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OBJECTIVE: To investigate the diagnostic utility of targeted next-generation sequencing (tNGS) in the diagnosis of lower respiratory tract infections. METHODS: Patients with lower respiratory tract infection in East Area of Yantai Yantaishan Hospital from December 2021 to September 2023 were retrospectively analyzed. Sputum samples were tested using both tNGS technology and conventional microbiological examination. Data were collected on general clinical features and test outcomes. The study evaluated the efficacy of tNGS by comparing its positive detection rate against traditional methods and analyzing detection differences among patients with varying clinical characteristics. Receiver operating characteristic (ROC) analysis was used to determine the diagnostic accuracy of both testing methods. RESULTS: A total of 281 patients were included, with corresponding sputum specimens. The tNGS method showed a higher positivity rate of 90.0%, significantly outperforming the conventional method's rate of 70.82% (P<0.05). Among 199 patients with concordant positive results, 38.22% fully agreed, while 53.40% completely disagreed between the two methods. Mycobacterium tuberculosis, Candida albicans, and Pseudomonas aeruginosa were the most frequently detected pathogens, respectively. tNGS significantly reduced the time required for pathogen detection (P<0.001) and identified a higher rate of mixed infections compared to conventional methods (49.11% vs 2.85%, P<0.001). Positive tNGS detection rates significantly differed between patients with abnormal vs normal C-reactive protein or procalcitonin levels. The AUC for tNGS was 0.867, indicating superior diagnostic accuracy over the conventional method (P<0.05). CONCLUSIONS: tNGS technology demonstrates a high positivity rate and rapid pathogen detection in lower respiratory tract infections, with notable advantages in identifying mixed infections. This method shows potential for enhancing diagnostic accuracy and treatment decisions in clinical settings.
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Viral lower respiratory tract infections (LRTIs), including rhinovirus and respiratory syncytial virus during early childhood, have been linked to subsequent asthma. However, the impact of other respiratory viruses remains unclear. We analyzed nationwide Korean data from January 1, 2008, to December 31, 2018, utilizing the national health insurance database. Our study focused on 19 169 meticulously selected children exposed to severe respiratory infections requiring hospitalization with documented viral pathogens, matched with 191 690 unexposed children at a ratio of 1:10 using incidence density sampling. Our findings demonstrate that asthma exacerbation rates were higher among the exposed cohort than the unexposed cohort over a mean follow-up of 7.8 years. We observed elevated risks of asthma exacerbation and newly developed asthma compared to the unexposed cohort. Hospitalization due to rhinovirus, respiratory syncytial virus, influenza, metapneumovirus, and adenovirus was related to increased asthma exacerbations. Notably, we found a stronger association in cases of multiple LRTI hospitalizations. In conclusion, our study shows that early childhood respiratory viral infections are related to subsequent asthma exacerbations and new asthma diagnoses.
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Asma , Hospitalización , Infecciones del Sistema Respiratorio , Humanos , Asma/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Hospitalización/estadística & datos numéricos , Masculino , Preescolar , Femenino , Lactante , República de Corea/epidemiología , Niño , Virosis/epidemiología , Incidencia , Factores de Riesgo , Infecciones por Virus Sincitial Respiratorio/epidemiología , Rhinovirus/aislamiento & purificaciónRESUMEN
BACKGROUND: Bacterial pneumonia is among the leading causes of morbidity and mortality worldwide. The extensive misuse and overuse of antibiotics observed during the Corona Virus Disease 2019 (COVID-19) pandemic may have changed the patterns of pathogens causing bacterial pneumonia and their antibiotic susceptibility profiles. This study was designed to establish the prevalence of culture-confirmed bacterial pneumonia and describe their antimicrobial susceptibility profile in adult patients who presented with signs and symptoms of lower respiratory tract infections (LRTIs) during the COVID-19 pandemic. METHODOLOGY: This hospital-based cross-sectional study was conducted from July 2021 to July 2022 at a zonal referral hospital and two district hospitals in Mwanza, Tanzania. Demographic and clinical data were collected using a standardized questionnaire. Sputum samples were processed by conventional culture followed by the identification of isolates and antibiotic susceptibility testing. Descriptive data analysis was performed using STATA version 15.0. RESULTS: A total of 286 patients with a median age of 40 (IQR 29-60) years were enrolled in the study. More than half of the patients enrolled were females (52.4%, n = 150). The overall prevalence of bacterial pneumonia was 34.3% (n = 98). The majority of the bacterial pathogens isolated were Gram-negative bacteria (GNB) (61.2%, 60/98), with a predominance of Klebsiella spp., 38.8% (38/98), followed by Streptococcus pyogenes (21.4%, 21/98). Multi drug resistant (MDR) bacteria were detected in 72/98 (73.5%) of the isolates. The proportions of GNB-resistant strains were 60.0% (36/60) for ciprofloxacin, 60% (36/60) for amoxicillin, 60% (36/60) for amoxicillin, 68.3% (41/60) for trimethoprim-sulfamethoxazole and 58.3% (35/60) for ceftriaxone. CONCLUSION: One-third of the patients with signs and symptoms of LRTIs had laboratory-confirmed bacterial pneumonia with a predominance of Gram negative MDR bacteria. This calls for continuous antimicrobial resistance (AMR) surveillance and antimicrobial stewardship programs in the study setting and other settings in developing countries as important strategies for tackling AMR.
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BACKGROUND: The true burden of acute lower respiratory tract diseases (aLRTD; includes acute lower respiratory tract infection, acute exacerbation of pre-existing heart failure and chronic lung disease) among adults presenting to primary care, and the proportion that are potentially vaccine preventable, is unknown. AIMS: To describe aLRTD incidence in adults presenting to primary care; estimate proportions caused by RSV, SARS-CoV-2 and pneumococcus; and investigate disease burden from patient and NHS perspectives. DESIGN & SETTING: Primary care prospective cohort study conducted in six representative General Practices (total Ì´83 000 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 and 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.
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Human parainfluenza viruses (HPIVs) are a significant cause of acute lower respiratory tract infections (ALRTIs) among young children and elderly individuals worldwide. The four types of HPIVs (HPIV1-4) can cause recurrent infections and pose a significant economic burden on health care systems globally. However, owing to the limited availability of complete genome sequences, the genetic evolution of these viruses and the development of vaccines and antiviral treatments are hampered. To address this issue, this study utilized next-generation sequencing to obtain 156 complete genome sequences of HPIV1-4, which were isolated from hospitalized children with ALRTIs in six regions of China between 2015 and 2021. This study revealed multiple clades, lineages, or sublineages of HPIVs circulating in mainland China, with a novel clade D of HPIV1 identified as geographically restricted to China. Moreover, this study identified the endemic dominant genotype of HPIV3, lineage C3, which has widely spread and continuously circulated in China. Bioinformatic analysis of the genome sequences revealed that the proteins of HPIV3 possessed the most variable sites, with the P protein showing more diversity than the other proteins among all types of HPIVs. The HN proteins of HPIV1-3 are all under negative/purifying selection, and two amino acid substitutions in the HN proteins correspond to known mAb neutralizing sites in the two HPIV3 strains. These findings provide crucial insights into the genetic diversity and evolutionary dynamics of HPIVs circulating among children in China and may facilitate research on the molecular diagnosis, vaccine development, and surveillance of HPIVs.IMPORTANCEPhylogenetic analysis revealed the prevalence of multiple clades, lineages, or sublineages of human parainfluenza viruses (HPIVs) circulating in mainland China. Notably, a unique evolutionary branch of HPIV1 containing only Chinese strains was identified and designated clade D. Furthermore, in 2023, HPIV3 strains from Pakistan and Russia formed a new lineage within clade C, named C6. The first HPIV4b sequence obtained in this study from China belongs to lineage C2. Evolutionary rate assessments revealed that both the HN and whole-genome sequences of HPIV3 presented the lowest evolutionary rates compared with those of the other HPIV types, with rates of 6.98E-04 substitutions/site/year (95% HPD: 5.87E-04 to 8.25E-03) and 5.85E-04 substitutions/site/year (95% HPD: 5.12E-04 to 6.62E-04), respectively. Recombination analysis revealed a potential recombination event in the F gene of an HPIV1 strain in this study. Additionally, all the newly obtained HPIV1-3 strains exhibited negative selection pressure, and two mutations were identified in the HN protein of two HPIV3 strains at monoclonal antibody-binding sites.
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Introduction: Off-season upsurge of respiratory syncytial virus (RSV) infection with changed characteristics and heightened clinical severity during the post-COVID-19 era are raising serious concerns. This study aimed to develop and validate a nomogram for predicting the risk of severe acute lower respiratory tract infection (SALRTI) in children hospitalized for RSV infection during the post-COVID-19 era using machine learning techniques. Methods: A multicenter retrospective study was performed in nine tertiary hospitals in Yunnan, China, enrolling children hospitalized for RSV infection at seven of the nine participating hospitals during January-December 2023 into the development dataset. Thirty-nine variables covering demographic, clinical, and laboratory characteristics were collected. Primary screening and dimension reduction of data were performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression, followed by identification of independent risk factors for RSV-associated SALRTI using Logistic regression, thus finally establishing a predictive nomogram model. Performance of the nomogram was internally evaluated by receiver operating characteristic (ROC) curve, calibration curve, and decision curve analysis (DCA) based on the development dataset. External validation of our model was conducted using same methods based on two independent RSV cohorts comprising pediatric RSV inpatients from another two participating hospitals between January-March 2024. Results: The development dataset included 1102 patients, 239 (21.7%) of whom developed SALRTI; while the external validation dataset included 249 patients (142 in Lincang subset and 107 in Dali subset), 58 (23.3%) of whom were diagnosed as SALRTI. Nine variables, including age, preterm birth, underlying condition, seizures, neutrophil-lymphocyte ratio (NLR), interleukin-6 (IL-6), lactate dehydrogenase (LDH), D-dimer, and co-infection, were eventually confirmed as the independent risk factors of RSV-associated SALRTI. A predictive nomogram was established via integrating these nine predictors. In both internal and external validations, ROC curves indicated that the nomogram had satisfactory discrimination ability, calibration curves demonstrated good agreement between the nomogram-predicted and observed probabilities of outcome, and DCA showed that the nomogram possessed favorable clinical application potential. Conclusion: A novel nomogram combining several common clinical and inflammatory indicators was successfully developed to predict RSV-associated SALRTI. Good performance and clinical effectiveness of this model were confirmed by internal and external validations.
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COVID-19 , Hospitalización , Nomogramas , Infecciones por Virus Sincitial Respiratorio , SARS-CoV-2 , Humanos , Infecciones por Virus Sincitial Respiratorio/diagnóstico , Infecciones por Virus Sincitial Respiratorio/epidemiología , COVID-19/diagnóstico , COVID-19/epidemiología , Masculino , Femenino , Lactante , Estudios Retrospectivos , Preescolar , China/epidemiología , Niño , Índice de Severidad de la Enfermedad , Factores de Riesgo , Infecciones del Sistema Respiratorio/diagnóstico , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Aprendizaje Automático , Recién Nacido , Curva ROCRESUMEN
Background: Viral causes of lower respiratory tract infections (LRTIs) are associated with increased mortality in children aged <5 years (U5). Human adenovirus (HAdV) has been associated with severe LRTI; however, its relationship with HIV and malnutrition in South Africa (SA) is not understood. Objectives: To identify the prevalence of and factors associated with HAdV LRTIs in hospitalised U5 childen. Methods: Clinical and viral data on U5 children hospitalised with severe LRTI from January 2018 to June 2020 at King Edward VIII Hospital, Durban, SA, including results of a multiplex polymerase chain reaction (PCR) panel assay for respiratory viruses, were retrieved from inpatient files and laboratory databases and retrospectively analysed. Standard descriptive statistics and Pearson's χ², Fisher's exact and Mann-Whitney tests were used to determine significant associations with HAdV LRTI. Results: Among the 206 viral assays analysed (15.6% of all LRTI admissions), HAdV was the most common virus identified. The cohort had a median (interquartile range) age of 5 (2 - 13) months, 47.3% had perinatal HIV exposure, and 34.5% had severe acute malnutrition (SAM). No seasonal pattern with HAdV could be demonstrated. SAM and prematurity were significant risk factors for readmission, and perinatal HIV exposure was a significant risk factor for presence of multiple viruses on analysis of a respiratory specimen. Detection of HAdV was not associated with an increased risk of requiring oxygen or ventilatory support. Conclusion: HAdV was the most common virus found on analysis of multiplex PCR panel results in children hospitalised with severe LRTI in SA, where high rates of HIV exposure may result in increased susceptibility to viral co-infections. The role of HAdV as a cause of severe LRTI in SA infants, who have high rates of HIV exposure, requires greater scrutiny. Study synopsis: What the study adds. This study provides retrospective data identifying human adenovirus (HAdV) as the most common cause of severe lower respiratory tract infection (LRTI) in children aged <5 years (U5). The impact of respiratory syncytial virus as a common pathogen in children is well established. The study confirms anecdotal evidence that HAdV is an important disease-causing pathogen associated with LRTI. Children with perinatal HIV exposure and severe acute malnutrition (SAM) may be particularly susceptible.Implications of the findings. HAdV must be considered a major cause of severe LRTI in U5 children. Children with LRTI who had perinatal HIV exposure and those with SAM need to be tested for HAdV and to be monitored for severe disease.
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BACKGROUND: Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics. OBJECTIVE: This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research. METHODS: Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section. RESULTS: Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.
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This case report details the diagnostic challenges and management of a middle-aged man who presented with complaints of fever and breathlessness. He was initially suspected of lower respiratory tract infection and diabetic ketoacidosis on clinical examination and treated with intravenous fluids, antibiotics, and insulin infusion. The point of care ultrasound (POCUS), as part of the primary survey, showed right atrium (RA)-right ventricle (RV) dilation and a D-shaped left ventricle, which was highly suspicious of pulmonary embolism and was later confirmed with computed tomography pulmonary angiogram (CTPA). The patient was successfully managed for pulmonary embolism, diabetic ketoacidosis, and lower respiratory tract infection.
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Background Pediatric respiratory infections, mainly bronchiolitis, are a substantial clinical burden. The most common etiology is respiratory syncytial virus (RSV). Other viruses include human rhinovirus, human metapneumovirus, influenza, adenovirus, coronavirus, and parainfluenza viruses. Objective We aimed to study the epidemiology and clinical characteristics of children with confirmed viral bronchiolitis and flu after the COVID-19 pandemic season and compare the behavior of each virus. Methods This retrospective observation study was done over seven months, from October 2022 to April 2023. All children (0-14) were included in the study if they met the clinical diagnosis of bronchiolitis or flu. Viral etiology is confirmed by PCR, using the respiratory panel available in our center which included the detection of four viruses: COVID-19, RSV, influenza A, and B. Clinical data, lab results, and X-rays were collected and correlated with each viral infection for all admitted patients. Results We recruited 237 children with bronchiolitis and flu symptoms from October 2022 to April 2023. The peak of infections (41%) was in November. Seasonal variations for each virus showed distinct patterns across the year. RSV peaked at the beginning of the season, gradually declining after that. In contrast, influenza A and B maintained a relatively consistent presence throughout the season. Meanwhile, COVID-19 reached its peak during March and April. One hundred forty-four (60%) of the patients were under two years of age. RSV was predominant in 150 patients (63.3%). COVID-19 was only detected in 25 patients (10%), whereas influenza A and B were equally isolated in 31 (13%) patients each. Fifty-one children (21%) were initially sick and required pediatric intensive care unit (PICU) admission, with no deaths reported. Notably, COVID-19 had a milder disease course, a shorter length of stay (LOS) in the hospital (two days) and a shorter duration of illness (five days) compared to other viruses. RSV infection was linked to more profound hypoxia and more sick children with more extended hospital stays. Conclusion Our study showed that, following the pandemic and the release of lockdown measures, there was another peak of upper respiratory tract infections (URTI) and flu, which was more aggressive, primarily due to other viruses, especially RSV. This resurgence was associated with more severe respiratory symptoms and an increased need for hospitalization. Notably, children with COVID-19 were in better condition compared to those with RSV.
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DISCLAIMER: In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. PURPOSE: Prescribing excess antibiotic duration at hospital discharge is common. A pharmacist-led Antimicrobial Stewardship Program Transition of Care (ASP TOC) intervention was associated with improved discharge prescribing. To improve the sustainability of this service, an electronic scoring system (ESS), which included the ASP TOC electronic variable, was implemented in the electronic medical record to prioritize pharmacist workload. The purpose of this study was to evaluate the implementation of the ASP TOC variable in the ESS in patients with community-acquired pneumonia (CAP) or chronic obstructive pulmonary disease (COPD). METHODS: This institutional review board-approved, retrospective quasi-experiment included patients discharged on oral antibiotics for CAP or COPD exacerbation (lower respiratory tract infection) from November 1, 2021, to March 1, 2022 (the preintervention period) and November 1, 2022, to March 1, 2023 (the postintervention period). The primary endpoint was optimized discharge antimicrobial regimen. A sample of at least 194 patients was required to achieve 80% power to detect a 20% difference in the frequency of optimized therapy. Multivariable logistic regression was used to identify factors associated with optimized regimens. RESULTS: Similar baseline characteristics were observed in both study groups (n = 100 for both groups). The frequency of optimized discharge regimens improved from 69% to 82% (P = 0.033). The percentage of ASP TOC interventions documented as completed by a pharmacist increased from 4% to 25% (P < 0.001). ASP TOC intervention, female gender, and COPD were independently associated with an optimized discharge regimen (adjusted odds ratios, 6.57, 1.61, and 3.89, respectively; 95% CI, 1.51-28.63, 0.81-3.17, and 1.85-8.20, respectively). CONCLUSION: After the launch of the ASP TOC variable, there was an increase in optimized discharge regimens and ASP TOC interventions completed. Pharmacists' use of the ASP TOC variable through an ESS can aid in improving discharge prescribing.
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Background: Respiratory syncytial virus (RSV) is one of the most significant respiratory pathogens that causes acute lower respiratory tract infections (LRTI) early in life. Most children have a history of RSV infection within 24 months of age, and recurrent infections are common throughout life. Methods: Children under five years of age were identified through a review of medical records with a diagnosis of RSV-LRTI between 2016 and 2020. Severe RSV-LRTI was defined as a prolonged length of stay (> 7 days), admission to the intensive care unit, need for mechanical ventilation, non-invasive positive pressure ventilation, or in-hospital mortality. Factors associated with severe RSV-LRTI were investigated using univariate and multivariate analyses. Results: During the study period, 620 patients were diagnosed with RSV-LRTI and 249 (40.16%) patients had severe RSV-LRTI. In the multivariable logistic regression analysis, the factors for severe RSV-LRTI were being under 3 months (aOR 2.18 CI 1.39-3.43, p0.001), cardiovascular disease (aOR 3.55 CI 1.56-8.06, p0.002), gastrointestinal disease (aOR 5.91 CI 1.90-18.46, p0.002), genetic disease (aOR 7.33 CI 1.43-37.54, p0.017), and pulmonary disease (aOR 9.50, CI 4.56-19.80, p<0.001). Additionally, the presence of ≥ 2 co-morbidities (aOR 6.23 CI 2.81-14.81, p<0.016), experiencing illness for more than 5 days (aOR 3.33 CI 2.19-5.06, p<0.001), co-detection of influenza (aOR 8.62 CI 1.49-38.21, p0.015), and nosocomial RSV infection (aOR 9.13 CI 1.98-41.30, p0.012), markedly increased the risk of severe RSV-LTRI. The severe RSV-LRTI group demonstrated higher hospitalization expenses (median, US $720.77 vs $278.00, respectively; p<0.001), and three infants died in-hospital. Conclusion: Children at high risk for RSV-LRTI due to underlying genetic and gastrointestinal diseases are at an increased risk for severe RSV-LRTI. Further studies to determine the cost-effectiveness of RSV immunization in these potential co-morbidities should be initiated to prioritize RSV immunization, especially in resource-constrained regions with limited availability of nirsevimab.
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Hospitales Universitarios , Infecciones por Virus Sincitial Respiratorio , Humanos , Infecciones por Virus Sincitial Respiratorio/epidemiología , Lactante , Masculino , Femenino , Preescolar , Factores de Riesgo , Hospitalización , Virus Sincitial Respiratorio Humano , Recién Nacido , Estudios Retrospectivos , Infecciones del Sistema Respiratorio/virología , Infecciones del Sistema Respiratorio/epidemiología , Niño Hospitalizado/estadística & datos numéricosRESUMEN
INTRODUCTION: Lower respiratory tract infections (LRTIs) are one of the most commonly encountered infections with significant mortality and morbidity. Sputum is the most frequently obtained sample for LRTI diagnosis. However, sputum samples carry the risk of being non-representative due to the risk of contamination with oral colonizers. To overcome the dilemma with respect to representative sampling, the use of a scoring system such as the Bartlett scoring system is emphasized. This study probes the bacterial profile of sputum samples among patients presenting with LRTIs and their antibiotic susceptibility profile in relation to the Bartlett scoring system. METHODOLOGY: Retrospective data for a period of three years, comprising 4960 sputum samples from patients presenting with LRTI, were collected to study the bacterial profile and antibiogram in comparison with the sputum quality analyzed by the Bartlett scoring system. RESULTS: Out of the 4960 sputum samples analyzed from patients with LRTI, 31.18% yielded the growth of bacterial pathogens, and 98.64% of the sputum samples yielding pathogenic growth had a significant Bartlett score. CONCLUSION: Sputum samples are non-invasive representative samples of lower airway infective pathologies. Sputum quality assessment by Bartlett scoring serves as a proxy marker to rule out respiratory colonization and aid culture-based diagnosis.
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There were several factors associated with respiratory syncytial virus (RSV) severe acute lower respiratory infection (RSV-sALRI) in infants and young children. It is vital to develop a convenient scoring system to predict RSV-sALRI in children. Pediatric patients with RSV-ALRI from January 2009 to December 2021 were recruited retrospectively. Two-third of them were randomly grouped into the development set and one-third to the validation set. In the development set, risk factors for RSV-sALRI were transferred into the logistic regression analysis, then their receiver operating characteristic (ROC) curves were built to obtain the area under the ROC curve (AUC), and regression coefficients for each predictor were converted to points. Finally, the value of the scoring system was evaluated in the validation set. A total of 1 066 children with RSV-ALRI were recruited, including 710 in the development set and 356 in the validation set. By logistic regression analysis, six factors (younger than 2 years, gestational age <37 weeks, have siblings, birth weight ≤2500 g, artificial/mix feeding, CHD) showed statistical difference and then were scored with points according to the coefficient value (OR) in the development set. In the validation set, the sensitivity of the scoring system was 70.25%, the specificity 85.53%, the positive predictive value 71.43%, the negative predictive value 84.81%, and coincidence rate 0.80. The Kolmogorov-Smirnov test showed the distribution of AUC 0.765 (SE = 0.027; 95% CI = 0.713-0.818; p < 0.001). A simplified scoring system was developed in the study with high prediction value for RSV-sALRI in children.
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OBJECTIVES: To describe the symptoms, duration, severity, and microbiology of lower respiratory tract infection (LRTI) in outpatients. METHODS: Prospective cohort study of adults in US primary or urgent care with a chief complaint of cough and symptoms consistent with LRTI. Baseline data included demographics, signs, symptoms, and PCR for 46 viruses and bacteria. The severity of symptoms reported for ≤28 days follow-up via diary and text message. The Bronchitis severity score assessed severity at baseline; overall severity was defined as the area under the symptom severity curve. RESULTS: Of 718 patients with complete baseline data, 618 had valid PCR results, and 443 were followed until symptoms resolved. Of those with valid PCR, 100 (16.2%) had 1+ viruses detected, 211 (34.1%) had 1+ bacteria, and 168 (27.2%) had both. Symptoms more likely with viral or mixed infection included feverishness (36.7-38.4% vs. 18.5%), chills or sweats (36.0-38.1% vs. 17.9%), being generally unwell (78.2-81.3% vs. 64.9%), and myalgias (42.7-48.2% vs. 28.6%). Coloured sputum (42.9% vs. 23.2-29.5%) was more common with a bacterial infection. The mean duration of cough was 14.7 days with viruses (95% CI: 13.2-16.2), 17.3 with bacteria (95% CI: 15.9-18.6), 16.9 with mixed infection (95% CI: 15.2-18.6), and 18.4 with no detection (95% CI: 16.1-20.8). Overall severity of cough was lower for viral infections (20.9 points, 95% CI: 18.6-23.3) than for other groups (range 24.2-26.3). The most common potential bacterial pathogens were Haemophilus influenza (28.0%), Moraxella catarrhalis (16.2%), and Streptococcus pneumoniae (10.2%), whereas the most common viral pathogens were rhinovirus (17.3%), influenza (12.8%), SARS-CoV-2 (11.5%), and seasonal coronaviruses (8.1%). DISCUSSION: The mean duration of cough was 16.4 days. Consistent with European studies, the type of infection or potential pathogen was not an important predictor of the duration or severity of LRTI.
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Background: Lower respiratory tract infection (LRTI) is a leading cause of infant morbidity and mortality globally. LRTI may be caused by viral or bacterial infections, individually or in combination. We investigated associations between LRTI and infant nasopharyngeal (NP) viruses and bacteria in a South African birth cohort. Methods: In a case-control study of infants enrolled in the Drakenstein Child Health Study (DCHS), LRTI cases were identified prospectively and age-matched with controls from the cohort. NP swabs were tested using quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing. We calculated adjusted Conditional Odds Ratios (aORs) for qPCR targets and used mixed effects models to identify differentially abundant taxa between LRTI cases and controls and explore viral-bacterial interactions. Results: Respiratory Syncytial Virus (RSV) [aOR: 5.69, 95% CI: 3.03-10.69], human rhinovirus (HRV) [1.47, 1.03-2.09], parainfluenza virus [3.46, 1.64-7.26], adenovirus [1.99, 1.08-3.68], enterovirus [2.32, 1.20-4.46], Haemophilus influenzae [1.72, 1.25-2.37], Klebsiella pneumoniae [2.66, 1.59-4.46], or high-density (> 6.9 log10 copies/mL) Streptococcus pneumoniae [1.53, 1.01-2.32] were associated with LRTI. Using 16S sequencing, LRTI was associated with increased relative abundance of Haemophilus (q = 0.0003) and decreased relative abundance of Dolosigranulum (q = 0.001), Corynebacterium (q = 0.091) and Neisseria (q = 0.004). In samples positive for RSV, Staphylococcus and Alloprevotella were present at lower relative abundance in cases than controls. In samples positive for parainfluenza virus or HRV, Haemophilus was present at higher relative abundance in cases. Conclusions: The associations between bacterial taxa and LRTI are strikingly similar to those identified in high-income countries, suggesting a conserved phenotype. RSV was the major virus associated with LRTI. H. influenzae appears to be the major bacterial driver of LRTI, acting synergistically with viruses. The Gram-positive bacteria Dolosigranulum and Corynebacteria may protect against LRTI, while Staphylococcus was associated with reduced risk of RSV-related LRTI. Funding: National Institutes of Health of the USA, Bill and Melinda Gates Foundation, National Research Foundation South Africa, South African Medical Research Council, L'Oréal-UNESCO For Women in Science South Africa, Australian National Health and Medical Research Council.
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Respiratory tract infections (RTIs) pose a substantial health burden worldwide, especially among immunocompromised groups like cancer patients. The aim of this prospective cohort study was to explore lower respiratory tract infections in cancer patients. We followed 107 cases with clinically or radiologically suspected lower respiratory tract infections until discharge or death, comprising 65 males and 42 females across diverse age groups. Clinical evaluations, including patient history, examination, and malignancy diagnosis, were conducted. Nasopharyngeal swabs (NPSs), sputum samples, and blood samples were collected within 24 h of symptom onset. Multiplex Real-Time PCR allowed for the simultaneous detection of viral, bacterial, and fungal infections, while conventional microbiological culture methods were used for bacterial and fungal analysis. SARS-CoV-2 infection was excluded in all of the enrolled patients using real-time RT-PCR. Hematological and biochemical analyses included hemoglobin, lymphocyte, neutrophil, and platelet counts, along with ALT, AST, creatinine, and CRP levels. Significant differences were noted in clinical presentations, management outcomes, and prognostic markers among patients with different hematological malignancies. Distinct clinical profiles were identified for leukemia, lymphoma, and solid tumors, with variations in age distribution and symptom prevalence. ICU admission rates varied significantly, with solid tumor patients exhibiting higher rates. The hematological and biochemical biomarkers differed across malignancies, with notable associations between lymphopenia, thrombocytopenia, and mortality following respiratory episodes. This study highlights the critical role of rapid pathogen detection and infection control measures in safeguarding vulnerable cancer patients from nosocomial transmission.
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Biomarcadores , Neoplasias , Infecciones del Sistema Respiratorio , Humanos , Masculino , Femenino , Estudios Prospectivos , Persona de Mediana Edad , Infecciones del Sistema Respiratorio/mortalidad , Infecciones del Sistema Respiratorio/sangre , Infecciones del Sistema Respiratorio/diagnóstico , Anciano , Neoplasias/complicaciones , Neoplasias/sangre , Neoplasias/mortalidad , Adulto , Biomarcadores/sangre , Biomarcadores/análisis , Estudios de Cohortes , Anciano de 80 o más AñosRESUMEN
The aim of this study was to investigate the epidemiological characteristics of respiratory syncytial virus (RSV) infections in children in Zhejiang from 2019 to 2023. Data from pediatric patients who visited the Children's Hospital of Zhejiang University School of Medicine for RSV infection between 2019 and 2023 were analyzed. Nasopharyngeal swabs were collected for RSV antigen detection, and relevant patient information was collected. Factors such as age were analyzed. A total of 673 094 specimens were included from 2019 to 2023, with a rate of positive specimens of 4.74% (31 929/673 094). The highest rate of positive specimens of 10.82%, was recorded in 2021, while the remaining years had a rate of approximately 3%-5%. In terms of seasonal prevalence characteristics, the rate of positive specimens in 2019, 2020, and 2022 peaked in the winter months at approximately 8% and decreased in the summer months, where the rate of positive specimens remained at approximately 0.5%. In contrast, summer is the peak period for RSV incidence in 2021 and 2023, with the rate of positive specimens being as high as 9%-12%. Based on the prevalence characteristics of gender and age, this study found that the detection rate of positive specimens was higher in boys than in girls in 2019-2023. In 2019-2022, among the different age groups, the highest rate of positive specimens was found in children aged 0 to <6 months, and it decreased with age. In 2023, the rate of positive specimens was above 8% in the 0 to <6 months, 6 to <12 months, and 1-2 years age groups, with the highest rate of positive specimens in the 1-2 years age group, and a gradual decrease in the rate of positive specimens with age for children over 3 years of age. Between 2019 and 2023, the epidemiological pattern of RSV changed. A summer peak was observed in 2021 and 2023.
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Hospitales Pediátricos , Infecciones por Virus Sincitial Respiratorio , Virus Sincitial Respiratorio Humano , Estaciones del Año , Humanos , Infecciones por Virus Sincitial Respiratorio/epidemiología , Infecciones por Virus Sincitial Respiratorio/virología , Infecciones por Virus Sincitial Respiratorio/diagnóstico , Masculino , Femenino , China/epidemiología , Lactante , Preescolar , Prevalencia , Hospitales Pediátricos/estadística & datos numéricos , Niño , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Recién Nacido , Nasofaringe/virología , Adolescente , IncidenciaRESUMEN
BACKGROUND: Nonpharmaceutical interventions (NPIs) implemented to reduce the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have suppressed the spread of other respiratory viruses during the coronavirus disease 2019 (COVID-19) pandemic. This study aimed to explore the epidemiological trends and clinical characteristics of Mycoplasma pneumoniae (MP) infection among inpatient children with lower respiratory tract infection (LRTI) before and during the COVID-19 pandemic, and investigate the long-term effects of China's NPIs against COVID-19 on the epidemiology of MP among inpatient children with LRTI. METHODS: Children hospitalised for LRTI at the Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine (Hangzhou, China) between January 2019 and December 2022 were tested for common respiratory pathogens, including Mycoplasma pneumoniae (MP), Chlamydia trachomatis (CT) and other bacteria. Clinical data on age, sex, season of onset, disease spectrum, and combined infection in children with MP-induced LRTI in the past 4 years were collected and analysed. RESULTS: Overall, 15909 patients were enrolled, and MP-positive cases were 1971 (34.0%), 73 (2.4%), 176 (5.8%), and 952 (20.6%) in 2019, 2020, 2021, and 2022, respectively, with a significant statistical difference in the MP-positive rate over the 4 years (p <0.001). The median age of these children was preschool age (3-6 years), except for 2022, when they were school age (7-12 years), with statistical differences. Comparing the positive rates of different age groups, the school-age children (7-12 years) had the highest positive rate, followed by the preschoolers (3-6 years) in each of the 4 years. Compared among different seasons, the positive rate of MP in children with LRTI was higher in summer and autumn, whereas in 2020, it was highest in spring. The monthly positive rate peaked in July 2019, remained low from 2020 to 2021, and rebounded until 2022. Regarding the disease spectrum, severe pneumonia accounted for the highest proportion (46.3%) pre-pandemic and lowest (0%) in 2020. CONCLUSION: Trends in MP detection in children with LRTIs suggest a possible correlation between COVID-19 NPIs and significantly reduced detection rates. The positivity rate of MP gradually rose after 2 years. The epidemic season showed some differences, but school-age children were more susceptible to MP before and during the COVID-19 pandemic.
Asunto(s)
COVID-19 , Mycoplasma pneumoniae , Neumonía por Mycoplasma , Infecciones del Sistema Respiratorio , Humanos , China/epidemiología , COVID-19/epidemiología , Niño , Preescolar , Masculino , Femenino , Neumonía por Mycoplasma/epidemiología , Neumonía por Mycoplasma/microbiología , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Adolescente , Lactante , SARS-CoV-2 , PandemiasRESUMEN
Background: Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Leveraging the advancements in metagenomic next-generation sequencing (mNGS) technology alongside the emergence of machine learning, it is now viable to compare the attributes of lower respiratory tract microbial communities among patients across diverse age groups, diseases, and infection types. Method: We collected bronchoalveolar lavage fluid samples from 138 patients diagnosed with lower respiratory tract infections and conducted mNGS to characterize the lung microbiota. Employing various machine learning algorithms, we investigated the correlation of key bacteria in patients with concurrent bronchiectasis and developed a predictive model for hospitalization duration based on these identified key bacteria. Result: We observed variations in microbial communities across different age groups, diseases, and infection types. In the elderly group, Pseudomonas aeruginosa exhibited the highest relative abundance, followed by Corynebacterium striatum and Acinetobacter baumannii. Methylobacterium and Prevotella emerged as the dominant genera at the genus level in the younger group, while Mycobacterium tuberculosis and Haemophilus influenzae were prevalent species. Within the bronchiectasis group, dominant bacteria included Pseudomonas aeruginosa, Haemophilus influenzae, and Klebsiella pneumoniae. Significant differences in the presence of Pseudomonas phage JBD93 were noted between the bronchiectasis group and the control group. In the group with concomitant fungal infections, the most abundant genera were Acinetobacter and Pseudomonas, with Acinetobacter baumannii and Pseudomonas aeruginosa as the predominant species. Notable differences were observed in the presence of Human gammaherpesvirus 4, Human betaherpesvirus 5, Candida albicans, Aspergillus oryzae, and Aspergillus fumigatus between the group with concomitant fungal infections and the bacterial group. Machine learning algorithms were utilized to select bacteria and clinical indicators associated with hospitalization duration, confirming the excellent performance of bacteria in predicting hospitalization time. Conclusion: Our study provided a comprehensive description of the microbial characteristics among patients with lower respiratory tract infections, offering insights from various perspectives. Additionally, we investigated the advanced predictive capability of microbial community features in determining the hospitalization duration of these patients.