Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays

Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses

Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98.4 % and 93.8 %, respectively, and 6 discrepant results were observed. The BioFire was identified as the platform with the highest relative sensitivity. Overall, the platforms performed similarly and are all suitable for syndromic testing of respiratory samples.

Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait

Background

The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen.

Results

Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years).

Conclusion

Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.

Antimicrobial De-Escalation in Critically Ill Patients

Antimicrobial de-escalation (ADE) is defined as the discontinuation of one or more antimicrobials in empirical therapy, or the replacement of a broad-spectrum antimicrobial with a narrower-spectrum antimicrobial. The aim of this review is to provide an overview of the available literature on the effectiveness and safety of ADE in critically ill patients, with a focus on special conditions such as anti-fungal therapy and high-risk categories. Although it is widely considered a safe strategy for antimicrobial stewardship (AMS), to date, there has been no assessment of the effect of de-escalation on the development of resistance. Conversely, some authors suggest that prolonged antibiotic treatment may be a side effect of de-escalation, especially in high-risk categories such as neutropenic critically ill patients and intra-abdominal infections (IAIs). Moreover, microbiological documentation is crucial for increasing ADE rates in critically ill patients with infections, and efforts should be focused on exploring new diagnostic tools to accelerate pathogen identification. For these reasons, ADE can be safely used in patients with infections, as confirmed by high-quality and reliable microbiological samplings, although further studies are warranted to clarify its applicability in selected populations.

Implementing Community-Based Strategies for Improved Pneumonia Care in Children: Insights From a Pilot Study

INTRODUCTION

Respiratory ailments, encompassing a spectrum of disorders, are a leading cause of mortality and morbidity in children, with pneumonia being particularly significant, accounting for 16% of child mortality. To ensure timely engagement with healthcare services, it is imperative to instill awareness through Information, Education, and Communication (IEC) initiatives targeting mothers of children under five. The primary objective of this pilot study is to assess the feasibility of a community-based intervention on health-seeking behaviour, knowledge, and practice measures concerning the management and prevention of pneumonia in children.

METHODOLOGY

The pilot study mirrored the main study's procedures in two villages, Bhuvanahalli and Gavanahalli, each randomly assigned as either an experimental or a control group. We selected 12 mothers with children under the age of five who had community-acquired pneumonia, employing a straightforward random technique, with six mothers from each group. These mothers were interviewed using a structured questionnaire focusing on health-seeking behaviour, knowledge, and practices related to the management and prevention of pneumonia. Mothers in the experimental group received a community-based intervention, specifically an educational set focusing on health-seeking behaviour, knowledge, and practice measures concerning the management and prevention of pneumonia in children, while those in the control group continued with their routine practices. We collected post-test data from the mothers in both groups at the 2nd, 4th, and 6th months of the intervention. The data analysis was conducted using the IBM SPSS Statistics for Windows, Version 28 (Released 2021; IBM Corp., Armonk, New York) software. The Mann-Whitney test and Kruskal-Wallis analyses indicated a notable and statistically significant shift in health-seeking behaviour, knowledge, and practices pertaining to the management and prevention of pneumonia in children as a result of the community-based educational intervention implemented in the experimental group (P<0.05).

CONCLUSION

Community-based intervention is crucial to preventing mortality and morbidity in children. The findings of the pilot study affirm its feasibility and lay a strong foundation for further investigation and implementation.

Multi-criteria decision analysis method for differential diagnosis of tropical febrile diseases

This paper employs the Analytical Hierarchy Process (AHP) to enhance the accuracy of differential diagnosis for febrile diseases, particularly prevalent in tropical regions where misdiagnosis may have severe consequences. The migration of health workers from developing countries has resulted in frontline health workers (FHWs) using inadequate protocols for the diagnosis of complex health conditions. The study introduces an innovative AHP-based Medical Decision Support System (MDSS) incorporating disease risk factors derived from physicians' experiential knowledge to address this challenge. The system's aggregate diagnostic factor index determines the likelihood of febrile illnesses. Compared to existing literature, AHP models with risk factors demonstrate superior prediction accuracy, closely aligning with physicians' suspected diagnoses. The model's accuracy ranges from 85.4% to 96.9% for various diseases, surpassing physicians' predictions for Lassa, Dengue, and Yellow Fevers. The MDSS is recommended for use by FHWs in communities lacking medical experts, facilitating timely and precise diagnoses, efficient application of diagnostic test kits, and reducing overhead expenses for administrators.

Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes

BACKGROUND

Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes.

METHODS

Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients.

RESULTS

The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections.

CONCLUSIONS

Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.

Prevalence and Outpatient Clinical Diagnostic Approaches for Common Acute Respiratory Tract Infections in Children Under Five Years of Age: A Cross-Sectional Study

Background

Acute respiratory tract infections are among the leading causes of child morbidity and mortality worldwide. Although the diagnosis of acute respiratory tract infections requires simple outpatient medical techniques and care, it is still misdiagnosed among primary care physicians, leading to delayed treatment and increased mortality. This study described the prevalence of common acute respiratory tract infections and simple techniques that effectively detect and diagnose children presenting with acute respiratory symptoms to primary healthcare physicians in remote settings.

Patients and Methods

This descriptive cross-sectional study was conducted at the pediatric outpatient clinic of a tertiary hospital in western Uganda in April, May and June 2019. A total of 896 children aged 2-59 months attending the clinic were recruited consecutively into the study and examined for the presence of acute respiratory infection. Participants' sociodemographic and clinical data were collected through history taking and clinical examination using a validated Uganda Ministry of Health Uganda outpatient clinical checklist (FORM 5). The outcome variable was the presence of an acute upper or lower respiratory condition. Data was analyzed using STATA version 13.0 (StataCorp, College Station, USA) and summarized using descriptive statistics.

Results

The overall period prevalence of acute respiratory tract infections among children aged 2 to 59 months was 36.9% (36,942 per 100,000 population). Upper respiratory tract infections with a prevalence of 24.8% were more common than lower respiratory tract infections. The most frequent upper respiratory tract infection in this setting was common cold (52%), followed by tonsillopharyngitis (10.7%), while pneumonia (26%) was the most frequent lower respiratory tract infection.

Conclusion

Acute respiratory tract infections contribute to the high burden of disease in pediatric outpatient clinics. Simple, affordable, and approved diagnostic clinical techniques that involve physical examination of the upper and lower respiratory systems can precisely diagnose acute respiratory tract infections in resource-limited settings where there is no access to sophisticated diagnostic equipment.

LAMPPrimerBank, a manually curated database of experimentally validated loop-mediated isothermal amplification primers for detection of respiratory pathogens

PURPOSE AND METHODS

The emergence of coronavirus disease 2019 (COVID-19) has once again affirmed the significant threat of respiratory infections to global public health and the utmost importance of prompt diagnosis in managing and mitigating any pandemic. The nucleic acid amplification test (NAAT) is the primary detection method for most pathogens. Loop-mediated isothermal amplification (LAMP) is a rapid, simple, sensitive, and specific epitome of isothermal NAAT performed using a set of four to six primers. Primer design is a fundamental step in LAMP assays, with several complexities and experimental screening requirements. To address this challenge, an online database is presented here. Its workflow comprises three steps: literature aggregation, data curation, and database and website implementation.

RESULTS

LAMPPrimerBank ( https://lampprimerbank.mathematik.uni-marburg.de ) is a manually curated database dedicated to experimentally validated LAMP primers, their peculiarities of assays, and accompanying literature, with a primary emphasis on respiratory pathogens. LAMPPrimerBank, with its user-friendly web interface and an open application programming interface, enables the accelerated and facile exploration, comparison, and exportation of LAMP primer sequences and their respective information from the massively scattered literature. LAMPPrimerBank currently comprises LAMP primers for diagnosing viral, bacterial, and fungal respiratory pathogens. Additionally, to address the challenge of false-positive results generated by nonspecific amplifications, LAMPPrimerBank computationally predicted and visualized the sizes of LAMP products for recorded primer sets in the database.

CONCLUSION

LAMPPrimerBank, as a pioneering database in the rapidly expanding field of isothermal NAAT, endeavors to confront the two challenges of the LAMP: primer design and discrimination of false-positive results.

Respiratory virus infections after allogeneic stem cell transplantation: Current understanding, knowledge gaps, and recent advances

Before the COVID-19 pandemic, common community-acquired seasonal respiratory viruses (CARVs) were a significant threat to the health and well-being of allogeneic hematopoietic cell transplant (allo-HCT) recipients, often resulting in severe illness and even death. The pandemic has further highlighted the significant risk that immunosuppressed patients, including allo-HCT recipients, face when infected with SARS-CoV-2. As preventive transmission measures are relaxed and CARVs circulate again among the community, including in allo-HSCT recipients, it is crucial to understand the current state of knowledge, gaps, and recent advances regarding CARV infection in allo-HCT recipients. Urgent research is needed to identify seasonal respiratory viruses as potential drivers for future pandemics.

Advancements in Rapid and Affordable Diagnostic Testing for Respiratory Infectious Diseases: Evaluation of Aptamer Beacon Technology for Rapid and Sensitive Detection of SAR-CoV-2 in Breath Condensate

The demand for rapid and efficient diagnostic point-of-care tests for respiratory infectious diseases has become increasingly critical in the current landscape. The emphasis on accessibility has been underscored over the past year, making it crucial to have biological components that exhibit fast and accurate kinetics. The foundation for precise, swift, and effective testing relies on the availability of highly responsive biological agents. Two published aptamer DNA sequences designated Song and MSA52 and their truncated internal stem-loop structures were studied for their potential to serve as aptamer beacons for rapid COVID detection. The candidate beacons were covalently labeled with Atto 633 dye attached to their 5' ends and Iowa Black quencher attached to their 3' ends. The whole aptamer structures exhibited the greatest fluorescence signal intensities and higher fluorescence background than their truncated internal stem-loop beacon structures suggesting that the distance between fluorophores and quenchers was greater for the whole aptamer beacon candidates versus the isolated stem-loop structures. Beacon candidates were tested against two heat- or gamma radiation-killed SARS-CoV-2 Washington 1/2020 virus samples and three different COVID spike (S) proteins to test their effectiveness. Despite the higher background fluorescence, the whole aptamer beacons showed better signal-to-noise ratios and were selected for further investigation. Limit of detection (LOD) studies revealed that both the whole Song and whole MSA52 aptamer beacon candidates had a LOD of 9.61 × 103 genome equivalents in phosphate-buffered saline using the red channel of a Promega Quantus™ fluorometer which correlated well with confirmatory spectrofluorometry. Cross-reactivity studies using numerous COVID variants, related coronaviruses, and other common respiratory pathogens suggested greater COVID selectivity for the whole MSA52 versus the whole Song aptamer beacon candidate, indicating promise for specific COVID detection. Importantly, both whole aptamer beacon candidates exhibited very rapid "bind and detect" fluorescence increases within the first 1-2 min of mixing the beacons with killed SARS-CoV-2 viruses in 100 µl samples. Overall, this work illustrates the strong potential for aptamer beacons for rapid, on-site detection and presumptive diagnosis of COVID in breath condensates or other small liquid samples. This research highlights the strong potential of aptamer beacons for addressing the need for fast and convenient diagnostic tools in global health contexts, especially in resource-limited settings.

The Interventions and Challenges of Antimicrobial Stewardship in the Emergency Department

Over the last decades, we have witnessed a constant increase in infections caused by multi-drug-resistant strains in emergency departments. Despite the demonstrated effectiveness of antimicrobial stewardship programs in antibiotic consumption and minimizing multi-drug-resistant bacterium development, the characteristics of emergency departments pose a challenge to their implementation. The inclusion of rapid diagnostic tests, tracking microbiological results upon discharge, conducting audits with feedback, and implementing multimodal educational interventions have proven to be effective tools for optimizing antibiotic use in these units. Nevertheless, future multicenter studies are essential to determine the best way to proceed and measure outcomes in this scenario.

Co-Circulation of SARS-CoV-2 and Other Respiratory Pathogens in Upper and Lower Respiratory Tracts during Influenza Season 2022-2023 in Lazio Region

Lower respiratory tract infections (LRTIs) occur when there is a lower airway tract infection. They are well-known for increasing the susceptibility of patients to bacterial/fungal co-infections and super-infections. In this study, we present the results of our investigation, which involved 381 consecutive patients admitted to our hospital during the Influenza season from October 2022 to April 2023. Among the 381 specimens, 75 were bronchoalveolar (BAL), and 306 were nasopharyngeal swabs (NPSs). Notably, 34.4% of the examined samples tested positive for SARS-CoV-2. Of these, we observed that 7.96% of NPSs showed positivity only for other respiratory viruses, while a substantial percentage (77%) of BAL specimens exhibited positive results only for bacterial co-infections. The results of our study not only confirm the importance of co-infections in COVID-19 but also emphasize the significance of utilizing rapid diagnostic tests (RDTs) for the timely diagnosis of LRTIs. In fact, RDTs allow for the identification of multiple pathogens, providing clinicians with useful and timely information to establish effective therapy.

Modulation of the Host Response as a Therapeutic Strategy in Severe Lung Infections

Respiratory pathogens such as influenza and SARS-CoV-2 can cause severe lung infections leading to acute respiratory distress syndrome (ARDS). The pathophysiology of ARDS includes an excessive host immune response, lung epithelial and endothelial cell death and loss of the epithelial and endothelial barrier integrity, culminating in pulmonary oedema and respiratory failure. Traditional approaches for the treatment of respiratory infections include drugs that exert direct anti-pathogen effects (e.g., antivirals). However, such agents are typically ineffective or insufficient after the development of ARDS. Modulation of the host response has emerged as a promising alternative therapeutic approach to mitigate damage to the host for the treatment of respiratory infections; in principle, this strategy should also be less susceptible to the development of pathogen resistance. In this review, we discuss different host-targeting strategies against pathogen-induced ARDS. Developing therapeutics that enhance the host response is a pathogen-agnostic approach that will help prepare for the next pandemic.

Evaluation of Five Host Inflammatory Biomarkers in Early Diagnosis of Ventilator-Associated Pneumonia in Critically Ill Children: A Prospective Single Center Cohort Study

Background: Early diagnosis of ventilator-associated pneumonia (VAP) remains a challenge due to subjective clinical criteria and the low discriminative power of diagnostic tests. We assessed whether rapid molecular diagnostics in combination with Clinically Pulmonary Index Score (CPIS) scoring, microbiological surveillance and biomarker measurements of PTX-3, SP-D, s-TREM, PTX-3, IL-1β and IL-8 in the blood or lung could improve the accuracy of VAP diagnosis and follow-up in critically ill children. Methods: A prospective pragmatic study in a Pediatric Intensive Care Unit (PICU) was conducted on ventilated critically ill children divided into two groups: high and low suspicion of VAP according to modified Clinically Pulmonary Index Score (mCPIS). Blood and bronchial samples were collected on days 1, 3, 6 and 12 after event onset. Rapid diagnostics were used for pathogen identification and ELISA for PTX-3, SP-D, s-TREM, IL-1β and IL-8 measurements. Results: Among 20 enrolled patients, 12 had a high suspicion (mCPIS > 6), and 8 had a low suspicion of VAP (mCPIS < 6); 65% were male; and 35% had chronic disease. IL-1β levels at day 1 correlated significantly with the number of mechanical ventilation days (r_s = 0.67, p < 0.001) and the PICU stay (r = 0.66; p < 0.002). No significant differences were found in the levels of the other biomarkers between the two groups. Mortality was recorded in two patients with high VAP suspicion. Conclusions: PTX-3, SP-D, s-TREM, IL-1β and IL-8 biomarkers could not discriminate patients with a high or low suspicion of VAP diagnosis.

Are ELISA and PCR Discrepancies in the Identification of Chlamydia pneumoniae Caused by the Presence of "Chlamydia-Related Bacteria"?

Chlamydia are Gram-negative, intracellular pathogens colonizing the epithelial mucosa. They cause primarily atypical pneumonia and have recently been associated with chronic diseases. Diagnostics rely almost exclusively on serological methods; PCR tests are used rarely because in patients with positive ELISA, it is nearly impossible to identify chlamydial DNA. To understand this issue, we elaborated a reliable and sensitive nested PCR method (panNPCR) for identifying all Chlamydiales species, not only in sputa, but also in clotted blood. Sequencing of the PCR product revealed that 41% of positive sputa samples and 66% of positive blood samples were not infected by Chlamydia but with "Chlamydia-related bacteria" such as Rhabdochlamydia sp., Parachlamydia sp., Protochlamydia sp., Neochlamydia sp., Mesochlamydia elodeae and lacustris, Piscichlamydia salmonis, and Estrella lausannensis. Consequently, we propose that there might be more than four human pathogenic Chlamydia species. We did not find any clear correlation between increased levels of antibodies and the presence of their DNA. Chlamydialles DNA was found in sputa samples from individuals positive for IgG or IgA but not in blood samples. Thus, elevated IgG and IgA levels are not reliable markers of chronic infection, and the presence of persistent forms should be proved by panNPCR. Apparently, the differences between ELISA and DNA amplification results have three main methodological reasons. The first one is the threshold occurrence of chlamydial genetic material in sputum and blood. The second one is the fact that a significant part of the samples can have DNA with sequences different from those of other species of the order Chlamydiales. The third one is the high background characteristic for ELISA, the absence of paired sera, and the vague interpretation of the gray zone.