Aetiology of lower respiratory tract infection in adults in primary care: a prospective study in 11 European countries

General Population and Healthcare Professionals' Level of Knowledge of the Burden and Prevention of Respiratory Syncytial Virus in France

Introduction

This study aimed to assess the level of knowledge among the general population and French healthcare professionals regarding respiratory syncytial virus (RSV) burden and prevention.

Methods

An online survey was conducted in the Ipsos Access Panel Online database using two questionnaires, respectively addressed to a large representative sample of the French general population, including at‐risk individuals and independent healthcare professionals. The main topics covered were epidemiology and risk groups, clinical presentations, perceived dangerousness, and attitudes towards preventive measures.

Results

In October 2022, 5000 individuals representing the French general population and 501 independent healthcare professionals, including pharmacists, physicians, and nurses, were surveyed.

Healthcare professionals acknowledge, at 60%, having limited knowledge of respiratory viruses, impacting the care and advice provided to their patients. Both caregivers and patients predominantly call for better education on the subject, leading to a rethink of seasonal awareness campaigns.

More than 90% of the French population and around two‐thirds of healthcare professionals are insufficiently aware of RSV infection.

Vaccination recommendations against respiratory viral infections are widely insufficient in the general population and among vulnerable individuals, despite the majority being willing to do so with detailed information. Eighty‐three percent of at‐risk individuals are inclined to be vaccinated against RSV to protect themselves or others.

Conclusion

The French population and healthcare professionals are insufficiently informed about RSV. Rethinking public health information campaigns will be of paramount importance considering the recently approved RSV vaccines for older adults.

Hidden in plain sight: the impact of human rhinovirus infection in adults

BACKGROUND

Human rhinovirus (HRV), a non-enveloped RNA virus, was first identified more than 70 years ago. It is highly infectious and easily transmitted through aerosols and direct contact. The advent of multiplex PCR has enhanced the detection of a diverse range of respiratory viruses, and HRV consistently ranks among the most prevalent respiratory pathogens globally. Circulation occurs throughout the year, with peak incidence in autumn and spring in temperate climates. Remarkably, during the SARS-CoV-2 pandemic, HRV transmission persisted, demonstrating its resistance to stringent public health measures aimed at curbing viral transmission.

MAIN BODY

HRV is characterised by its extensive genetic diversity, comprising three species and more than 170 genotypes. This diversity and substantial number of concurrently circulating strains allows HRVs to frequently escape the adaptive immune system and poses formidable challenges for the development of effective vaccines and antiviral therapies. There is currently a lack of specific treatments. Historically, HRV has been associated with self-limiting upper respiratory infection. However, there is now extensive evidence highlighting its significant role in severe lower respiratory disease in adults, including exacerbations of chronic airway diseases, such as asthma and chronic obstructive pulmonary disease (COPD), as well as pneumonia. These severe manifestations can occur even in immunocompetent individuals, broadening the clinical impact of this ubiquitous virus. Consequently, the burden of rhinovirus infections extends across various healthcare settings, from primary care to general hospital wards and intensive care units. The impact of HRV in adults, in terms of morbidity and healthcare utilisation, rivals that of the other major respiratory viruses, including influenza and respiratory syncytial virus. Recognition of this substantial burden underscores the critical need for novel treatment strategies and effective management protocols to mitigate the impact of HRV infections on public health.

CONCLUSION

This review examines the epidemiology, clinical manifestations, and risk factors associated with severe HRV infection in adults. By drawing on contemporary literature, we aim to provide a comprehensive overview of the virus's significant health implications. Understanding the scope of this impact is essential for developing new, targeted interventions and improving patient outcomes in the face of this persistent and adaptable pathogen.

Antibiotic susceptibility of pathogens isolated in respiratory tract samples of recently hospitalized patients

Community-acquired lower respiratory tract infections (CA-LRTIs) treatment is largely empirical as microbiologic testing is rarely performed. Here, we provide microbiologic data of severe CA-LRTI cases requiring hospitalization. We aim to describe the distribution and susceptibility patterns of pathogens causing severe CA-LRTI. We analyzed respiratory samples from recently admitted patients with CA-LRTIs to assess pathogen distribution and antibiotic susceptibility patterns. We divided patients into three groups: CA-LRTI and no prior healthcare exposure, CA-LRTI with healthcare exposure, and patients diagnosed with LRTI 48 to 7 days of hospital admission. In a sub-cohort, we assessed the bacteria's susceptibility to cefditoren. A total of 1,395, 2,212, and 2,760 samples were included in the three study groups. Gram-negative bacteria were the most common bacteria isolated. Streptococcus pneumoniae was over-represented in patients admitted to the intensive care unit (ICU) in the first two study groups, and was fully susceptible to penicillin in only ~50% of cases, and to fluoroquinolones and third-generation cephalosporins including cefditoren in >95% of cases. Susceptibility of Gram-negative bacteria to penicillins and to second-generation cephalosporins was lower than 50%. Age, admission to an ICU or surgical department, healthcare-associated infections, and infections with Gram-negative bacteria, Staphylococcus aureus, and Stenotrophomonas/Acinetobacter baumannii were associated with increased mortality. These results highlight pathogen diversity and concerning antibiotic susceptibility patterns in LRTI. These findings emphasize the importance of improving diagnostics and addressing antibiotic resistance in the effective management of LRTI.IMPORTANCEThis survey aims to describe the microbiologic aspects of community-acquired lower respiratory tract infections (CA-LRTI) in a large cohort of patients recently admitted to hospital. In a small sub-study, we assessed antibiotic susceptibility to cefditoren, an oral third-generation cephalosporin not used in Israel. By analyzing specimens from recently admitted patients with CA-LRTI, we aim to provide physicians with the relevant microbiologic data of the more severe CA-LRTI cases, i.e., those that resulted in hospital admission. Such microbiological data would provide primary care and emergency room physicians with additional insights as to the causative agents of severe CA-LRTI.

Metagenomic next-generation sequencing on treatment strategies and prognosis of patients with lower respiratory tract infections: A systematic review and meta-analysis

OBJECTIVES

Controversy exists regarding the benefits of metagenomic next-generation sequencing (mNGS) in lower respiratory tract infections (LRTIs). We assessed the impact of mNGS on the treatment and prognosis of LRTI patients through a systematic review and meta-analysis.

METHODS

A literature search was conducted in PubMed, Embase, and CENTRAL databases up to 19 February 2024. Studies investigating the clinical value of mNGS in patients with LRTIs were included. The Risk-of-Bias Tool for randomized controlled trials and the Newcastle-Ottawa scale for observational studies were used to assess risk of bias. Antibiotic change rates and prognostic outcomes were evaluated using random-effects analyses with 95% confidence intervals (CIs). This study is registered with PROSPERO, CRD42024509738.

RESULTS

Twelve studies were included in the meta-analysis. The use of mNGS was associated with a higher rate of antibiotic change (odds ratio, 2.47; 95% CI, 1.42-4.28; P < 0.01). Consistent findings were observed in adults, patients with severe LRTIs, and in those who underwent mNGS testing exclusively on bronchoalveolar lavage fluid. We also observed a reduction in in-hospital mortality (odds ratio, 0.49; 95% CI, 0.36-0.67; P < 0.01), though no significant impact on length of hospital stay was observed (mean difference, -1.79; 95% CI, -5.20 -1.63; P = 0.31).

CONCLUSIONS

This meta-analysis indicates that the application of mNGS may lead to changes in antibiotic prescriptions for patients with LRTIs, and might reduce the risk of mortality. However, large-scale randomized controlled clinical trials are urgently needed to validate the findings of this study.

Diagnostic value of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

BACKGROUND

Current diagnostic methods of lower respiratory tract infections (LRTIs) often lack specificity, underscoring the necessity for advanced technologies such as metagenomic next-generation sequencing (mNGS).

METHODS

This retrospective study compared bronchoalveolar lavage fluid (BALF) analysis using mNGS and conventional microbiological tests (CMT) to evaluate their effectiveness in pathogen identification and alignment with clinical diagnoses.

RESULTS

In this study involving 369 patients suspected of LTRIs, mNGS identified pathogens in 342 cases (92.7%), showing superior diagnostic performance compared to CMT (58.8%). The positive agreement and negative agreement rates of mNGS were 92.7% and 96.3%, respectively, both significantly higher than those of CMT (both p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were significantly higher than those of CMT, with values of 99.7% vs. 57.1%, 68.4% vs. 26.3%, 96.5% vs. 87.1%, and 96.3% vs. 6.3%, respectively (all p<0.001). Pathogen detection rates among the patients showed that 89.7% had evidence of LRTIs, with bacterial infections (20.1%), mycoplasma (13.6%), mycobacterium (4.3%), fungal (4.1%), viral (3.3%), and mixed infections (44.4%) being the most common. Furthermore, the study also differentiated the distribution of pathogens between adults and pediatric patients, and assessed the impact of pathogen types on severe outcomes using multivariate logistic regression, revealing that viral and fungal infections were more likely associated with severe symptoms, whereas mycoplasma infections typically presented with milder symptoms.

CONCLUSIONS

BALF mNGS proves effective for rapid, comprehensive pathogen detection in LRTIs, warranting its early use for enhanced diagnosis and management, especially across different age groups.

How likely is it that a virus or bacteria is causing a patient's symptoms? A new approach to interpret the outcome from multi-pathogen PCR

BACKGROUND

Whether a detected virus or bacteria is a pathogen that may require treatment, or is merely a commensal 'passenger', remains confusing for many infections. This confusion is likely to increase with the wider use of multi-pathogen PCR.

OBJECTIVES

To propose a new statistical procedure to analyse and present data from case-control studies clarifying the probability of causality.

METHODS

We conducted a case-control study in US outpatient settings that enrolled patients aged 18 to 75 years with acute lower respiratory tract infection and controls without respiratory symptoms. Patients underwent multi-pathogen PCR testing. The positive etiologic predictive value was calculated to estimate the probability that each potential pathogen was the cause of symptoms. The outcome was illustrated using a modified forest plot and by classifying pathogens into five categories clarifying the probability for causality.

RESULTS

We enrolled 618 adult cases and 497 asymptomatic controls. The modified forest plot and the classification of risk for causality aimed to facilitate understanding. Pathogens likely to be causative when present included influenza A and B, SARS-CoV-2, rhinovirus, and parainfluenza viruses, while Staphylococcus aureus is almost always commensal. Broad confidence intervals for the positive etiologic predictive value made it difficult to draw conclusions for potential pathogens with low prevalence.

CONCLUSION

This pilot study shows that the proposed statistical approach is likely to be practical for analysing larger case-control studies or for a meta-analysis of multiple studies. This method may help when interpreting the results from multi-pathogen PCR.

A new pathogen pattern of acute respiratory tract infections in primary care after COVID-19 pandemic: a multi-center study in southern China

BACKGROUND

After the coronavirus disease 2019 (COVID-19) pandemic, no studies on bacterial and atypical pathogens were conducted in primary care. We aimed to describe the etiological composition of acute respiratory tract infections (ARTIs) presenting to primary care with limited resources after the pandemic.

METHODS

1958 adult patients with ARTIs from 17 primary care clinics were recruited prospectively from January 2024 to March 2024. 17 and 62 pathogens in throat swab samples were tested using polymerase chain reaction (PCR) and targeted next-generation sequencing (tNGS), respectively. We analyzed the pathogen spectrum and co-infectious pattern of viral, bacterial or atypical pathogens. Then, the associations between clinical characteristics and pathogens were investigated.

RESULTS

In PCR test, the positive rate of any pathogens was 80.3%, consisting of 60.2% for viruses, 41.8% for bacteria and 21.7% for viral-bacterial co-infection. In tNGS test, the positive rate was 89.1%, consisting of 64.7% for viruses, 55.2% for bacteria and 30.9% for viral-bacterial co-infection. Influenza virus B (18.2%), influenza virus A (16.8%) and severe acute respiratory syndrome coronavirus 2 (14.1%) were the three leading viral pathogens, and H. influenzae (36.1%), S. anginosus (15.7%) and S. pneumoniae (8.4%) were the three leading bacterial pathogens. Few M. pneumoniae (1.6%) were detected. The mixed bacterial or mixed viral-bacterial co-infections were the most common co-infectious patterns. The mixed bacterial or mixed viral-bacterial co-infections were the most common co-infectious patterns. Overall, patients with viral infection or viral-bacterial co-infection had more clinical symptoms, and patients with bacterial infection had higher inflammatory indicators.

CONCLUSIONS

After the COVID-19 pandemic, the main viral pathogens of ARTIs were unevenly distributed, and less bacterial and atypical pathogens were detected in primary care. The microbiological evidences can optimize the precision diagnosis and treatment of ARTIs in primary care with limited resources.

Analysis of the potentially pathogenic bacteria of lower respiratory tract infections in children per-, during and post-COVID-19: a retrospective study

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has caused significant changes in lower respiratory tract infections (LRTIs). This study aimed to characterize potentially pathogenic bacterial infections in paediatric patients hospitalized for LRTIs per-, during and post-COVID-19.

METHODS

Sputum culture data from 85,659 children with LRTIs at the Children's Hospital of Soochow University from January 2016 to May 2024 were analyzed for eight bacteria: Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. The data during the pandemic (2020-2022, during COVID-19) and after the pandemic (January 2023-May 2024, post-COVID-19) were compared with those before the pandemic (2016-2019).

RESULTS

Overall, 85,659 children with LRTIs were enrolled. Of these, 42,567 cases (49.7%) were diagnosed in the pre-COVID-19 period, 22,531 cases (26.3%) during the COVID-19 period and 20,561 cases (24.0%) in the post-COVID-19 period. The overall positive rate for pathogenic bacteria was 37.1%, with the top three being S. pneumoniae (14.5%), H. influenzae (12.1%) and S. aureus (6.5%). Compared to the average pre-COVID-19 levels, the bacterial pathogen positive rate decreased by 3.5% during the COVID-19 period (OR: 0.94, 95% CI: 0.91-0.98) and by 23.4% in the post-COVID-19 period (OR: 0.66, 95% CI: 0.64-0.69). During the COVID-19 period, the positive rates for S. pneumoniae, H. influenzae, E. coli, K. pneumoniae and mixed infections decreased by 11.7%, 35.3%, 22.2%, 33.3% and 45.7% respectively, while the positive rates for S. aureus, M. catarrhalis and P. aeruginosa increased by 21.7%, 44.7% and 25% respectively. In the post-COVID-19 period, the positive rates for S. pneumoniae, H. influenzae, E. coli, P. aeruginosa, K. pneumoniae, A. baumannii and mixed infections decreased by 50.0%, 7.4%, 22.2%, 50.0%, 44.4%, 60.0% and 32.6% respectively, while there was no statistical change in the positive rates for S. aureus and M. catarrhalis. Bacteria case detection decreases in 2020 (67.0%), 2021 (60.5%), 2022 (76.3%) and 2023 (72.7%) compared to predicted cases.

CONCLUSIONS

Measures to restrict COVID-19 as a driver of declining bacterial positive rates. Respiratory bacteria in children are change across COVID-19 phases, age groups and seasons. After COVID-19, clinicians should continue to increase surveillance for pathogenic bacteria, especially drug-resistant flora.

Persistent microbial infections and idiopathic pulmonary fibrosis - an insight into non-typeable Haemophilus influenza pathogenesis

Interstitial lung disease (ILD) is characterized by chronic inflammation and scarring of the lungs, of which idiopathic pulmonary fibrosis (IPF) is the most devastating pathologic form. Idiopathic pulmonary fibrosis pathogenesis leads to loss of lung function and eventual death in 50% of patients, making it the leading cause of ILD-associated mortality worldwide. Persistent and subclinical microbial infections are implicated in the acute exacerbation of chronic lung diseases. However, while epidemiological studies have highlighted pollutants, gastric aspirate, and microbial infections as major causes for the progression and exacerbation of IPF, the role of persistent microbial infections in the pathogenesis of IPF remains unclear. In this review, we have focused on the role of persistent microbial infections, including viral, bacterial, and fungal infections, and their mechanisms of action in the pathogenesis of IPF. In particular, the mechanisms and pathogenesis of the Gram-negative bacteria Non-typeable Haemophilus influenzae (NTHi) in ILDs are discussed, along with growing evidence of its role in IPF, given its unique ability to establish persistent intracellular infections by leveraging its non-capsulated nature to evade host defenses. While antibiotic treatments are presumably beneficial to target the extracellular, interstitial, and systemic burden of pathogens, their effects are significantly reduced in combating pathogens that reside in the intracellular compartments. The review also includes recent clinical trials, which center on combinatorial treatments involving antimicrobials and immunosuppressants, along with antifibrotic drugs that help mitigate disease progression in IPF patients. Finally, future directions focus on mRNA-based therapeutics, given their demonstrated effectiveness across a wide range of clinical applications and feasibility in targeting intracellular pathogens.

Multicenter Evaluation of the QIAstat-Dx and the BioFire Multiplex Panel Tests for the Detection of Respiratory Pathogens

Syndromic multiplex panel testing enables simultaneous detection of multiple respiratory pathogens, but limited data is available on the comparative diagnostic performance of different testing systems. In this multicenter prospective study, we aimed to compare the QIAstat-Dx Respiratory Panel 2.0 (QIAstat-Dx-RP2.0) with the widely used BioFire-RP2.1, using 269 respiratory clinical specimens. Concordant test results were obtained in 232 (86.3%) cases. Discordant test results included 33 BioFire-RP2.1(+)/QIAstat-Dx-RP2.0(-) and 4 BioFire-RP2.1(-)/QIAstat-Dx-RP2.0(+) results. Discordant samples showed significantly lower pathogen loads than concordant ones (p < 0.01). Overall, the QIAstat-Dx-RP2.0 showed an analytical sensitivity of 50%-100% depending on the respiratory target, with an analytical specificity ≥ 99.0%. Most significant differences were found for the detection of adenovirus, human coronaviruses, respiratory syncytial virus, human rhinovirus/enterovirus and SARS-CoV-2 (kappa-score: 0.67-0.91). Co-detections of respiratory pathogens were identified in 47 cases by BioFire-RP2.1 and 29 by QIAstat-Dx-RP2.0. Agreement rates between the two multiplex panel tests decreased from 91.8% for single pathogen detections to 65.0% and 42.9% for co-detecting two and three pathogens, respectively. Pathogen loads were significantly lower in co-detections compared to single pathogen detections (p < 0.01), potentially explaining the lower detection rates with the QIAstat-Dx-RP2.0 in cases of multiple pathogens. In conclusion, our prospective multicenter evaluation showed good diagnostic performance of the QIAstat-Dx-RP2.0 assay, but lower detection rates for some respiratory targets compared to BioFire-RP2.1. As QIAstat-Dx-RP2.0 offers advantages in handling, noise emission, cost effectiveness, and provides semi-quantitative results compared to BioFire-RP2.1 an updated version with enhanced analytical sensitivity would be a viable alternative syndromic testing system for detecting respiratory pathogens.

Estimating the burden of vaccine-preventable lower respiratory tract disease in UK primary care: protocol for a prospective surveillance study (AvonCAP GP2)

BACKGROUND

The true burden of acute lower respiratory tract disease (aLRTD; includes acute lower respiratory tract infection [aLRTI] and presumed non-infective exacerbations of chronic lung disease and heart failure) among adults presenting to primary care, and the proportion that are potentially vaccine preventable is unknown.

AIM

To describe aLRTD incidence in adults presenting to primary care; estimate proportions caused by respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Streptococcus pneumoniae (SP); and investigate disease burden from patient and NHS perspectives.

DESIGN & SETTING

Primary care prospective cohort study conducted in six representative general practices (total ∼86 000 registered adults) in Bristol, UK.

METHOD

Adults (aged ≥18 years) registered at participating general practices and presenting to primary care (in-hours or out-of-hours) or emergency department (if not admitted) with aLRTD will be eligible. They will be identified by real-time primary care record searches. Researchers will screen electronic GP records, including free text, contact patients to assess eligibility, and offer enrolment in a surveillance study and an enhanced diagnostic study (urine, saliva, and respiratory samples; physical examination; and symptom diaries). Data will be collected for all aLRTD episodes, with patients assigned to one of three arms: surveillance; embedded diagnostic; and descriptive dataset. Outcome measures will include clinical and pathogen-defined aLRTD incidence rates, symptom severity and duration, NHS contacts and costs, health-related quality-of-life changes, and mortality (≤30 days post-identification).

CONCLUSION

This comprehensive surveillance study of adults presenting to primary care with aLRTD, with embedded detailed data and sample collection, will provide an accurate assessment of aLRTD burden due to vaccine-preventable infections.

Triggering Toll-Like Receptor 5 Signaling During Pneumococcal Superinfection Prevents the Selection of Antibiotic Resistance

Toll-like receptor 5 (TLR5) signaling plays a key role in antibacterial defenses. We previously showed that respiratory administration of flagellin, a potent TLR5 agonist, in combination with amoxicillin (AMX) improves the treatment of primary pneumonia or superinfection caused by AMX-sensitive or AMX-resistant Streptococcus pneumoniae. Here, the impact of adjunct flagellin therapy on antibiotic dose/regimen and the selection of antibiotic-resistant S. pneumoniae was investigated using superinfection with isogenic antibiotic-sensitive and antibiotic-resistant bacteria and population dynamics analysis. Our findings demonstrate that flagellin allows for a 200-fold reduction in the antibiotic dose, achieving the same therapeutic effect observed with antibiotic alone. Adjunct treatment also reduced the selection of antibiotic-resistant bacteria in contrast to the antibiotic monotherapy. A mathematical model was developed that captured the population dynamics and estimated a 20-fold enhancement immune-modulatory factor on bacterial clearance. This work paves the way for the development of host-directed therapy and refinement of treatment by modeling.

Supporting vaccine (co)-administration decisions: Development and validation of a tool for assessing the risk of severe outcomes due to lower respiratory tract infections

OBJECTIVE

To develop and validate a score to predict the 90-day risk of hospitalization/death in patients with low respiratory tract infections (LRTIs) with the aim to support clinical decision making on vaccine (co)-administration.

METHODS

We formed a cohort of patients aged 18 years or older being diagnosed with LRTIs in the period between January 1, 2012 and December 31, 2022. Each patient was followed until occurrence of respiratory-related hospitalization/death up to the end of the study period (December 31, 2022). Along with age and sex, forty determinants were adopted to assemble the respiratory tract infection (RTI)-Health Search (HS) core using the development sub-cohort. The prediction accuracy of the score was therefore assessed in the validation sub-cohort.

RESULTS

We identified 252,319 patients being diagnosed with LRTIs (females: 54.7 %; mean age: 60 (SD:18.1)). When the risk of LRTIs-related hospitalizations/deaths was estimated via RTI-HScore, its predicted value was equal to 1.4 % over a 90-day event horizon. The score showed explained variation and discrimination accuracy were equal to 45 % (95 % CI: 44-47 %) and 81 % (95 % CI: 79-84 %), respectively. The calibration slope did not significantly differ from the unit (p = 0.8314).

CONCLUSIONS

The RTI-HScore was featured by good accuracy for prediction of LRTIs-related complications over a 90-day follow-up. Such a tool might therefore support general practitioners to enhance patients' care by facilitating approaches for (co)-administration of vaccines for respiratory infections through a score-based decision support system.

Literature review on micro-organisms from domestic goats potentially causing human pneumonia

Background: In the Netherlands, living in proximity to goat farms has been consistently associated with an increased incidence of community-acquired pneumonia (CAP). The cause remains largely unknown though airborne microbial agents could play a role. Objective: The aim of this study is to explore micro-organisms present in goats that can cause human pneumonia. Methods: An extensive literature review was conducted to identify all micro-organisms detected in goats that are associated with human pneumonia. Additionally, the identified micro-organisms were prioritized using a self-developed scoring system and expert opinion. Results: Through extensive literature review, 4309 references describing 302 different micro-organisms in goats or on goat farms were identified. Additional searches and reviews for human respiratory disease caused by each of these micro-organisms yielded a final list of 76 bacteria, 7 viruses, 7 fungi, and 6 protozoa. They were assigned scores based on pneumonia type, diagnosis of respiratory disease, patient immune status, and evidence strength. Based on these scores, the most likely potential causal micro-organisms included Moraxella spp. Chlamydia psittaci, Staphylococcus aureus, and Streptococcus pneumoniae. Subsequently, the list of micro-organisms was reviewed by external experts on their perceived likelihood of the organism causing this CAP. Conclusion: Results of this literature study can give insight into the possible causes of pneumonia. Nonetheless, no unambiguous conclusion on the actual cause of the increased CAP risk around goat farms can be drawn solely based on these results.

The optimal antibiotic treatment duration for community-acquired pneumonia in adults diagnosed in general practice in Denmark (CAP-D): an open-label, pragmatic, randomised controlled trial

BACKGROUND

Use of antibiotics is the main driver of antimicrobial resistance which is considered one of the biggest threats to human health. In Denmark, most antibiotics are prescribed in general practice. Acute lower respiratory tract infections, including community-acquired pneumonia (CAP), are among the most frequent indications for antibiotic prescribing. Phenoxymethylpenicillin is established as first-line treatment in general practice in Denmark. However, the treatment duration with phenoxymethylpenicillin is mostly based on traditions. Both 5 and 7 days of treatment is recommended in Danish guidelines, and when asking the general practitioners about what treatment duration, they prescribe the variation is even bigger. Several hospital-based studies have proven short course (≤ 6 days) antibiotic treatment non-inferior to long course (≥ 7 days) treatment of CAP. No evidence exists on the optimal treatment duration for CAP in non-hospitalised patients. This randomised controlled trial aim to investigate the optimal treatment duration with phenoxymethylpenicillin for CAP in adults diagnosed in general practice in Denmark.

METHODS

This is an open-label, pragmatic, randomised controlled, five-arm DURATIONS trial. Participants will be recruited from at least 24 general practices in Denmark. Eligible participants are adults, with no pre-existing lung disease, presenting with symptoms of CAP, and in whom the general practitioner finds it relevant to treat with antibiotics. The study will compare treatment with phenoxymethylpenicillin 1.2 MIE q.i.d. in 3, 4, 5, 6, and 7 days.

DISCUSSION

This study will provide evidence for the optimal antibiotic treatment duration of CAP in general practice and inform future guidelines on CAP in all countries using phenoxymethylpenicillin for the treatment of acute respiratory tract infections in adults. The results of this study might also be used to guide treatment recommendations in other countries using phenoxymethylpenicillin. Moreover, a (potential) reduction in antibiotic use might lower the development of antimicrobial resistance, increase patient treatment adherence, reduce risks of adverse events, and lower the economical exp TRIAL REGISTRATION: ClinicalTrials.gov: NCT06295120. Registered 28 February 2024.  The Scientific Ethics Committee for the North Denmark Region: N-20230039.

Cost-Effectiveness Analysis of Routine Childhood Immunization with 20-Valent versus 15-Valent Pneumococcal Conjugate Vaccines in Germany

This study aimed to evaluate the cost-effectiveness of routine childhood immunization with the 20-valent pneumococcal conjugate vaccine (PCV20) in a four-dose regimen (3 + 1 schedule) versus the 15-valent PCV (PCV15/V114) in a three-dose regimen (2 + 1) in Germany. The study utilized a decision-analytic Markov model to estimate lifetime costs and effectiveness outcomes for a single birth cohort in Germany. The model tracked the incidence of acute pneumococcal infections and long-term pneumococcal meningitis sequelae for both vaccination strategies. The vaccine effectiveness data were derived from published clinical trials and observational studies of PCV7 and PCV13. Indirect effects, such as herd protection and serotype replacement, were included in the model. The model adopted a societal perspective, including direct medical, direct non-medical, and indirect costs. Scenario and sensitivity analyses were performed. In the base case, PCV20 prevented more pneumococcal disease cases and deaths, with an expected gain of 96 quality-adjusted life years (QALYs) compared to V114. However, PCV20 was associated with a total incremental cost of EUR 48,358,424, resulting in an incremental cost-effectiveness ratio (ICER) of EUR 503,620/QALY. Most of the scenario and sensitivity analyses estimated that the ICER for PCV20 exceeded EUR 150,000/QALY. Routine childhood immunization with PCV20 instead of V114 may not be an economically efficient use of healthcare resources in Germany.

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.

Global Epidemiology and Seasonality of Human Seasonal Coronaviruses: A Systematic Review

Background

We characterized the global epidemiology and seasonality of human coronaviruses (HCoVs) OC43, NL63, 229E, and HKU1.

Methods

In this systematic review, we searched MEDLINE, EMBASE, Web of Science, SCOPUS, CINAHL, and backward citations for studies published until 1 September 2023. We included studies with ≥12 months of consecutive data and tested for ≥1 HCoV species. Case reports, review articles, animal studies, studies focusing on SARS-CoV-1, SARS-CoV-2, and/or Middle East respiratory syndrome, and those including <100 cases were excluded. Study quality and risk of bias were assessed using Joanna Briggs Institute Critical Appraisal Checklist tools. We reported the prevalence of all HCoVs and individual species. Seasonality was reported for studies that included ≥100 HCoVs annually. This study is registered with PROSPERO, CRD42022330902.

Results

A total of 201 studies (1 819 320 samples) from 68 countries were included. A high proportion were from China (19.4%; n = 39), whereas the Southern Hemisphere was underrepresented. Most were case series (77.1%, n = 155) with samples from secondary care (74.1%, n = 149). Seventeen (8.5%) studies included asymptomatic controls, whereas 76 (37.8%) reported results for all 4 HCoV species. Overall, OC43 was the most prevalent HCoV. Median test positivity of OC43 and NL63 was higher in children, and 229E and HKU1 in adults. Among 18 studies that described seasonality (17 from the Northern Hemisphere), circulation of all HCoVs mostly peaked during cold months.

Conclusions

In our comprehensive review, few studies reported the prevalence of individual HCoVs or seasonality. Further research on the burden and circulation of HCoVs is needed, particularly from Africa, South Asia, and Central/South America.

Nasal sprays and behavioural interventions compared with usual care for acute respiratory illness in primary care: a randomised, controlled, open-label, parallel-group trial

BACKGROUND

A small amount of evidence suggests that nasal sprays, or physical activity and stress management, could shorten the duration of respiratory infections. This study aimed to assess the effect of nasal sprays or a behavioural intervention promoting physical activity and stress management on respiratory illnesses, compared with usual care.

METHODS

This randomised, controlled, open-label, parallel-group trial was done at 332 general practitioner practices in the UK. Eligible adults (aged ≥18 years) had at least one comorbidity or risk factor increasing their risk of adverse outcomes due to respiratory illness (eg, immune compromise due to serious illness or medication; heart disease; asthma or lung disease; diabetes; mild hepatic impairment; stroke or severe neurological problem; obesity [BMI ≥30 kg/m2]; or age ≥65 years) or at least three self-reported respiratory tract infections in a normal year (ie, any year before the COVID-19 pandemic). Participants were randomly assigned (1:1:1:1) using a computerised system to: usual care (brief advice about managing illness); gel-based spray (two sprays per nostril at the first sign of an infection or after potential exposure to infection, up to 6 times per day); saline spray (two sprays per nostril at the first sign of an infection or after potential exposure to infection, up to 6 times per day); or a brief behavioural intervention in which participants were given access to a website promoting physical activity and stress management. The study was partially masked: neither investigators nor medical staff were aware of treatment allocation, and investigators who did the statistical analysis were unaware of treatment allocation. The sprays were relabelled to maintain participant masking. Outcomes were assessed using data from participants' completed monthly surveys and a survey at 6 months. The primary outcome was total number of days of illness due to self-reported respiratory tract illnesses (coughs, colds, sore throat, sinus or ear infections, influenza, or COVID-19) in the previous 6 months, assessed in the modified intention-to-treat population, which included all randomly assigned participants who had primary outcome data available. Key secondary outcomes were possible harms, including headache or facial pain, and antibiotic use, assessed in all randomly assigned participants. This trial was registered with ISRCTN, 17936080, and is closed to recruitment.

FINDINGS

Between Dec 12, 2020, and April 7, 2023, of 19 475 individuals screened for eligibility, 13 799 participants were randomly assigned to usual care (n=3451), gel-based nasal spray (n=3448), saline nasal spray (n=3450), or the digital intervention promoting physical activity and stress management (n=3450). 11 612 participants had complete data for the primary outcome and were included in the primary outcome analysis (usual care group, n=2983; gel-based spray group, n=2935; saline spray group, n=2967; behavioural website group, n=2727). Compared with participants in the usual care group, who had a mean of 8·2 (SD 16·1) days of illness, the number of days of illness was significantly lower in the gel-based spray group (mean 6·5 days [SD 12·8]; adjusted incidence rate ratio [IRR] 0·82 [99% CI 0·76-0·90]; p<0·0001) and the saline spray group (6·4 days [12·4]; 0·81 [0·74-0·88]; p<0·0001), but not in the group allocated to the behavioural website (7·4 days [14·7]; 0·97 [0·89-1·06]; p=0·46). The most common adverse event was headache or sinus pain in the gel-based group: 123 (4·8%) of 2556 participants in the usual care group; 199 (7·8%) of 2498 participants in the gel-based group (risk ratio 1·61 [95% CI 1·30-1·99]; p<0·0001); 101 (4·5%) of 2377 participants in the saline group (0·81 [0·63-1·05]; p=0·11); and 101 (4·5%) of 2091 participants in the behavioural intervention group (0·95 [0·74-1·22]; p=0·69). Compared with usual care, antibiotic use was lower for all interventions: IRR 0·65 (95% CI 0·50-0·84; p=0·001) for the gel-based spray group; 0·69 (0·45-0·88; p=0·003) for the saline spray group; and 0·74 (0·57-0·94; p=0·02) for the behavioural website group.

INTERPRETATION

Advice to use either nasal spray reduced illness duration and both sprays and the behavioural website reduced antibiotic use. Future research should aim to address the impact of the widespread implementation of these simple interventions.

FUNDING

National Institute for Health and Care Research.

Rapid respiratory microbiological point-of-care-testing and antibiotic prescribing in primary care: Protocol for the RAPID-TEST randomised controlled trial

BACKGROUND

Antibiotics are prescribed for over 50% of respiratory tract infections in primary care, despite good evidence of there being no benefit to the patient, and evidence of over prescribing driving microbial resistance. The high treatment rates are attributed to uncertainty regarding microbiological cause and clinical prognosis. Point-of-care-tests have been proposed as potential antibiotic stewardship tools, with some providing microbiological results in 15 minutes. However, there is little research on their impact on antibiotic use and clinical outcomes in primary care.

METHODS

This is a multi-centre, individually randomised controlled trial with mixed-methods investigation of microbial, behavioural and antibiotic mechanisms on outcomes in patients aged 12 months and over presenting to primary care in the UK with a suspected respiratory tract infection, where the clinician and/or patient thinks antibiotic treatment may be, or is, necessary. Once consented, all participants are asked to provide a combined nose and throat swab sample and randomised to have a rapid microbiological point-of-care-test or no point-of-care-test. For intervention patients, clinicians review the result of the test, before contacting the patient to finalise treatment. Treatment decisions are made as per usual care in control group patients. The primary outcome is whether an antibiotic is prescribed at this point. All swab samples are sent to the central laboratory for further testing. Patients are asked to complete a diary to record the severity and duration of symptoms until resolution or day 28, and questionnaires at 2 months about their beliefs and intention to consult for similar future illnesses. Primary care medical records are also reviewed at 6-months to collect further infection consultations, antibiotic prescribing and hospital admissions. The trial aims to recruit 514 patients to achieve 90% power with 5% significance to detect a 15% absolute reduction in antibiotic prescribing. Qualitative interviews are being conducted with approximately 20 clinicians and 30 participants to understand any changes in beliefs and behaviour resulting from the point-of-care-test and generate attributes for clinician and patient discrete choice experiments.

DISCUSSION

This trial will provide evidence of efficacy, acceptability and mechanisms of action of a rapid microbiological point-of-care test on antibiotic prescribing and patient symptoms in primary care.

TRIAL REGISTRATION

ISRCTN16039192, prospectively registered on 08/11/2022.

Surveillance of pneumococcal serotypes in adults hospitalised with acute lower respiratory tract infection in Bristol, UK

INTRODUCTION

Pneumococcus remains a major cause of adult lower respiratory tract infections (LRTI). Few data exist on the relative contribution of serotypes included in pneumococcal vaccines to community-acquired pneumonia (CAP) and non-pneumonic (NP) LRTI. We measured the burden of all and vaccine-serotype pneumococcal respiratory infection following SARS-CoV-2 emergence to inform evidence-based vaccination policy.

METHODS

A prospective cohort study at two Bristol hospitals (UK) including all adults age ≥ 18-years hospitalised with acute lower respiratory tract disease (aLRTD) from Nov2021-Nov2022. LRTI patients were classified as: a) radiographically-confirmed CAP (CAP+/RAD+), b) clinically-diagnosed CAP without radiological confirmation (CAP+/RAD-), or c) NP-LRTI. Pneumococcus was identified by blood culture, BinaxNOW™and serotype-specific urine antigen detection assays (UAD).

RESULTS

Of 12,083 aLRTD admissions, 10,026 had LRTI and 2,445 provided urine: 1,097 CAP + RAD+; 207 CAP + RAD-; and 1,141 NP-LRTI. Median age was 71.1y (IQR57.9-80.2) and Charlson comorbidity index = 4 (IQR2-5); 2.7 % of patients required intensive care, and 4.4 % died within 30-days of hospitalisation. Pneumococcus was detected in 280/2445 (11.5 %) participants. Among adults aged ≥ 65y and 18-64y, 12.9 % (198/1534) and 9.0 % (82/911), respectively, tested pneumococcus positive. We identified pneumococcus in 165/1097 (15.0 %) CAP + RAD+, 23/207 (11.1 %) CAP + RAD-, and 92/1141 (8.1 %) NP-LRTI cases. Of the 280 pneumococcal cases, 102 (36.4 %) were due to serotypes included in PCV13 + 6C, 115 (41.7 %) in PCV15 + 6C, 210 (75.0 %) in PCV20 + 6C/15C and 228 (81.4 %) in PPV23 + 15C. The most frequently identified serotypes were 8 (n = 78; 27.9 % of all pneumococcus), 7F (n = 25; 8.9 %), and 3 (n = 24; 8.6 %).

DISCUSSION

Among adults hospitalised with respiratory infection, pneumococcus is an important pathogen across all subgroups, including CAP+/RAD- and NP-LRTI. Despite 20-years of PPV23 use in adults ≥ 65-years and herd protection due to 17-years of PCV use in infants, vaccine-serotype pneumococcal disease still causes a significant proportion of LRTI adult hospitalizations. Direct adult vaccination with high-valency PCVs may reduce pneumococcal disease burden.

PLUS-IS-LESS project: Procalcitonin and Lung UltraSonography-based antibiotherapy in patients with Lower rESpiratory tract infection in Swiss Emergency Departments: study protocol for a pragmatic stepped-wedge cluster-randomized trial

BACKGROUND

Lower respiratory tract infections (LRTIs) are among the most frequent infections and a significant contributor to inappropriate antibiotic prescription. Currently, no single diagnostic tool can reliably identify bacterial pneumonia. We thus evaluate a multimodal approach based on a clinical score, lung ultrasound (LUS), and the inflammatory biomarker, procalcitonin (PCT) to guide prescription of antibiotics. LUS outperforms chest X-ray in the identification of pneumonia, while PCT is known to be elevated in bacterial and/or severe infections. We propose a trial to test their synergistic potential in reducing antibiotic prescription while preserving patient safety in emergency departments (ED).

METHODS

The PLUS-IS-LESS study is a pragmatic, stepped-wedge cluster-randomized, clinical trial conducted in 10 Swiss EDs. It assesses the PLUS algorithm, which combines a clinical prediction score, LUS, PCT, and a clinical severity score to guide antibiotics among adults with LRTIs, compared with usual care. The co-primary endpoints are the proportion of patients prescribed antibiotics and the proportion of patients with clinical failure by day 28. Secondary endpoints include measurement of change in quality of life, length of hospital stay, antibiotic-related side effects, barriers and facilitators to the implementation of the algorithm, cost-effectiveness of the intervention, and identification of patterns of pneumonia in LUS using machine learning.

DISCUSSION

The PLUS algorithm aims to optimize prescription of antibiotics through improved diagnostic performance and maximization of physician adherence, while ensuring safety. It is based on previously validated tests and does therefore not expose participants to unforeseeable risks. Cluster randomization prevents cross-contamination between study groups, as physicians are not exposed to the intervention during or before the control period. The stepped-wedge implementation of the intervention allows effect calculation from both between- and within-cluster comparisons, which enhances statistical power and allows smaller sample size than a parallel cluster design. Moreover, it enables the training of all centers for the intervention, simplifying implementation if the results prove successful. The PLUS algorithm has the potential to improve the identification of LRTIs that would benefit from antibiotics. When scaled, the expected reduction in the proportion of antibiotics prescribed has the potential to not only decrease side effects and costs but also mitigate antibiotic resistance.

TRIAL REGISTRATION

This study was registered on July 19, 2022, on the ClinicalTrials.gov registry using reference number: NCT05463406.

TRIAL STATUS

Recruitment started on December 5, 2022, and will be completed on November 3, 2024. Current protocol version is version 3.0, dated April 3, 2023.

Endemic Human Coronavirus-Specific Nasal Immunoglobulin A and Serum Immunoglobulin G Dynamics in Lower Respiratory Tract Infections

Endemic human coronaviruses (HCoV) NL63, 229E, OC43, and HKU1 cause respiratory infection. Following infection, a virus-specific serum antibody rise is usually observed, coinciding with recovery. In some cases, an infection is not accompanied by an immunoglobulin G (IgG) antibody rise in serum in the first month after HCoV infection, even though the infection has cleared in that month and the patient has recovered. We investigated the possible role of nasal immunoglobulin A (IgA). We measured spike (S) and nucleocapsid (N)-specific nasal IgA during and after an HCoV lower respiratory tract infection (LRTI) and compared the IgA responses between subjects with and without a significant IgG rise in serum (IgG responders (n = 31) and IgG non-responders (n = 14)). We found that most IgG responders also exhibited significant nasal IgA rise in the first month after the infection, whereas such an IgA rise was lacking in most IgG non-responders. Interestingly, the serum IgG non-responders presented with a significantly higher nasal IgA when they entered this study than during the acute phase of the LRTI. Our data suggest that nasal IgA could be part of a fast acute response to endemic HCoV infection and may play a role in clearing the infection.

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.

Chitosan-Based Nanocarriers for Pulmonary and Intranasal Drug Delivery Systems: A Comprehensive Overview of their Applications

The optimization of respiratory health is important, and one avenue for achieving this is through the application of both Pulmonary Drug Delivery System (PDDS) and Intranasal Delivery (IND). PDDS offers immediate delivery of medication to the respiratory system, providing advantages, such as sustained regional drug concentration, tunable drug release, extended duration of action, and enhanced patient compliance. IND, renowned for its non-invasive nature and swift onset of action, presents a promising path for advancement. Modern PDDS and IND utilize various polymers, among which chitosan (CS) stands out. CS is a biocompatible and biodegradable polysaccharide with unique physicochemical properties, making it well-suited for medical and pharmaceutical applications. The multiple positively charged amino groups present in CS facilitate its interaction with negatively charged mucous membranes, allowing CS to adsorb easily onto the mucosal surface. In addition, CS-based nanocarriers have been an important topic of research. Polymeric Nanoparticles (NPs), liposomes, dendrimers, microspheres, nanoemulsions, Solid Lipid Nanoparticles (SLNs), carbon nanotubes, and modified effective targeting systems compete as important ways of increasing pulmonary drug delivery with chitosan. This review covers the latest findings on CS-based nanocarriers and their applications.

Rhinovirus dynamics across different social structures

Rhinoviruses (RV), common human respiratory viruses, exhibit significant antigenic diversity, yet their dynamics across distinct social structures remain poorly understood. Our study delves into RV dynamics within Kenya by analysing VP4/2 sequences across four different social structures: households, a public primary school, outpatient clinics in the Kilifi Health and Demographics Surveillance System (HDSS), and countrywide hospital admissions and outpatients. The study revealed the greatest diversity of RV infections at the countrywide level (114 types), followed by the Kilifi HDSS (78 types), the school (47 types), and households (40 types), cumulatively representing >90% of all known RV types. Notably, RV diversity correlated directly with the size of the population under observation, and several RV type variants occasionally fuelled RV infection waves. Our findings highlight the critical role of social structures in shaping RV dynamics, information that can be leveraged to enhance public health strategies. Future research should incorporate whole-genome analysis to understand fine-scale evolution across various social structures.

Positive and negative viral associations in patients with acute respiratory tract infections in primary care: the ECOVIR study

Introduction

Acute respiratory infections (ARIs) are the most common viral infections encountered in primary care settings. The identification of causal viruses is still not available in routine practice. Although new strategies of prevention are being identified, knowledge of the relationships between respiratory viruses remains limited.

Materials and methods

ECOVIR was a multicentric prospective study in primary care, which took place during two pre-pandemic seasons (2018-2019 and 2019-2020). Patients presenting to their General practitioner (GP) with ARIs were included, without selecting for age or clinical conditions. Viruses were detected on nasal swab samples using a multiplex Polymerase Chain Reaction test focused on 17 viruses [Respiratory Syncytial Virus-A (RSV-A), RSV-B, Rhinovirus/Enterovirus (HRV), human Metapneumovirus (hMPV), Adenovirus (ADV), Coronaviruses (CoV) HKU1, NL63, 229E, OC43, Influenza virus (H1 and H3 subtypes), Influenza virus B, Para-Influenza viruses (PIVs) 1-4, and Bocavirus (BoV)].

Results

Among the 668 analyzed samples, 66% were positive for at least one virus, of which 7.9% were viral codetections. The viral detection was negatively associated with the age of patients. BoV, ADV, and HRV occurred more significantly in younger patients than the other viruses (p < 0.05). Codetections were significantly associated with RSV, HRV, BoV, hMPV, and ADV and not associated with influenza viruses, CoV, and PIVs. HRV and influenza viruses were negatively associated with all the viruses. Conversely, a positive association was found between ADV and BoV and between PIVs and BoV.

Conclusion

Our study provides additional information on the relationships between respiratory viruses, which remains limited in primary care.

The potential clinical value of pairing procalcitonin and lung ultrasonography to guide antibiotic therapy in patients with community-acquired pneumonia: a narrative review

INTRODUCTION

Lower respiratory tract infections (LRTIs) are among the most frequent infections and are prone to inappropriate antibiotic treatments. This results from a limited accuracy of diagnostic tools in identifying bacterial pneumonia. Lung ultrasound (LUS) has excellent sensitivity and specificity in diagnosing pneumonia. Additionally, elevated procalcitonin (PCT) levels correlate with an increased likelihood of bacterial infection. LUS and PCT appear to be complementary in identifying patients with bacterial pneumonia who are likely to benefit from antibiotics.

AREAS COVERED

This narrative review aims to summarize the current evidence for LUS to diagnose pneumonia, for PCT to guide antibiotic therapy and the clinical value of pairing both tools.

EXPERT OPINION

LUS has excellent diagnostic accuracy for pneumonia in different settings, regardless of the examiner's experience. PCT guidance safely reduces antibiotic prescription in LRTIs. The combination of both tools has demonstrated an enhanced accuracy in the diagnosis of pneumonia, including CAP in the ED and VAP in the ICU, but randomized controlled studies need to validate the clinical impact of a combined approach.

Infection Prevalence at a Tertiary Hospital in Hail, Saudi Arabia: A Single-Center Study to Identify Strategies to Improve Antibiotic Usage

Objective

Identifying the burden of disease and the condition of the Saudi population is in high demand from both a surveillance and analytical standpoint. The objective of this study was to determine the most prevalent infections among hospitalized patients (both community-acquired and hospital-acquired), the antibiotics prescribing pattern, and their relationship with patient characteristics like age and gender.

Methods

A retrospective study was conducted comprising 2646 patients with infectious diseases or complications admitted to a tertiary hospital in the Hail region of Saudi Arabia. A standardized form was used to collect information from patient's medical records. Demographic data such as age, gender, prescribed antibiotics, and culture-sensitivity tests were included in the study.

Results

Males represented about two-thirds (66.5%, n = 1760) of the patients. Most patients (45.9%) who suffered from infectious diseases were between the ages of 20 and 39. The most prevalent infectious ailment was respiratory tract infection (17.65%, n = 467). Furthermore, the most common multiple infectious diseases were gallbladder calculi with cholecystitis (40.3%, n = 69). Similarly, COVID-19 had the greatest impact on people over 60. Beta-lactam antibiotics were the most commonly prescribed (37.6%), followed by fluoroquinolones (26.26%) and macrolides (13.45%). But performing culture sensitivity tests were rather uncommon (3.8%, n = 101). For multiple infections, beta-lactam antibiotics (such as amoxicillin and cefuroxime) were the most commonly prescribed antibiotics (2.26%, n = 60), followed by macrolides (such as azithromycin and Clindamycin) and fluoroquinolones (eg, ciprofloxacin and levofloxacin).

Conclusion

Respiratory tract infections are the most prevalent infectious disease among hospital patients, who are primarily in their 20s. The frequency of performing culture tests is low. Therefore, it is important to promote culture sensitivity testing in order to support the prudent use of antibiotics. Guidelines for anti-microbial stewardship programs are also highly recommended.

Predicted Public Health and Economic Impact of Respiratory Syncytial Virus Vaccination with Variable Duration of Protection for Adults ≥60 Years in Belgium

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infection (ARI) in older adults. This study used a static, cohort-based decision-tree model to estimate the public health and economic impact of vaccination against RSV in Belgians aged ≥60 years compared with no vaccination for different vaccine duration of protection profiles from a healthcare payer perspective. Three vaccine protection durations were compared (1, 3, and 5 years), and several sensitivity and scenario analyses were performed. Results showed that an RSV vaccine with a 3-year duration of protection would prevent 154,728 symptomatic RSV-ARI cases, 3688 hospitalizations, and 502 deaths over three years compared to no vaccination in older adults and would save EUR 35,982,857 in direct medical costs in Belgium. The number needed to vaccinate to prevent one RSV-ARI case was 11 for the 3-year duration profile, while it was 28 and 8 for the 1- and 5-year vaccine duration profiles, respectively. The model was generally robust in sensitivity analyses varying key input values. This study suggested that vaccination could substantially decrease the public health and economic burden of RSV in adults ≥60 years in Belgium, with benefits increasing with a longer duration of vaccine protection.

Viral etiology of lower respiratory tract infections in adults in the pre-COVID-19 pandemic era: A cross-sectional study in a single center experience from Cameroon

BACKGROUND AND AIMS

Respiratory viruses are responsible for the majority of lower respiratory tract infections (LRTIs) worldwide. However, there is a gap on the epidemiology of viral LRTIs in adults in sub-Saharan African countries. In Cameroon, like in other countries, the role of viral respiratory pathogens in the etiology of LRTIs in adults is helpful for clinical management. This study aimed to determine the viral aetiologies of LRTIs among hospitalized adults in a reference center for respiratory diseases in the town of Yaounde in Cameroon and its surroundings.

METHODS

A cross-sectional study was conducted from January 2017 to January 2018 at Jamot Hospital in Yaounde (Cameroon). Clinical and demographic information; BAL and sputa were collected from hospitalized patients meeting LRTI case definitions. The clinical samples were investigated for respiratory pathogens with a commercial Reverse Transcriptase Real-Time Polymerase Chain Reaction (RT-PCR) targeting 21 viruses, cultures for bacterial and fungal infections.

RESULTS

The 77 included adult patients with LRTIs had an appropriate clinical sample for microbial investigations. A viral agent was detected in 22.1% (17/77) samples. The main viruses detected included rhinovirus (10/77), coronavirus (hCoV-OC43 and hCoV-229E), and influenza A virus (3/77 each). A concomitant viral and bacterial co-infection occurred in 7.8% of patients (6/77) while viral co-infection occurred in one patient (1.3%). No Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) was detected in clinical samples. Most patients were under antimicrobials before getting diagnosed.

CONCLUSIONS

Respiratory viruses account for 22.1% of LRTIs in hospitalized patients in this study. Despite prior antimicrobial therapy and delay, rhinovirus, coronavirus and influenza A virus were the most detected in patients in the pre-COVID-19 pandemic era in a single center experience from Cameroon.

Pulse Oximetry as an Aid to Rule Out Pneumonia among Patients with a Lower Respiratory Tract Infection in Primary Care

Guidelines recommend chest X-rays (CXRs) to diagnose pneumonia and guide antibiotic treatment. This study aimed to identify clinical predictors of pneumonia that are visible on a chest X-ray (CXR+) which could support ruling out pneumonia and avoiding unnecessary CXRs, including oxygen saturation. A secondary analysis was performed in a clinical trial that included patients with suspected pneumonia in Swiss primary care. CXRs were reviewed by two radiologists. We evaluated the association between clinical signs (heart rate > 100/min, respiratory rate ≥ 24/min, temperature ≥ 37.8 °C, abnormal auscultation, and oxygen saturation < 95%) and CXR+ using multivariate analysis. We also calculated the diagnostic performance of the associated clinical signs combined in a clinical decision rule (CDR), as well as a CDR derived from a large meta-analysis (at least one of the following: heart rate > 100/min, respiratory rate ≥ 24/min, temperature ≥ 37.8 °C, or abnormal auscultation). Out of 469 patients from the initial trial, 107 had a CXR and were included in this study. Of these, 26 (24%) had a CXR+. We found that temperature and oxygen saturation were associated with CXR+. A CDR based on the presence of either temperature ≥ 37.8 °C and/or an oxygen saturation level < 95% had a sensitivity of 69% and a negative likelihood ratio (LR-) of 0.45. The CDR from the meta-analysis had a sensitivity of 92% and an LR- of 0.37. The addition of saturation < 95% to this CDR increased the sensitivity (96%) and decreased the LR- (0.21). In conclusion, this study suggests that pulse oximetry could be added to a simple CDR to decrease the probability of pneumonia to an acceptable level and avoid unnecessary CXRs.

Overruling of Procalcitonin-Guided Antibiotics for Lower Respiratory Tract Infections in Primary Care: Ancillary Study of a Randomized Controlled Trial

BACKGROUND

Lower respiratory tract infections (LRTIs) in primary care are a promising target for antibiotic stewardship. A clinical trial in Switzerland showed a large decrease in antibiotic prescriptions with procalcitonin guidance (cut-off < 0.25 µg/L) compared with usual care. However, one-third of patients with low procalcitonin at baseline received antibiotics by day 28.

AIM

To explore the factors associated with the overruling of initial procalcitonin guidance.

DESIGN AND SETTING

Secondary analysis of a cluster randomized trial in which patients with an LRTI were included.

METHOD

Using the characteristics of patients, their disease, and general practitioners (GPs), we conducted a multivariate logistic regression, adjusted for clustering.

RESULTS

Ninety-five out of 301 (32%) patients with low procalcitonin received antibiotics by day 28. Factors associated with an overruling of procalcitonin guidance were: a history of chest pain (adjusted OR [aOR] 1.81, 95% confidence interval 1.03-3.17); a prescription of chest X-ray by the GP (aOR 4.65, 2.32-9.34); a C-reactive protein measured retrospectively above 100 mg/L (aOR 7.48, 2.34-23.93, reference ≤ 20 mg/L); the location of the GP practice in an urban setting (aOR 2.27, 1.18-4.37); and the GP's number of years of experience (aOR per year 1.05, 1.01-1.09).

CONCLUSIONS

Overruling of procalcitonin guidance was associated with GPs' socio-demographic characteristics, pointing to the general behavioral problem of overprescription by physicians. Continuous medical education and communication training might support the successful implementation of procalcitonin point-of-care tests aimed at antibiotic stewardship.

Impact of point-of-care C-reactive protein testing intervention on non-prescription dispensing of antibiotics for respiratory tract infections in private community pharmacies in Nigeria: a cluster randomized controlled trial

OBJECTIVES

To ascertain if access to C-reactive protein (CRP) test kits-and staff training on how to use them in respiratory tract infection (RTI) management-in private community pharmacies (PCPs) can reduce non-prescription antibiotic dispensing for RTI.

METHODS

A parallel cluster randomized controlled trial was conducted in Nigeria. The clusters-which were equally the participating units-were PCPs with blood testing experience. Stratified block randomization was done. PCPs were stratified by the baseline value of the primary outcome. PCPs were not blinded. The intervention PCPs were provided with CRP kits and trained to use them to make decisions regarding non-prescription antibiotic dispensing for RTI. The control PCPs received no intervention. The primary outcome was the non-prescription antibiotic dispensing rate for RTI. Data were collected by blinded simulated clients who visited each PCP 30 times before and after the intervention without prescriptions. Analyses were by intention-to-treat.

RESULTS

Twenty PCPs were randomized, 1:1. Ten PCPs were analyzed in each arm. Each PCP contributed 30 data points to the multiple imputation analysis where antibiotic dispensing decreased by 15.66% (209/300 [intervention] vs 256/300 [control]) in the adjusted analysis (odds ratio = 0·279, 95% confidence interval = 0.107-0.726; P-value = 0.0090) and 16% (208/300 [intervention] vs 256/300 [control]) in the crude analysis (odds ratio = 0.299, 95% confidence interval = 0.098-0.911; P-value = 0.034).

CONCLUSION

Access to CRP kits-and staff training on how to use them in RTI management-in PCPs reduced non-prescription antibiotic dispensing for RTI.

The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections

OBJECTIVE

Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce.

METHODS

A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms.

RESULTS

The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group.

CONCLUSION

In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.

The Design and Implementation of the ECOVIR Project: A Primary Health Care Surveillance System to Strengthen Co-Detection of Respiratory Viruses in Normandy

Acute respiratory infections (ARIs) need to be better understood and treated, as they are critical to public health, especially during crises such as the SARS-CoV2 pandemic. These are the most abundant infections in the general population and are seen primarily in primary care by general practitioners (GPs). Many different viruses are involved, according to epidemic variations. Viral co-detections account for a significant proportion of ARIs in hospital cohorts. The objective of the ECOVIR cohort was to study viral co-detections by setting up a biobank of respiratory tract samples from patients consulting their general practitioner for ARI symptoms. We report here on the course of the study: the design, the conduct, and the difficulties encountered. ECOVIR (Etude des CO-detections VIrales dans les prélèvements Respiratoires) was a prospective, multicenter cohort conducted in France during two epidemic seasons (2018-2019 and 2019-2020). We recruited GPs. Each GP investigator (GPI) saw patients weekly for examination, clinical data collection, and nasopharyngeal swabbing. Each sample was sent to the virology unit for biobanking and molecular analysis. Clinical and sociodemographic data were collected 7 days after inclusion. ECOVIR involved 36 GPIs. Patients with symptoms of an ARI were included (n = 685). The median number of inclusions was 16 patients per GPI over both seasons (IC_25-75% [4.75; 27]). Patients aged 18 to 64 years were the most numerous (57%), followed by children (30%), and the elderly (13% over 65 years). This age distribution emphasizes the young adult and middle-aged population. Residents participated in the project and called patients on day 7 to obtain clinical and sociodemographic data. Our study triggered the creation of an original network, which plans to establish a functional link between research and primary health care. Primary care is unfortunately poorly represented in research protocols, particularly in respiratory infections, even though it is a cornerstone of our French health care system, as demonstrated every day in this period of crisis.

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections

Respiratory viruses such as influenza viruses, respiratory syncytial virus (RSV), and coronaviruses initiate infection at the mucosal surfaces of the upper respiratory tract (URT), where the resident respiratory microbiome has an important gatekeeper function. In contrast to gut-targeting administration of beneficial bacteria against respiratory viral disease, topical URT administration of probiotics is currently underexplored, especially for the prevention and/or treatment of viral infections. Here, we report the formulation of a throat spray with live lactobacilli exhibiting several in vitro mechanisms of action against respiratory viral infections, including induction of interferon regulatory pathways and direct inhibition of respiratory viruses. Rational selection of Lactobacillaceae strains was based on previously documented beneficial properties, up-scaling and industrial production characteristics, clinical safety parameters, and potential antiviral and immunostimulatory efficacy in the URT demonstrated in this study. Using a three-step selection strategy, three strains were selected and further tested in vitro antiviral assays and in formulations: Lacticaseibacillus casei AMBR2 as a promising endogenous candidate URT probiotic with previously reported barrier-enhancing and anti-pathogenic properties and the two well-studied model strains Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1 that display immunomodulatory capacities. The three strains and their combination significantly reduced the cytopathogenic effects of RSV, influenza A/H1N1 and B viruses, and HCoV-229E coronavirus in co-culture models with bacteria, virus, and host cells. Subsequently, these strains were formulated in a throat spray and human monocytes were employed to confirm the formulation process did not reduce the interferon regulatory pathway-inducing capacity. Administration of the throat spray in healthy volunteers revealed that the lactobacilli were capable of temporary colonization of the throat in a metabolically active form. Thus, the developed spray with live lactobacilli will be further explored in the clinic as a potential broad-acting live biotherapeutic strategy against respiratory viral diseases.

Cost-utility analysis of the universal pneumococcal vaccination programme for older adults in Norway

The aim of this study was to establish whether the universal pneumococcal vaccination for older adults in Norway is likely to be cost-effective from the perspective of the health care provider. A decision tree model developed by the Public Health Agency of Sweden was adapted to the Norwegian setting. Two cohorts, consisting of 65-year-olds and 75-year-olds grouped into vaccinated and unvaccinated, were followed over a 5-year time horizon. In the base case, the 23-valent polysaccharide vaccine (PPV23) was used while the 13-valent pneumococcal conjugate vaccine (PCV13) was included in scenario analyses only. The costs and health benefits (measured in quality adjusted life years (QALY) gained) were compared in the two cohorts between the vaccinated and unvaccinated groups. The impact of indirect effects of the vaccine, such as herd immunity and serotype replacement, were not investigated. The relative importance of change in price was assessed by performing one-way sensitivity analyses. Under base-case assumptions, the programme for the 75-year-old cohort is expected to be dominant (cost-effective) from the health care perspective at the current maximal pharmacy retail price and at 75% vaccination coverage. In comparison, for the 65-year-old cohort the cost per QALY gained is approximately NOK 601,784 (EUR 61,281) under the base-case assumptions. A reduction in the cost of the vaccine to one quarter of its current level also brings the cost per QALY gained within the acceptable ranges in a Norwegian context for both the 65- and 75-year-old cohorts. There is no exact cost-effectiveness threshold in Norway. However, introducing a vaccination programme against pneumococcal disease for 65-year-olds in Norway is likely to fall within the acceptable range while for the 75-year-old cohort the universal programme appears to be dominant (cost-effective).

Recent infection with HCoV-OC43 may be associated with protection against SARS-CoV-2 infection

Antibodies against seasonal human coronaviruses (HCoVs) are known to cross-react with SARS-CoV-2, but data on cross-protective effects of prior HCoV infections are conflicting. In a prospective cohort of healthcare workers (HCWs), we studied the association between seasonal HCoV (OC43, HKU1, 229E and NL63) nucleocapsid protein IgG and SARS-CoV-2 infection during the first pandemic wave in the Netherlands (March 2020 - June 2020), by 4-weekly serum sampling. HCW with HCoV-OC43 antibody levels in the highest quartile, were less likely to become SARS-CoV-2 seropositive when compared with those with lower levels (6/32, 18.8%, versus 42/97, 43.3%, respectively: p = 0.019; HR 0.37, 95% CI 0.16-0.88). We found no significant association with HCoV-OC43 spike protein IgG, or with antibodies against other HCoVs. Our results indicate that the high levels of HCoV-OC43-nucleocapsid antibodies, as an indicator of a recent infection, are associated with protection against SARS-CoV-2 infection; this supports and informs efforts to develop pancoronavirus vaccines.

A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia

Purpose

Plasma metagenomic next-generation sequencing (mNGS) has emerged as an attractive and minimally invasive technique for pathogen detection. However, few studies have demonstrated the need for simultaneous plasma and bronchoalveolar lavage fluid (BALF) mNGS in patients with severe pneumonia.

Patients and Methods

This study retrospectively performed a paired comparison of BALF and plasma mNGS in critically ill patients with suspected severe pneumonia from April 2019 to December 2020. The diagnostic performance of BALF and plasma mNGS was compared using the clinical composite diagnosis as the reference standard.

Results

In total, 57 patients were included in this study. Patients with positive plasma mNGS had shorter hospital stay days at the time of specimen acquisition (4.5 vs 11, P = 0.028) and a higher positivity rate of BALF culture (50% vs 22.9%, P = 0.033) than patients with negative plasma mNGS. Fifty-three patients (93%) were finally diagnosed with severe pneumonia. Significant differences were observed in the sensitivity of BALF and plasma mNGS (100% vs 42%, P < 0.001), and the diagnostic accuracy was 96% and 46%, respectively. The proportion of virus in positive plasma mNGS results was higher than that in BALF mNGS (23% vs 11%, P = 0.173) without significant difference. Although plasma mNGS detected additional microorganisms in 11/53 patients, the beneficial effect was observed in only 5/53 (9%) patients.

Conclusion

In this study, the clinical effect of simultaneously conducting mNGS of BALF and plasma samples was found to be limited. For patients with the suspected virus infection, plasma mNGS may be a supplementary test. Further studies are needed to identify the optimal indications for plasma mNGS.

The Opportunity of Point-of-Care Diagnostics in General Practice: Modelling the Effects on Antimicrobial Resistance

OBJECTIVES

Antimicrobial resistance (AMR) is a public health threat associated with antibiotic consumption. Community-acquired acute respiratory tract infections (CA-ARTIs) are a major driver of antibiotic consumption in primary care. We aimed to quantify the investments required for a large-scale rollout of point-of care (POC) diagnostic testing in Dutch primary care, and the impact on AMR due to reduced use of antibiotics.

METHODS

We developed an individual-based model that simulates consultations for CA-ARTI at GP practices in the Netherlands and compared a scenario where GPs test all CA-ARTI patients with a hypothetical diagnostic strategy to continuing the current standard-of-care for the years 2020-2030. We estimated differences in costs and future AMR rates caused by testing all patients consulting for CA-ARTI with a hypothetical diagnostic strategy, compared to the current standard-of-care in GP practices.

RESULTS

Compared to the current standard-of-care, the diagnostic algorithm increases the total costs of GP consultations for CA-ARTI by 9% and 19%, when priced at €5 and €10, respectively. The forecast increase in Streptococcus pneumoniae resistance against penicillins can be partly restrained by the hypothetical diagnostic strategy from 3.8 to 3.5% in 2030, albeit with considerable uncertainty.

CONCLUSIONS

Our results show that implementing a hypothetical diagnostic strategy for all CA-ARTI patients in primary care raises the costs of consultations, while lowering antibiotic consumption and AMR. Novel health-economic methods to assess and communicate the potential benefits related to AMR may be required for interventions with limited gains for individual patients, but considerable potential related to antibiotic consumption and AMR.

Age-Specific Characteristics of Adult and Pediatric Respiratory Viral Infections: A Retrospective Single-Center Study

This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups were then subdivided based on age: 0−6, 7−12, 13−18, 19−49, 50−64, and ≥65 years old. These groups were compared to evaluate the differences in the pattern of respiratory viral infections. Among a total of 4058 pediatric patients (mean age 3.0 ± 2.9 years, n = 1793 females), 2829 (48.9%) had mono-infections, while 1229 (51.1%) had co-infections. Co-infections were the most common in the 0−6-year-old group (31.6%). Among 1550 adult patients (mean age 70.2 ± 15.3 years, n = 710 females), 1307 (85.6%) had mono-infections and 243 (14.4%) had co-infections. Co-infections were most common in the ≥65-year-old group (16.8%). Viral infection and co-infection rates decreased with age in pediatric patients but increased with increasing age in adults. In pediatric patients, the rates of viral infections and co-infections were high; the rate of co-infections was higher in younger patients. In adult patients, the rates of viral infections and co-infections were lower than those in pediatric patients; the rate of co-infections was higher in older patients.

Respiratory etiological surveillance among quarantined patients with suspected lower respiratory tract infection at a medical center in southern Taiwan during COVID-19 pandemic

Background

A comprehensive study of respiratory pathogens was conducted in an area with a low prevalence of COVID-19 among the adults quarantined at a tertiary hospital.

Methods

From March to May 2020, 201 patients suspected lower respiratory tract infection (LRTI) were surveyed for etiologies by multiplex polymerase chain reaction (PCR: FilmArray TM Respiratory Panel) test combination with cultural method, viral antigen detection and serologic surveys.

Results

Total 201 patients tested with FilmArray TM Respiratory Panel were enrolled, of which 68.2% had sputum bacterial culture, 86.1% had pneumococcus and Legionella urine antigen test. Their median age was 72.0 year-old with multiple comorbidities, and 11.4% were nursing home residents. Bacteria accounted for 59.7% of identified pathogens. Atypical pathogens were identified in 31.3% of total pathogens, of which viruses accounted for 23.9%. In comparison to patients with bacterial infection, patients with atypical pathogens were younger (median= 77.2 vs 67.1, years, P = 0.017) and had shorter length of hospital (8.0 vs 4.5, days, P = 0.007).

Conclusions

Patients with LRTI caused by atypical pathogens was indistinguishable from those with bacterial pathogens by clinical manifestations or biomarkers. Multiplex PCR providing rapid diagnosis of atypical pathogens enhance patient care and decision making when rate of sputum culture sampling was low in quarantine ward during pandemic.

Clinical prediction of laboratory-confirmed influenza in adults with influenza-like illness in primary care. A randomized controlled trial secondary analysis in 15 European countries

BACKGROUND

Clinical findings do not accurately predict laboratory diagnosis of influenza. Early identification of influenza is considered useful for proper management decisions in primary care.

OBJECTIVE

We evaluated the diagnostic value of the presence and the severity of symptoms for the diagnosis of laboratory-confirmed influenza infection among adults presenting with influenza-like illness (ILI) in primary care.

METHODS

Secondary analysis of patients with ILI who participated in a clinical trial from 2015 to 2018 in 15 European countries. Patients rated signs and symptoms as absent, minor, moderate, or major problem. A nasopharyngeal swab was taken for microbiological identification of influenza and other microorganisms. Models were generated considering (i) the presence of individual symptoms and (ii) the severity rating of symptoms.

RESULTS

A total of 2,639 patients aged 18 or older were included in the analysis. The mean age was 41.8 ± 14.7 years, and 1,099 were men (42.1%). Influenza was microbiologically confirmed in 1,337 patients (51.1%). The area under the curve (AUC) of the model for the presence of any of seven symptoms for detecting influenza was 0.66 (95% confidence interval [CI]: 0.65-0.68), whereas the AUC of the symptom severity model, which included eight variables-cough, fever, muscle aches, sweating and/or chills, moderate to severe overall disease, age, abdominal pain, and sore throat-was 0.70 (95% CI: 0.69-0.72).

CONCLUSION

Clinical prediction of microbiologically confirmed influenza in adults with ILI is slightly more accurate when based on patient reported symptom severity than when based on the presence or absence of symptoms.

Utility of Polymerase Chain Reaction in Nasopharyngeal Swabs for Identifying Respiratory Bacteria Causing Community-Acquired Pneumonia

Timely identification of a pathogen in lower respiratory tract infections (LRTI) can support appropriate antibiotics use. The difficulty of obtaining lower respiratory tract (LRT) samples limits the utility of point-of-care syndromic molecular assays. We assessed the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in nasopharyngeal (NP) swab for detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Patients in the study included retrospectively consenting adults who attended the emergency department of Lausanne University Hospital between February 2019 and August 2020 for a community-acquired LRTI, with available NP swab and a high-quality LRT sample. These samples were tested with the FilmArray PP (cutoff of ≥10⁴ copies/mL). Positive (PPA) and negative percent agreement (NPA) of FilmArray PP in NP swab were calculated, using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. To assess the performance of a lower detection cutoff, NP samples were also tested with an in-house PCR (cutoff of ≥10 copies/mL) for S. pneumoniae and H. influenzae. Overall, 118 patients were included. FilmArray PP in LRT sample and standard microbiology tests detected S. pneumoniae in 19/118 and 12/118, H. influenzae in 44/118 and 19/118, and M. catarrhalis in 14/118 and 0/118, respectively. Using LRT FilmArray PP as reference, PPA and NPA of FilmArray PP on NP were 58% and 100% for S. pneumoniae, 61% and 100% for H. influenzae, and 57% and 99% for M. catarrhalis. Using standard diagnostic tests as reference, PPA and NPA were 58% and 96% for S. pneumoniae, 74% and 87% for H. influenzae, and indefinite and 92% for M. catarrhalis. Using a lower cutoff on NP (≥10² copies/mL), PPA was 68% for S. pneumoniae and 77% for H. influenzae with LRT FilmArray PP as reference. FilmArray PP in NP swabs has a limited PPA for identifying the most common etiologies of community-acquired LRTI irrespective of the reference standard, preventing its use for withholding antibiotics. The PCR detection cutoff does not explain the low PPA. The excellent NPA suggests the use of NP PCR results for rapidly targeted antimicrobial therapy.

IMPORTANCE Timely identification of a pathogen in patients with lower respiratory tract infections is of paramount importance to avoid inappropriate antibiotic prescription. We aimed to evaluate the performance of a rapid syndromic molecular assay in nasopharyngeal swabs for identifying the most common bacterial causes of lower respiratory tract infections in adults (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis). Our data show that nasopharyngeal molecular assay has a good concordance with lower respiratory tract sample when positive but not when negative. A positive result is therefore concordant with a lower respiratory tract infection and can be used to target antibiotics. Nevertheless, a negative result does not have a good concordance, so it cannot be used to withhold antibiotics. Our findings illustrate the potential utility of these easily collected samples for the management of patients with lower respiratory tract infections.

Atypical Antibody Dynamics During Human Coronavirus HKU1 Infections

Human coronavirus HKU1 (HCoV-HKU1) is one of the four endemic coronaviruses. It has been suggested that there is a difference in incidence, with PCR-confirmed HCoV-NL63 and HCoV-OC43 infections occurring more commonly, whereas HCoV-HKU1 is the least seen. Lower incidence of HCoV-HKU1 infection has also been observed in serological studies. The current study aimed to investigate antibody dynamics during PCR-confirmed HCoV-HKU1 infections using serum collected during infection and 1 month later. We expressed a new HCoV-HKU1 antigen consisting of both the linker and carboxy-terminal domain of the viral nucleocapsid protein and implemented it in ELISA. We also applied a spike-based Luminex assay on serum samples from PCR-confirmed infections by the four endemic HCoVs. At least half of HCoV-HKU1-infected subjects consistently showed no antibody rise via either assay, and some subjects even exhibited substantial antibody decline. Investigation of self-reported symptoms revealed that HCoV-HKU1-infected subjects rated their illness milder than subjects infected by other HCoVs. In conclusion, HCoV-HKU1 infections reported in this study displayed atypical antibody dynamics and milder symptoms when compared to the other endemic HCoVs.

Multiplex bacterial PCR in the bronchoalveolar lavage fluid of non-intubated patients with suspected pulmonary infection: a quasi-experimental study

Background

Early pathogen identification in pulmonary infection is crucial to guide antibacterial therapy and decrease length of hospital stay. We hypothesise that compared to conventional diagnostic methods, a multiplex bacterial polymerase chain reaction assay has a higher diagnostic yield in bronchoalveolar lavage (BAL) fluid and improved clinical outcomes in patients with suspicion of pulmonary infection.

Methods

A prospective, monocentric, quasi-experimental, observational study was carried out. Unselected patients with suspected pulmonary infection who underwent bronchoscopy with BAL were included in the study over a period of 1 year. In addition to conventional diagnostic methods, a multiplex PCR bacterial assay was performed in BAL on a 2 week on: 1 week off pre-determined schedule. No therapeutic recommendations were provided to the treating physician.

Results

605 cases were included, 54% of whom were immunosuppressed. Conventional diagnostic methods detected 56% of the bacteria evidenced by PCR. PCR failed to detect bacteria in 4% of the cases with a positive conventional diagnostic result. After bronchoscopy, 42% of the patients received antibacterial therapy for pulmonary infection for a median of 12 antibiotic days. There was no statistically significant difference in length of hospital stay (median 8 versus 8; p=0.839), antibiotic exposure (median 11 versus 14; p=0.362) or number of antibiotics prescribed (median 2 versus 2; p=0.595) between the two groups.

Conclusions

A multiplex bacterial PCR detected more bacteria in BAL fluid than conventional diagnostic methods. However, without a specific antibiotic stewardship approach and a clear understanding of the clinical implications of a positive or negative PCR result, the PCR results did not influence clinical outcomes.

[ECOVIR: Study of a primary care cohort in of patients with Acute Respiratory Infections in Normandy, an example of pluri-professional hospital-primary care coordination]

Acute Respiratory Infections (ARI) need be better understood and more effectively treated, especially insofar as they are of pivotal importance in public health, particularly during a crisis such as the SARS-CoV2 pandemic. The prospective, multicentric cohort study of viral codetections in respiratory samples study known as ECOVIR was conducted in Normandy, France during two winters (2018-2019, 2019-2020). The objective of the project was to create a biobank of respiratory tract samples from patients consulting their general practitioner (GP) for ARI symptoms. ECOVIR involved 36 GP investigators (GPI), from 8 health care centers throughout Normandy. Six hundred and eighty-five patients with ARI symptoms were included; naso-pharyngeal samples were taken by the GPIs and subsequently analyzed in virology laboratories for the purposes of viral codetection. The median of inclusions was 16 patients for each of the 31 actively participating GPIs over the two winters (CI25-75% [4.75; 27]). By D7, 92% of the patients contacted had responded to our call for participation, enabling us to obtain clinical, environmental and socio-demographic data. Through this study, we created an original functional network, thereby establishing a viable link between research and primary care, which is generally underrepresented in research protocols, even though it constitutes the cornerstone of the French health care system, especially during this prolonged period of sanitary crisis.