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Objective: To describe the association of respiratory viral test results and the risk of invasive bacterial infection (IBI) for febrile young infants presenting to emergency care., Design: A planned secondary analysis within the Febrile Infants Diagnostic assessment and Outcome (FIDO) study, a prospective multicentre observational cohort study conducted across the UK and Ireland., Setting: 35 paediatric emergency departments and assessment units across the UK and Ireland between 6 July 2022 and 31 August 2023., Patients: Febrile infants aged 90 days and under presenting to emergency care., Main Outcome Measures: IBI (meningitis or bacteraemia) among febrile infants, undergoing respiratory viral testing for respiratory syncytial virus (RSV), influenza and SARS-CoV-2., Results: 1395 out of 1821 participants underwent respiratory viral testing, of those tested 339 (24.5%) tested positive for at least one of, SARS-CoV-2, RSV or influenza. A total of 45 infants (3.2%) were diagnosed with IBI. Of these, IBI occurred in 40 out of 1056 (3.8%) participants with a negative viral test and 5 out of 339 (1.5%) occurred in participants with a positive viral respiratory test (p=0.034). Infants aged 29 days and older with a positive respiratory viral test had a significantly lower rate of IBI (0.7%) compared with those with a negative test (3.2%) (p=0.015)., Conclusions: Young febrile infants with a positive respiratory viral test for SARS-CoV-2, RSV or influenza are at lower risk of IBI. Infants over 28 days of age with a positive viral test represent the lowest risk cohort., Trial Registration Number: NCT05259683., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

Multiple respiratory viruses lead to high morbidity and mortality, yet global surveillance platforms focus primarily on seasonal influenza viruses. The COVID-19 pandemic and new RSV vaccines highlight the importance of a broader approach. Upper respiratory tract swabs from children aged 24-59 months presenting with influenza-like illness in The Gambia were collected during follow-up of a live-attenuated influenza vaccine randomised controlled trial in 2017-18. A microfluidic quantitative polymerase chain reaction (qPCR) assay was established and used to detect 21 respiratory viruses. 76.6% of samples had one or more viruses detected (n = 121/158). The viruses detected most frequently were rhinovirus (n = 37/158, 23.4%) and adenovirus (n = 34/158, 21.5%), followed by parainfluenza virus 3, influenza B and human metapneumovirus B. A third of positive samples had multiple viruses detected (two n = 31/121, 25.6%; three n = 9/121, 7.4%). Our data demonstrates how microfluidic qPCR is a useful tool for high-throughput, comprehensive detection of multiple respiratory viruses in surveillance platforms. Rapidly changing epidemiology exemplifies the need for new, broader approaches to virus surveillance in low-resource settings to respond to future epidemics and to guide the need for and use of new prevention and therapeutic measures., Competing Interests: Declarations Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in <24 h. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR testing. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential, de novo assembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Using in silico analysis, we showed that after removal of all human viral sequences from the reference database, 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus facilitating a robust and rapid response to the next viral pandemic., Competing Interests: Competing interests C.Y.C. is a founder of Delve Bio and on the scientific advisory board for Delve Bio, Flightpath Biosciences, Biomeme, Mammoth Biosciences, BiomeSense and Poppy Health. He is also an inventor on US patent 11380421, “Pathogen detection using next generation sequencing”, under which algorithms for taxonomic classification, filtering, and pathogen detection are used by SURPI+ software. C.Y.C. receives research support from Delve Bio and Abbott Laboratories, Inc. The other authors declare no competing interests., (© 2024. The Author(s).)

The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging-especially in the case of respiratory viruses-due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2,000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 625.1 copies/µL of influenza A virus. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.IMPORTANCETarget capture sequencing has been developed and applied for direct genome sequencing of viruses in clinical specimens to overcome the low detection sensitivity of metagenomic next-generation sequencing. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A, focusing on clinical specimens containing low copy numbers of viral genomes. Our results showed that the target capture sequencing yielded dramatically higher read counts than metagenomic sequencing for both viruses. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with other viruses, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies., Competing Interests: The authors declare no conflict of interest.

Case Presentation: A 10-month-old boy with a weight of 5 kg demonstrated recurrent respiratory infections after birth, respiratory distress after feeding, and slow weight gain. At the time of presentation, he had been experiencing a cough accompanied by pyrexia for > 20 days. Prenatal ultrasound examinations revealed no abnormalities. He was born at full term via cesarean delivery and weighed 2.9 kg at birth. He was hospitalized three times because of pneumonia., Competing Interests: Financial/Nonfinancial Disclosures None declared., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Objectives: Although human bocavirus (HBoV) is primarily linked to respiratory tract infections, its exact role as a respiratory pathogen remains unclear. This study aims to investigate HBoV detection rates, as well as clinical, laboratory, microbiological, and radiological characteristics, length of stay in the emergency department (ED), rate of hospitalization, and severity of illness in cases where HBoV is detected in respiratory secretions., Methods: We conducted a retrospective analysis of all consecutive patients under 18 years who visited a large-volume tertiary pediatric ED from January to December 2023 and tested positive for HBoV in their respiratory viral panel (RVP)., Results: Among the 14,315 patients who underwent RVP testing during the study period, 591 (4%) tested positive for HBoV. After excluding those with incomplete data, 528 patients (57% male) were included in the analyses. The median age was 2.8 [1.2-4.9] years. The most common symptoms were cough (67%), fever (58%), runny nose/nasal congestion/sore throat (34%), and respiratory distress (24%). Thirty percent of the patients had a history of antibiotic use before admission. Thirteen percent of the patients had at least one chronic illness. Co-infection with HBoV occurred in 37% of the patients, with respiratory syncytial virus (RSV) being the most frequently co-detected virus (45%). Lymphopenia was documented in 12% of patients, and 36% had elevated C-reactive protein levels (median 21 [12-38] g/dl). Abnormal chest X-rays were noted in 85% of patients. The management approach included outpatient care for more than half of the patients (69%). Clinical severity was classified as high in 11% of patients ( n  = 60), necessitating ICU admission., Conclusion: Although typically mild, HBoV infections can escalate to severe respiratory illnesses, requiring respiratory support and intensive care.

Background: Long-term care facility (LTCF) residents are twice as likely to receive antibiotics compared with elderly living in the community, and studies have reported up to half of prescriptions in LTCFs as inappropriate., Aim: To identify factors contributing to general and inappropriate antibiotic prescription among LTCF residents with lower respiratory tract infections (LRTIs)., Methods: In this prospective, multicentric, observational study, residents with LRTIs were recruited among 32 LTCFs in Western Switzerland during winter 2022-2023. Residents underwent lung ultrasound (LUS) within three days of LRTI onset, serving as the pneumonia diagnosis reference standard. Multivariate logistic regression and backward selection were used with P < 0.1 cut-off to identify factors among demographics, vital signs, diagnostic tests, and LTCF characteristics associated with (i) antibiotic prescription and (ii) inappropriate prescription., Findings: A total of 114 residents were included, 63% female, median age 87 years. Fifty-nine (52%) residents underwent diagnostic tests: 50 (44%) polymerase chain reaction (PCR) for respiratory viruses and 16 (14%) blood test with C-reactive protein and/or blood count. Sixty-three (55%) residents received antibiotics. Factors associated with antibiotic prescriptions were Rockwood Clinical Frailty Scale score ≥7, oxygen saturation <92%, performing a blood test, rural LTCFs, and female physician. Among residents receiving antibiotics, 48 (74%) had inappropriate prescriptions, with performance of respiratory virus PCR test as the only protective factor., Conclusion: Whereas half of LRTI residents received antibiotics, falling within lower ranges of European LTCFs prescription rates (53-80%), most antibiotic prescriptions were inappropriate. Utilization of diagnostic tests correlates with lower overall and inappropriate prescription, advocating for their use to optimize prescription practices in LTCFs., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Early and accurate identification of pathogens in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is critically important. The clinical usefulness of metagenomic next-generation sequencing (mNGS) in the diagnosis of pulmonary infections after allo-HSCT remains under discussion. This multicenter retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in identifying the pathogens of pulmonary infections in allo-HSCT recipients. One hundred forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs performed on bronchoalveolar lavage fluid specimens showed 71.4% positivity on mNGS compared to 55.0% positivity on CMTs. mNGS identified 182 pathogens, including bacteria (n = 88), fungi (n = 35) and viruses (n = 59), compared to 106 pathogens detected by CMTs (bacteria, n = 31; fungi, n = 24; viruses, n = 51). Pulmonary infection was finally diagnosed in 98 patients, including 22 bacterial, 7 fungal, 18 viral, and 48 mixed infections and 3 infections with an unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections was 88.8% and 69.4%, respectively (P = .001), and the specificity were 81.0% and 85.7%, respectively (P = .688). Our findings suggest that mNGS may be a promising technology for diagnosing pulmonary infections in allo-HSCT recipients., (Copyright © 2024 The American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc. All rights reserved.)

Introduction: Telehealth has emerged as an important clinical setting for managing acute respiratory tract infections (ARIs), potentially reducing emergency department and urgent care overcrowding, and reducing nosocomial transmission. Many current algorithms for ARI management incorporate information on patient vital signs. However, the accuracy of vital signs collected by patients using readily available home devices and techniques has not been studied. Methods: A cross-sectional sample of patients seen for urgent conditions at a hospital emergency and urgent care center were given instructions and low-cost, readily available devices to collect their vital signs. A trained research coordinator collected a parallel set of vital signs using standard hospital equipment, serving as the gold standard. We analyzed the performance of patient-collected vital signs compared with vital signs collected by a trained research coordinator. Results: A total of 300 patients completed the study. Patient-collected vital signs were highly specific for traditional levels of abnormalities (HR >100 beats per min, RR >24 breaths per min, temperature >100.4 degrees Fahrenheit, oxygen saturation <94 percent); however, sensitivity was poor for elevated heart rate by pulse estimation (25%) and elevated respiratory rate (60%). Heart rate and oxygen saturation by pulse oximeter and oral temperature had higher sensitivity. Conclusions: Vital signs measured and provided by patients are not uniformly accurate, particularly when using manual techniques rather than automated devices. Telehealth algorithms that rely on these values could provide incorrect triage and management advice.

Objectives: Acute respiratory tract infections (ARTIs) are a heterogenous group of diseases. Often, it is difficult to obtain a precise diagnosis in general practice but also difficult to determine when the patient is recovered. The lack of a precise definition of recovery after ARTI complicates scientific research aiming to optimize diagnostics and compare treatments. The study aimed to define cutoff points to determine the end of an ARTI as a proxy for recovery in patients diagnosed with ARTI in general practice using a validated patient-reported outcome instrument; The ARTI Questionnaire (ARTIQ)., Methods: A total of 259 participants was divided in 2 groups-1 with ARTI and 1 without. Histograms and area under the curve were calculated for each of the 5 dimensions within the ARTIQ to evaluate the discriminative effect. For the most discriminative dimensions receiver operating comparison curves were performed to determine relevant cutoff points for having or not having ARTI symptoms and serve as a proxy for recovery in clinical research., Results: The highest discriminative effect was found in 2 dimensions: "physical-upper airways" and "physical-lower airways." When combining these dimensions, the area under the curve was 0.97. Sensitivity, specificity, and predictive values were calculated for selected cutoff points., Conclusion: Cutoff points serving as proxy for recovery from ARTI using a patient-reported outcome were identified. The specific cutoff point for a certain research project must be selected considering the specific clinical situation of interest., Competing Interests: Author Disclosures Author disclosure forms can be accessed below in the Supplemental Material section., (Copyright © 2024. Published by Elsevier Inc.)

Context: Influenza-like illness (ILI) is commonly used in clinical and public health settings to identify influenza cases. CDC defines ILI as fever and either cough or sore throat, with symptom onset within 7 days. Objective: Assess performance of ILI criteria in two settings (clinical and community), comparing symptom profiles and laboratory detection of influenza in children. Study Design and Analysis: Retrospective analyses of data from medically attended influenza (MAI) surveillance and a communitybased study. Datasets were analyzed separately to assess predictors of influenza cases. Analyses were limited to specimens collected within 7 days of symptom onset. Relationships between influenza and each categorical variable were described by the confusion matrix, sensitivity, and specificity. Associations were tested using chi-square tests. Unadjusted and adjusted logistic regression models were used for all variables with RT-PCR result as the outcome. Setting or Dataset: The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a respiratory infection study based in the Oregon School District (Dane County, WI). The Wisconsin Influenza Incidence Surveillance Project (IISP) is a MAI surveillance system operating in five family medicine clinics in Dane County. Population Studied: Children aged 4-18 years with acute respiratory infections. Intervention/Instrument: Oropharyngeal specimens, collected by research staff (ORCHARDS) or clinicians (IISP), were tested for influenza via RT-PCR and for multiple respiratory viruses at the Wisconsin State Laboratory of Hygiene. Extensive demographic and symptoms data were collected from all participants. Outcome Measures: Influenza(+)PCR. Results: From 9/7/2010-3/12/2020, 1,338 and 2,359 specimens meeting inclusion criteria were collected for IISP and ORCHARDS, respectively. Cough, fever, and ILI classification were significantly associated with influenza (sensitivity ≥92.8%, ≥85.9%, and ≥84.5%, respectively). Receiver operator curve analysis confirmed ILI had high predictive ability in both settings, improved by the inclusion of seasonality and influenza vaccination status (IISP: 0.61 vs 0.76, ORCHARDS: 0.68 vs 0.78). Conclusions: ILI performed well in both clinical and community contexts. Factors most highly associated with increased odds of RT-PCR(+) results were cough, fever, and ILI. Inclusion of seasonality and influenza vaccination status improved the predictive value of ILI in both datasets., Competing Interests: Authors report none., (2023 Annals of Family Medicine, Inc.)

Human bocavirus (HBoV) has emerged as a significant pathogen primarily associated with respiratory infections in children. This study aimed to evaluate the clinical relevance of HBoV infection by quantifying viral loads in nasopharyngeal swabs from hospitalized children with acute respiratory infections (ARIs) and investigating correlations with clinical outcomes. A total of 957 children were tested, with HBoV detected in 73 cases (7.6%), either as a sole infection or co-infection with other respiratory viruses. Quantitative polymerase chain reaction (qPCR) was employed to measure viral load, and a threshold of 10 4 copies/mL was used to differentiate high and low viral concentrations. Results have shown that children with lower respiratory tract infections (LRTIs) had significantly higher viral loads, most notably in cases where HBoV was the sole pathogen. Additionally, children with pre-existing health conditions were more likely to have elevated HBoV concentrations compared to those who were previously healthy. Children with higher viral loads were more likely to require oxygen supplementation and receive empirical antibiotic therapy, indicating a more severe clinical course. This study underscores the importance of considering HBoV viral load in clinical diagnostics, as higher concentrations were associated with more severe presentations, including the need for oxygen support. Future research should focus on refining diagnostic thresholds and exploring HBoV's role in co-infections to enhance patient care strategies.

Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics., (© 2024. The Author(s).)

Background: Respiratory tract infections are a common health problem. Cytokines/chemokines play a critical role in the regulation of the immune system. Their defective production may predispose to recurrent respiratory tract infections (RRIs), and an excessive immune response may lead to chronic inflammation and cause damage to the respiratory tract. Another biomarker of respiratory infections may be immunoglobulin-IgG4. Its meaning has still been little explored. We wanted to assess the suitability of the levels of biomarkers tested: interleukin (IL)-17A, IL-18, IL-23, normal T cells expressed and secreted (RANTES), and induced protein (IP)-10, as well as immunoglobilun G4 (IgG4) to predict recurrent infections. Methods: The study group (SG) included a total of 130 children (68 girls, 62 boys) between 3 and 17 years of age with RRI. The control group (CG) included 86 healthy children with no symptoms of inflammatory or allergic diseases (44 girls and 42 boys) of the same age. Blood samples were collected in fasting state and then serum samples were frozen and stored until biomarker assay. Results: Serum RANTES, IL-18, IL-23, and IgG4 concentration were higher in all children with recurrent infections vs. those in the CG ( p   < 0001). Serum levels of IL-17A and IP-10 were also significantly higher in the SG than in the CG, but only in the youngest children. Among the six serum markers, RANTES demonstrated the highest area under the receiver operating characteristic curve (area under curve) value (0.998, 95% confidence interval [CI]: 0.98-1.0, p < 0.001) for the diagnosis of RRIs, followed by IL-23 (0.99, 95% CI 0.966-0,999, p < 0.001) and IL-18 (0.957, 95% CI 0.921-0.980, p < 0.001). Conclusions: RANTES, IL-23, and IL-18 could be strong predictors of respiratory infections recurrence in children., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2024 Edyta Machura et al.)

Respiratory pathogen infections are seasonally prevalent and are likely to cause co-infections or serial infections during peak periods of infection. Since they often cause similar symptoms, simultaneous and on-site detection of respiratory pathogens is essential for accurate diagnosis and efficient treatment of these infectious diseases. However, molecular diagnostic techniques for multiple pathogens in this field are lacking. Herein, we developed a microfluidic LAMP and real-time fluorescence assay for rapid detection of multiple respiratory pathogens using a ten-channel microfluidic chip with pathogen primers pre-embedded in the chip reaction well. The microfluidic chip provided a closed reaction environment, effectively preventing aerosol contamination and improving the accuracy of the detection results. Its corresponding detection instrument could automatically collect and display the fluorescence curve in real time, which was more conducive to the interpretation of results. The results showed that the developed method could specifically recognize the nucleic acid of influenza A(H1N1), Mycoplasma pneumoniae , respiratory syncytial virus type A, and SARS-CoV-2 with low detection limits of 10 4 copies per mL or 10 3 copies per mL. The test results on clinical samples demonstrated that the developed method has high sensitivity (92.00%) and high specificity (100.00%) and even has the capability to differentiate mixed-infection samples. With simple operation and high detection efficiency, the present portable and simultaneous detection assay could significantly improve the efficiency of on-site detection of respiratory infectious diseases and promote the accurate treatment, efficient prevention and control of the diseases.

A 24/7 AI sound-based coughing monitoring system was applied in combination with oral fluids (OFs) and bioaerosol (AS)-based screening for respiratory pathogens in a conventional pig nursery. The objective was to assess the additional value of the AI to identify disease patterns in association with molecular diagnostics to gain information on the etiology of respiratory distress in a multimicrobially infected pig population. Respiratory distress was measured 24/7 by the AI and compared to human observations. Screening for swine influenza A virus (swIAV), porcine reproductive and respiratory disease virus (PRRSV), Mycoplasma (M.) hyopneumoniae , Actinobacillus (A.) pleuropneumoniae , and porcine circovirus 2 (PCV2) was conducted using qPCR. Except for M. hyopneumoniae , all of the investigated pathogens were detected within the study period. High swIAV-RNA loads in OFs and AS were significantly associated with a decrease in respiratory health, expressed by a respiratory health score calculated by the AI The odds of detecting PRRSV or A. pleuropneumoniae were significantly higher for OFs compared to AS. qPCR examinations of OFs revealed significantly lower Ct-values for swIAV and A. pleuropneumoniae compared to AS. In addition to acting as an early warning system, AI gained respiratory health data combined with laboratory diagnostics, can indicate the etiology of respiratory distress.

Background: Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited., Methods: This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU., Results: Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P < 0.05), both in the immunocompromised group (95.0% vs 58.75%, P < 0.05) and the immunocompetent group (93.51% vs 71.43%, P < 0.05). mNGS detected more pathogens than CMTs did (167 vs 51), identifying 116 organisms that were missed by CMTs. The proportion of antibiotic regimen adjustments based on mNGS results was significantly higher compared to CMTs in both the immunocompromised (70.00% vs 17.50%, P < 0.05) and immunocompetent groups (48.70% vs 15.58%, P < 0.05). In the immunocompromised group, patients who had their antibiotic treatment adjusted on mNGS results had improved prognosis, with significantly lower ICU mortality (8.93% vs 50%, P < 0.05) and 28-day mortality rates (30.36% vs 68.75%, P < 0.05) than CMTs. In the immunocompetent group, no statistically significant differences were observed in ICU mortality or 28-day mortality (20.00% vs 33.33%, P > 0.05; 42.67% vs 45.83%, P > 0.05)., Conclusion: mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis., (© 2024. The Author(s).)

Introduction: Febrile infants under 3 months of age are at risk of invasive bacterial infection (IBI). It is currently unclear if testing for respiratory viruses may have a role in IBI risk stratification. If found to be associated with the likelihood of IBI, respiratory viral point-of-care testing may improve patient and caregiver experience, reduce costs and enhance antimicrobial stewardship., Methods and Analysis: This is a study protocol for a systematic review and meta-analysis that aims to answer the following question: In young febrile infants presenting to emergency care settings does a positive respiratory viral test for RSV, Influenza or SARS-CoV2 (relative to a negative test) add value to current risk stratification pathways for the exclusion of invasive bacterial infection, subsequently enabling safe de-escalation of investigation and treatment ?A search strategy will include MEDLINE, EMBASE, Web of Science, The Cochrane Library and grey literature. Abstracts and then full texts will be independently screened for selection. Data extraction and quality assessment will be completed by two independent authors.The primary objective is to analyse the ability of a positive respiratory viral test to identify the overall risk of IBI. The secondary objective is to perform a subgroup analysis to investigate how the risk stratification alters based on other variables including virus type, patient characteristics and the presence of an identified source of fever.Bivariate random-effects meta-analysis will be undertaken. Diagnostic odds ratios (OR), sensitivity, specificity and positive and negative likelihood ratios will be calculated. The degree of heterogeneity and publication bias will be investigated and presented., Ethics and Dissemination: Ethical approval is not required. We will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to disseminate the study results through publication and conference presentations., Prospero Registration Number: This protocol is registered in PROSPERO-ID number: CRD42023433716., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Objective: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment., Results: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance., (© 2024. The Author(s).)

Background: Recurrent respiratory tract infections (rRTIs) are a common reason for immunodiagnostic testing in children, which relies on serum antibody level measurements. However, because RTIs predominantly affect the respiratory mucosa, serum antibodies may inaccurately reflect local immune defences. We investigated antibody responses in saliva and their interplay with the respiratory microbiota in relation to RTI severity and burden in young children with rRTIs., Methods: We conducted a prospective cohort study including 100 children aged <10 years with rRTIs, their family members and healthy healthcare professionals. Total and polyreactive antibody concentrations were determined in serum and saliva (ELISA); respiratory microbiota composition (16S rRNA sequencing) and respiratory viruses (quantitative PCR) were characterised in nasopharyngeal swabs. Proteomic analysis (Olink) was performed on saliva and serum samples. RTI symptoms were monitored with a daily mobile phone application and assessed using latent class analysis and negative binomial mixed models., Results: Serum antibody levels were not associated with RTI severity. Strikingly, 28% of salivary antibodies and only 2% of serum antibodies displayed polyreactivity (p<0.001). Salivary polyreactive IgA was negatively associated with recurrent lower RTIs (adjusted OR 0.80, 95% CI 0.67-0.94) and detection of multiple respiratory viruses (adjusted OR 0.76, 95% CI 0.61-0.96). Haemophilus influenzae abundance was positively associated with RTI symptom burden (regression coefficient 0.05, 95% CI 0.02-0.08)., Conclusion: These results highlight the importance of mucosal immunity in RTI severity and burden, and suggest that the level of salivary polyreactive IgA and H. influenzae abundance may serve as indicators of infection severity and burden in young children with rRTIs., Competing Interests: Conflict of interest: D. Bogaert reports grants from GSK and OM Pharma, speaker fees from MedImmune, and a leadership role as Treasurer of the International Society of Pneumonia and Pneumococcal Diseases, all outside the submitted work. The authors have no other conflicts of interest to disclose., (Copyright ©The authors 2024.)

Recurrent respiratory papillomatosis is a chronic infection of the airway mucosa by the human papilloma virus, in the form of recurrent exophytic papilloma. Two clinical forms are distinguished: juvenile and adult onset. Depending on their size and location, papilloma can cause dysphonia, pharyngeal discomfort, until obstruction of the airway. There is no curative treatment. The management strategy is to surgically remove symptomatic disease by transoral approach, but some recurrent disease require multiple interventions and -adjuvant therapies. The symptoms caused by the disease as well as treatments' side effects have a major impact on patient's quality of life. Vaccination against HPV currently represents the best strategy to prevent disease., Competing Interests: Les auteurs n’ont déclaré aucun conflit d’intérêts en relation avec cet article.

We report a considerable increase in enterovirus D68 (EV-D68) cases since July 2024, culminating in an ongoing outbreak of acute respiratory infections in northern Italy, accounting for nearly 90% of all enterovirus infections. The outbreak was identified by community- and hospital-based surveillance systems, detecting EV-D68 in individuals with mild-to-severe respiratory infections. These strains belonged to B3 and a divergent A2 lineage. An increase in adult cases was observed. Enhanced surveillance and molecular characterisation of EV-D68 across Europe are needed.

Objective: To evaluate and summarise the evidence from published Meta-analyses/systematic reviews (MAs/SRs) of Traditional Chinese Medicine (TCM) in the treatment of recurrent respiratory tract infections (RRTIs) and to provide a scientific basis for the clinical treatment of RRTIs with TCM., Methods: Studies were retrieved from Chinese and English databases including the China National Knowledge Infrastructure, Wanfang database, China Science and Technology Journal Database, SinoMed, PubMed, Web of Science, the Cochrane Library and EMbase from their establishment date to March 2023. Involved studies were screened, extracted, and evaluated for quality by two researchers independently. The a measurement tool to assess systematic reviews (AMSTAR) 2 scale was used for methodological quality evaluation, as well as the preferred reporting items for systematic reviews and Meta-analyses (PRISMA) 2020 statement for report quality evaluation, the risk of bias in systematic reviews (ROBIS) tool for risk of bias, and the grading of recommendations, assessment, development and evaluation (GRADE) quality assessment tool for evidence quality., Results: Twenty MAs/SRs studies were included, including analyses of 274 original studies involving 38 335 patients with RRTIs. The AMSTAR 2 scale evaluation results showed that 19 studies were of very low quality and one of moderate quality. The ROBIS evaluation results showed that 11 MAs/SRs were at high risk and nine at low risk of bias. The PRISMA 2020 report quality showed the included studies had scores between 23.5 and 35.5, among them one with high quality, 17 with moderate quality and two with low quality. The GRADE system results showed that among 126 outcome indicators, only 17 had moderate quality of evidence, 27 had low quality, 82 had very low quality, and none had high quality., Conclusions: The MAs/SRs methodological quality of using TCM for treatment RRTIs is generally poor, the quality of reports as well as of evidence is generally low, and the risk of bias is high; therefore we should treat these results with caution.

Competing Interests: Declaration of interests The authors declare no conflict of interest.

Respiratory syncytial virus (RSV), an RNA virus spread by droplet infection that affects all ages, is increasingly recognised as an important pathogen in adults, especially among older people living with comorbidities. Distinguishing RSV from other acute viral infections on clinical grounds alone, with sufficient precision to be clinically useful, is not possible. The reference standard diagnosis is by PCR: point-of-care tests perform less well with lower viral loads. Testing samples from a single respiratory tract site could result in underdetection. RSV is identified in 6-11% of outpatient respiratory tract infection (RTI) consultations in older adults (≥60 years, or ≥65 years, depending on the study) and accounts for 4-11% of adults (≥18 years) hospitalised with RTI, with 6-15% of those hospitalised admitted to intensive care, and 1-12% of all adults hospitalised with RSV respiratory tract infection dying. Community-based studies estimate the yearly incidence of RSV infection at around 3-7% in adults aged 60 years and older in high-income countries. Although RSV accounts for a similar disease burden as influenza in adults, those hospitalised with severe RSV disease are typically older (most ≥60 years) and have more comorbidities, more respiratory symptoms, and are frequently without fever. Long-term sequelae are common and include deterioration of underlying disease (typically heart failure and COPD). There are few evidence-based RSV-specific treatments currently available, with supportive care being the main modality. Two protein subunit vaccines for protection from severe RSV in adults aged 60 years and older were licensed in 2023, and a third-an mRNA-based vaccine-recently gained market approval in the USA. The phase 3 studies in these three vaccines showed good protection against severe disease. Data on real-world vaccine effectiveness in older adults, including subgroups at high risk for RSV-associated hospitalisation, are needed to establish the best use of these newly approved RSV vaccines. New diagnostics and therapeutics are being developed, which will also need rigorous evaluation within their target populations to ensure they are used only for those in whom there is evidence of improved outcomes. There is an urgent need to reconceptualise this illness from one that is serious in children, but far less important than influenza in older people, to thinking of RSV as also a major risk to health for older people that needs targeted prevention and treatment., Competing Interests: Declaration of interests CCB contributed to an advisory board on RSV for Moderna; has received funding for prospective observational research on the epidemiology of RSV, and other viral infections in older people in primary care, through the European Clinical Research Alliance on Infectious Diseases from Sanofi; and was an investigator on the prospective observational RESCEU study of RSV in older adults, funded by the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement 116019. JGW has been an investigator for clinical trials funded by IMI/Horizon2020 and ZonMw, and clinical trials sponsored by pharmaceutical companies including AstraZeneca, Merck, Pfizer, Sanofi, and Janssen. All funds have been paid to University Medical Centre Utrecht. JGW participated in advisory boards of Janssen and Sanofi, and was a speaker at a symposium sponsored by Sanofi, with honoraria paid to University Medical Centre Utrecht. DML has received personal fees from Gilead for an educational video, and from Merck for a roundtable discussion, speaker fees from Biotest, Takeda, and AstraZeneca, and support from Octapharma to attend a conference. DML also holds research grants from GlaxoSmithKline and Bristol Myers Squibb, and has received consultancy fees from GSK (paid to institution). JFS has undertaken consultancy for Adrenomed, Proveca, Clinsearch, and GARD-P, and has participated in a data safety and monitoring board for GlaxoSmithKline (all fees paid to institution)., (Copyright © 2024 Elsevier Ltd. All rights reserved, including those for text and data mining, AI training, and similar technologies.)

Background: Whole genome sequencing (WGS) of respiratory viruses from rapid antigen tests (RAT-WGS) is a novel approach to expanding genomic surveillance of respiratory infections. To date however, there are limited data on the genomic stability of these viruses on RATs. In this study, we investigated the effect of storage conditions and nucleic acid preservatives on the ability to enhance stability and improve recovery of respiratory virus genomes from RATs., Methods: A mixture of common respiratory viruses was used to inoculate RATs at different environmental temperatures (4°C, 20°C and 36°C), with two preservative reagents (RNALater and DNA/RNA shield) Nucleic acid was extracted from RATs at two different timepoints (72 h and seven days) and subject to real-time multiplex respiratory PCR to detect a range of respiratory viruses. WGS was performed using target-enrichment with the TWIST Comprehensive Viral Research Panel. Defined metrics from an automated in-house bioinformatic pipeline were used to assess and compare viral genome recovery under different conditions., Results: Nucleic acid degradation (indicated by relative change in PCR cycle threshold and WGS-based metrics) was most notable at 20 °C and 36 °C. Storage in either RNALater or DNA / RNA shield improved genome recovery for respiratory viruses across all temperature conditions, although this was most pronounced for RNALater. Subtyping of Influenza viruses demonstrated the applicability of RAT-WGS in downstream genomic epidemiological surveillance., Conclusions: Under simulated conditions, RAT-WGS demonstrated that (i) viral genomes were generally stable at 4°C at 72 h and 1 week, (ii) RNALater has a more significant preservation of nucleic acids compared to DNA/RNA Shield and (iii) genome recovery can be achieved using a sequencing depth of 500,000 reads per sample in RNALater, across all respiratory viruses and conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Crown Copyright © 2024. Published by Elsevier B.V. All rights reserved.)

Objective: To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection., Methods: We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics., Results: The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

We report the use of a new multiplex Real-Time PCR platform to simultaneously identify 24 pathogens and 3 antimicrobial-resistance genes directly from respiratory samples of COVID-19 patients. Results were compared to culture-based diagnosis. Secondary infections were detected in 60% of COVID-19 patients by molecular analysis and 73% by microbiological assays, with no significant differences in accuracy, indicating Gram-negative bacteria as the predominant species. Among fungal superinfections, Aspergillus spp. were detected by both methods in more than 7% of COVID-19 patients. Oxacillin-resistant S. aureus and carbapenem-resistant K. pneumoniae were highlighted by both methods. Secondary microbial infections in SARS-CoV-2 patients are associated with poor outcomes and an increased risk of death. Since PCR-based tests significantly reduce the turnaround time to 4 hours and 30 minutes (compared to 48 hours for microbial culture), we strongly support the routine use of molecular techniques, in conjunction with microbiological analysis, to identify co/secondary infections., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper, (Copyright © 2024 Elsevier Inc. All rights reserved.)

Competing Interests: JMM declares that AAZ Laboratory supplied rapid immunochromatographic All In Triplex devices. EDH, CB, IC, and PT declare no competing interests.

Objectives: In the fall-winter of 2023, China experienced its first epidemic season of respiratory diseases since the COVID-19 pandemic. Gathering timely data about pathogenetic characteristics of respiratory infections is crucial to complement current respiratory surveillance mechanisms in China. Data from direct-to-consumer (DTC) multi-respiratory pathogen (MRP) testing could serve as a novel source of multi-pathogen data for community-based surveillance., Methods: A pioneering initiative was launched to detect multiple respiratory pathogens in Beijing and Guangzhou, China. DTC MRP tests were used to provide proactive surveillance ahead of medical services., Results: A total of 28,018 participants were enrolled between 22 August and 10 December 2023. Positive findings for at least one respiratory pathogen were observed in 26,202 (93.5%) participants. Influenza virus A, respiratory syncytial virus (RSV), and human adenovirus are the three leading viral pathogens detected with proportions of 18.0%, 10.6%, and 8.8%. Viral-bacterial pathogens were co-detected in 9736 (34.7%) of participants, which reduced to 22.2% for bacterial-bacterial co-detection, and 22.0% for bacterial mono-detection. The epidemiological ecology of respiratory pathogens within both viral clusters and specific pathogens varied among cities. The peak of RSV epidemics in Guangzhou occurred in the fall of 2023, earlier than in Beijing., Conclusion: The innovative program offered enhanced surveillance capabilities beyond traditional methods, enabling prompt feedback about test results and mitigating the risk of cross-infection caused by waits in healthcare facilities., Competing Interests: Declarations of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objective: To examine whether or not viral positive patients experienced worse outcomes and assess differences in surgical outcomes between viral-positive patients with and without viral symptoms within 30 days of surgery., Methods: This retrospective study reviewed charts of pediatric patients who underwent congenital heart surgery and routine viral testing at a single institution over a consecutive 3-year period (2017-2019). Patients with a history of heart transplants, pacemaker changes, or implants, and mediastinal washouts were excluded from the study. Surgical outcomes were compared by viral status and viral symptoms, using the Fisher exact and Wilcoxon rank sum tests., Results: Among 1041 patients, 374 patients underwent routine preoperative viral testing, with 107 patients testing positive and 267 testing negative for viral swabs before surgery. There were no significant differences observed in surgical outcomes by viral status, including no differences in mortality. Among the 107 patients with positive viral swabs before surgery, comparisons between 24 patients with viral symptoms and 83 without symptoms within 30 days of surgery detected no significant differences in mortality or complication rates. However, symptomatic versus asymptomatic patients had significantly longer postoperative stay (23.4 vs 13.4 days; P = .02) and intubation time (9.8 vs 4.9 hours; P = .004)., Conclusions: Patients who test positive before congenital heart surgery and are asymptomatic beyond the incubation period may proceed to surgery with no further delay. Patients who are viral positive and symptomatic have a longer postoperative stay and intubation time. A prospective study is needed to assess the importance of routine viral testing., Competing Interests: Conflict of Interest Statement The authors reported no conflicts of interest. The Journal policy requires editors and reviewers to disclose conflicts of interest and to decline handing manuscripts for which they may have a conflict of interest. The editors and reviewers of this article have no conflicts of interest., (Copyright © 2024 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.)

Introduction: The current gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis by real-time reverse transcriptase polymerase chain reaction (RT-PCR) is limited by the number of genes that can be detected. In this study, we developed a low-cost and high-throughput next-generation sequencing technology that can overcome the limitations of real time RT-PCR., Methodology: A targeted sequencing panel (TSP) consisting of approximately 500 amplicons was designed. This panel could simultaneously detect a broad range of gene loci of SARS-CoV-2, and genes for the most common infectious viruses that affect the respiratory tract, in a single run and could include up to 96 samples. Four hundred and forty-eight samples and 31 control samples were analyzed independently with both TSP and RT-PCR, and the results were compared for accuracy and other indicators., Results: TSP identified 50 SARS-CoV-2 positive samples with a 99.33% match to RT-PCR results. It is not surprising that TSP also identified multiple infections from the 96 samples, whereas RT-PCR could not. Thus, TSP was able to accurately diagnose the samples which could not be identified based on single RT-PCR test., Conclusions: Our data demonstrated that TSP is a fast and accurate testing method for identifying multiple pathogen infections of the respiratory tract., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2024 Changyan Ju, Chengbosen Zhou, Zhezhi Deng, Jingwei Gao, Weizhao Jiang, Hanbing Zeng, Haiwei Huang, Yongxiang Duan, David X Deng.)

Respiratory pathogens infecting the human respiratory system are characterized by their diversity, high infectivity, rapid transmission, and acute onset. Traditional detection methods are time-consuming, have low sensitivity, and lack specificity, failing to meet the needs of rapid clinical diagnosis. Nucleic acid aptamers, as an emerging and innovative detection technology, offer novel solutions with high specificity, affinity, and broad target applicability, making them particularly promising for respiratory pathogen detection. This review highlights the progress in the research and application of nucleic acid aptamers for detecting respiratory pathogens, discussing their selection, application, potential in clinical diagnosis, and future development. Notably, these aptamers can significantly enhance the sensitivity and specificity of detection when combined with detection techniques such as fluorescence, colorimetry and electrochemistry. This review offers new insights into how aptamers can address the limitations of traditional diagnostic methods and advance clinical diagnostics. It also highlights key challenges and future research directions for the clinical application of nucleic acid aptamers., (© 2024. The Author(s).)

Background: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited., Methods: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis., Results: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS., Conclusion: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS., (© 2024. The Author(s).)

The epidemiological relevance of viral acute respiratory infections (ARIs) has been dramatically highlighted by COVID-19. However, other viruses cannot be neglected, such as influenza virus, respiratory syncytial virus, human adenovirus. These viruses thrive in closed spaces, influenced by human and environmental factors. High-risk closed communities are the most vulnerable settings, where the real extent of viral ARIs is often difficult to evaluate, due to the natural disease progression and case identification complexities. During the COVID-19 pandemic, wastewater-based epidemiology has demonstrated its great potential for monitoring the circulation and evolution of the virus in the environment. The "Prevention of ARIs in indoor environments and vulnerable communities" study (Stell-ARI) addresses the urgent need for integrated surveillance and early detection of ARIs within enclosed and vulnerable communities such as long-term care facilities, prisons and primary schools. The rapid transmission of ARIs in such environments underscores the importance of comprehensive surveillance strategies to minimise the risk of outbreaks and safeguard community health, enabling proactive prevention and control strategies to protect the health of vulnerable populations. This study consists of designing and validating tools for integrated clinical and environmental-based surveillance for each setting, coupled with analytical methods for environmental matrices. The clinical surveillance involves specialized questionnaires and nasopharyngeal swabs for virus identification, while the environmental surveillance includes air and surface microbiological and chemical monitoring, and virological analysis of wastewater. Integrating this information and the collection of behavioural and environmental risk factors into predictive and risk assessment models will provide a useful tool for early warning, risk assessment and informed decision-making. The study aims to integrate clinical, behavioural, and environmental data to establish and validate a predictive model and risk assessment tool for the early warning and risk management of viral ARIs in closed and vulnerable communities prior to the onset of an outbreak., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Carducci et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Objective: Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients., Methods: 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared., Results: Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3 ± 14.7 vs. 27.9 ± 19.0 days, P = 0.044; 18.9 ± 15.0 vs. 29.5 ± 17.7 days, P = 0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P = 0.049)., Conclusion: Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection., (© 2024. The Author(s).)

Background: Pentraxin 3 (PTX3) is an acute-phase reactant that is elevated in the plasma during inflammatory responses. We aimed to evaluate the utility of PTX3 as a clinical marker in children with lower respiratory tract infections (LRTIs) and the association between PTX3 and LRTIs severity., Methods: We included 60 patients admitted to Fayoum University Hospital with LRTIs fulfilling the WHO criteria for diagnosing LRTIs. We collected data on peak temperature, respiratory rate, heart rate, oxygen saturation upon admission, and length of hospital stay. The complete blood count (CBC), C-reactive protein (CRP) level, and PTX3 were measured upon admission., Results: PTX3 levels were significantly correlated with peak temperature, duration of hospital stay, the Pediatric Respiratory Severity Score (PRESS), total leucocytic count (TLC), CRP, and blood cultures., Conclusion: PTX-3 represented the severity of the disease and predicted the prognosis. Pentraxin levels demonstrate a statistically significant sensitivity of (93.3%) and a specificity of (70%) at the cut-off value (of 8.84) with an area under the curve (90.7%) in the diagnosis of LRTIs., (© 2024. The Author(s).)

Coughing may impair the quality of life, for instance by interfering with sleep or social interactions. Acute cough is almost invariably caused by a viral respiratory tract infection and seldom warrants medical consultation or treatment. Red flags in cough (haemoptysis, high fever or severe illness) may be indicative of a life threatening underlying disease. Wet and dry cough often have the same aetiology, and a different approach is therefore not needed.

We analyzed the records of 869 children who underwent flexible bronchoscopy. We found procedural complications in 6.7% (n = 59), with severe events in 3.2% (n = 28). Age < 1 y, recurrent respiratory papillomatosis, and finding lower airway malacia on bronchoscopy were identified as independent risk factors for developing complications with adjusted odds ratio (95% CI) of 2.6 (1.3, 4.9); P = 0.004; 5.4 (1.7, 17.6); P = 0.005 and 2.1 (1.1, 4.0); P = 0.031, respectively.

At present, the diagnosis of lower respiratory tract infections (LRTIs) is difficult, and there is an urgent need for better diagnostic methods. This study enrolled 136 patients from 2020 to 2021 and collected bronchoalveolar lavage fluid (BALF) specimens. We used metatranscriptome to analyze the lower respiratory tract microbiome (LRTM) and host immune response. The diversity of the LRTM in LRTIs significantly decreased, manifested by a decrease in the abundance of normal microbiota and an increase in the abundance of opportunistic pathogens. The upregulated differentially expressed genes (DEGs) in the LRTIs group were mainly enriched in infection immune response-related pathways. Klebsiella pneumoniae had the most significant increase in abundance in LRTIs, which was strongly correlated with host infection or inflammation genes TNFRSF1B, CSF3R, and IL6R. We combined LRTM and host transcriptome data to construct a machine-learning model with 12 screened features to discriminate LRTIs and non-LRTIs. The results showed that the model trained by Random Forest in the validate set had the best performance (ROC AUC: 0.937, 95% CI: 0.832-1). The independent external dataset showed an accuracy of 76.5% for this model. This study suggests that the model integrating LRTM and host transcriptome data can be an effective tool for LRTIs diagnosis., (© 2024. The Author(s).)

Primary ciliary dyskinesia (PCD) is a heterogeneous genetic disorder associated with abnormalities in ciliary structure and function. Here, we report A 22-year-old non-smoking Chinese man with recurrent episodes of respiratory tract infections and sinusitis since high school period. The diagnosis is more complicated by the atypical symptoms and the late age of onset. We summarized the clinical characteristics of this case and literature review. This report aimed to improve the clinical understanding of primary ciliary dyskinesia.

SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa , Staphylococcus aureus , Haemophilus influenzae , and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia , Inquilinus , Achromobacter , Ralstonia , and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus , although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia , Inquilinus , Achromobacter , Ralstonia , and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices., Competing Interests: Lisa Saiman receives grant funding (provided to institution) from the U.S. CF Foundation and serves as a consultant to the CF Foundation. Valerie Waters receives grant funding from the U.S. CF Foundation and CF Canada. John J. LiPuma receives grant funding from the U.S. CF Foundation. Lucas R. Hoffman receives grant funding from the U.S. CF Foundation. Kevin Alby has no conflicts of interest to report. Sean X. Zhang receives grant funding from the U.S. CF Foundation. Yvonne C. Yau receives grant funding from the U.S. CF Foundation and CF Canada. Damian G. Downey receives grants from the CF Trust and U.S. CF Foundation. He receives support from the European CF Society and U.S. CF Foundation for travel to meetings. He is the Director of the European CF Society Clinical Trials Network. Isabelle Sermet-Gaudelus receives funding from the European Cystic Fibrosis Society and the UK Cystic Fibrosis Trust. Jean-Philippe Bouchara receives funding from Vaincre la Mucoviscidose, La Pierre Le Bigaut, Association Grégory Lemarchal, and Anjou Muco. Timothy J Kidd has no conflicts of interest to report. Scott C. Bell receives grant funding from the U.S. CF Foundation, the Australian National Health and Medical Research Council, and the Medical Research Future's Fund. A. Whitney Brown is an employee of the U.S. CF Foundation.

Background: Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method., Methods: A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated., Results: Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay ( n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched., Conclusion: Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection., Competing Interests: Author HL, BH, and BY are employed by Vision Medicals Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Li, Tan, Zhang, Long, Chen, Xiang, Wu, Guo, Liu, Hu, Yang and Hu.)

Respiratory infectious disease has become ahead of all the children's diseases, with the trend of continuously increasing global incidence, antimicrobial resistance and simultaneous infection with multiple pathogens. Diagnosis of this disease is mainly based on clinical symptoms and pathogenic detection. However, there are some differences in clinical manifestations, progression and prognosis between pediatric patients and adults, which prompting clinical diagnosis mainly depending on clinical laboratory test. Therefore, fast, convenient and accurate methods are urgently needed to clarify the type of infectious pathogen and carry out differentiated treatment, and reduce the burden on families and public health-care systems in schools. This article aims to elaborate the laboratory methods of children's respiratory infectious diseases and explore the opportunities and challenges, which can provide ideas for prevention, early screening and diagnosis, prognosis and treatment monitoring.

Testing for respiratory viruses has changed greatly over the past decade, owing to advances in technology, drug development, vaccine research, and a growing recognition of the importance of improving patient access. Here, we focus on the most common respiratory viruses and review preanalytic variables (eg, collection and storage) that affect test results, testing methods including nucleic acid amplification testing (NAAT), and controversies, challenges, and trends in diagnostic testing relevant to clinicians., (Copyright © 2024 The Cleveland Clinic Foundation. All Rights Reserved.)

Background: Shotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice., Methods: We used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed., Findings: mp-tNGS and hc-tNGS took 10.3 and 16 h, respectively, with low sequencing data sizes of 0.1 M and 1 M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450 CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P < 0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS., Interpretation: tNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections., Funding: National Natural Science Foundation of China (81625014 and 82202535)., Competing Interests: Declaration of interests P.Z., Y.L., J.L., and C.H. are employees of Guangzhou KingCreate Biotechnology Co., Ltd. The other authors declare no conflicts of interest., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Introduction. Recently, the incidence of Mycoplasma pneumoniae ( M. pneumoniae ) infection in children has been increasing annually. Early differential diagnosis of M. pneumoniae infection can not only avoid the abuse of antibiotics, but also is essential for early treatment and reduction of transmission. Gap statement. The change of routine blood parameters may have important clinical significance for the diagnosis of M. pneumoniae infection, but it has not been reported so far. Aim. This study aims to establish a predictive model for M. pneumoniae infection and explore the changes and clinical value of routine blood parameters in children with M. pneumoniae infection, serving as auxiliary indicators for the diagnosis and differentiation of clinical M. pneumoniae infection. Methodology. A total of 770 paediatric patients with respiratory tract infections were enrolled in this study, including 360 in the M. pneumoniae group, 40 in the SARS-CoV-2 group, 200 in the influenza A virus group, and 170 in the control group. The differences of routine blood parameters among all groups were compared, and risk factors were analysed using multivariate logistics analysis, and the diagnostic efficacy of differential indicators using ROC curves. Results. This study revealed that Mono% (OR: 3.411; 95% CI: 1.638-7.102; P =0.001) was independent risk factor associated with M. pneumoniae infection, and Mono% (AUC=0.786, the optimal cutoff at 7.8%) had a good discriminative ability between patients with M. pneumoniae infection and healthy individuals. Additionally, Mono% (OR: 0.424; 95% CI: 0.231-0.781; P =0.006) and Lymp% (OR: 0.430; 95% CI: 0.246-0.753; P =0.003) were independent risk factors for distinguishing M. pneumoniae infection from influenza A virus infection, and the Lymp% (AUC=0.786, the optimal cutoff at 22.1%) and Net% (AUC=0.761, the optimal cutoff at 65.2%) had good discriminative abilities between M. pneumoniae infection and influenza A infection. Furthermore, platelet distribution width (OR: 0.680; 95% CI: 0.538-0.858; P =0.001) was independent risk factor for distinguishing M. pneumoniae infection from SARS-CoV-2 infection. Meanwhile, the ROC curve demonstrated that PDW (AUC=0.786, the optimal cutoff at 15%) has a good ability to differentiate between M. pneumoniae infection and SARS-CoV-2 infection. Conclusion. This study demonstrates that routine blood parameters can be used as auxiliary diagnostic indicators for M. pneumoniae infection and provide reference for the diagnosis and differentiation of clinical M. pneumoniae infection.

Background: An understanding of viral testing rates is crucial to accurately estimate the pathogen-specific hospitalisation burden. We aimed to estimate the patterns of testing for respiratory syncytial virus (RSV), influenza virus, parainfluenza virus (PIV) and human metapneumovirus (hMPV) by geographical location, age and time in children <5 years old in Western Australia., Methods: We conducted a population-based cohort study of children born between 1 January 2010 and 31 December 2021, utilising linked administrative data incorporating birth and death records, hospitalisations and respiratory viral surveillance testing records from state-wide public pathology data. We examined within-hospital testing rates using survival analysis techniques and identified independent predictors of testing using binary logistic regression., Results: Our dataset included 46,553 laboratory tests for RSV, influenza, PIV, or hMPV from 355,021 children (52.5% male). Testing rates declined in the metropolitan region over the study period (RSV testing in infants: from 242.11/1000 child-years in 2012 to 155.47/1000 child-years in 2018) and increased thereafter. Conversely, rates increased in non-metropolitan areas (e.g., RSV in Goldfields: from 364.92 in 2012 to 504.37/1000 child-years in 2021). The strongest predictors of testing were age <12 months (adjusted odds ratio [aOR] = 2.25, 95% CI 2.20-2.31), preterm birth (<32 weeks: aOR = 2.90, 95% CI 2.76-3.05) and remote residence (aOR = 0.77, 95% CI 0.73-0.81)., Conclusion: These current testing rates highlight the potential underestimation of respiratory virus hospitalisations by routine surveillance and the need for estimation of the true burden of respiratory virus admissions., (© 2024 The Author(s). Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.)

In 2023, the EBMT Practice harmonization and Guidelines Committee partnered with the EBMT Infection Diseases Working Party (IDWP) to undertake the task of delivering best practice recommendations, aiming to harmonize by expert consensus, the already existing definitions and future epidemiological and clinical studies among centers of the EBMT network. To attain this objective, a group of experts in the field was convened. The workgroup identified and discussed some critical aspects in definitions of community-acquired respiratory viruses (CARV) and adenovirus (ADV) infections in recipient of hematopoietic cell transplant (HCT). The methodology involved literature review and expert consensus. For CARV, expert consensus focused on defining infection severity, infection duration, and establishing criteria for lower respiratory tract disease (LRTD). For ADV, the expert consensus focused on surveillance methods and the definitions of ADV infection, certainty levels of disease, response to treatment, and attributable mortality. This consensus workshop provided indications to EBMT community aimed at facilitating data collection and consistency in the EBMT registry for respiratory viral infectious complications., Competing Interests: Declaration of competing interest DA: No conflict of interest to declare. AB: No conflict of interest to declare. SC: No conflict of interest to declare. RdC: Participation in advisory boards for Astra-Zeneca, Astella, Moderna and MSD. Speaker for MSD, Gilead. None of these conflicts were related to this manuscript. RG: speaking honoraria from Biotest, Pfizer, Medac, Neovii and Magenta; none of the mentioned conflicts of interest were related to financing of the content of this manuscript. For non-profit organization, she is a co-chair of the EBMT PH & G committee. PL: Participation in advisory boards for Astra-Zeneca and Moderna. Speaker for MSD. None of these conflicts were related to this manuscript. MM: No conflict of interest to declare. DN: No conflict of interest to declare. FO: Declares no conflict of interest related to this work. For non-profit organization, he is a co-chair of the EBMT PH & G committee. JLP: Declares no conflict of interest related to this work. PV: Participation in advisory boards and speaking honoraria for Gilead Sciences, Pfizer, Mundipharma, F2G and Shionogi. Honoraria were paid to my institute. None of these conflicts were related to this manuscript. ISO: Declares no conflict of interest related to this work. For non-profit organization, she is the current secretary of the EBMT PH & G committee. JS: Declares no conflict of interest related to this work. IYA: Declares no conflict of interest related to this work. For non-profit organization, he is the current chair of the EBMT PH & G committee., (Copyright © 2024. Published by Elsevier Masson SAS.)