cases in Shanghai from 2015 to 2019

Objective: To study the epidemiological characteristics and mixed infection of adenovirus in acute respiratory tract infections in Shanghai from 2015 to 2019, and to provide scientific basis for the prevention and control of adenovirus. Methods: Acute respiratory tract infections were collected from 3 hospitals in Shanghai from 2015 to 2019. Relevant information was registered and respiratory specimens were sampled for detection of respiratory pathogens by multiplex PCR. Results: A total of 1 543 cases of acute respiratory tract infection were included. The positive rate of adenovirus was 2.92%(45/1 543), the positive rates of influenza like illness (ILI) and severe acute respiratory illness (SARI) were 2.74%(29/1 058) and 3.30%(16/485), respectively. The positive rate of ILI during January-May 2019 was 5.43%(7/129), higher than that in the same period of 2015- 2018 (0.52%-4.48%) (Fisher's exact test value=8.92, P=0.036). The incidence of adenovirus-positive cases was mainly distributed in the first and second quarters, accounting for 62.22% (28/45). The difference of the incidence of adenovirus-positive cases in each quarter was significant (χ(2)= 12.52, P=0.006). The positive rate in the second quarter was highest (6.03%), which was higher than that in other quarters (1.89%-2.93%). There were significant differences among different age groups (χ(2)=16.94, P=0.001), and the positive rate decreased with age (χ(2)=10.16, P=0.001). The positive rate of 13-19 years old group (9.43%) was higher than that of other age groups (1.48%-4.81%). The positive rate of student group (12.07%) was higher than that of other occupations (2.61%). The difference was systematic (χ(2)=11.53, P=0.001). Mixed infection accounted for 31.11% (14/45) of 45 adenovirus positive cases. The mixed infection rates of ILI and SARI were 34.48% (10/29) and 25.00% (4/16), respectively. Among 14 cases of mixed infection, the main mixed infection pathogens of adenovirus were influenza A virus and coronavirus. Conclusion: Adenovirus surveillance should be further strengthened in adolescents with a focus on students and other key groups in the second quarter.

Repeat Molecular Testing for Respiratory Pathogens: Diagnostic Gain or Diminishing Returns?

BackgroundUpper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management.MethodsWe evaluated the test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test.ResultsOur study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results.ConclusionsOur findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.

Rapid Detection of Airway Pathogens in Lung Transplant Donors

Final culture results are often unavailable at the time of donor organ offers, despite their importance in the evaluation of donor organ quality. We hypothesized that a rapid multiplex molecular assay could improve time to results and facilitate treatment initiation in the donors prior to organ recovery. The "Rapid Detection of Airway Pathogens for Lung Transplantation" trial (NCT03933878) is a prospective observational clinical trial investigating the efficiency and accuracy of the BioFire Pneumonia Panel in the context of donor bronchoscopy. This assay tests the presence and/or quantity for 26 common airway pathogens in 2 hours. Bronchoalveolar lavagewas collected from brain dead donors at the time of lung procurement. Molecular assay results were compared to standard of care cultures. Time to result between molecular assay and standard of care was compared by Wilcoxon signed-rank test. Agreement between assays was assessed by Cohen's kappa. A total of 35 donor samples were included. From the time of sample collection to time to result, the median time was 7.01 hours [6.59-9.18] versus 57.7 hours [44.6-72.6] (p <0.001) for the molecular and standard of care assay results, respectively. Molecular assays detected bacterial pathogens in 21 cases (60%) and viruses in 2 cases (6%), versus 57% and 3% for standard of care assays, respectively. The agreement between assays for bacteria was 0.82 (p <0.001) and 0.65 (p <0.001) for viruses. Molecular detection of lower respiratory pathogens significantly reduces the time to result while maintaining agreement with standard of care clinical cultures in the context of candidate lung allografts. Such data could inform quality assessment and facilitate timely donor management prior to organ recovery.

Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens

ObjectivesThe performance of the investigational-use-only version of the BioFire FilmArray Pneumonia Panel (FA-Pneumo), a high-order nested multiplex PCR, was evaluated for the detection of typical respiratory bacterial pathogens and antibiotic resistance genes in sputa and endotracheal aspirate (ETA) specimens. MethodsThirty-one sputa and 69 ETA specimens were analyzed. The diagnostic performance of FA-Pneumo was assessed using routine microbiological methods as the reference standard. ResultsOverall sensitivity and specificity for organism detection using FA-Pneumo were 98.5% and 76.5%, respectively. The sensitivity for each pathogen was 100%, except for Klebsiella aerogenes, and the range of specificity was 83.3–99.0%. FA-Pneumo detected antimicrobial resistance genes in 17 out of 18 specimens (94.4%) that were resistant by antimicrobial susceptibility testing. FA-Pneumo additionally detected 25 resistance genes in 22 specimens, and sequencing for the presence of resistance genes confirmed the majority of these results (20/25, 80%). Semi-quantitative analysis of bacterial nucleic acid amounts by FA-Pneumo revealed that 88.2% of the identified bacteria (67/76) with ≥106 copies/ml also gave culture-positive results with significant amounts of bacteria. ConclusionsFA-Pneumo is a rapid test with high sensitivity for the detection of bacteria and antimicrobial resistance genes in sputum and ETA specimens and could aid in determining antibiotic therapy.