Practical Guidance for Clinical Microbiology Laboratories: Updated guidance for processing respiratory tract samples from people with cystic fibrosis.

SUMMARYThis guidance presents recommendations for clinical microbiology laboratories for processing respiratory samples from people with cystic fibrosis (pwCF). Appropriate processing of respiratory samples is crucial to detect bacterial and fungal pathogens, guide treatment, monitor the epidemiology of cystic fibrosis (CF) pathogens, and assess therapeutic interventions. Thanks to CF transmembrane conductance regulator modulator therapy, the health of pwCF has improved, but as a result, fewer pwCF spontaneously expectorate sputum. Thus, the collection of sputum samples has decreased, while the collection of other types of respiratory samples such as oropharyngeal and bronchoalveolar lavage samples has increased. To optimize the detection of microorganisms, including Pseudomonas aeruginosa, Staphylococcus aureus, Haemophilus influenzae, and Burkholderia cepacia complex; other less common non-lactose fermenting Gram-negative bacilli, e.g., Stenotrophomonas maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species; and yeasts and filamentous fungi, non-selective and selective culture media are recommended for all types of respiratory samples, including samples obtained from pwCF after lung transplantation. There are no consensus recommendations for laboratory practices to detect, characterize, and report small colony variants (SCVs) of S. aureus, although studies are ongoing to address the potential clinical impact of SCVs. Accurate identification of less common Gram-negative bacilli, e.g., S. maltophilia, Inquilinus, Achromobacter, Ralstonia, and Pandoraea species, as well as yeasts and filamentous fungi, is recommended to understand their epidemiology and clinical importance in pwCF. However, conventional biochemical tests and automated platforms may not accurately identify CF pathogens. MALDI-TOF MS provides excellent genus-level identification, but databases may lack representation of CF pathogens to the species-level. Thus, DNA sequence analysis should be routinely available to laboratories for selected clinical circumstances. Antimicrobial susceptibility testing (AST) is not recommended for every routine surveillance culture obtained from pwCF, although selective AST may be helpful, e.g., for unusual pathogens or exacerbations unresponsive to initial therapy. While this guidance reflects current care paradigms for pwCF, recommendations will continue to evolve as CF research expands the evidence base for laboratory practices.

Influenza virus and pneumococcal neuraminidases enhance catalysis by similar yet distinct sialic acid-binding strategies.

Influenza A viruses and the bacterium Streptococcus pneumoniae (pneumococci) both express neuraminidases that catalyze release of sialic acid residues from oligosaccharides and glycoproteins. Although these respiratory pathogen neuraminidases function in a similar environment, it remains unclear if these enzymes use similar mechanisms for sialic acid cleavage. Here, we compared the enzymatic properties of neuraminidases from two influenza A subtypes (N1 and N2) and the pneumococcal strain TIGR4 (NanA, NanB, and NanC). Insect cell-produced N1 and N2 tetramers exhibited calcium-dependent activities and stabilities that varied with pH. In contrast, E. coli-produced NanA, NanB, and NanC were isolated as calcium insensitive monomers with stabilities that were more resistant to pH changes. Using a synthetic substrate (MUNANA), all neuraminidases showed similar pH optimums (pH 6-7) that were primarily defined by changes in catalytic rate rather than substrate binding affinity. Upon using a multivalent substrate (fetuin sialoglycans), much higher specific activities were observed for pneumococcal neuraminidases that contain an additional lectin domain. In virions, N1 and especially N2 also showed enhanced specific activity toward fetuin that was lost upon the addition of detergent, indicating the sialic acid-binding capacity of neighboring hemagglutinin molecules likely contributes to catalysis of natural multivalent substrates. These results demonstrate that influenza and pneumococcal neuraminidases have evolved similar yet distinct strategies to optimize their catalytic activity.

Tiny swabs: nasal swabs integrated into tube caps facilitate large-scale self-collected SARS-CoV-2 testing.

The COVID-19 pandemic spurred the development of innovative solutions for specimen collection and molecular detection for large-scale community testing. Among these developments is the RHINOstic nasal swab, a plastic anterior nares swab built into the cap of a standard matrix tube that facilitates automated processing of up to 96 specimens at a time. In a study of unsupervised self-collection utilizing these swabs, we demonstrate comparable analytic performance and shipping stability compared to traditional anterior nares swabs, as well as significant improvements in laboratory processing efficiency. The use of these swabs may allow laboratories to accommodate large numbers of sample collections during periods of high testing demand. Automation-friendly nasal swabs are an important tool for high-throughput processing of samples that may be adopted in response to future respiratory viral pandemics.

Analyzing infections caused by 11 respiratory pathogens in children: Pre- and post-COVID-19 pandemic trends in China.

With the lifting of coronavirus disease 2019 (COVID-19) restrictions in December 2022 in China, the population was widely infected with COVID-19. We aim to analyzed changes in the epidemiological characteristics of other respiratory pathogens in children before and after the COVID-19 pandemic. We conducted a retrospective analysis of 44 704 children with acute respiratory infections who underwent 11 respiratory pathogen tests based on multiplex polymerase chain reaction between February and December in both 2022 and 2023. The total pathogen detection rate (24861, 74.80% vs. 6423, 56.01%; p = 0.000) and detection rates of coinfection (4059, 12.21% vs. 676, 5.89%; p = 0.000) in 2023 was significantly higher than that in 2022. The detection rates of influenza A (2567, 7.72% vs. 222, 1.94%; p = 0.000), influenza B (383, 1.15% vs. 37, 0.32%; p = 0.000), human parainfluenza virus (2175, 6.54% vs. 602, 5.25%; p = 0.000), human metapneumovirus (1354, 4.07% vs. 346, 3.01%; p = 0.000), respiratory syncytial virus (3148, 9.47% vs. 870, 7.59%; p = 0.000), and Mycoplasma pneumonia (MP; 9494, 28.56% vs. 1790, 15.61%; p = 0.000) in 2023 were significantly higher than those in 2022, whereas the detection rates of human adenovirus (1124, 3.38% vs. 489, 4.26%; p = 0.000) and human bocavirus (629, 1.89% vs. 375, 3.27%; p = 0.000) were significantly lower than those in 2022. Chlamydia, human rhinovirus, and human coronavirus showed similar detection rates between 2023 and 2022. In 2023, the influenza virus and human parainfluenza virus regained seasonal characteristic, an outbreak of MP infection occurred, the epidemic season of respiratory syncytial virus changed, and the proportion of children with acute respiratory infection aged 0-28 days and over 3 years old increased. Influenza B, metapneumovirus, and human bocavirus were detected in children aged 0-28 days in 2023, but not in 2022. After the COVID-19 pandemic, we should be alert to the increase of respiratory diseases and the change of epidemic season and susceptible age.

Changing respiratory pathogens infection patterns after COVID-19 pandemic in Shanghai, China.

To assess the positive rate of 11 respiratory pathogens in 2023, providing a comprehensive summary and analysis of the respiratory infection patterns after COVID-19 pandemic. The study comprised 7544 inpatients suspected of respiratory infections who underwent respiratory pathogen multiplex polymerase chain reaction tests from July 2022 to December 31, 2023. We analyzed the positive rate of 11 pathogens over 18 months and the characterization of infection patterns among different age groups and immune states. Among 7544 patients (age range 4 months to 104 years, 44.99% female), the incidence of infected by at least one of the 11 pathogens was 26.07%. Children (55.18%, p < 0.05) experienced a significantly higher infection probability than adults (20.88%) and old (20.66%). Influenza A virus (8.63%), Mycoplasma pneumoniae (5.47%), and human rhinovirus (5.12%) were the most common pathogens. In children, M. pneumoniae (35.96%) replaced the predominant role of human respiratory syncytial virus (HRSV) (5.91%) in the pathogen spectrum. Age, immunosuppressed state, and respiratory chronic conditions were associated with a significantly higher risk of mixed infection. Immunosuppressed patients were more vulnerable to human coronavirus (4.64% vs. 1.65%, p < 0.05), human parainfluenza virus (3.46% vs. 1.69%, p < 0.05), and HRSV (2.27% vs. 0.55%, p < 0.05). Patterns in respiratory infections changed following regional epidemic control measures and the COVID-19 pandemic.

Simple, sensitive, and visual detection of 12 respiratory pathogens with one-pot-RPA-CRISPR/Cas12a assay.

Respiratory infections pose a serious threat to global public health, underscoring the urgent need for rapid, accurate, and large-scale diagnostic tools. In recent years, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system, combined with isothermal amplification methods, has seen widespread application in nucleic acid testing (NAT). However, achieving a single-tube reaction system containing all necessary components is challenging due to the competitive effects between recombinase polymerase amplification (RPA) and CRISPR/Cas reagents. Furthermore, to enable precision medicine, distinguishing between bacterial and viral infections is essential. Here, we have developed a novel NAT method, termed one-pot-RPA-CRISPR/Cas12a, which combines RPA with CRISPR molecular diagnostic technology, enabling simultaneous detection of 12 common respiratory pathogens, including six bacteria and six viruses. RPA and CRISPR/Cas12a reactions are separated by paraffin, providing an independent platform for RPA reactions to generate sufficient target products before being mixed with the CRISPR/Cas12a system. Results can be visually observed under LED blue light. The sensitivity of the one-pot-RPA-CRISPR/Cas12a method is 2.5 × 100 copies/µL plasmids, with no cross-reaction with other bacteria or viruses. Additionally, the clinical utility was evaluated by testing clinical isolates of bacteria and virus throat swab samples, demonstrating favorable performance. Thus, our one-pot-RPA-CRISPR/Cas12a method shows immense potential for accurate and large-scale detection of 12 common respiratory pathogens in point-of-care testing.

Advances in nucleic acid aptamer-based detection of respiratory virus and bacteria: a mini review.

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

Impacts of environmental factors on the aetiological diagnosis and disease severity of community-acquired pneumonia in China: a multicentre, hospital-based, observational study.

Environmental exposures are known to be associated with pathogen transmission and immune impairment, but the association of exposures with aetiology and severity of community-acquired pneumonia (CAP) are unclear. A retrospective observational study was conducted at nine hospitals in eight provinces in China from 2014 to 2019. CAP patients were recruited according to inclusion criteria, and respiratory samples were screened for 33 respiratory pathogens using molecular test methods. Sociodemographic, environmental and clinical factors were used to analyze the association with pathogen detection and disease severity by logistic regression models combined with distributed lag nonlinear models. A total of 3323 CAP patients were included, with 709 (21.3%) having severe illness. 2064 (62.1%) patients were positive for at least one pathogen. More severe patients were found in positive group. After adjusting for confounders, particulate matter (PM) 2.5 and 8-h ozone (O3-8h) were significant association at specific lag periods with detection of influenza viruses and Klebsiella pneumoniae respectively. PM10 and carbon monoxide (CO) showed cumulative effect with severe CAP. Pollutants exposures, especially PM, O3-8h, and CO should be considered in pathogen detection and severity of CAP to improve the clinical aetiological and disease severity diagnosis.

Epidemiological trends of respiratory tract pathogens detected via mPCR in Australian adult patients before COVID-19.

BACKGROUND: Respiratory tract infections (RTIs) are a major global health burden due to their high morbidity and mortality. This retrospective study described the epidemiology of respiratory pathogens in adults over a 5-year period at an Australian tertiary healthcare network. METHODS: All multiplex reverse transcription polymerase chain reaction respiratory samples taken between the 1st of November 2014 and the 31st of October 2019 were included in this study. Overall prevalence and variations according to seasons, age groups and sex were analysed, as well as factors associated with prolonged hospital and intensive care length of stay. RESULTS: There were 12,453 pathogens detected amongst the 12,185 positive samples, with coinfection rates of 3.7%. Picornavirus (Rhinovirus), Influenza A and respiratory syncytial virus were the most commonly detected pathogens. Mycoplasma pneumoniae was the most commonly detected atypical bacteria. Significant differences in the prevalence of Chlamydia pneumoniae and Human metapneumovirus infections were found between sexes. Longest median length of intensive care and hospital stay was for Legionella species. Seasonal variations were evident for certain pathogens. CONCLUSIONS: The high rates of pathogen detection and hospitalisation in this real-world study highlights the significant burden of RTIs, and the urgent need for an improved understanding of the pathogenicity as well as preventative and treatment options of RTIs.

Epidemiological changes in respiratory pathogen transmission among children with acute respiratory infections during the COVID-19 pandemic in Kunming, China.

BACKGROUND: Acute respiratory infections are a leading cause of morbidity and mortality in children. However, studies on the prevalence of respiratory viruses among children with acute respiratory infections in Kunming, China, are lacking. Therefore, we aimed to investigate the epidemiological characteristics of respiratory pathogens among children with acute respiratory infections in Kunming during the coronavirus disease 2019 pandemic. METHODS: Nasopharyngeal swab samples were collected from 4956 children with acute respiratory infections at Yunnan Provincial First People's Hospital between January 2020 and December 2022, patients with COVID-19 were excluded from the study. Multiplex reverse transcription polymerase chain reaction was used to detect respiratory pathogens. RESULTS: The frequency of respiratory pathogens among children was significantly lower in 2020 than in 2021 and 2022. The following pathogens had the highest prevalence rates (in descending order) from 2020 to 2022: HRV > RSV > PIV > ADV > MP; HRV > RSV > HADV > PIV > MP and HRV > Mp > HADV > H3N2 > HMPV. The overall frequency of respiratory pathogens exhibited an inverted U-shape with increasing age among the children. Human bocavirus, human parainfluenza virus, and human respiratory syncytial virus were the dominant respiratory viruses in children aged ≤ 3 years, whereas Mycoplasma pneumoniae was the dominant respiratory pathogen in children aged > 3 years. HRV has the highest prevalence and is the main pathogen of mixed infection. The prevalence of the influenza A virus has decreased significantly, whereas HRSV and Mp are found to be seasonal. CONCLUSIONS: Our findings offer an objective evaluation of transmission dynamics and epidemiological shifts in respiratory pathogens during the coronavirus disease 2019 pandemic in Kunming, serving as a basis for informed decision-making, prevention, and treatment strategies.

Co-detection of respiratory pathogens among ILI patients: characterization of samples collected during the 2018/19 and 2019/20 pre-pandemic seasons.

Influenza-like illness (ILI) patients co-detected with respiratory pathogens exhibit poorer health outcomes than those with single infections. To address the paucity of knowledge concerning the incidence of concurrent respiratory pathogens, their relationships, and the clinical differences between patients detected with single and multiple pathogens, we performed an in-depth characterization of the oropharyngeal samples of primary care patients collected in Genoa (Northwest Italy), during winter seasons 2018/19-2019/20.The apriori algorithm was employed to evaluate the incidence of viral, bacterial, and viral-bacterial pairs during the study period. The grade of correlation between pathogens was investigated using the Phi coefficient. Factors associated with viral, bacterial or viral-bacterial co-detection were assessed using logistic regression.The most frequently identified pathogens included influenza A, rhinovirus, Haemophilus influenzae and Streptococcus pneumoniae. The highest correlations were found between bacterial-bacterial and viral-bacterial pairs, such as Haemophilus influenzae-Streptococcus pneumoniae, adenovirus-Haemophilus influenzae, adenovirus-Streptococcus pneumoniae, RSV-A-Bordetella pertussis, and influenza B Victoria-Bordetella parapertussis. Viruses were detected together at significantly lower rates. Notably, rhinovirus, influenza, and RSV exhibited significant negative correlations with each other. Co-detection was more prevalent in children aged < 4, and cough was shown to be a reliable indicator of viral co-detection.Given the evolving epidemiological landscape following the COVID-19 pandemic, future research utilizing the methodology described here, while considering the circulation of SARS-CoV-2, could further enrich the understanding of concurrent respiratory pathogens.

Are secondary bacterial pneumonia mortalities increased because of insufficient pro-resolving mediators?

Respiratory viral infections, including respiratory syncytial virus (RSV), parainfluenza viruses and type A and B influenza viruses, can have severe outcomes. Bacterial infections frequently follow viral infections, and influenza or other viral epidemics periodically have higher mortalities from secondary bacterial pneumonias. Most secondary bacterial infections can cause lung immunosuppression by fatty acid mediators which activate cellular receptors to manipulate neutrophils, macrophages, natural killer cells, dendritic cells and other lung immune cells. Bacterial infections induce synthesis of inflammatory mediators including prostaglandins and leukotrienes, then eventually also special pro-resolving mediators, including lipoxins, resolvins, protectins and maresins, which normally resolve inflammation and immunosuppression. Concurrent viral and secondary bacterial infections are more dangerous, because viral infections can cause inflammation and immunosuppression before the secondary bacterial infections worsen inflammation and immunosuppression. Plausibly, the higher mortalities of secondary bacterial pneumonias are caused by the overwhelming inflammation and immunosuppression, which the special pro-resolving mediators might not resolve.

The impact of the COVID-19 pandemic on the circulation, seasonal distribution, and research of other respiratory pathogens in Turkey.

INTRODUCTION: Respiratory infections are one of the world's most common infectious diseases. Following the species, numbers, and seasonal distribution of acute respiratory agents is important for the protection of public health. Our study aimed to determine the effect of the COVID-19 pandemic on the circulation and seasonal distribution of non-SARS-CoV-2 respiratory tract agents and research on non-SARS-CoV-2 agents. METHODS: The results of the Multiplex PCR respiratory panel of 3702 nasopharyngeal swab samples sent between January 2018 and December 2021 were evaluated retrospectively. Scientific articles on acute respiratory infections between 2010 and 2021 from Turkey were analyzed in Scopus for bibliometric analysis. RESULTS: 1.382 pathogens were detected. During the pandemic, the number of non-SARS-CoV-2 pathogens was found to be statistically significantly lower than before the pandemic. It was determined that while the most frequent agent before the pandemic was the Adenovirus, the most frequent agent was the RSV-A during the pandemic. Our network analysis of keywords indicated that academic interest in 2020-21 was directed toward COVID-19, which coincides with the pandemic period. CONCLUSIONS: Our study determined the fact that the incidence, species, and seasonal distribution of non-SARS-COV-2 respiratory agents changed after the onset of the pandemic. Increasing the identification and following-up of these pathogens in health organizations and also presenting these data to literature and sharing with academics is important. We are of the opinion that the results of our study shall shed light on the epidemiology of changing respiratory infections and the prevention and following-up of future health problems.

Shared sanitation facilities and risk of respiratory virus transmission in resource-poor settings: A COVID-19 modeling case study.

Water supply and sanitation are essential household services frequently shared in resource-poor settings. Shared sanitation can increase the risk of enteric pathogen transmission due to suboptimal cleanliness of facilities used by large numbers of individuals. It also can potentially increase the risk of respiratory disease transmission. As sanitation is an essential need, shared sanitation facilities may act as important respiratory pathogen transmission venues even with strict control measures such as stay-at-home recommendations in place. This analysis explores how behavioral and infrastructural conditions surrounding shared sanitation may individually and interactively influence respiratory pathogen transmission. We developed an individual-based community transmission model using COVID-19 as a motivating example parameterized from empirical literature to explore how transmission in shared latrines interacts with transmission at the community level. We explored mitigation strategies, including infrastructural and behavioral interventions. Our review of empirical literature confirms that shared sanitation venues in resource-poor settings are relatively small with poor ventilation and high use patterns. In these contexts, shared sanitation facilities may act as strong drivers of respiratory disease transmission, especially in areas reliant on shared facilities. Decreasing dependence on shared latrines was most effective at attenuating sanitation-associated transmission. Improvements to latrine ventilation and handwashing behavior were also able to decrease transmission. The type and order of interventions are important in successfully attenuating disease risk, with infrastructural and engineering controls being most effective when administered first, followed by behavioral controls after successful attenuation of sufficient alternate transmission routes. Beyond COVID-19, our modeling framework can be extended to address water, sanitation, and hygiene measures targeted at a range of environmentally mediated infectious diseases.

Association of antenatal and early childhood air pollution and greenspace exposures with respiratory pathogen upper airway acquisitions and respiratory health outcomes.

The association of air pollution and greenspace with respiratory pathogen acquisition and respiratory health was investigated in a community-based birth-cohort of 158 Australian children. Weekly nasal swabs and daily symptom-diaries were collected for 2-years, with annual reviews from ages 3-7-years. Annual exposure to fine-particulate-matter (PM2.5), nitrogen-dioxide (NO2), and normalised-difference-vegetation-index (NDVI) was estimated for pregnancy and the first 2-years-of-life. We examined rhinovirus, any respiratory virus, Streptococcus pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae detections in the first 3-months-of-life, age at initial pathogen detection, wheezing in the first 2-years, and asthma at ages 5-7-years. Our findings suggest that higher NDVI was associated with fewer viral and M. catarrhalis detections in the first 3-months, while increased PM2.5 and NO2 were linked to earlier symptomatic rhinovirus and H. influenzae detections, respectively. However, no associations were observed with wheezing or asthma. Early-life exposure to air pollution and greenspace may influence early-life respiratory pathogen acquisition and illness. .

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

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

High incidence of the virus among respiratory pathogens in children with lower respiratory tract infection in northwestern China.

Lower respiratory tract infection (LRTI) is one of the major reasons for childhood mortality that threaten the health of the public. We aimed to investigate the epidemiological pathogens and their infection analysis among children with LRTI. Sputum specimens were collected for polymerase chain reaction detection and microbiological tests to identify the viral infection and bacterial infection. The serological specimens were separated from venous blood using for Mycoplasma pneumoniae and Chlamydia pneumoniae detection. The virus was confirmed in 86.2% of the children. Human rhinovirus (38.3%), respiratory syncytial virus (32.1%), and parainfluenza virus type 3 (27.2%) were the most frequently identified pathogens. Patients with viral and bacterial coinfection showed younger age (p = 0.032), a higher proportion of wheezing rales (p = 0.032), three depressions sign (p = 0.028), and tachypnea (p = 0.038), and more likely associated with severe pneumonia (p = 0.035). Additionally, older children were more susceptible to viral-atypical bacterial coinfection (p = 0.032). Vomiting (p = 0.011) and fever (p = 0.003) were more likely to occur in children with viral-atypical bacterial coinfection. Attention should be paid to the virus infection of LRTI, as viral-bacterial coinfection and viral-atypical bacterial co-infection may have a detrimental impact on the gravity of LTRI.

High detection rate of viral pathogens in nasal discharge in children aged 0 till 5 years.

Respiratory tract infections (RTI) in children remain a cause of disease burden worldwide. Nasopharyngeal (NP) & oropharyngeal (OP) swabs are used for respiratory pathogen detection, but hold disadvantages particularly for children, highlighting the importance and preference for a child friendly detection method. We aimed to evaluate the performance and tolerability of a rhinorrhea swab (RS) in detecting viral pathogens when compared to a combined OP(/NP) or mid-turbinate (MT) nasal swab. This study was conducted between September 2021 and July 2022 in the Netherlands. Children aged 0-5 years, with an upper RTI and nasal discharge, were included and received a combined swab and a RS. Multiplex polymerase chain reaction (PCR) and severe acute respiratory syndrome coronavirus-2 PCR were used for viral pathogen detection. Tolerability was evaluated with a questionnaire and visual analog scale (VAS) scores. During 11 months 88 children were included, with a median age of 1.00 year [interquartile range 0.00-3.00]. In total 122 viral pathogens were detected in 81 children (92%). Sensitivity and specificity of the RS compared to a combined swab were respectively 97% (95% confidence interval [CI] 91%-100%) and 78% (95% CI 45%-94%). Rhinorrhea samples detected more pathogens than the (combined) nasal samples, 112 versus 108 respectively. Median VAS scores were significantly lower for the RS in both children (2 vs. 6) and their parents (0 vs. 5). A RS can therefore just as effectively/reliably detect viral pathogens as the combined swab in young children and is better tolerated by both children and their parents/caregivers.

Comparison of common human respiratory pathogens among hospitalized children aged ≤ 6 years in Hainan Island, China, during spring and early summer in 2019-2021.

The coronavirus disease 2019 (COVID-19) pandemic and related public health intervention measures have been reported to have resulted in the reduction of infections caused by influenza viruses and other common respiratory viruses. However, the influence may be varied in areas that have different ecological, economic, and social conditions. This study investigated the changing epidemiology of 8 common respiratory pathogens, including Influenza A (IFVA), Influenza B (IFVB), Respiratory syncytial virus (HRSV), rhinovirus (RV), Human metapneumovirus Adenovirus, Human bocavirus, and Mycoplasma pneumoniae, among hospitalized children during spring and early summer in 2019-2021 in two hospitals in Hainan Island, China, in the COVID-19 pandemic era. The results revealed a significant reduction in the prevalence of IFVA and IFVB in 2020 and 2021 than in 2019, whereas the prevalence of HRSV increased, and it became the dominant viral pathogen in 2021. RV was one of the leading pathogens in the 3 year period, where no significant difference was observed. Phylogenetic analysis revealed close relationships among the circulating respiratory viruses. Large scale studies are needed to study the changing epidemiology of seasonal respiratory viruses to inform responses to future respiratory virus pandemics.

Used paper tissues for pathogen identification in acute respiratory infection.

During the Belgian winter and spring season 2022-2023, we investigated the potential of used paper tissue (UPT) as a noninvasive sampling method for the diagnosis of acute respiratory infections. Screening for respiratory pathogens was done using an in-house developed respiratory panel for simultaneous detection of 22 respiratory viruses and seven nonviral pathogens. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. Pathogens that were identified in nasal swabs could also be detected in concurrent UPT from the same patient. In all cases that tested positive on an antigen-detection rapid diagnostic test, the corresponding virus could be detected in UPT. The collection of UPT could be useful in epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 and other coronaviruses, as well as other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses including EV-D68, parainfluenzaviruses, and Streptococcus pneumoniae. Multiple respiratory pathogens could be detected in UPTs of collectivities, confirming its applicability for community testing. This is especially interesting for screening in nursing homes, centers for the disabled, schools or other settings were taking nasal or nasopharyngeal samples is cumbersome.