Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses

Prevalence of EBV, HHV6, HCMV, HAdV, SARS-CoV-2, and Autoantibodies to Type I Interferon in Sputum from Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients

An exhausted antiviral immune response is observed in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and post-SARS-CoV-2 syndrome, also termed long COVID. In this study, potential mechanisms behind this exhaustion were investigated. First, the viral load of Epstein-Barr virus (EBV), human adenovirus (HAdV), human cytomegalovirus (HCMV), human herpesvirus 6 (HHV6), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was determined in sputum samples (n = 29) derived from ME/CFS patients (n = 13), healthy controls (n = 10), elderly healthy controls (n = 4), and immunosuppressed controls (n = 2). Secondly, autoantibodies (autoAbs) to type I interferon (IFN-I) in sputum were analyzed to possibly explain impaired viral immunity. We found that ME/CFS patients released EBV at a significantly higher level compared to controls (p = 0.0256). HHV6 was present in ~50% of all participants at the same level. HAdV was detected in two cases with immunosuppression and severe ME/CFS, respectively. HCMV and SARS-CoV-2 were found only in immunosuppressed controls. Notably, anti-IFN-I autoAbs in ME/CFS and controls did not differ, except in a severe ME/CFS case showing an increased level. We conclude that ME/CFS patients, compared to controls, have a significantly higher load of EBV. IFN-I autoAbs cannot explain IFN-I dysfunction, with the possible exception of severe cases, also reported in severe SARS-CoV-2. We forward that additional mechanisms, such as the viral evasion of IFN-I effect via the degradation of IFN-receptors, may be present in ME/CFS, which demands further studies.

Pulmonary microbiology and microbiota in adults with non-cystic fibrosis bronchiectasis: a systematic review and meta-analysis

BACKGROUND

Non-cystic fibrosis bronchiectasis is associated with frequent and diverse microbial infections, yet an overall understanding of microbial presence across different disease stages is lacking.

METHODS

A meta-analysis assessed lung microbes in adults with non-CF bronchiectasis, collecting data using both culture-based and sequencing approaches through three international databases and three Chinese databases. Subgroups were categorized by disease stage: the stable group (S), the exacerbation group (E), and unclassified data consolidated into the undetermined group (U). Culture data were analysed in random-effects meta-analyses while sequencing data were processed using QIIME 2.

RESULTS

A total of 98 studies were included with data from 54,384 participants worldwide. Pseudomonas aeruginosa was the most frequently isolated bacterium (S: 26[19-34]%, E: 23[20-25]%, U: 20[16-25]%), while not specified Mycobacterium avium complex exhibited the highest mycobacterial prevalence (S: 3[1-5]%, E: 4[2-5]%, U: 15[3-27]%). Aspergillus spp. (S: 15[-10-39]%, E: 2[1-3]%, U: 10[5-15]%) and Candida spp. (S: not applicable, E: 11[2-20]%, U: 10[-8-27]%) were predominant in fungi culture with variable distributions among groups. Rhinovirus was the most commonly detected virus with varying prevalence across airway sample types rather than disease stages (S-sputum: 18[-16-53]%, S-nasopharyngeal: 4[-1-9]%, E-sputum: 22[16-29]%, E-nasopharyngeal: 6[4-8]%). Sequencing results revealed notable antibiotic persistence of Pseudomonas in 16S, and significant domination of Candida in ITS.

CONCLUSION

Our findings indicate consistent bacterial patterns throughout bronchiectasis stages in both culture and sequencing results. Viruses are extensively detected in stable patients but vary across different airway sample types. Lower bacterial diversity and higher fungal diversity may be associated with exacerbation risks.

Faecal shedding of SARS-CoV-2 from patients with asymptomatic and mild COVID-19 without gastrointestinal symptoms in Ghana

OBJECTIVE

In this study, we sought to determine whether faecal shedding occurs among SARS-COV-2 positive Ghanaians, as reported elsewhere. Hence we assayed for SARS-COV-2 in the stools of 48 SARS-COV-2 confirmed patients at the Ho Municipal Hospital in Ghana.

RESULTS

Of the 48 COVID-19 patients, 45 (93.8%) had positive tests for SARS-CoV-2 faecal shedding. About 60% reported no respiratory symptoms, while only 2% (1 patient) reported gastrointestinal (GI) symptoms in the form of nausea. Other symptoms reported included headache (57.9%), weakness (57.9%), cough (52.6%), blocked/runny nose (47.4%), fever (31.6%), sore throat (31.6%), and shortness of breath (21.1%). One person complained of nausea (5.3%) Semi-quantitative comparison of the SARS COV-2 viral loads in matched respiratory and faecal samples using the cycle threshold (CT) values revealed no statistical differences. Furthermore, the duration between collection of respiratory and faecal samples did not have any direct influence on the differences in the CT values. This suggests that treatment and use of sewage for environmental surveillance of SARS COV-2 could be a potential public health countermeasure.

Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness

BACKGROUND

Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis.

METHODS

Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication.

RESULTS

Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected.

CONCLUSIONS

Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.

Nasal discharge: A unique enhanced alternative for the detection of respiratory pathogens in adults

Upper respiratory tract infections are a significant cause of social- and disease burden worldwide. Currently, invasive and uncomfortable molecular detection methods are used for respiratory pathogen detection. We aimed to assess the ability and bearability of a rhinorrhea swab (RS) to detect respiratory pathogens in comparison to the combined nasopharyngeal and oropharyngeal swab (NP/OP). This study was performed at a Public Health Service severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) testing facility between November and December 2022 in the Netherlands. Adults aged 16 years and older, being subjected to a standard of care NP/OP swab with nasal discharge, were included and received an additional RS. Respiratory pathogen detection was evaluated using SARS-CoV-2 polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification (MLPA) PCR. Bearability was evaluated using visual analog scale (VAS) scores and a questionnaire. A total of 100 adults with a mean age ± SD of 46 ± 16 years were included. The NP/OP swab detected 104 pathogens, the RS 83 pathogens (p < 0.001), and in total 108 respiratory pathogens were identified in 89 adults (89%). The ability to detect respiratory pathogens compared between the RS and the combined NP/OP swab revealed a sensitivity of 82% (95% CI 73%-89%) and specificity of 100% (95% CI 72%-100%). RS were significantly more bearable than the combined NP/OP swab (p value < 0.001). Therefore, nasal discharge found in adults can be used as an adequate reliable medium for respiratory pathogen detection using SARS-CoV-2 PCR and MLPA PCR.

Underascertainment of Respiratory Syncytial Virus Infection in Adults Due to Diagnostic Testing Limitations: A Systematic Literature Review and Meta-analysis

BACKGROUND

Most observational population-based studies identify respiratory syncytial virus (RSV) by nasal/nasopharyngeal swab reverse transcriptase real-time PCR (RT-PCR) only. We conducted a systematic review and meta-analyses to quantify specimen and diagnostic testing-based underascertainment of adult RSV infection.

METHODS

EMBASE, PubMed, and Web of Science were searched (January 2000-December 2021) for studies including adults using/comparing >1 RSV testing approach. We quantified test performance and RSV detection increase associated with using multiple specimen types.

RESULTS

Among 8066 references identified, 154 met inclusion. Compared to RT-PCR, other methods were less sensitive: rapid antigen detection test (RADT; pooled sensitivity, 64%), direct fluorescent antibody (DFA; 83%), and viral culture (86%). Compared to singleplex PCR, multiplex PCR's sensitivity was lower (93%). Compared to nasal/nasopharyngeal swab RT-PCR alone, adding another specimen type increased detection: sputum RT-PCR, 52%; 4-fold rise in paired serology, 44%; and oropharyngeal swab RT-PCR, 28%. Sensitivity was lower in estimates limited to only adults (for RADT, DFA, and viral culture), and detection rate increases were largely comparable.

CONCLUSIONS

RT-PCR, particularly singleplex testing, is the most sensitive RSV diagnostic test in adults. Adding additional specimen types to nasopharyngeal swab RT-PCR testing increased RSV detection. Synergistic effects of using ≥3 specimen types should be assessed, as this approach may improve the accuracy of adult RSV burden estimates.

Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis

Concentrations of nucleic acids from a range of respiratory viruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from excretions deposited in toilets or drains. To relate measured concentrations in wastewater at a treatment plant to the number of community infections, viral nucleic-acid concentrations in human excretions are needed as inputs to a mass balance model. Here, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus, metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. We identified 220 data sets from 50 articles and reported viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). Most articles only reported the presence or absence of the virus in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.

Diagnosis of Respiratory Syncytial Virus in Adults Substantially Increases When Adding Sputum, Saliva, and Serology Testing to Nasopharyngeal Swab RT-PCR

INTRODUCTION

Nearly all existing respiratory syncytial virus (RSV) incidence estimates are based on real-time polymerase chain reaction (RT-PCR) testing of nasal or nasopharyngeal (NP) swabs. Adding testing of additional specimen types to NP swab RT-PCR increases RSV detection. However, prior studies only made pairwise comparisons and the synergistic effect of adding multiple specimen types has not been quantified. We compared RSV diagnosis by NP swab RT-PCR alone versus NP swab plus saliva, sputum, and serology.

METHODS

This was a prospective cohort study over two study periods (27 December 2021 to 1 April 2022 and 22 August 2022 to 11 November 2022) of patients aged ≥ 40 years hospitalized for acute respiratory illness (ARI) in Louisville, KY. NP swab, saliva, and sputum specimens were collected at enrollment and PCR tested (Luminex ARIES platform). Serology specimens were obtained at acute and convalescent timepoints (enrollment and 30-60-day visit). RSV detection rate was calculated for NP swab alone and for NP swab plus all other specimen type/test.

RESULTS

Among 1766 patients enrolled, 100% had NP swab, 99% saliva, 34% sputum, and 21% paired serology specimens. RSV was diagnosed in 56 (3.2%) patients by NP swab alone, and in 109 (6.2%) patients by NP swab plus additional specimens, corresponding to a 1.95 times higher rate [95% confidence interval (CI) 1.62, 2.34]. Limiting the comparison to the 150 subjects with all four specimen types available (i.e., NP swab, saliva, sputum, and serology), there was a 2.60-fold increase (95% CI 1.31, 5.17) compared to NP swab alone (3.3% versus 8.7%). Sensitivities by specimen type were: NP swab 51%, saliva 70%, sputum 72%, and serology 79%.

CONCLUSIONS

Diagnosis of RSV in adults was several-fold greater when additional specimen types were added to NP swab, even with a relatively low percentage of subjects with sputum and serology results available. Hospitalized RSV ARI burden estimates in adults based solely on NP swab RT-PCR should be adjusted for underestimation.

Usefulness of Combining Sputum and Nasopharyngeal Samples for Viral Detection by Reverse Transcriptase PCR in Adults Hospitalized with Acute Respiratory Illness

Nasopharyngeal swabs (NPS) or washings have traditionally been used to diagnose respiratory tract infections. Reverse transcriptase PCR (RT-PCR) is widely used for rapid viral detection using samples from the upper respiratory tract. However, RT-PCR is rarely applied to sputum samples, mainly due to the viscosity of sputum. Thus, we assessed the detection rates of respiratory viruses from NPS, sputum samples, and combined NPS and sputum samples using multiplex RT-PCR (Allplex respiratory panels I, II, and III; Seegene, Seoul, South Korea). Paired NPS and sputum samples were collected from 219 patients admitted to the hospital with acute respiratory illnesses from October to December 2019. RT-PCR was performed on each sample for virus detection. Combined samples for virus detection were produced using remnant NPS and sputum samples with a positive virus signal. Respiratory viral nucleic acid was identified in 92 (42%) of 219 patients. Among the 92 viral detections, 61 (28%) were detected by both NPS and sputum samples. Twenty-four (11%) were sputum positive/NPS negative, and seven (3%) were sputum negative/NPS positive. For the combined NPS-sputum samples (n = 92), all paired samples positive in both specimens (n = 61) were also positive in the combined NPS-sputum sample. Twenty-seven (87%) of the 31 discordant paired samples were positive in the combined samples. Out of the total of 103 viruses identified before combining the samples, the detection rate of the combined samples was 94% (97/103), which was higher than the detection rates of sputum (88%; 91/103) and NPS (71%; 73/103). Because additional tests incur additional costs, our findings suggest that combining samples instead of testing separate samples using RT-PCR is likely the most cost-effective method of viral testing for patients with acute respiratory illnesses. IMPORTANCE This study reveals that RT-PCR utilizing sputum significantly increased the detection rate for respiratory viral nucleic acids among adult patients admitted to the hospital, compared to nasopharyngeal swabs (NPS). Notably, combined samples of sputum and NPS maintained the majority of the improved sputum detection rate with only a few positive signal losses from NPS samples. In order to detect respiratory viruses in adult patients with acute respiratory illness, it is important to choose the optimal respiratory samples. This study helped to improve our understanding of this process.

Comparison of sputum specimens and nasopharyngeal swab specimens for diagnosis of acute human metapneumovirus-related lower respiratory tract infections in adults

BACKGROUND

To detect human metapneumovirus, tests besides reverse transcription-polymerase chain reaction (RT-PCR) on nasopharyngeal swab specimens are less accessible. Immunochromatography assays are rapid and simple without the need of any special equipment but sometimes are insufficiently sensitive. This study describes the usefulness of immunochromatography assays to detect human metapneumovirus in adult patients with human metapneumovirus-related acute lower respiratory tract infection using sputum specimens.

METHODS

This prospective single-center study enrolled adults and adolescents aged ≥16 years with signs and symptoms of an acute respiratory illness who were diagnosed with acute lower respiratory tract infection. The presence of human metapneumovirus infection was confirmed by seroconversion. Immunochromatography assays and real-time RT-PCR were performed to compare the efficacy of nasopharyngeal swab specimens and sputum specimens. Comparative results were obtained via McNemar's test.

RESULTS

Overall, 337 patients were recruited in this study; 63 (18.7%) patients were seroconverted. Sputum specimens showed significantly higher positivity rates than nasopharyngeal swab specimens with both immunochromatography assays (p = 0.0008) and real-time RT-PCR (p = 0.014). Among 29 patients with pneumonia who had concordant positive real-time RT-PCR results for both nasopharyngeal swab specimens and sputum specimens, 21 (72.4%) had a higher viral load in the sputum specimens.

CONCLUSIONS

Sputum specimens are more useful in detecting human metapneumovirus than nasopharyngeal swab specimens in adult patients with acute lower respiratory tract infection.

Association between lipid profiles and viral respiratory infections in human sputum samples

Background

Respiratory infections such as influenza account for significant global mortality each year. Generating lipid profiles is a novel and emerging research approach that may provide new insights regarding the development and progression of priority respiratory infections. We hypothesized that select clusters of lipids in human sputum would be associated with specific viral infections (Influenza (H1N1, H3N2) or Rhinovirus).

Methods

Lipid identification and semi-quantitation was determined with liquid chromatography and high-resolution mass spectrometry in induced sputum from individuals with confirmed respiratory infections (influenza (H1N1, H3N2) or rhinovirus). Clusters of lipid species and associations between lipid profiles and the type of respiratory viral agent was determined using Bayesian profile regression and multinomial logistic regression.

Results

More than 600 lipid compounds were identified across the sputum samples with the most abundant lipid classes identified as triglycerides (TG), phosphatidylethanolamines (PE), phosphatidylcholines (PC), Sphingomyelins (SM), ether-PC, and ether-PE. A total of 12 lipid species were significantly different when stratified by infection type and included acylcarnitine (AcCar) (10:1, 16:1, 18:2), diacylglycerols (DG) (16:0_18:0, 18:0_18:0), Lysophosphatidylcholine (LPC) (12:0, 20:5), PE (18:0_18:0), and TG (14:1_16:0_18:2, 15:0_17:0_19:0, 16:0_17:0_18:0, 19:0_19:0_19:0). Cluster analysis yielded three clusters of lipid profiles that were driven by just 10 lipid species (TGs and DGs). Cluster 1 had the highest levels of each lipid species and the highest prevalence of influenza A H3 infection (56%, n = 5) whereas cluster 3 had lower levels of each lipid species and the highest prevalence of rhinovirus (60%; n = 6). Using cluster 3 as the reference group, the crude odds of influenza A H3 infection compared to rhinovirus in cluster 1 was significantly (p = 0.047) higher (OR = 15.00 [95% CI: 1.03, 218.29]). After adjustment for confounders (smoking status and pulmonary comorbidities), the odds ratio (OR) became only marginally significant (p = 0.099), but the magnitude of the effect estimate was similar (OR = 16.00 [0.59, 433.03]).

Conclusions

In this study, human sputum lipid profiles were shown to be associated with distinct types of viral infection. Better understanding the relationship between respiratory infections of global importance and lipids contributes to advancing knowledge of pathogenesis of infections including identifying populations with increased susceptibility and developing effective therapeutics and biomarkers of health status.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-022-02091-w.

Does the timing of saliva collection affect the diagnosis of SARS-CoV-2 infection?

We evaluated the optimal timing of saliva sample collection to diagnose the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We obtained 150 saliva samples at four specific time points from 13 patients with confirmed SARS-CoV-2 infection. The time points were (1) early morning (immediately after waking), (2) immediately after breakfast before tooth brushing, (3) 2 h after breakfast, and (4) before lunch. On the 2nd hospital day, patients collected saliva at the four time points by themselves. We collected samples at two time points, (1) and (3), from the 3rd hospital day to day 9 following symptom onset. In 52 samples collected at the four time points, there was no significant difference. Meanwhile, there was no significant difference in the positive proportion or the viral load between the two time points in both analyses by the day from symptom onset and by all samples. In this study, there was no difference in the positive proportions in saliva collected at various time points within 9 days after symptom onset. The timing of saliva collection was not affected by the diagnosis of SARS-CoV-2 infection.

Rates of Medically-Attended RSV among US Adults: A Systematic Review and Meta-Analysis

Background

Adult respiratory syncytial virus (RSV) vaccines are in late stages of development. A comprehensive synthesis of adult RSV burden is needed to inform public health decision-making.

Methods

We performed a systematic review and meta-analysis of studies describing the incidence of medically-attended RSV (MA-RSV) among US adults. We also identified studies reporting nasopharyngeal (NP) or nasal swab RT-PCR results with paired serology (four-fold-rise) or sputum (RT-PCR) to calculate RSV detection ratios quantifying improved diagnostic yield after adding a second specimen type (ie, serology or sputum).

Results

We identified 14 studies with 15 unique MA-RSV incidence estimates, all based on NP or nasal swab RT-PCR testing alone. Pooled annual RSV-associated incidence per 100,000 adults ≥65 years of age was 178 (95%CI: 152‒204; n = 8 estimates) hospitalizations (4 prospective studies: 189; 4 model-based studies: 157), 133 (95%CI: 0‒319, n = 2) emergency department (ED) admissions, and 1519 (95%CI: 1109‒1929, n = 3) outpatient visits. Based on 6 studies, RSV detection was ∼1.5 times higher when adding paired serology or sputum. After adjustment for this increased yield, annual RSV-associated rates per 100,000 adults ≥65 years were 267 hospitalizations (UI: 228‒306) (prospective: 282; model-based: 236), 200 ED admissions (UI: 0‒478), and 2278 outpatient visits (UI: 1663‒2893). Persons &lt;65 years with chronic medical conditions were 1.2−28 times more likely to be hospitalized for RSV depending on risk condition.

Conclusions

The true burden of RSV has been underestimated and is significant among older adults and individuals with chronic medical conditions. A highly effective adult RSV vaccine would have substantial public-health impact.

Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study

BACKGROUND

Respiratory tract infections (RTIs) caused by contagious viruses are common among patients presenting to the emergency department (ED). Early detection of these viruses can help prevent nosocomial transmission.

AIM

To investigate the efficacy of three rapid molecular methods, namely FilmArray^® Pneumonia Panel plus (FAP plus), ID NOW^™ Influenza A and B 2 (ID NOW2) point-of-care test, and an in-house real-time polymerase chain reaction (RT-PCR) test, to identify patients with viral RTIs requiring isolation in an emergency setting.

METHODS

We included a FilmArray^® Pneumonia Panel plus in the initial workup of patients with suspected RTIs during a flu season. The RT-PCR and the influenza point-of-care test were performed as part of routine diagnostics, on demand from the treating physicians. We compared viral detections and compared time to positive test results for each method.

FINDINGS

The FAP plus significantly reduced the turnaround time and was able to identify 95% patients with potential contagious viral RTI. Routine diagnostics ordered by the treating physician had a turnaround time of a median 22 h and detected 87% of patients with potential contagious viral RTI. In patients that had all three tests, the ID NOW2 detected 62% of patients with influenza.

CONCLUSIONS

The FAP plus was able to rapidly and reliably identify patients with potential contagious viral RTIs; its use was feasible in the ED setting. Failing to test patients with viral RTI and using tests with long turnaround time may lead to nosocomial transmission of viral infections and adverse patient outcomes.

Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients

Scaling up of diagnostic capacity is needed to mitigate the global pandemic of SARS-CoV2. However, there are challenges including shortage of sample collection swabs and transport medium. Saliva has been recommended as a simple, low-cost, non-invasive option. However, data from different populations and settings are limited. Here, we showed that saliva could be a good alternative sample to diagnose COVID-19 patients. Pair of NPS-saliva samples was collected from 152 symptomatic; confirmed COVID-19 patients, and compared their positivity rate, viral load, and duration of viral shedding. From 152 patients, 80 (52.63%) tested positive and 72 (47.37%) were negative for SARSA-CoV2 in NPS sample. In saliva, 129 (92.14%) were tested positive and 11 (7.86%) were negative on the day of admission to hospital. The overall percent agreement of RT-PCR result of Saliva to NPS was 70% (196/280). A comparison of viral load from 72 NPS-saliva pair samples on day of admission shows saliva contains significantly higher viral load (P < 0.001). In conclusion, saliva has higher yield in detecting SARS-CoV2, and COVID-19 patients show higher viral load and prolonged period of viral shedding in saliva. Therefore, we recommend saliva as a better alternative sample to NPS to diagnose COVID-19 patients.

Comparison of microbiota in the upper versus lower respiratory tract in children during health and respiratory disease: protocol for a systematic review

BACKGROUND

The upper respiratory tract of children is colonized by various microbial species during the healthy state, whereas the lungs are believed to be sterile. In children with respiratory infections, micro-organisms can be recovered from the upper respiratory sites, as well as the lungs. However, the correlation of microbial yield between the two sites is unclear. This systematic review is designed to explore the microbial composition of the respiratory system in healthy children, comparing the organisms identified in the upper airways versus the lungs. We will also compare the prevalence and pattern of upper respiratory micro-organisms in healthy children versus those with various respiratory diseases. We will additionally compare the organisms identified in the upper airway versus the lungs in children with respiratory disease.

METHODS

We will search the following electronic databases: Epistemonikos and Cochrane Library for systematic reviews and MEDLINE (through PubMed), EMBASE, Cochrane CENTRAL, LIVIVO, Web of Science, Scopus, and CINAHL databases for primary studies. Reference lists of relevant studies will be examined for links to potential related articles. Two reviewers will independently determine eligibility for inclusion. The methodological quality and risk of bias of the included observational studies will be scored using the Newcastle-Ottawa Scale tool, and JBI Critical Appraisal Checklist for case series. We will present the data with descriptive statistics and provide pooled estimates of outcomes, wherever it is feasible to perform a meta-analysis. Heterogeneity in studies will be explored by using the Higgins and Thompson I² method. Sensitivity analysis will be done to explore the impact of study quality, and subgroup analysis will be done based on age, health condition, type of respiratory specimen, and method of identifying organisms. We will prepare a summary of findings' table and assess the confidence in the evidence using the GRADE methodology.

RESULTS

This is a protocol; hence, there are no results at this stage.

DISCUSSION

The proposed systematic review will provide comparisons of the microbiota in the upper respiratory tract versus the lungs, in children, during health as well as respiratory disease. Similarly, the site-specific yield will be compared between healthy children and those with respiratory disease. This will provide clinicians, microbiologists, and respiratory therapists a better understanding of the respiratory system microbiota, suitability (or otherwise) of upper airway specimens in various respiratory diseases, and the potential role of upper airway colonization on specific respiratory diseases. We will disseminate the review through a peer-reviewed journal publication. Data that cannot be included in the published version will be made available on request.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42020202115 .

Prediction of in-hospital recurrence and false-negative results in patients with COVID-19 by red blood cell values on admission

The clinical characteristics and risk factors of patients with coronavirus disease 2019 (COVID-19) with re-positive or false-negative test results have so far remained to be determined. The present study provides a cross-sectional observational study on 134 hospitalized patients selected from Huoshenshan Hospital (Wuhan, China) using cluster sampling. A total of 68 patients had reduced red blood cell (RBC) counts, 55 a decrease in the hemoglobin concentration (HBC) and 73 a decline in hematocrit (HCT). The false-negative rate of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA detection in pharyngeal swab specimens was 18.7%. The absolute lymphocyte count (ALC), RBC, HBC and HCT levels in false-negative patients were significantly higher than those in patients who tested positive for viral nucleic acids. Multivariate logistic regression analysis indicated that RBC [odds ratio (OR)=0.43, 95% CI: 0.18-0.99], HBC (OR=0.97, 95% CI: 0.94-0.99) and ALC (OR=0.43, 95% CI: 0.20-0.91) were the factors influencing the negative testing results for viral nucleic acid. The rate of re-positive patients was 16.4%. The white blood cell, RBC, HBC and HCT values in re-positive patients were lower than those in non-re-positive patients. The median (interquartile range) values for RBC, HBC and HCT of male re-positive patients were 3.95 (3.37, 4.2) x10¹²/l, 123 (103, 133) g/l and 36.6 (31.1, 39.2)%, respectively, while the RBC, HBC and HCT of female re-positive patients were 3.54 (3.13, 3.74) x10¹²/l, 115 (102, 118) g/l and 34.2 (28.5, 34.9)%, respectively. It was determined that RBC, HBC and HCT values had moderate accuracy in predicting SARS-CoV-2 recurrence in patients with COVID-19 using receiver operating curve analysis. The present study suggested that RBC may have an important role in the pathogenesis of COVID-19.

Etiology and clinical characteristics of SARS-CoV-2 and other human coronaviruses among children in Zhejiang Province, China 2017-2019

BACKGROUND

A novel coronavirus (SARS-CoV-2) emerging has put global public health institutes on high alert. Little is known about the epidemiology and clinical characteristics of human coronaviruses infections in relation to infections with other respiratory viruses.

METHODS

From February 2017 to December 2019, 3660 respiratory samples submitted to Zhejiang Children Hospital with acute respiratory symptoms were tested for four human coronaviruses RNA by a novel two-tube multiplex reverse transcription polymerase chain reaction assays. Samples were also screened for the occurrence of SARS-CoV-2 by reverse transcription-PCR analysis.

RESULTS

Coronavirus RNAs were detected in 144 (3.93%) specimens: HCoV-HKU1 in 38 specimens, HCoV-NL63 in 62 specimens, HCoV-OC43 in 38 specimens and HCoV-229E in 8 specimens. Genomes for SARS-CoV-2 were absent in all specimens by RT-PCR analysis during the study period. The majority of HCoV infections occurred during fall months. No significant differences in gender, sample type, year were seen across species. 37.5 to 52.6% of coronaviruses detected were in specimens testing positive for other respiratory viruses. Phylogenic analysis identified that Zhejiang coronaviruses belong to multiple lineages of the coronaviruses circulating in other countries and areas.

CONCLUSION

Common HCoVs may have annual peaks of circulation in fall months in the Zhejiang province, China. Genetic relatedness to the coronaviruses in other regions suggests further surveillance on human coronaviruses in clinical samples are clearly needed to understand their patterns of activity and role in the emergence of novel coronaviruses.

Is it enough for COVID-19 screening test? Limitation of swab test and general characteristics of mild symptom patients

The most common method for SARS-CoV-2 testing is throat or nasal swabbing by real-time reverse transcription polymerase chain reaction (RT-PCR) assay. In South Korea, drive-through swab test is used for screening system and community treatment centers (CTCs), which admit and treat confirmed COVID-19 patients with mild symptoms, are being used. This retrospective study was conducted on patients admitted to a CTC on March 6, 2020. A total of 313 patients were admitted. The nasal and throat swabs were collected from the upper respiratory tract, and a sputum test was performed to obtain lower respiratory samples. The positive rate of the first set of test, sputum test was higher than that of the swab test (p = 0.011). In the second set of test, 1 week after the first ones, the rate of positive swab tests was relatively high (p = 0.026). In the first set of test, 66 of 152 (43.4%) patients showed 24-h consecutive negative swab test results, when the sputum test results were considered together, that number fell to 29 patients (19.1%) (p < 0.001). Also, in the second set of test, 63 of 164 (38.4%) patients met the discharge criteria only when the swab test was considered; that number fell to 30 (18.3%) when the sputum test results were also considered (p < 0.001). Using the swab test alone is insufficient for screening test and discharge decision. Patients who may have positive result in the sputum test can be missed.

Enhanced Detection of Community-Acquired Pneumonia Pathogens With the BioFire® Pneumonia FilmArray® Panel

BACKGROUND

Although most observational studies identify viral or bacterial pathogens in 50% or less of patients hospitalized with community-acquired pneumonia (CAP), we previously demonstrated that a multi-test bundle (MTB) detected a potential pathogen in 73% of patients. This study compares detection rates for potential pathogens with the MTB versus the Biofire® Pneumonia FilmArray® panel (BPFA) multiplex PCR platform and presents an approach for integrating BPFA results as a foundation for subsequent antibiotic stewardship (AS) activities.

METHODS

Between January 2017 to March 2018, all patients admitted for CAP were enrolled. Patients were considered evaluable if all elements of the MTB and the BPFA were completed, and they met other a priori inclusion criteria. The primary endpoint was the percentage of potential pathogens detected using the MTB (8 viral and 6 bacterial targets) versus the BPFA (8 viral and 18 bacterial targets). Blood and sputum cultures were performed on all patients. Two or more procalcitonin (PCT) levels assisted clinical assessments as to whether detected bacteria were invading or colonizing.

RESULTS

Of 585 enrolled patients, 274 were evaluable. A potential viral pathogen was detected in 40.5% with MTB versus 60.9% of patients with BPFA with an odds ratio (95% CI) of 9.00 (4.12 to 23.30) p<0.01. A potential bacterial pathogen was identified in 66.4% with the MTB vs 75.5% with the BPFA odds ratio (95% CI) of 2.09 (1.24 to 3.59), p 0.003). Low PCT levels helped identify detected bacteria as colonizers.

Catalytic amplification by transition-state molecular switches for direct and sensitive detection of SARS-CoV-2

Despite the importance of nucleic acid testing in managing the COVID-19 pandemic, current detection approaches remain limited due to their high complexity and extensive processing. Here, we describe a molecular nanotechnology that enables direct and sensitive detection of viral RNA targets in native clinical samples. The technology, termed catalytic amplification by transition-state molecular switch (CATCH), leverages DNA-enzyme hybrid complexes to form a molecular switch. By ratiometric tuning of its constituents, the multicomponent molecular switch is prepared in a hyperresponsive state-the transition state-that can be readily activated upon the binding of sparse RNA targets to turn on substantial enzymatic activity. CATCH thus achieves superior performance (~8 RNA copies/μl), direct fluorescence detection that bypasses all steps of PCR (<1 hour at room temperature), and versatile implementation (high-throughput 96-well format and portable microfluidic assay). When applied for clinical COVID-19 diagnostics, CATCH demonstrated direct and accurate detection in minimally processed patient swab samples.

Comparison of detection rate of 16 sampling methods for respiratory viruses: a Bayesian network meta-analysis of clinical data and systematic review

BACKGROUND

Respiratory viruses (RVs) is a common cause of illness in people of all ages, at present, different types of sampling methods are available for respiratory viral diagnosis. However, the diversity of available sampling methods and the limited direct comparisons in randomised controlled trials (RCTs) make decision-making difficult. We did a network meta-analysis, which accounted for both direct and indirect comparisons, to determine the detection rate of different sampling methods for RVs.

METHODS

Relevant articles were retrieved comprehensively by searching the online databases of PubMed, Embase and Cochrane published before 25 March 2020. With the help of R V.3.6.3 software and 'GeMTC V.0.8.2' package, network meta-analysis was performed within a Bayesian framework. Node-splitting method and I ² test combined leverage graphs and Gelman-Rubin-Brooks plots were conducted to evaluate the model's accuracy. The rank probabilities in direct and cumulative rank plots were also incorporated to rank the corresponding sampling methods for overall and specific virus.

RESULTS

16 sampling methods with 54 438 samples from 57 literatures were ultimately involved in this study. The model indicated good consistency and convergence but high heterogeneity, hence, random-effect analysis was applied. The top three sampling methods for RVs were nasopharyngeal wash (NPW), mid-turbinate swab (MTS) and nasopharyngeal swab (NPS). Despite certain differences, the results of virus-specific subanalysis were basically consistent with RVs: MTS, NPW and NPS for influenza; MTS, NPS and NPW for influenza-a and b; saliva, NPW and NPS for rhinovirus and parainfluenza; NPW, MTS and nasopharyngeal aspirate for respiratory syncytial virus; saliva, NPW and MTS for adenovirus and sputum; MTS and NPS for coronavirus.

CONCLUSION

This network meta-analysis provides supporting evidences that NPW, MTS and NPS have higher diagnostic value regarding RVs infection, moreover, particular preferred methods should be considered in terms of specific virus pandemic. Of course, subsequent RCTs with larger samples are required to validate our findings.

Molecular diagnostic technologies for COVID-19: Limitations and challenges

BACKGROUND

To curb the spread of the COVID-19 (coronavirus disease 2019) pandemic, the world needs diagnostic systems capable of rapid detection and quantification of the novel coronavirus (SARS-CoV-2). Many biomedical companies are rising to the challenge and developing COVID-19 diagnostics. In the last few months, some of these diagnostics have become commercially available for healthcare workers and clinical laboratories. However, the diagnostic technologies have specific limitations and reported several false-positive and false-negative cases, especially during the early stages of infection.

AIM

This article aims to review recent developments in the field of COVID-19 diagnostics based on molecular technologies and analyze their clinical performance data.

KEY CONCEPTS

The literature survey and performance-based analysis of the commercial and pre-commercial molecular diagnostics address several questions and issues related to the limitations of current technologies and highlight future research and development challenges to enable timely, rapid, low-cost, and accurate diagnosis of emerging infectious diseases.

Respiratory virus-associated infections in HIV-infected adults admitted to the intensive care unit for acute respiratory failure: a 6-year bicenter retrospective study (HIV-VIR study)

Introduction

Acute respiratory failure is the main reason for admission to the intensive care unit (ICU) in HIV-infected adults. There is little data about the epidemiology of respiratory viruses in this population.

Methods

HIV-infected adults admitted to two intensive care units over a 6-year period for an acute respiratory failure and explored for respiratory viruses with multiplex polymerase chain reaction (mPCR) were retrospectively selected. Objectives were to describe the prevalence of respiratory viruses, coinfections with non-viral pathogens, and hospital outcome.

Results

A total of 123 episodes were included. An HIV infection was newly diagnosed in 9% of cases and 72% of the population were on antiretroviral therapy. Real-time mPCR tests identified at least one respiratory virus in the respiratory tract of 33 (27%) patients, but with a non-viral copathogen in two-thirds of cases. Rhinovirus was predominant, documented in 15 patients, followed by Influenza and Respiratory Syncytial Viruses (both n = 6). The prevalence of respiratory virus-associated infection did not vary along with the level of the CD4 T-cell deficiency, except for Rhinovirus which was more prevalent in patients with a CD4 lymphocyte count below 200 cells/µL (n = 13 (20%) vs. n = 2 (4%), p < 0.01). In multivariate analysis, respiratory virus-associated infection was not associated with a worse prognosis.

Conclusions

Viruses are frequently identified in the respiratory tract of HIV-infected patients with acute respiratory failure that requires ICU admission, but with a non-viral copathogen in two-thirds of cases. Rhinovirus is the predominant viral specie; its prevalence is highest in patients with a CD4 lymphocyte count below 200 cells/µL.

Analysis of pressure-driven membrane preconcentration for point-of-care assays

Point-of-care diagnostic devices for both physicians and patients themselves are now ubiquitous, but often not sensitive enough for highly dilute analytes (e.g., pre-symptomatic viral detection). Two primary methods to address this challenge include (1) increasing the sensitivity of molecular recognition elements with greater binding affinity to the analyte or (2) increasing the concentration of the analyte being detected in the sample itself (preconcentration). The latter approach, preconcentration, is arguably more attractive if it can be made universally applicable to a wide range of analytes. In this study, pressure-driven membrane preconcentration devices were developed, and their performance was analyzed for detecting target analytes in biofluids in the form of point-of-care lateral-flow assays (LFAs). The demonstrated prototypes utilize negative or positive pressure gradients to move both water and small interferents (salt, pH) through a membrane filter, thereby concentrating the analyte of interest in the remaining sample fluid. Preconcentration up to 33× is demonstrated for influenza A nucleoprotein with a 5 kDa pore polyethersulfone membrane filter. LFA results are obtained within as short as several minutes and device operation is simple (very few user steps), suggesting that membrane preconcentration can be preferable to more complex and slow conventional preconcentration techniques used in laboratory practice.

Viral shedding dynamics reveals sputum as a reliable and cost-saving specimen for SARS-CoV-2 diagnosis within the first 10 days since symptom onset: A prospective cohort study

BACKGROUND

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome virus (SARS-CoV-2) is challenging global public health, due to an increasing demand for testing and the shortage of diagnostic supplies. Nasopharyngeal swab (NPS) is considered the optimal sample for SARS-CoV2 diagnosis and sputum (SPT) has been proposed as an economic alternative. However, the temporal concordance of diagnosis in NPS and SPT has not been addressed.

METHODS

Through a longitudinal study we compared the shedding dynamics of SARS-CoV-2 RNA evaluated by RT-qPCR in serially collected SPT and NPS obtained from 82 ambulatory and hospitalized patients during acute infection and convalescence. The concordance during the follow-up and cost analysis between both collected specimens was evaluated.

FINDINGS

We analyzed 379 samples, 177 NPS and 202 SPT. The highest proportion of positive samples was detected within the first 15 days after the symptoms onset. The median time of positivity was higher for NPS (median= 25 days) than SPT (median= 21 days). There was no significant difference in the median RT-qPCR CT values between both sample types. The temporal categorization of matched-paired samples indicated substantial correlation (r=0.6023) and substantial agreement (87.23%) during the first ten days since symptoms onset (kappa = 0.697). A cost analysis demonstrated a significant saving when the SPT specimen was used.

INTERPRETATION

Sputum is a feasible and cost-saving alternative to NPS, providing an equivalent value for the detection and follow-up of SARS-CoV-2 RNA.

The Yield and Consistency of the Detection of SARS-CoV-2 in Multiple Respiratory Specimens

Background

Few studies have compared the yield of reverse transcription polymerase chain reaction (RT-PCR) assays in nasopharyngeal swabs, oropharyngeal swabs, and sputum for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection.

Methods

We conducted an observational study in Beijing Ditan Hospital, China. Specimens including nasopharyngeal swabs, oropharyngeal swabs, and sputum from confirmed coronavirus 2019 patients were collected for RT-PCR testing. Disease duration was calculated from the date of symptom onset to the date of specimen collection and divided into 3 groups: ≤14 days, 14–21 days, and >21 days. We compared positive rates across the 3 specimens collected. The kappa coefficient was used to evaluate the consistency of RT-PCR results between different specimens.

Results

A total of 291 specimens were collected and tested from 43 confirmed patients. Among specimens collected with a disease duration of ≤14 days, the positive rate was highest in sputum (79.2%); this rate was significantly higher than that in nasopharyngeal swabs (37.5%; P = .003) and oropharyngeal swabs (20.8%; P < .001). Similar findings were observed with the disease durations of 14–21 days and >21 days. The consistency of testing results between nasopharyngeal swabs and oropharyngeal swabs was low with the disease durations of ≤14 days and >21 days. The consistency between the sputum and oropharyngeal swabs and between the sputum and nasopharyngeal swabs was very low across all 3 disease durations, with statistical significance.

Conclusions

Compared with nasopharyngeal swabs and oropharyngeal swabs, sputum had the highest yield of SARS-CoV-2 detection. Nasopharyngeal swabs and oropharyngeal swabs had a similar yield. If sputum is not feasible, a nasopharyngeal swab can be recommended for the detection of SARS-CoV-2, and early testing is needed.

Epidemiological and clinical characteristics of coronavirus disease (COVID-19) cases at a screening clinic during the early outbreak period: a single-centre study

Introduction. Coronavirus disease 2019 (COVID-19) is an infectious disease caused by Severe Acute Respiratory Corona Virus-2 (SARS-CoV-2). The disease was first identified in December 2019 in Wuhan, the capital of China's Hubei province, and has since spread globally, resulting in the ongoing 2019-2020 corona virus pandemic. SARS-CoV-2 is closely related to the original SARS-CoV. It is thought to have a zoonotic origin. The virus is primarily spread between people during close contact, often via small droplets produced by coughing, sneezing or talking. People may also become infected by touching a contaminated surface and then touching their face. COVID-19 patients currently remain the primary source of infection. An epidemiological survey indicated that the general population is susceptible to SARS-CoV-2. The spectrum of this disease ranges from mild to life-threatening. Fever is the most common symptom, although older people and those with comorbidities may experience fever later in the disease. Other common symptoms include cough, loss of appetite, fatigue, shortness of breath, sputum production, and muscle and joint pains. Symptoms such as nausea, vomiting and diarrhea have been observed in varying percentages. Some cases might progress promptly to acute respiratory distress syndrome (ARDS) and/or multiple organ function failure. Asymptomatic carriers and those in the incubation period may also be infectious.Aim. To determine the epidemiological and clinical characteristics of patients presenting with COVID-19 at the screening clinic of a tertiary care hospital in Peshawar, Pakistan.Methodology. In this descriptive study, we analysed data of patients presenting to a newly established Covid-19 screening clinic in Rehman Medical Institute. Anyone who reported with new onset fever and/or cough was tested for SARS-CoV-2 in the screening clinic. We documented and analysed demographic, epidemiological and clinical characteristics, which included age, sex, travel history, clinical features, comorbidities and laboratory data of patients confirmed by real-time reverse-transcription (RT)-PCR at Rehman Medical Institute, Peshawar, Pakistan from 15 March till 21 April 2020. Paired specimens of throat swabs and nasal swabs were obtained from 845 patients, ribonucleic acid (RNA) was extracted and tested for SARS-CoV-2 by the RT-PCR assay.Results. A total of 845 specimens were taken as described above. The positive rate for SARS-CoV-2 was about 14.3%. Male and older population had a significantly higher positive rate. Of the 121 patients infected with SARS-CoV-2, the mean age was 43.19 years (sd, 17.57) and the infections were more frequent among male gender accounting for 85 (70.25 %) patients. Common symptoms included fever (88 patients, 72 %), cough (72 patients, 59.5 %) and shortness of breath (69 patients, 57 %). Twenty-two (18 %) patients had recent travel history outside Pakistan in the previous 14 days, the majority of whom had returned back from Saudi Arabia.Conclusion. In this single-centre, prospective, descriptive study, fever, cough and shortness of breath were the most common symptoms. Old age (>50 years), chronic underlying comorbidities and travel history may be risk factors. Therefore, we concluded that viral nucleic acid amplification tests (NAAT) played an important role in identifying SARS-CoV-2 infection in a screening clinic, which helped with isolation and cohorting of these patients.

SARS-CoV-2 detection in different respiratory sites: A systematic review and meta-analysis

Background

The accurate detection of SARS-CoV-2 through respiratory sampling is critical for the prevention of further transmission and the timely initiation of treatment for COVID-19. There is a diverse range of SARS-CoV-2 detection rates in reported studies, with uncertainty as to the optimal sampling strategy for COVID-19 diagnosis and monitoring.

Methods

We performed a systematic review and meta-analysis of studies comparing respiratory sampling strategies for the detection of SARS-CoV-2 RNA. The inclusion criteria were studies that assessed at least two respiratory sampling sites (oropharyngeal swab, nasopharyngeal swab, and sputum) in participants with COVID-19. The percentage positive tests were compared between sampling modalities by constructing a Z-test assuming independence and using the standard errors obtained from the random effects meta-analysis.

Findings

From 1039 total studies, we identified 11 studies that met our inclusion criteria, with SARS-CoV-2 testing results from a total of 3442 respiratory tract specimens. Compared to nasopharyngeal swab sampling, sputum testing resulted in significantly higher rates of SARS-CoV-2 RNA detection while oropharyngeal swab testing had lower rates of viral RNA detection. Earlier sampling after symptom onset was associated with improved detection rates, but the differences in SARS-CoV-2 RNA detection by sampling method was consistent regardless of the duration of symptoms.

Interpretation

The results support sputum sampling as a valuable method of COVID-19 diagnosis and monitoring, and highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis.

Funding

This study was funded in part by the NIH grants U01AI106701 and by the Harvard University for AIDS Research (NIAID 5P30AI060354).

Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2)-infected pneumonia (COVID-19)

Objectives In December 2019, a novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) occurred in Wuhan, China. Laboratory-based diagnostic tests utilized real-time reverse transcriptase polymerase chain reaction (RT-PCR) on throat samples. This study evaluated the diagnostic value to analyzing throat and sputum samples in order to improve accuracy and detection efficiency. Methods Paired specimens of throat swabs and sputum were obtained from 54 cases, and RNA was extracted and tested for 2019-nCoV (equated with SARS-CoV-2) by the RT-PCR assay. Results The positive rates of 2019-nCoV from sputum specimens and throat swabs were 76.9% and 44.2%, respectively. Sputum specimens showed a significantly higher positive rate than throat swabs in detecting viral nucleic acid using the RT-PCR assay (p = 0.001). Conclusions The detection rates of 2019-nCoV from sputum specimens were significantly higher than those from throat swabs. We suggest that sputum would benefit for the detection of 2019-nCoV in patients who produce sputum. The results can facilitate the selection of specimens and increase the accuracy of diagnosis.

Comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (SARS-Cov-2)-infected pneumonia (COVID-19)

Objectives In December 2019, a novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) occurred in Wuhan, China. Laboratory-based diagnostic tests utilized real-time reverse transcriptase polymerase chain reaction (RT-PCR) on throat samples. This study evaluated the diagnostic value to analyzing throat and sputum samples in order to improve accuracy and detection efficiency. Methods Paired specimens of throat swabs and sputum were obtained from 54 cases, and RNA was extracted and tested for 2019-nCoV (equated with SARS-CoV-2) by the RT-PCR assay. Results The positive rates of 2019-nCoV from sputum specimens and throat swabs were 76.9% and 44.2%, respectively. Sputum specimens showed a significantly higher positive rate than throat swabs in detecting viral nucleic acid using the RT-PCR assay (p = 0.001). Conclusions The detection rates of 2019-nCoV from sputum specimens were significantly higher than those from throat swabs. We suggest that sputum would benefit for the detection of 2019-nCoV in patients who produce sputum. The results can facilitate the selection of specimens and increase the accuracy of diagnosis.

Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection

BACKGROUND

Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray.

METHODS

We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray.

RESULTS

Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant.

CONCLUSIONS

In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.

Prediction model for pneumonia in primary care patients with an acute respiratory tract infection: role of symptoms, signs, and biomarkers

BACKGROUND

Diagnosing pneumonia can be challenging in general practice but is essential to distinguish from other respiratory tract infections because of treatment choice and outcome prediction. We determined predictive signs, symptoms and biomarkers for the presence of pneumonia in patients with acute respiratory tract infection in primary care.

METHODS

From March 2012 until May 2016 we did a prospective observational cohort study in three radiology departments in the Leiden-The Hague area, The Netherlands. From adult patients we collected clinical characteristics and biomarkers, chest X ray results and outcome. To assess the predictive value of C-reactive protein (CRP), procalcitonin and midregional pro-adrenomedullin for pneumonia, univariate and multivariate binary logistic regression were used to determine risk factors and to develop a prediction model.

RESULTS

Two hundred forty-nine patients were included of whom 30 (12%) displayed a consolidation on chest X ray. Absence of runny nose and whether or not a patient felt ill were independent predictors for pneumonia. CRP predicts pneumonia better than the other biomarkers but adding CRP to the clinical model did not improve classification (- 4%); however, CRP helped guidance of the decision which patients should be given antibiotics.

CONCLUSIONS

Adding CRP measurements to a clinical model in selected patients with an acute respiratory infection does not improve prediction of pneumonia, but does help in giving guidance on which patients to treat with antibiotics. Our findings put the use of biomarkers and chest X ray in diagnosing pneumonia and for treatment decisions into some perspective for general practitioners.

Comparison of respiratory pathogen yields from Nasopharyngeal/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya

Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). However, nasopharyngeal/oropharyngeal (NP/OP) swabs may not accurately reflect etiologic agents from the lower respiratory tract where sputum specimens are considered as a more representative sample. The pathogen yields from NP/OP against sputum specimens have not been extensively explored, especially in tropical countries. We compared pathogen yields from NP/OP swabs and sputum specimens from patients ≥18 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar's test. The agreement for pathogen detection between NP/OP and sputum specimens ranged between 85-100%. More viruses were detected from NP/OP specimens whereas Klebsiella pneumoniae and Mycobacterium tuberculosis were more common in sputum specimens. There was no clear advantage in using sputum over NP/OP specimens to detect pathogens of ALRI in adults using TAC in the context of this tropical setting.

Comparing the yield of oropharyngeal swabs and sputum for detection of 11 common pathogens in hospitalized children with lower respiratory tract infection

Background

Advances in molecular laboratory techniques are changing the prospects for the diagnosis of viral infectious diseases. Multiplex polymerase chain reaction assay (multiplex-PCR) can detect dozens of pathogens simultaneously, greatly reducing turnaround time (TAT) and improving detection sensitivity. But as a double-edged sword, due to the high sensitivity of PCR, the type of respiratory specimens is critical to diagnosis. In this work, we performed a head-to-head comparison to evaluate the multiplex-PCR yields between two samples, sputum and flocked oropharyngeal swabs (OPS).

Methods

Eleven common respiratory pathogens were tested in hospitalized children< 13 years of age who met the criteria for lower respiratory tract infection by GeXP-based multiplex-PCR of paired OPS and sputum.

Results

From January to June 2018, 440 children with paired OPS and sputum were tested. The positive rate was 84% (369/440) for OPS and 88% (386/440) for sputum (p = .007). The frequency of detection of HRV, RSV, Influenza A virus, HMPV, parainfluenza virus, adenovirus, M. pneumoniae, coronavirus, bocavirus and C. pneumoniae in sputa was higher than that of OPSs (all p < .001). Both types of specimens had similarly very good kappa values for most of pathogens, except for Mycoplasma pneumonia (κ = 0.61) and Chlamydia pneumoniae (κ = 0.24). Additionally, 79.3% (349/440) of cases showed consistent results between the two types of samples, and they were significantly younger than patients with inconsistent results (p = .002).

Conclusions

Flocked oropharyngeal swabs and sputum performed similarly for the detection of common respiratory pathogens in hospitalized children by multiplex-PCR, except for Mycoplasma pneumoniae and Chlamydia pneumoniae. Young patients are likely to have consistent results between the two specimens.

Electronic supplementary material

The online version of this article (10.1186/s12985-019-1177-x) contains supplementary material, which is available to authorized users.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections

•

Pulmonary samples and nasopharyngeal aspirates have a similar diagnostic sensitivity for viruses detection by multiplex PCR.

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Pulmonary samples have a higher efficiency for detection of Legionella pneumophila.

Background

PCR-based techniques for the diagnosis of community- acquired severe lower respiratory tract infections are becoming the standard of care. However, their relative ability to identify either atypical bacteria or viruses that cause LRTI from clinical samples from various sources is yet to be determined.

Objectives and study design

The aim of our study was to compare the diagnostic yield of nasopharyngeal aspirates with that of pulmonary samples for the etiological diagnosis of severe acute lower respiratory tract infections by multiplex PCR. Patients were adults with community-acquired pneumonia or acute exacerbation of chronic obstructive pulmonary disease.

Results

We obtained concordant results for 81 (79%) of the 103 pairs of samples. In 14 of the 22 discordant results, more pathogens were evidenced in the lower respiratory tract samples.

Conclusions

Pulmonary samples had a similar diagnostic sensitivity for virus detection by multiplex PCR as nasopharyngeal aspirates. In contrast, in our study, the diagnostic efficacy of pulmonary samples for Legionella pneumophila over simple aspirates was clearly superior.

Automated TruTip nucleic acid extraction and purification from raw sputum

Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.

Laboratory epidemiology of respiratory viruses in a large children's hospital: A STROBE-compliant article

Acute respiratory tract infection (ARTI) is the most common causes of outpatient visit and hospital admission for children. The study aimed to report epidemiological data on respiratory viruses in a university-affiliated children's hospital.The study was a retrospective study conducted in a university affiliated children's hospital from 2016 May to 2017 April. The results of all nasopharyngeal swab and sputum samples sent for the test for respiratory viruses (adenovirus, influenza A, influenza B, and respiratory syncytial virus) were extracted from the electronic healthcare records. Clinical characteristics were compared between groups with positive versus negative results for respiratory viruses. Multivariable regression models were employed by including age, gender, type of sample (swab vs sputum), source (emergency department vs others), and season to explore the independent factors associated with positive results for respiratory viruses.A total of 34,961 samples were identified during the study period. A total of 3102 (8.9%) samples were positive for adenovirus, 2811 (8.0%) were positive for influenza A, 3460 (9.9%) were positive for influenza B, and 4527 (13.0%) were positive for respiratory syncytial virus. The positive rate of adenovirus was highest in April (50.8%), and lowest in November (3%). The absolute number of positive samples for adenovirus was highest in June (n = 587) and April (n = 544). For the test of influenza A, age was independently associated with positive result. With 1 year increase in age, the odds of positive result increased by 12% (odds ratio [OR]: 1.12; 95% confidence interval [CI]: 1.11-1.13; P < .001). As compared with the autumn, the summer showed significantly lower rate of positive for RSV (OR: 0.49; 95% CI: 0.38-0.62; P < .001), whereas the winter had higher risk of positive result (OR: 3.88; 95% CI: 3.37-4.50; P < .001).The study reported epidemiological data on the prevalence of respiratory viruses in a large tertiary care children's hospital. Age, gender, type of sample, source, and season were associated with the positive rates for respiratory viruses.

Effectiveness of inactivated influenza vaccine against laboratory-confirmed influenza pneumonia among adults aged ≥65 years in Japan

BACKGROUND

The effectiveness of inactivated influenza vaccine (IIV) against laboratory-confirmed influenza pneumonia in older adults remains to be established.

METHODS

Pneumonia patients aged ≥65 years who visited a study hospital in Chiba, Japan, were prospectively enrolled from February 2012 to January 2014. Sputum samples were collected from participants and tested for influenza virus by polymerase chain reaction assays. Influenza vaccine effectiveness (IVE) against laboratory-confirmed influenza pneumonia was estimated by a test-negative design.

RESULTS

Among a total of 814 pneumonia patients, 42 (5.2%) tested positive for influenza: 40 were positive for influenza A virus, and two were positive for influenza B virus. The IVE against laboratory-confirmed influenza pneumonia was 58.3% (95% confidence interval, 28.8-75.6%). The IVE against influenza pneumonia hospital admission, severe pneumonia, and death was 60.2% (95% CI, 22.8-79.4%), 65.5% (95% CI, 44.3-78.7%), and 71% (95% CI, -62.9% to 94.8%), respectively. In the subgroup analyses, the IVE against influenza pneumonia was higher for patients with immunosuppressive conditions (85.9%; 95% CI, 67.4-93.9%) than for those without (48.7%; 95% CI, 2.7-73%) but did not differ by patients' statin use status.

CONCLUSION

IIV effectively reduces the risk of laboratory-confirmed influenza pneumonia in older adults.

Respiratory syncytial virus infection in elderly adults

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and young children. Reinfections are common throughout adult life with more severe presentations occurring in immunocompromised individuals, subjects with underlying high-risk cardiopulmonary diseases, and in the elderly. There is now a significant body of literature indicating that the impact of RSV in elderly adults is similar to that of non-pandemic influenza, both in the community and in nursing homes. Clinical manifestations of RSV infections are similar to those caused by other viral respiratory pathogens, including influenza viruses. Molecular tests (reverse transcription-PCR) now provide a rapid diagnosis. The sputum sample combined with nasopharyngeal swab increases the diagnostic yield. At the present time, treatment is mainly symptomatic. The prevention of RSV consists in various infection control strategies, such as standard precautions, especially hand washing and droplet precautions to limit the nosocomial spread. Vaccines and antiviral agents for the prevention and treatment of RSV infections in elderly adults are currently not available, but they are being developed.

Comparing the Yield of Nasopharyngeal Swabs, Nasal Aspirates, and Induced Sputum for Detection of Bordetella pertussis in Hospitalized Infants

Background. Advances in molecular laboratory techniques are changing the landscape of Bordetella pertussis illness diagnosis. Polymerase chain reaction (PCR) assays have greatly improved the sensitivity detection and the turnaround time to diagnosis compared to culture. Moreover, different respiratory specimens, such as flocked nasopharyngeal swabs (NPSs), nasopharyngeal aspirates (NPAs), and induced sputum, have been used for B. pertussis detection, although there is limited head-to-head comparison to evaluating the PCR yield from the 3 sampling methods.

Methods. Hospitalized infants <6 months of age who fulfilled a broad syndromic criteria of respiratory illness were tested for B. pertussis infection by PCR on paired NPSs and NPAs; or paired NPSs and induced sputum. An exploratory analysis of B. pertussis culture was performed on induced sputum specimens and in a subset of NPSs.

Results. From November 2014 to May 2015, 484 infants with paired NPSs and NPAs were tested; 15 (3.1%) PCR-confirmed pertussis cases were identified, 13 of which were PCR positive on both samples, while 1 each were positive only on NPS or NPA. From March to October 2015, 320 infants had NPSs and induced sputum collected, and 11 (3.4%) pertussis cases were identified by PCR, including 8 (72.7%) positive on both samples, 1 (9.1%) only positive on NPS, and 2 (18.2%) only positive on induced sputum. The 3 types of specimens had similar negative predictive value >99% and sensitivity >83%. Compared to PCR, culture sensitivity was 60% in induced sputum and 40% in NPSs.

Conclusions. Flocked nasopharyngeal swabs, nasopharyngeal aspirates, and induced sputum performed similarly for the detection of B. pertussis infection in young infants by PCR.

Respiratory RNA Viruses

Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.

Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens

Respiratory illness causes significant morbidity especially in children, the elderly and the immunocompromised. The sample type taken and the quality of that sample are of great significance in providing an accurate diagnosis. Gargle samples are easy to take and sample the same area as a throat swab (THS). In this study, we assessed the utility of gargle samples for the molecular detection of common respiratory infections. Paired gargle and THS samples collected on the same day from the same patient were compared. We also included in our analysis paired THS and gargle samples that were collected within three days of each other as these samples are likely to have been taken during the same illness. Overall the data suggests that gargle samples are a more sensitive sample type than THS samples as overall the diagnostic yield was higher in the gargle samples and the Ct value of the gargle samples was stronger for the majority of samples in comparison to THS samples. Similar data was seen in the paired samples collected within one to three days of each other, as although the diagnostic yield between the sample types was similar (similar discrepant results), the majority of gargles had stronger Ct values than THS samples. This paper highlights the usefulness of gargle samples as non-invasive sensitive respiratory sample in comparison to THS samples. We recommend that other testing sites should consider using gargle samples for respiratory diagnosis as it will bring benefits in terms of sensitivity and sampling ease of use.

Additional molecular testing of saliva specimens improves the detection of respiratory viruses

Emerging infectious diseases in humans are often caused by respiratory viruses such as pandemic or avian influenza viruses and novel coronaviruses. Microbiological testing for respiratory viruses is important for patient management, infection control and epidemiological studies. Nasopharyngeal specimens are frequently tested, but their sensitivity is suboptimal. This study evaluated the incremental benefit of testing respiratory viruses in expectorated saliva using molecular assays. A total of 258 hospitalized adult patients with suspected respiratory infections were included. Their expectorated saliva was collected without the use of any special devices. In the first cohort of 159 patients whose nasopharyngeal aspirates (NPAs) tested positive for respiratory viruses during routine testing, the viral load was measured using quantitative reverse transcription PCR. Seventeen percent of the patients (27/159) had higher viral loads in the saliva than in the NPA. The second cohort consisted of 99 patients whose NPAs tested negative for respiratory viruses using a direct immunofluorescence assay. Their NPA and saliva specimens were additionally tested using multiplex PCR. In these patients, the concordance rate by multiplex PCR between NPA and saliva was 83.8%. Multiplex PCR detected viruses in saliva samples from 16 patients, of which nine (56.3%) had at least one virus that was not detected in the NPA. Decisions on antiviral or isolation precautions would be affected by salivary testing in six patients. Although NPAs have high viral loads and remain the specimen of choice for most patients with respiratory virus infections, supplementary molecular testing of saliva can improve the clinical management of these patients.

Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR

Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens (P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies.