Contemporary Situation of Community-acquired Pneumonia in China: A Systematic Review

Application of Targeted Next-Generation Sequencing in Bronchoalveolar Lavage Fluid for the Detection of Pathogens in Pulmonary Infections

Objective

This study aims to evaluate the utility of targeted next-generation sequencing (tNGS) in bronchoalveolar lavage fluid (BALF) for hospitalized patients with pulmonary infections.

Methods

A cohort of 358 patients who received diagnosis and treatment for respiratory infections in the department of Respiratory Medicine at Wenzhou People's hospital from January 2023 to April 2024 were selected for this study. The BALF of the patients was analyzed using tNGS, and the diagnostic efficacy of tNGS was subsequently compared with that of conventional testing methods (CTs) for pathogen detection.

Results

Through the analysis of tNGS from the cohort, the pathogen detection rate in BALF using tNGS was significantly higher than that of CTs (90.22% VS 57.26%, P=0.001). Among them, Tropheryma Whipplei (6.15%), Bordetella pertussis (2.51%), Non-tuberculous mycobacteria (1.96%), Mycobacteria tuberculosis (1.40%), Chlamydia pneumoniae (1.96%), Chlamydia psittaci (0.56%), Legionella pneumophila (0.28%) were detected using tNGS alone, and the CTs results of these microorganisms were all negative. Among the various types of mixed infections observed, concurrent presence of bacteria and viruses was the most common, accounting for 37.15%. The detection rates of tNGS and CTs have statistical significance (66.87% VS 35.12%, P=0.001). Furthermore, a total of 61 cases of antimicrobial resistance genes were detected, including 34 cases of 23S rRNA A2063G, 6 cases of KPC, 5 cases of OXA, 2 cases of CTX-M, 3 cases of IMP, 1 case of NDM and 13 cases of mecA. Using the clinical diagnosis as references, the positive coincidence rate of the tNGS was significantly higher compared to that of the CTs (P=0.012).

Conclusion

Compared to CTs, the application of tNGS enables the identification of a greater diversity of organisms and exhibits superior accuracy, effectively identifying pathogens that are undetectable by CTs, especially fastidious and atypical organisms. Consequently, it holds immense potential in pathogen diagnosis and offers valuable clinical guidance for patients with pulmonary infections.

Protective immunity induced by a novel P1 adhesin C-terminal anchored mRNA vaccine against Mycoplasma pneumoniae infection in BALB/c mice

Mycoplasma pneumoniae (Mp), a unique pathogen devoid of a cell wall, is naturally impervious to penicillin antibiotics. This bacterium is the causative agent of M. pneumoniae pneumonia, an acute pulmonary affliction marked by interstitial lung damage. Non-macrolide medications may have potential adverse effects on the developmental trajectory of children, thereby establishing macrolides as the preferred treatment for M. pneumoniae in pediatric patients. However, the emergence of macrolide-resistant and multidrug-resistant strains of M. pneumoniae presents significant challenges to clinical management and public health. Vaccines, particularly those based on mRNA technology, are regarded as a promising avenue for preventing and controlling M. pneumoniae infections due to their inherent safety, immunogenicity, and adaptability. Our research delves into the P1 adhesin of M. pneumoniae, a protein that binds to host cell receptors with its immunodominant epitopes located at the carboxyl terminus, known to provoke robust immune responses and pulmonary inflammation. We have developed an mRNA vaccine harnessing this dominant antigenic epitope and assessed its protective immunity in BALB/c mice against M. pneumoniae infection. The vaccine elicited potent humoral and cellular immune responses, effectively diminishing inflammation. It notably decreased IL-6 levels in the lungs of infected mice and concurrently elevated IL-4, IL-10, and IFN-γ levels post-immunization. The vaccine also reduced pathological changes in the lungs and the M. pneumoniae DNA copy numbers in the infected animals. Collectively, these findings underscore the mRNA vaccine's remarkable immunogenicity and protective potential against M. pneumoniae infections, offering valuable insights for the development of mRNA vaccines targeting mycoplasma infections.IMPORTANCEM. pneumoniae, a bacteria without a cell wall, is known for causing pneumonia and is resistant to penicillin. The increasing prevalence of macrolide-resistant strains has complicated treatment options, emphasizing the need for new strategies. Our research explores an mRNA vaccine candidate that targets the P1 adhesin of M. pneumoniae, a protein critical for the bacteria's interaction with host cells. In a mouse model, this vaccine has shown potential by inducing immune responses and suggesting a possible reduction in inflammation, as indicated by changes in cytokine levels and lung pathology. While further research is required, the vaccine's preliminary results hint at a potential new direction in managing mycoplasma infections, offering a promising avenue for future therapeutic development. This study contributes to the ongoing search for effective preventive measures against M. pneumoniae.

Establishment of a rapid detection method for Mycoplasma pneumoniae based on RPA-CRISPR-Cas12a technology

Mycoplasma pneumoniae can cause respiratory infections and pneumonia, posing a serious threat to the health of children and adolescents. Early diagnosis of Mycoplasma pneumoniae infection is crucial for clinical treatment. Currently, diagnostic methods for Mycoplasma pneumoniae infection include pathogen detection, molecular biology techniques, and bacterial culture, all of which have certain limitations. Here, we developed a rapid, simple, and accurate detection method for Mycoplasma pneumoniae that does not rely on large equipment or complex operations. This technology combines the CRISPR-Cas12a system with recombinase polymerase amplification (RPA), allowing the detection results to be observed through fluorescence curves and immunochromatographic lateral flow strips.It has been validated that RPA-CRISPR/Cas12a fluorescence analysis and RPA-CRISPR/Cas12-immunochromatographic exhibit no cross-reactivity with other common pathogens, and The established detection limit was ascertained to be as low as 102 copies/µL.Additionally, 49 clinical samples were tested and compared with fluorescence quantitative polymerase chain reaction, demonstrating a sensitivity and specificity of 100%. This platform exhibits promising clinical performance and holds significant potential for clinical application, particularly in settings with limited resources, such as clinical care points or resource-constrained areas.

Epidemiological characteristics of community-acquired Mycoplasma pneumoniae in hospitalized children around COVID-19 from Jiangsu Province, China: a multicenter retrospective study

Background

It has been reported that the emergence of coronavirus disease 2019 (COVID-19) has changed the epidemiological characteristics of many pathogens, but the epidemiological characteristics of Mycoplasma (MP) infection in hospitalized children with community-acquired pneumonia (CAP) are not clear. The aim of this study was to answer this question.

Methods

Children with CAP in three tertiary hospitals (hospitals A, B and C) from 2018 to 2023 were selected. Data on gender, age, number and date of MP infection were obtained from the medical record. The intensity of the epidemic was measured as a percentage of the number of CAP.

Results

In hospitals A and B, before the pandemic (in 2018 and 2019), the number of hospitalized children with MP pneumonia and the proportion of total pneumonia had shown a significant upward trend, but the control measures led to a slight decline. In hospital C, the number and percentage of hospitalized children with MP pneumonia were low before and during the COVID-19 period. After the epidemic control was lifted, the number and percentage of children with MP pneumonia in the three hospitals increased sharply, and the proportion of children aged more than 7 years old increased significantly in 2022 and 2023.

Conclusions

From 2018 to 2019, there was already an epidemic trend of MP in the study hospital. From 2020 to 2022, after the outbreak of COVID-19, the incidence of MP pneumonia stabilized, but after the epidemic control was lifted, it broke out. This may be due to the severe restrictive measures taken early during the COVID-19 pandemic that effectively controlled the spread of MP, pausing its pandemic.

Comparison of targeted next-generation sequencing and traditional microbial culture in the diagnosis of pulmonary infections

This study investigated the diagnostic potential of targeted next-generation sequencing (tNGS) for pulmonary infections. The positivity rate of tNGS was significantly higher than that of traditional microbial culture (92.6 % vs 25.2 %, χ2 = 378.272, P < 0.001). The proportion of two or more species of pathogens detected using tNGS exceeded that detected using microbial culture (χ2 = 337.283, P < 0.001). There were inconsistencies between the results of the tNGS antibiotic resistance gene and the drug susceptibility test resistance phenotype. The tNGS technique demonstrates rapid and effective capabilities in identifying bacteria, fungi, viruses, and specific pathogens, with a detection sensitivity that surpasses that of conventional culture methodologies. Microbial drug resistance genotypes detected by tNGS cannot accurately predict drug resistance phenotypes and require further improvement or integration with traditional microbial culture to establish a foundation for effective clinical treatment.

CAP-PIRO Scoring System's Performance in Predicting Prognosis and Severity of Community-Acquired Pneumonia: A Single-Center Prospective Study

Background

Community-acquired pneumonia (CAP) is a significant global health issue, leading to high morbidity and mortality rates. Despite the existence of various severity scoring systems, accurately predicting patient outcomes remains challenging. The CAP-PIRO (Predisposition, Insult, Response, and Organ dysfunction) scoring system offers a comprehensive approach to evaluating CAP severity and prognosis.

Objective

This study aimed to assess the effectiveness of the CAP-PIRO scoring system in predicting the prognosis and severity of CAP patients, focusing on the development of acute respiratory distress syndrome (ARDS) and 28-day mortality.

Methods

A total of 875 CAP patients were prospectively enrolled from the emergency department of Beijing Chao-yang Hospital between November 2017 and December 2023. Clinical data, including patient demographics, medical history, vital signs, and laboratory findings, were collected within 6 hours of admission. CAP-PIRO, CURB-65, and PSI scores were calculated. Patients were stratified based on ARDS development, 28-day mortality, and PaO2/FiO2 categories (≤100 mmHg, 100-200 mmHg, 200-300 mmHg).

Results

Significant differences were observed in PCT, blood lactate (Lac), CURB-65, PSI, and CAP-PIRO scores between patients with and without ARDS, as well as between survivors and non-survivors at 28 days (P<0.05). CAP-PIRO and Lac were identified as independent predictors for ARDS development and 28-day mortality. The area under the ROC curve (AUC) for CAP-PIRO was higher than that for CURB-65 and PSI in predicting 28-day mortality. The combination of CAP-PIRO and Lac demonstrated improved predictive accuracy for ARDS. Notably, significant differences in CAP-PIRO scores were observed across different PaO2/FiO2 groups.

Conclusion

CAP-PIRO demonstrates strong predictive ability for adverse outcomes and, when combined with lactate, shows enhanced predictive power. These findings underscore the value of CAP-PIRO for clinical risk stratification in CAP patients.

Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation

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

Efficacy of azithromycin combined with intravenous immunoglobulin in the treatment of refractory mycoplasma pneumoniae pneumonia in children: a meta-analysis

BACKGROUND

The incidence of refractory Mycoplasma pneumoniae pneumonia (RMPP) in children is increasing, posing a serious threat to life safety. Intravenous immunoglobulin (IVIG) has demonstrated the ability to modulate the immune system and has shown the potential to treat RMPP. This study evaluated the clinical efficacy and safety of azithromycin combined with IVIG in the treatment of RMPP in children through a meta-analysis.

METHODS

A comprehensive search was conducted in seven databases including PubMed and Cochrane Library, and the studies on the treatment of RMPP in children with azithromycin combined with IVIG were screened. After data extraction, meta-analysis and sensitivity analysis were performed to assess heterogeneity and stability.

RESULTS

Thirteen randomized controlled trials and two cohort studies were included, totaling 1,142 children. The results of meta-analysis showed a higher clinical efficacy rate (RR = 1.18, 95% CI: 1.11-1.25, P < 0.01) and shorter time to defervescence (MD = -2.12, 95% CI: -2.69--1.55), time to disappearance of pulmonary rales (MD = -2.90, 95% CI: -3.57--2.23), time to disappearance of cough (MD = -3.59, 95% CI: -4.51--2.67), and hospital length of stay (MD = -5.72, 95% CI: -8.80--2.64) in the experimental group receiving azithromycin combined with IVIG treatment compared to the control group treated with azithromycin alone. Additionally, there was no significant publication bias in this meta-analysis.

CONCLUSION

Treatment with azithromycin combined with IVIG is more effective than treatment with azithromycin alone for children with RMPP.

CLINICAL TRIAL NUMBER

Not applicable.

Comparative study on the incidence of non-COVID-19 viral pneumonia before and after the COVID-19 pandemic: A retrospective analysis based on respiratory non-COVID viral nucleic acid results

Background

The impact of the coronavirus disease 2019 (COVID-19) pandemic on the etiology of non-COVID-19 viral pneumonia remains to be identified. We investigated the evolution of non-COVID-19 viral pneumonia in hospitalized patients before and after the COVID-19 pandemic.

Methods

This is a single-center retrospective study. Patients who came to West China Hospital of Sichuan University diagnosed with non-COVID-19 viral pneumonia from January 1, 2016 to December 31, 2021, were included and divided into pre- and post-COVID-19 groups according to the date of the COVID-19 outbreak in China. The results of 13 viral nucleic acid tests were compared between the two groups.

Results

A total of 5937 patients (3954 in the pre-COVID-19 group and 1983 in the post-COVID-19 group) were analyzed. Compared with the pre-COVID-19 group, the proportion of patients tested for respiratory non-COVID-19 viral nucleic acid was significantly increased in the post-COVID-19 group (14.78% vs. 22.79%, P <0.05). However, the non-COVID-19 virus-positive rates decreased from 37.9% to 14.6% after the COVID-19 outbreak (P < 0.001). Notably, non-COVID-19 viral pneumonia caused by the influenza A virus H1N1 (InfAH1N1) (2009) dropped to 0% after the pandemic. The top three viruses were InfAH1N1 (2009) (13.9%), human rhinovirus (7.4%), and human adenovirus (3.4%) in the pre-COVID-19 group, and human rhinovirus (3.8%), human respiratory syncytial virus (2.0%), human parainfluenza virus (1.1%) and InfAH3N2 (1.1%) in the post-COVID-19 group.

Conclusions

The proportion of non-COVID-19 viral pneumonia decreased significantly after the COVID-19 outbreak, among which InfAH1N1 (2009) pneumonia decreased the most dramatically.

Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection

BACKGROUND

Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited.

METHODS

To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis.

RESULTS

In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS.

CONCLUSION

In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.

Clinical utility of metagenomic next-generation sequencing on bronchoalveolar lavage fluid in diagnosis of lower respiratory tract infections

BACKGROUND

In this study, we aimed to evaluate the clinical utility of Metagenomic Next-Generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) in diagnosis of Lower Respiratory Tract Infections (LRTIs).

METHODS

In this study, we retrospectively analyzed 186 hospitalized patients who were suspected with LRTIs and performed mNGS (DNA) test of BALF simultaneously at The Fifth Affiliated Hospital of Sun Yat-Sen University from March 2023 to August 2023. Suspected LRTI was based on LRTI related clinical manifestations or imaging examination. Among them, 155 patients had undergone conventional culture and mNGS (DNA) testing simultaneously. Finally, 138 cases (89.03%,138/155) were diagnosed as LRTI and 17 cases (10.97%,17/155) were diagnosed as non-LRTI. Both detecting rate and diagnostic efficacy of mNGS and conventional culture were compared.

RESULTS

The positive detection rates of pathogens between mNGS and conventional culture were significant different (81.29% VS 39.35%, P < 0.05). Compared with paired conventional culture result, the sensitivity of mNGS in diagnosis of LRTIs was more superior (88.41% VS 43.48%; P < 0.05), the specificity was opposite (76.47% VS 94.12%; P > 0.05). Furthermore, 77.54% and 35.51% of LRTI cases were being etiologically diagnosed by mNGS and culture respectively. Importantly, mNGS directly led to a change of treatment regimen in 58 (37.42%) cases, including antibiotic adjustment (29.68%) and ruling out active infection (7.74%). Moreover, treatment regimen remained unchanged in 97 (62.58%) cases, considering the current antibiotic therapy already covered the detected pathogens (36.13%) or empirical treatment was effective (11.61%).

CONCLUSIONS

mNGS can identify a wide range of pathogens in LRTIs, with improved sensitivity and being more superior at diagnosing LRTIs etiologically. mNGS has the potential to enhance clinical outcomes by optimizing the treatment regimens.

Mycoplasma pneumoniae infection outbreak in Guangzhou, China after COVID-19 pandemic

BACKGROUNDS

Mycoplasma pneumoniae (M. pneumoniae) is a common pathogen causing respiratory diseases in children. This study aimed to characterize epidemiological and disease severity shifts of M. pneumoniae: infections in Guangzhou, China during and after the coronavirus disease 2019 (COVID-19) pandemic.

METHODS

Throat swab samples were obtained from 5405 hospitalized patients with symptoms of acute respiratory infections to detect M. pneumoniae. Differences in epidemiological and clinical characteristics of M. pneumoniae: infections were investigated during 2020-2022 and after COVID-19 pandemic (2023).

RESULTS

M. pneumoniae were detected in 849 (15.6%, 849/5405) patients. The highest annual positive rate was 29.4% (754/2570) in 2023, followed by 5.3% (72/1367) in 2022, 1.2% (12/1015) in 2021, and 2.0% (11/553) in 2020, with significantly increasing annual prevalence from 2020 to 2023. M. pneumoniae incidence peaked between July and December post-COVID-19 pandemic in 2023, with the highest monthly positive rate (56.4%, 165/293). Clinical characteristics and outcomes of patients with M. pneumoniae did not vary between periods during and after COVID-19 pandemic except that patients with M. pneumoniae post-COVID-19 pandemic were more likely to develop fever. Patients with severe M. pneumoniae pneumonia (SMPP) were more likely to develop respiratory complications, myocardial damage, and gastrointestinal dysfunction than those with non-SMPP. Patients with SMPP had lower lymphocytes, CD3+ T cells, CD4+ T cells, CD8+ T cells, B cells, and higher IL-4, IL-6, IL-10 levels than those with non-SMPP. Bronchoalveolar lavage fluid specimens from infected patients were obtained to identify macrolide resistance mutations. Macrolide-resistant M. pneumoniae (MRMP) proportion in 2023 was 91.1% (215/236).

CONCLUSION

Outbreaks of M. pneumoniae: occurred in Guangzhou, China in 2023 upon Non-pharmaceutical interventions easing. Despite the increasing incidence of M. pneumoniae, the disease severity remained similar during and after the COVID-19 pandemic.

The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections

Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.

A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients

INTRODUCTION

Lower respiratory tract infections(LRTIs) in adults are complicated by diverse pathogens that challenge traditional detection methods, which are often slow and insensitive. Metagenomic next-generation sequencing (mNGS) offers a comprehensive, high-throughput, and unbiased approach to pathogen identification. This retrospective study evaluates the diagnostic efficacy of mNGS compared to conventional microbiological testing (CMT) in LRTIs, aiming to enhance detection accuracy and enable early clinical prediction.

METHODS

In our retrospective single-center analysis, 451 patients with suspected LRTIs underwent mNGS testing from July 2020 to July 2023. We assessed the pathogen spectrum and compared the diagnostic efficacy of mNGS to CMT, with clinical comprehensive diagnosis serving as the reference standard. The study analyzed mNGS performance in lung tissue biopsies and bronchoalveolar lavage fluid (BALF) from cases suspected of lung infection. Patients were stratified into two groups based on clinical outcomes (improvement or mortality), and we compared clinical data and conventional laboratory indices between groups. A predictive model and nomogram for the prognosis of LRTIs were constructed using univariate followed by multivariate logistic regression, with model predictive accuracy evaluated by the area under the ROC curve (AUC).

RESULTS

(1) Comparative Analysis of mNGS versus CMT: In a comprehensive analysis of 510 specimens, where 59 cases were concurrently collected from lung tissue biopsies and BALF, the study highlights the diagnostic superiority of mNGS over CMT. Specifically, mNGS demonstrated significantly higher sensitivity and specificity in BALF samples (82.86% vs. 44.42% and 52.00% vs. 21.05%, respectively, p < 0.001) alongside greater positive and negative predictive values (96.71% vs. 79.55% and 15.12% vs. 5.19%, respectively, p < 0.01). Additionally, when comparing simultaneous testing of lung tissue biopsies and BALF, mNGS showed enhanced sensitivity in BALF (84.21% vs. 57.41%), whereas lung tissues offered higher specificity (80.00% vs. 50.00%). (2) Analysis of Infectious Species in Patients from This Study: The study also notes a concerning incidence of lung abscesses and identifies Epstein-Barr virus (EBV), Fusobacterium nucleatum, Mycoplasma pneumoniae, Chlamydia psittaci, and Haemophilus influenzae as the most common pathogens, with Klebsiella pneumoniae emerging as the predominant bacterial culprit. Among herpes viruses, EBV and herpes virus 7 (HHV-7) were most frequently detected, with HHV-7 more prevalent in immunocompromised individuals. (3) Risk Factors for Adverse Prognosis and a Mortality Risk Prediction Model in Patients with LRTIs: We identified key risk factors for poor prognosis in lower respiratory tract infection patients, with significant findings including delayed time to mNGS testing, low lymphocyte percentage, presence of chronic lung disease, multiple comorbidities, false-negative CMT results, and positive herpesvirus affecting patient outcomes. We also developed a nomogram model with good consistency and high accuracy (AUC of 0.825) for predicting mortality risk in these patients, offering a valuable clinical tool for assessing prognosis.

CONCLUSION

The study underscores mNGS as a superior tool for lower respiratory tract infection diagnosis, exhibiting higher sensitivity and specificity than traditional methods.

Exploring the Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Unexplained Pulmonary Infection

Background

Pulmonary infections are significant global health burdens, and conventional diagnostic methods (culture and polymerase chain reaction), are often limited by slow results and low sensitivity. Metagenomic next-generation sequencing (mNGS) offers a rapid, comprehensive alternative for identifying diverse pathogens, including rare and mixed infections. Thus, we assessed the diagnostic performance of mNGS in pulmonary infections, compared the findings with those of traditional pathogen detection methods, and explored its potential to enhance clinical diagnostics and patient care.

Methods

We collected samples from 125 immunocompromised patients diagnosed with pulmonary infection at the Department of Respiratory Medicine of Shenzhen Longgang Central Hospital from March 2020 to July 2022. We compared the rate of pathogen positivity and pathogen distribution between conventional pathogen detection methods and mNGS using samples including sputum, blood, and bronchoalveolar lavage fluid.

Results

Among the 125 cases of unexplained pulmonary infection, 82 (65.6%) and 40 (32.0%) tested positive for pathogens using mNGS and routine culture, respectively (P < 0.05). Both methods of pathogen detection were positive in 28 (22.4%) cases (complete match, 9; complete mismatch, 13; partial match, 6). However, 43.2% of cases only tested positive using mNGS, 9.4% only tested positive using routine tests, and 24.8% tested negative using both methods. A viral infection was present in 55.2% of cases. The detection rate of mycobacteria using mNGS (12.8%) was higher than that using conventional pathogen detection methods (5.6%).

Conclusion

mNGS technology enhances pathogen detection in unexplained pulmonary infections, enabling targeted antimicrobial therapy and consequently helping to reduce broad-spectrum antibiotic use, aligning treatments more closely with the causative pathogens. Thus, mNGS offers significant clinical value by improving treatment efficacy and potentially reducing antibiotic resistance in pulmonary infection cases.

Clinical applications of metagenomics next-generation sequencing in infectious diseases

Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.

Intracardiac and Cerebral Thrombosis Complicated With Mycoplasma Pneumonia

A seven-year-old girl developed multiposition thrombosis after fever and respiratory symptoms. Chest computed tomography (CT) scan demonstrated bilateral infiltrates, consolidation of the right lower lobe, and pleural effusion in the right lung field. Brain magnetic resonance imaging (MRI) showed multiple abnormal signals in the brain with limited diffusion, and cerebral infarction could not be excluded. Echocardiography revealed hypoechoic mitral valve tips, which are likely to be suspected as vegetation. Mycoplasma pneumoniae infection was clarified by a four-fold increase in IgG antibodies to M. pneumoniae sera. D-dimer levels were elevated increasingly. We found and reported this rare pediatric case of an M. pneumoniae-induced severe pneumonia complicated with intracardiac and cerebral thrombosis. We investigate the clinical characteristics, diagnosis, and treatment of refractory mycoplasma pneumonia complicated with intracardiac and cerebral thrombosis in children.

Research status and challenges of Mycoplasma pneumoniae pneumonia in children: A bibliometric and visualization analysis from 2011 to 2023

BACKGROUND

Mycoplasma pneumoniae (MP) infections occur in regional outbreaks every 3 to 7 years, lasting up to 2 years. Since this fall, there has been a significant rise in MP infections among children in China, indicating a regional epidemiological trend that imposes an increased national public health burden. To date, bibliometric methods have not been applied to studies on MP infection in children.

METHODS

We searched for all relevant English publications on MP pneumonia in children published from 2011 to 2023 using Web of Science. Analytical software tools such as Citespace and VOSviewer were employed to analyze the collected literature.

RESULTS

993 articles on MP pneumonia in children were published in 338 academic journals by 5062 authors affiliated with 1381 institutions across 75 countries/regions. China led in global productivity with 56.19%. Among the top 10 prolific organizations, 8 were Chinese institutions, with Soochow University being the most active, followed by Capital Medical University and Zhejiang University. Zhimin Chen from Zhejiang University School of Medicine exhibited the highest H-index of 32. Keyword co-occurrence network analysis revealed 7 highly relevant clusters.

CONCLUSION

The current research hotspots and frontiers in this field are primarily MP pneumonia, refractory MP pneumonia, lactate dehydrogenase, asthma, and biomarker. We anticipate that this work will provide novel insights for advancing scientific exploration and the clinical application of MP pneumonia in children.

Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Metagenomic next-generation sequencing (mNGS) is widely used as a more promising technology than conventional tests. However, its clinical utility in the context of bronchoalveolar lavage fluid (BALF) samples for discriminating between non-severe and severe pneumonia is not well established. Thus, this study aimed to investigate the diagnostic performance of mNGS on BALF samples from 100 individuals suspected of pneumonia, and compared it with conventional microbiological tests (CMT) of BALF samples and the final clinical diagnosis. Twenty-seven cases of non-severe pneumonia and 73 cases of severe pneumonia patients were finally clinically diagnosed. Among 100 cases, diagnostic performance of mNGS and culture showed a significant difference; 65 cases had the same sample types, of which 25 cases were diagnosed as positive by mNGS only (38.46%) and 1 was diagnosed as positive by culture only (1.54%). Moreover, 24 cases were diagnosed positive in both mNGS and culture (36.92%) and 15 cases tested negative in both mNGS and culture (23.08%). Among 35 cases, 28 out of 35 cases were diagnosed as positive by mNGS, while only 4 out of 35 cases were diagnosed as positive by the indirect immunofluorescence method (IIFT). In addition, the positive rate of mNGS was higher than that of culture in cases regardless of prior antibiotic exposure. Mixed pathogens were found to be significantly more prevalent in severe pneumonia patients than in non-severe pneumonia patients. Importantly, among 38 cases who were diagnosed solely by mNGS, 25 patients experienced an improved outcome after physicians changed the therapy according to the mNGS results. In conclusion, the results showed that mNGS of BALF represents a potentially effective tool for detection of mixed pathogens in severe pneumonia.

Distribution Patterns of Pathogens Causing Lower Respiratory Tract Infection Based on Metagenomic Next-Generation Sequencing

Purpose

Lower Respiratory Tract Infection (LRTI) is a leading cause of morbidity and mortality worldwide. In this study, the distribution patterns of causative pathogens in LRTI were evaluated within a city-level hospital by combining conventional microbiological tests (CMT) with metagenomic next-generation sequencing (mNGS).

Patients and Methods

This retrospective cohort study involved 160 patients suspected of having LRTI in a single center. Specimens, including bronchoalveolar lavage fluid (BALF), blood, tissue, sputum, and pus were utilized to identify pathogens. The seasonal prevalence of pathogens and co-pathogens involved in multiple infections was analyzed.

Results

A total of 137 patients with 156 samples were included in this study. Pseudomonas aeruginosa, Corynebacterium striatum, Klebsiella pneumoniae, Candida, and human herpesvirus were the top prevalent pathogens. We observed seasonal dynamic variation in the top prevalent bacteria (Pseudomonas aeruginosa and Klebsiella pneumoniae) and herpesvirus (Epstein-Barr virus and Human herpesvirus-7). The majority of patients had single bacterial infections, followed by instances of bacterial-viral co-infections, as well as mixed infections involving bacteria, fungi, and viruses. Notably, the spectrum of co-infecting pathogens was broader among the elderly population, and positive Spearman correlations were observed among these co-infecting pathogens.

Conclusion

Co-infections were prevalent among patients with LRTI, and the pathogens displayed distinct seasonal distribution patterns. The findings underscored the significance of comprehending pathogen distribution and epidemic patterns, which can serve as a basis for early etiological identification.

Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort

Background

Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.

Methods

A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.

Results

Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).

Conclusions

mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.

The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science

Background

Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis.

Methods

The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3).

Results

In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections.

Conclusion

This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.

Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes

BACKGROUND

Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections.

METHODS

We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients.

RESULTS

A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups.

CONCLUSIONS

mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.

Prevalence and molecular characteristics of community-associated methicillin-resistant Staphylococcus aureus in the respiratory tracts of Chinese adults with community-acquired pneumonia

BACKGROUND

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an important pathogen causing healthcare-associated infections. In recent years, an increasing number of CA-MRSA clones have emerged and rapidly spread in the community and hospital settings in China.

OBJECTIVES

To investigate the molecular epidemiology and resistance of CA-MRSA in the respiratory tracts of Chinese adults with community-acquired pneumonia (CAP).

METHODS

A total of 243 sputum samples were collected from adult patients with CAP at the Nantong Hospital in China between 2018 and 2021. S. aureus was identified using PCR, and its susceptibility to 14 antimicrobials was tested using the broth dilution method. Genomic characterization of respiratory CA-MRSA and our previously collected intestinal CA-MRSA isolates was performed using whole-genome sequencing, and the evolutionary relationships of these isolates were assessed using phylogenetic analysis.

RESULTS

The CA-MRSA colonization rate among adults with CAP in China was 7.8 % (19/243). Antimicrobial resistance analysis revealed that the proportion of multidrug-resistant respiratory CA-MRSA isolates (100 %) was higher than that of intestinal CA-MRSA isolates (6.3 %). Among the 35 CA-MRSA isolates, 10 MLST types were identified and clustered into five clone complexes (CCs). CC5 (48.6 %) and CC88 (20 %) were predominant CA-MRSA clones. Notably, the CC5 clone ST764/ST6292-MRSA-II-t002 was identified as the major lineage causing respiratory tract infections in Chinese adults with CAP.

CONCLUSIONS

The prevalence of CA-MRSA among Chinese adults with CAP is high and often involves ST764/ST6292-MRSA-II-t002 as the causal pathogen.

The relationship between frailty and community-acquired pneumonia in older patients

PURPOSES

To explore the relationship between frailty and community-acquired pneumonia (CAP) in older patients.

METHODS

A prospective observational study included 109 older patients(≥ 65 years) hospitalized with CAP in respiratory department of Fuxing hospital, Capital Medical University from June 2018 to December 2020. Frailty scores(Frail Scale, range 0-5) and pneumonia severity CURB-65 scale(mild = 1, modest = 2, and severe ≥ 3) were measured. We extracted clinical variables including white blood cell(WBC), neutrophil-to-lymphocyte ratio (NLR), C-reactive protein(CRP), hemoglobin, and albumin. Charlson Comorbidity Index(CCI) was calculated as well. The correlations between the variables and frailty scores were investigated, respectively. After adjusting for covariates, binomial logistic regression analysis was used to assess independent effect of frailty scores on the outcome(discharge or death/progression) in older CAP patients.

RESULTS

The subjects had a median age 87(interquartile range,8.5) years, 60.6% male, 45.9% pre-frail, and 32.1% frail. There were positive correlations between frailty scores and CURB-65 scale (p = 0.000, r = 0.542), CCI(p = 0.000, r = 0.359) and NLR(p = 0.005, r = 0.268). Negative correlations were observed between frailty scores and hemoglobin (p = 0.002, r = - 0.298), albumin (p = 0.000, r = - 0.465). In multivariable logistic regression analysis, the factors associated with discharge or death/progression of CAP were frailty scores (OR = 1.623, p = 0.037), NLR (OR = 1.086, p = 0.008) and albumin (OR = 0.869, p = 0.034).

CONCLUSIONS

Frailty is correlated with CURB-65 scale, CCI and hemoglobin, and albumin in older patients with CAP. Frailty is also a correlate of increased risk for death or progression in these older people.

Cost-effectiveness of pneumococcal vaccines among adults aged 65 years and older in China: A comparative study

We aimed to assess the cost-effectiveness and health benefits of 23-valent pneumococcal polysaccharide vaccine (PPSV23), 13-valent pneumococcal conjunctive vaccine (PCV13), and PCV13-PPSV23 sequential vaccination strategies in preventing pneumonia and other pneumococcal diseases among the senior citizens (≥ 65 years) in China. The cost-effectiveness of pneumococcal vaccines compared to no vaccination was estimated using a decision-tree Markov model from a societal perspective. Parameters including epidemiological data, vaccine efficacy and cost data were obtained from previous studies. Cases and deaths averted, quality-adjusted life years (QALYs) gained, and incremental cost-effectiveness ratios (ICERs) were presented as outcomes. Sensitivity analyses were performed to explore the uncertainty in the model. In the base-case analysis, compared with no pneumococcal vaccination, the ICERs of PPSV23, PCV13 and PCV13-PPSV23 are US$10,776.7/QALY, $9,193.2/QALY, and $15,080.0/QALY, respectively. PCV13 is the most cost-effective strategy and the only cost-effective strategy based on a threshold of the one-time national GDP per capita, whereas PPSV23 vaccine strategy is provided with the lowest cost, and PCV13-PPSV23 demonstrates the greatest impact on pneumococcal disease burden. Sensitivity analyses reveal that the results are greatly influenced by serotype coverage, vaccine efficacy, CAP incidence and vaccine prices. The PCV13 vaccination for Chinese seniors is more cost-effective than PPSV23 vaccination and PCV13-PPSV23 sequential vaccination.

Comparison of next-generation sequencing with traditional methods for pathogen detection in cases of lower respiratory tract infection at a community hospital in Eastern China

Lower respiratory tract infection (LRTI) is still a threat to human health. Metagenomics next-generation sequencing (NGS) provides an efficient and unbiased way to identify LRTI pathogens, and has been shown to have several advantages over traditional methods. However, its application is currently limited in low-resource settings. Our aim was to collect and analyze data on LRTI cases at a county-level community hospital in Eastern China over one year, in order to compare the efficiency of NGS and traditional methods including culture, nucleic acid amplification and antibody techniques. We performed NGS of bronchoalveolar lavage fluid (BALF) for pathogen identification in 71 patients with LRTI. We compared the detection rates, identified pathogens, and turnaround time of NGS with traditional methods. Pathogens were detected using traditional methods in 19 cases, and the results were compared with those obtained with the NGS technique in 60 cases. The pathogen detection rate of NGS (84.5%) was much higher than that of the traditional methods (26.8%). Moreover, with the traditional methods considered the gold standard, the consistency rate between NGS and traditional methods was 68.4%. For the 19 cases in which the traditional method was used, the main pathogens included invasive Aspergillus (5 cases), Pseudomonas aeruginosa (3 cases), Candida albicans (3 cases), and Staphylococcus aureus (2 cases). Among the 60 cases detected by NGS, the main pathogens included Mycobacterium (12 cases), Streptococcus pneumoniae (5 cases), Klebsiella pneumoniae (3 cases), P. aeruginosa (3 cases), Haemophilus influenzae (3 cases), and S. aureus (3 cases), Aspergillus (9 cases), Pneumocystis jiroveci (5 cases), C. albicans (3 cases), Human Papilloma Virus (9 cases), Epstein-Barr virus (8 cases), and parvovirus (6 cases). In addition, 2 cases of chlamydia and 1 case of mycoplasma infection were detected by NGS. The time taken to perform the NGS tests was significantly shorter than that taken with the traditional method. NGS analysis of bronchoalveolar lavage fluid, in combination with traditional pathogen detection methods, can improve the efficiency of pathogen detection. More attention should be paid to the regional epidemic characteristics of infectious pathogens in LRTI.

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

Objective

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

Methods

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

Results

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

Conclusion

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

Mycoplasma pneumoniae triggers pneumonia epidemic in autumn and winter in Beijing: a multicentre, population-based epidemiological study between 2015 and 2020

The objective of this paper is to explore the characteristics of Mycoplasma pneumoniae (MP) epidemics in Beijing, China. Patients with acute respiratory tract infection (ARTI) were enrolled from 35 sentinel hospitals in Beijing, 2015–2020. Their medical records were reviewed and respiratory specimens were collected for assay for nucleic acids of 24 respiratory pathogens, including MP. The genotypes of MP were analysed using a real-time PCR method. The domain V of 23s rRNA gene was sequenced to identify macrolide-resistant mutations. A total of 41,677 specimens of ARTI patients were included, with an MP positive rate of 6.16%. MP prevalence mainly occurred between August and January, and peaked in October. The increase in the MP detection rate was coincident with the elevation of the reported number of patients with pneumonia in the 35 sentinel hospitals. One or more respiratory pathogens were co-detected in 27.1% of the MP-positive patients. Type 1 MP remained predominant, and the macrolide-resistant rate of MP had exceeded over 90%. A2063G mutation accounted for 99.0% of macrolide-resistant MP infections. MP epidemic in Beijing mainly occurred between August and January with a remarkable high macrolide-resistant rate. MP is one of the important contributors to the pneumonia epidemic in autumn and winter in Beijing.

Systematic review of the clinical outcomes of pneumonia with a penicillin-group resistant pneumococcus in respiratory and blood culture specimens in children in low- and middle-income countries

Background

Streptococcus pneumoniae is one of the most common bacteria causing pneumonia and the World Health Organization (WHO) recommends first-line treatment of pneumonia with penicillins. Due to increases in the frequency of penicillin resistance, this systematic review aimed to determine the clinical outcomes of children with pneumonia in low- and middle-income countries (LMICs), with penicillin-group resistant pneumococci in respiratory and/or blood cultures specimens.

Methods

English-language articles from January 2000 to November 2020 were identified by searching four databases. Systematic reviews and epidemiological studies from LMICs that included children aged one month to 9 years and reported outcomes of pneumonia with a penicillin-resistant pneumococcus in respiratory and blood culture specimens with or without comparison groups were included. Risk of bias was assessed using the Effective Public Health Practice Project (EPHPP) Quality Assessment Tool for Quantitative Studies. A narrative synthesis of findings based on the results of included studies was performed.

Results

We included 7 articles involving 2864 children. One strong- and four medium-quality studies showed no difference in clinical outcomes (duration of symptoms, length of hospital stay and mortality) between those children with penicillin non-susceptible compared to susceptible pneumococci. Two weak quality studies suggested better outcomes in the penicillin-susceptible group.

Conclusions

Current evidence suggests no difference in clinical outcomes of child pneumonia due to a penicillin-resistant S. pneumoniae and as such, there is no evidence to support a change in current WHO antibiotic guidelines.

Refractory Mycoplasma pneumoniae Pneumonia in Children: Early Recognition and Management

Refractory Mycoplasma pneumoniae pneumonia (RMPP) is a severe state of M. pneumoniae infection that has attracted increasing universal attention in recent years. The pathogenesis of RMPP remains unknown, but the excessive host immune responses as well as macrolide resistance of M. pneumoniae might play important roles in the development of RMPP. To improve the prognosis of RMPP, it is mandatory to recognize RMPP in the early stages, and the detection of macrolide-resistant MP, clinical unresponsiveness to macrolides and elevated proinflammatory cytokines might be clues. Timely and effective anti-mycoplasmal therapy and immunomodulating therapy are the main strategies for RMPP.

Efficacy and Safety of Ceftaroline Fosamil in Hospitalized Patients with Community-Acquired Pneumonia in China: Subset Analysis of an International Phase 3 Randomized Controlled Trial

Background

Methods

Results

Conclusion

Trial Registration

The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection

Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.

A post hoc analysis of two Phase III trials showing the efficacy and tolerability of ceftobiprole in East Asian patients

Aim: To evaluate the efficacy and safety of ceftobiprole in patients from East Asia. Materials & methods: A post hoc analysis was conducted of two randomized, double-blind, Phase III studies in patients with community- or hospital-acquired pneumonia. Results: Findings for East Asian patients were consistent with the overall study populations. A trend toward higher microbiological eradication rates and numerically lower rates of all-cause mortality were reported for ceftobiprole versus comparators (all-cause mortality [intent-to-treat]: community-acquired pneumonia, 1.5 vs 2.8%; hospital-acquired pneumonia excluding ventilator-associated pneumonia, 5.9 vs 11.4%). The incidence of adverse events was similar between treatment groups. Conclusion: This post hoc analysis supports the efficacy and tolerability of ceftobiprole in East Asian patients. ClinicalTrials.gov trial identifiers: NCT00326287, NCT00210964, NCT00229008.

Community-acquired bacterial pneumonia in adults: An update

Community-acquired pneumonia (CAP) is the prominent cause of mortality and morbidity with important clinical impact across the globe. India accounts for 23 per cent of global pneumonia burden with case fatality rates between 14 and 30 per cent, and Streptococcus pneumoniae is considered a major bacterial aetiology. Emerging pathogens like Burkholderia pseudomallei is increasingly recognized as an important cause of CAP in Southeast Asian countries. Initial management in the primary care depends on clinical assessment while the hospitalized patients require combinations of clinical scores, chest radiography and various microbiological and biomarker assays. This comprehensive diagnostic approach together with additional sampling and molecular tests in selected high-risk patients should be practiced. Inappropriate therapy in CAP in hospitalized patients lengthens hospital stay and increases cost and mortality. In addition, emergence of multidrug-resistant organisms poses tough challenges in deciding empirical as well as definitive therapy. Developing local evidence on the cause and management should be a priority to improve health outcomes in CAP.

Clinical Benefits and Cost-Effectiveness of Moxifloxacin as Initial Treatment for Community-Acquired Pneumonia: A Meta-Analysis and Economic Evaluation

PURPOSE

Moxifloxacin and levofloxacin are currently recommended as empirical initial treatment options for community-acquired pneumonia (CAP) in China according to guidelines. Most studies that evaluated the efficacy and safety of moxifloxacin and levofloxacin in treating CAP as initial empirical treatment were single-centered trials assessing different clinical end points. In addition, there is limited research investigating moxifloxacin's clinical benefits in the context of health care resource utilization and reimbursement from the payer's perspective in China. Hence, this study was aimed at comparing the clinical efficacy of moxifloxacin and levofloxacin by conducting a meta-analysis and assessing their economic value from the China payer's perspective through a cost-utility analysis model.

METHODS

For the meta-analysis, 6 bibliographic databases were searched for relevant publications from January 2000 to August 2020, and studies were assessed for eligibility under predetermined criteria. Meta-analysis was performed by using a random effects model when analyses included >2 trials. For the economic evaluation, a decision-tree model was constructed to investigate the cost-utility of moxifloxacin versus levofloxacin as initial regimens in the treatment of CAP inpatients. Parameter values were derived from meta-analysis, published literature, and clinician survey. The outcome was reported in the form of an incremental cost-effectiveness ratio. One-way sensitivity analysis and probabilistic sensitivity analysis were undertaken to assess the robustness of the model.

FINDINGS

Twenty-seven randomized controlled trials were included in the meta-analysis. Results indicated that the clinical response rate at the test-of-cure visit with initial treatment of moxifloxacin was significantly higher than that of levofloxacin (3441 patients; random effects model; I² = 49%; odds ratio, 3.35; 95% CI, 2.35-4.77; P < 0.001). In terms of the safety profile, total adverse events were not significantly different between the 2 groups (2770 patients; random effects model; I² = 40%; odds ratio, 0.77; 95% CI, 0.56-1.06; P = 0.11). Output of the cost-utility model showed that under the willingness-to-pay threshold of one-time China gross domestic product per capita, moxifloxacin is dominant over levofloxacin, being less costly and more efficacious (0.002 quality-adjusted life year gained, CNY 844 [US$131] saved in total cost, negative incremental cost-effectiveness ratio). Sensitivity analyses indicated the robustness of the model as moxifloxacin remained dominant when model parameter values fluctuated.

IMPLICATIONS

Moxifloxacin is more efficacious than levofloxacin as the initial empirical treatment for CAP. In addition, treatment of CAP with moxifloxacin instead of levofloxacin is expected to be cost-saving from the perspective of payers in China. However, for the cost-utility analysis, in the absence of a national representative database on costs for hospitalization in China, inputs in the cost-utility model could be underestimated or overestimated due to estimating errors applied to both treatment arms. (Clin Ther. 2021;43:XXX-XXX) © 2021 Elsevier HS Journals, Inc.

Mycoplasma pneumoniae Infections: Pathogenesis and Vaccine Development

Mycoplasma pneumoniae is a major causative agent of community-acquired pneumonia which can lead to both acute upper and lower respiratory tract inflammation, and extrapulmonary syndromes. Refractory pneumonia caused by M. pneumonia can be life-threatening, especially in infants and the elderly. Here, based on a comprehensive review of the scientific literature related to the respective area, we summarize the virulence factors of M. pneumoniae and the major pathogenic mechanisms mediated by the pathogen: adhesion to host cells, direct cytotoxicity against host cells, inflammatory response-induced immune injury, and immune evasion. The increasing rate of macrolide-resistant strains and the harmful side effects of other sensitive antibiotics (e.g., respiratory quinolones and tetracyclines) in young children make it difficult to treat, and increase the health risk or re-infections. Hence, there is an urgent need for development of an effective vaccine to prevent M. pneumoniae infections in children. Various types of M. pneumoniae vaccines have been reported, including whole-cell vaccines (inactivated and live-attenuated vaccines), subunit vaccines (involving M. pneumoniae protein P1, protein P30, protein P116 and CARDS toxin) and DNA vaccines. This narrative review summarizes the key pathogenic mechanisms underlying M. pneumoniae infection and highlights the relevant vaccines that have been developed and their reported effectiveness.

Frequency of Mycoplasma pneumoniae, Legionella pneumophila and Chlamydia spp. among patients with atypical pneumonia in Tehran

Mycoplasma pneumoniae, Legionella pneumophila and Chlamydia pneumoniae are the most common bacterial agents, which account for 15-40%, 2-15% and 5-10% of atypical community-acquired pneumonia (CAP) respectively. These agents are mostly associated with infection in the outpatient setting. The aim of this study was to evaluate the frequency of these pathogens among patients with CAP attending outpatient clinics in Tehran. A cross-sectional study was carried out of 150 patients attending to educational hospitals in Tehran with CAP. M. pneumoniae, L. pneumophila and Chlamydia spp. were detected by PCR assay, targeting the P1 adhesion gene, macrophage infectivity potentiator (mip) gene and 16S rRNA gene respectively from throat swabs obtained from each patient. A total of 86 (57.3%) of 150 patients were women; median age was 50 years (interquartile range, 35-65 years). M. pneumoniae, L. pneumophila and Chlamydia spp. were detected in 37 (24.7%), 25 (16.7%) and 11 (7.3%) patients respectively; of these, 66 patients (44%) were infected at least by one of these three pathogens. The frequency of L. pneumophila was significantly higher among patients over 60 years old (p 0.03). Coinfection was detected in seven patients (4.7%); six were infected by M. pneumoniae and L. pneumophila, and only one was infected by L. pneumophila and Chlamydia spp. M. pneumoniae was the most prevalent agent of atypical CAP, and L. pneumophila was more likely to infect elderly rather than younger people. Further studies on the prevalence of CAP and its aetiologic agents are needed to improve the diagnosis and treatment of CAP patients.

Blood and Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumonia

Background

Metagenomic next-generation sequencing (mNGS) has made a revolution in the mode of pathogen identification. We decided to explore the diagnostic value of blood and bronchoalveolar lavage fluid (BALF) as mNGS samples in pneumonia.

Methods

We retrospectively reviewed 467 mNGS results and assessed the diagnostic performance of paired blood and BALF mNGS in 39 patients with pneumonia.

Results

For bacteria and fungi, 16 patients had culture-confirmed pathogen diagnosis, while 13 patients were culture-negative. BALF mNGS was more sensitive than blood mNGS (81.3% vs. 25.0%, p=0.003), and the specificity in BALF and blood mNGS was not statistically significant different (76.9% vs. 84.6%, p=0.317). For 10 patients without culture test, treatments were changed in 2 patients. For viruses, Epstein-Barr virus was positive in blood mNGS in 9 patients. Human adenovirus was detected in both BALF and blood mNGS in 3 patients.

Conclusion

Our study suggests that BALF mNGS is more sensitive than blood mNGS in detecting bacteria and fungi, but blood also has advantages to identify the pathogens of pneumonia, especially for some viruses.

Etiology of Community-Acquired Pneumonia Requiring Hospital Admission in Adults with and Without Cancers: A Single-Center Retrospective Study in China

Background

The etiology and distribution of community-acquired pneumonia (CAP) vary periodically and geographically. The clinical evaluation of CAP among patients with cancers remains unknown.

Patients and Methods

This retrospective hospital-based study on adult CAP was conducted in Tang Du Hospital, China, from September 2018 to August 2019. The demographic characteristics, clinical manifestations and laboratory data were extracted from medical records and compared between CAP patients with and without cancers. Univariable and multivariable logistic regression methods were used to explore risk factors associated with CAP patients with and without cancers.

Results

Data from 149 CAP patients with cancers and 268 CAP patients without cancers were analyzed. Patients without cancers were more likely to show fever, cough and yellow sputum, higher level of neutrophil count than the cancer patients. Klebsiella pneumoniae (K. pneumoniae 14.77% vs 9.33%, p = 0.093) and Streptococcus pneumoniae (S. pneumoniae 16.11% vs 11.57%, p = 0.189) were among the most commonly encountered pathogens in both the groups. Pseudomonas aeruginosa (P. pneumoniae 26.50% vs 11.41%, p < 0.001), Mycoplasma pneumoniae (M. pneumoniae 8.21% vs 1.34%, p = 0.003), and filamentous fungi (10.82% vs 4.7%, p = 0.033) were predominant in CAP patients without cancers. Haemophilus influenzae (H. influenzae 22.15% vs 14.18%, p = 0.038) and methicillin-resistant Staphylococci (MRS 23.49 vs 15.68, p = 0.049) were more prevalent for CAP cancer patients. Certain pathogens were increasing in a cold season. In patients without cancers, MRS, H. influenzae and P. aeruginosa were associated with central nervous system (CNS) disease, connective tissue disease, bronchiectasis, respectively. In addition, healthy adults were likely to be infected with M. pneumoniae showing fever.

Conclusion

CAP patients with cancers had atypical clinical manifestations and showed no distinct increase in inflammatory markers. The predominant pathogens differed as well as similar between the CAP patients with and without cancers. Certain pathogens follow a seasonal pattern. CNS disease, connective tissue disease and bronchiectasis were associated with the predominant pathogens in patients without cancers.

Airway microbiome, host immune response and recurrent wheezing in infants with severe respiratory syncytial virus bronchiolitis

BACKGROUND

Early interactions between respiratory viruses and microbiota might modulate host immune responses and subsequently contribute to later development of recurrent wheezing and asthma in childhood. We aimed to study the possible association between respiratory microbiome, host immune response, and the development of recurrent wheezing in infants with severe respiratory syncytial virus (RSV) bronchiolitis.

METHODS

Seventy-four infants who were hospitalized at Beijing Children's Hospital during an initial episode of severe RSV bronchiolitis at 6 months of age or less were included and followed up until the age of 3 years. Sputum samples were collected, and their microbiota profiles, LPS, and cytokines were analyzed by 16S rRNA-based sequencing, ELISA, and multiplex immunoassay, respectively.

RESULTS

Twenty-six (35.1%) infants developed recurrent wheezing by the age of 3 years, and 48 (64.9%) did not. The relative abundance of Haemophilus, Moraxella, and Klebsiella was higher in infants who later developed recurrent wheezing than in those who did not (LDA score >3.5). Airway levels of LPS (P = .003), CXCL8 (P = .004), CCL5 (P = .029), IL-6 (P = .004), and IL-13 (P < .001) were significantly higher in infants who later developed recurrent wheezing than in those who did not. Moreover, high airway abundance of Haemophilus was associated with CXCL8 (r = 0.246, P = .037) level, and that of Moraxella was associated with IL-6 level (r = 0.236, P = .046) and IL-10 level (r = 0.266, P = .024).

CONCLUSION

Our study suggests that higher abundance of Haemophilus and Moraxella in airway microbiome might modulate airway inflammation during severe RSV bronchiolitis in infancy, potentially contributing to the development of subsequent recurrent wheezing in later childhood.

Burden of Community-Acquired Pneumonia and Unmet Clinical Needs

Community-acquired pneumonia (CAP) is the leading cause of death among infectious diseases and an important health problem, having considerable implications for healthcare systems worldwide. Despite important advances in prevention through vaccines, new rapid diagnostic tests and antibiotics, CAP management still has significant drawbacks. Mortality remains very high in severely ill patients presenting with respiratory failure or shock but is also high in the elderly. Even after a CAP episode, higher risk of death remains during a long period, a risk mainly driven by inflammation and patient-related co-morbidities. CAP microbiology has been altered by new molecular diagnostic tests that have turned viruses into the most identified pathogens, notwithstanding uncertainties about the specific role of each virus in CAP pathogenesis. Pneumococcal vaccines also impacted CAP etiology and thus had changed Streptococcus pneumoniae circulating serotypes. Pathogens from specific regions should also be kept in mind when treating CAP. New antibiotics for CAP treatment were not tested in severely ill patients and focused on multidrug-resistant pathogens that are unrelated to CAP, limiting their general use and indications for intensive care unit (ICU) patients. Similarly, CAP management could be personalized through the use of adjunctive therapies that showed outcome improvements in particular patient groups. Although pneumococcal vaccination was only convincingly shown to reduce invasive pneumococcal disease, with a less significant effect in pneumococcal CAP, it remains the best therapeutic intervention to prevent bacterial CAP. Further research in CAP is needed to reduce its population impact and improve individual outcomes.

Predictive Model for Discrimination of Tuberculous Pleural Effusion From Severe Mycoplasma pneumoniae Pneumonic Effusion in Children

BACKGROUND

Tuberculous pleural effusion (TPE) is often misdiagnosed as severe Mycoplasma pneumoniae pneumonic effusion (SMPPE) in children at early stage. The aim of this study was to develop a predictive model based on clinical and laboratory indices to make accurate differential diagnosis.

METHODS

Patients included in this study were 167 children (83 patients with TPE and 84 with SMPPE), containing 117 patients for predictive model development and 50 patients for external validation. Multivariate logistic regression analysis was conducted to select potentially useful characteristics for discrimination of TPEs. External validation was performed for model evaluation.

RESULTS

Multivariate analysis revealed that blood neutrophils and serum lactate dehydrogenase were significant independent factors to discriminate between TPEs and SMPPEs. The results indicated that blood neutrophils ≤69.6% and concentration of serum lactate dehydrogenase ≤297 U/L were the extremely important discrimination factors of TPEs. The area under the receiver operating characteristic curve of the model was 0.9839. The accuracy rate, sensitivity and specificity of the model were 94.02%, 98.28% and 89.83%, respectively. Meanwhile, the accuracy rate of the external validation from the 50 patients was 94.0%.

CONCLUSIONS

Applying a predictive model with clinical and laboratory indices can facilitate the differential diagnosis of TPE from SMPPE in children, which seems helpful when a microbiologic or histologic diagnosis of pleural tuberculosis could not be established.