Community-acquired pneumonia:

Deep diagnostic agent forest (DDAF): A deep learning pathogen recognition system for pneumonia based on CT

BACKGROUND

Even though antibiotics agents are widely used, pneumonia is still one of the most common causes of death around the world. Some severe, fast-spreading pneumonia can even cause huge influence on global economy and life security. In order to give optimal medication regimens and prevent infectious pneumonia's spreading, recognition of pathogens is important.

METHOD

In this single-institution retrospective study, 2,353 patients with their CT volumes are included, each of whom was infected by one of 12 known kinds of pathogens. We propose Deep Diagnostic Agent Forest (DDAF) to recognize the pathogen of a patient based on ones' CT volume, which is a challenging multiclass classification problem, with large intraclass variations and small interclass variations and very imbalanced data.

RESULTS

The model achieves 0.899 ± 0.004 multi-way area under curves of receiver (AUC) for level-I pathogen recognition, which are five rough groups of pathogens, and 0.851 ± 0.003 AUC for level-II recognition, which are 12 fine-level pathogens. The model also outperforms the average result of seven human readers in level-I recognition and outperforms all readers in level-II recognition, who can only reach an average result of 7.71 ± 4.10% accuracy.

CONCLUSION

Deep learning model can help in recognition pathogens using CTs only, which might help accelerate the process of etiological diagnosis.

Clinical metagenomics assessments improve diagnosis and outcomes in community-acquired pneumonia

Background

Identifying the causes of community-acquired pneumonia (CAP) is challenging due to the disease’s complex etiology and the limitations of traditional microbiological diagnostic methods. Recent advances in next generation sequencing (NGS)-based metagenomics allow pan-pathogen detection in a single assay, and may have significant advantages over culture-based techniques.

Results

We conducted a cohort study of 159 CAP patients to assess the diagnostic performance of a clinical metagenomics assay and its impact on clinical management and patient outcomes. When compared to other techniques, clinical metagenomics detected more pathogens in more CAP cases, and identified a substantial number of polymicrobial infections. Moreover, metagenomics results led to changes in or confirmation of clinical management in 35 of 59 cases; these 35 cases also had significantly improved patient outcomes.

Conclusions

Clinical metagenomics could be a valuable tool for the diagnosis and treatment of CAP.

Trial registration

Trial registration number with the Chinese Clinical Trial Registry: ChiCTR2100043628.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06039-1.

A randomized, controlled, multicenter clinical trial to evaluate the efficacy and safety of oral sitafloxacin versus moxifloxacin in adult patients with community-acquired pneumonia

OBJECTIVES

To evaluate the efficacy and safety of oral sitafloxacin versus oral moxifloxacin in the treatment of Chinese adults with community-acquired pneumonia (CAP).

PATIENTS AND METHODS

This is a multicenter, randomized, open-label, positive-controlled clinical trial (chinadrugtrials.org.cn identifier: CTR20130046). CAP patients received sitafloxacin tablets 100 mg once daily (qd) or 100 mg twice daily (bid) to compare with moxifloxacin tablets 400 mg qd, for 7-10 days. The primary outcome was non-inferiority of sitafloxacin to moxifloxacin in clinical cure rate at test of cure (TOC) visit in per-protocol set (PPS).

RESULTS

A total of 343 patients were randomized (sitafloxacin 100 mg qd, n = 117; sitafloxacin 100 mg bid, n = 116; moxifloxacin, n = 110), 291 patients were included in the PPS (sitafloxacin 100 mg qd, n = 96; sitafloxacin 100 mg bid, n = 94; moxifloxacin, n = 101). The clinical cure rate was 94.8% in the sitafloxacin 100 mg qd group, 96.8% in the sitafloxacin 100 mg bid group and 95.0% in the moxifloxacin group. At the TOC visit, the microbiological success rate was 97.0% (32/33) in the sitafloxacin 100 mg qd group, 97.1% (34/35) in the sitafloxacin 100 mg bid group and 94.9% (37/39) in the moxifloxacin group in the microbiological evaluable set (MES). The incidence of study-drug-related adverse events (AEs) was 23.3% (27/116) in the sitafloxacin 100 mg qd group, 29.8% (34/114) in the sitafloxacin 100 mg bid group and 28.2% (31/110) in the moxifloxacin group (p > .05). The common AEs related to study drug were dizziness, nausea, diarrhea, increased platelet count and alanine transaminase (ALT) elevation. All the AEs resolved completely after discontinuation of study drug.

CONCLUSION

Sitafloxacin 100 mg qd or 100 mg bid for 7-10 days is not inferior to moxifloxacin 400 mg qd for 7-10 days in clinical efficacy for adult CAP patients. Sitafloxacin provides a safety profile comparable to moxifloxacin.

Adult community-acquired pneumonia with unusually enlarged mediastinal lymph nodes: A case report

Adult community-acquired pneumonia (ACAP) is the most prevalent pulmonary infectious disease that may be asymptomatic or have varying clinical presentations. Patients with ACAP often present with enlarged mediastinal lymph nodes on their chest computed tomography images. However, large irregular swollen lymph nodes are rarely reported in ACAP, and may therefore be confused with enlarged lymph node masses. In the present case report, the patient presented with lymph node masses, which were ameliorated to their normal size following antimicrobial treatment. The patient was 24 years old and otherwise healthy, which led to a pronounced and excessive immune response to pneumonia in the lymph nodes. Atypical pneumonia is difficult to diagnose based on imaging features. The present case report demonstrates that patients with pneumonia may present with unusually enlarged mediastinal lymph nodes, which are most likely, a result of a strong immune response to pneumonia.

Community-acquired pneumonia

PURPOSE OF REVIEW

Community-acquired pneumonia (CAP) contributes significantly to morbidity and mortality, especially in the elderly. Recent advances aimed at improving outcomes and reducing CAP disease burden are summarized.

RECENT FINDINGS

Emerging data suggests that newer CAP risk stratification indices based on disease severity hold promise in predicting intensive care need. Additional evidence supports a role of procalcitonin and pro-adrenomedullin as biomarkers of disease severity and for guiding antimicrobial therapy. New diagnostic tools have greatly contributed to early diagnosis and better-targeted therapy. There is increasing recognition of the role of coinfections in CAP. In patients with severe disease, therefore, current guidelines advise against monotherapy. Although inclusion of coverage for atypical pathogens in nonsevere CAP has been challenged, evidence suggests that such coverage is beneficial in patients with severe disease. Use of steroids as adjunctive therapy for CAP, however, is associated with complications and prolonged hospitalization. Updated prevention strategies include approval of pneumococcal conjugate vaccine (PCV13) for adults at risk.

SUMMARY

Despite these developments research aimed at further reducing CAP-related morbidity and mortality is required. Increasing global life expectancy is likely to expand the at-risk population; therefore, research directed at CAP prevention in view of changing demography is essential.

Switch therapy in hospitalized patients with community-acquired pneumonia: tigecycline vs. levofloxacin

Background

Switch therapy is a management approach combining early discontinuation of intravenous (IV) antibiotics, switch to oral antibiotics, and early hospital discharge. This analysis compares switch therapy using tigecycline versus levofloxacin in hospitalized patients with community-acquired pneumonia (CAP).

Methods

A prospective, randomized, double-blind, Phase 3 clinical trial; patients were randomized to IV tigecycline (100 mg, then 50 mg q12h) or IV levofloxacin (500 mg q24h). Objective criteria were used to define time to switch therapy; patients were switched to oral levofloxacin after ≥6 IV doses if criteria met. Switch therapy outcomes were assessed within the clinically evaluable (CE) population.

Results

In the CE population, 138 patients were treated with IV tigecycline and 156 were treated with IV levofloxacin. The proportion of the population that met switch therapy criteria was 67.4% (93/138) for tigecycline and 66.7% (104/156) for levofloxacin. The proportion that actually switched to oral therapy was 89.9% (124/138) for tigecycline and 87.8% (137/156) for levofloxacin. Median time to actual switch therapy was 5.0 days each for tigecycline and levofloxacin. Clinical cure rates for patients who switched were 96.8% for tigecycline and 95.6% for levofloxacin. Corresponding cure rates for those that met switch criteria were 95.7% for tigecycline and 92.3% for levofloxacin.

Conclusions

Switch therapy outcomes in hospitalized patients with CAP receiving initial IV therapy with tigecycline are comparable to those of patients receiving initial IV therapy with levofloxacin. These data support the use of IV tigecycline in hospitalized patients with CAP when the switch therapy approach is considered.

ClinicalTrials.gov Identifier

NCT00081575

Oxygen therapy for pneumonia in adults

BACKGROUND

Oxygen therapy is widely used in the treatment of lung diseases. However, the effectiveness of oxygen therapy as a treatment for pneumonia is not well known.

OBJECTIVES

To determine the effectiveness and safety of oxygen therapy in the treatment of pneumonia in adults older than 18 years.

SEARCH METHODS

We searched the Cochrane Central Register of Controlled Trials (CENTRAL) 2011, Issue 4, part of The Cochrane Library, www.thecochranelibrary.com (accessed 9 December 2011), which includes the Cochrane Acute Respiratory Infections Group's Specialised Register, MEDLINE (1948 to November week 3, 2011) and EMBASE (1974 to December 2011).

SELECTION CRITERIA

Randomised controlled trials (RCTs) of oxygen therapy for adults with community-acquired pneumonia (CAP) and nosocomial (hospital-acquired) pneumonia (HAP or NP) in intensive care units (ICU).

DATA COLLECTION AND ANALYSIS

Two review authors independently reviewed abstracts and assessed data for methodological quality.

MAIN RESULTS

Three RCTs met our inclusion criteria. The studies enrolled 151 participants with CAP or immunosuppressed patients with pulmonary infiltrates. Overall, we found that non-invasive ventilation can reduce the risk of death in the ICU, odd ratio (OR) 0.28, 95% confidence interval (CI) 0.09 to 0.88; endotracheal intubation, OR 0.26, 95% CI 0.11 to 0.61; complications, OR 0.23, 95% CI 0.08 to 0.70; and shorten ICU length of stay, mean duration (MD) -3.28, 95% CI -5.41 to -1.61.Non-invasive ventilation and standard oxygen supplementation via a Venturi mask were similar when measuring mortality in hospital, OR 0.54, 95% CI 0.11 to 2.68; two-month survival, OR 1.67, 95% CI 0.53 to 5.28; duration of hospital stay, MD -1.00, 95% CI -2.05 to 0.05; and duration of mechanical ventilation, standard MD -0.26, 95% CI -0.66 to 0.14. Some outcomes and complications of non-invasive ventilation were varied according to different participant populations. We also found that some subgroups had a high level of heterogeneity when conducting pooled analyses.

AUTHORS' CONCLUSIONS

Non-invasive ventilation can reduce the risk of death in the ICU, endotracheal intubation, shorten ICU stay and length of intubation. Some outcomes and complications of non-invasive ventilation were varied according to different participant populations. Other than the oxygen therapy, we must mention the importance of standard treatment by physicians. The evidence is weak and we did not include participants with pulmonary tuberculosis and cystic fibrosis. More RCTs are required to answer these clinical questions. However, the review indicates that non-invasive ventilation may be more beneficial than standard oxygen supplementation via a Venturi mask for pneumonia.

Cost-effectiveness of adult vaccination strategies using pneumococcal conjugate vaccine compared with pneumococcal polysaccharide vaccine

CONTEXT

The cost-effectiveness of 13-valent pneumococcal conjugate vaccine (PCV13) compared with 23-valent pneumococcal polysaccharide vaccine (PPSV23) among US adults is unclear.

OBJECTIVE

To estimate the cost-effectiveness of PCV13 vaccination strategies in adults.

DESIGN, SETTING, AND PARTICIPANTS

A Markov state-transition model, lifetime time horizon, societal perspective. Simulations were performed in hypothetical cohorts of US 50-year-olds. Vaccination strategies and effectiveness estimates were developed by a Delphi expert panel; indirect (herd immunity) effects resulting from childhood PCV13 vaccination were extrapolated based on observed PCV7 effects. Data sources for model parameters included Centers for Disease Control and Prevention Active Bacterial Core surveillance, National Hospital Discharge Survey and Nationwide Inpatient Sample data, and the National Health Interview Survey.

MAIN OUTCOME MEASURES

Pneumococcal disease cases prevented and incremental costs per quality-adjusted life-year (QALY) gained.

RESULTS

In the base case scenario, administration of PCV13 as a substitute for PPSV23 in current recommendations (ie, vaccination at age 65 years and at younger ages if comorbidities are present) cost $28,900 per QALY gained compared with no vaccination and was more cost-effective than the currently recommended PPSV23 strategy. Routine PCV13 at ages 50 and 65 years cost $45,100 per QALY compared with PCV13 substituted in current recommendations. Adding PPSV23 at age 75 years to PCV13 at ages 50 and 65 years gained 0.00002 QALYs, costing $496,000 per QALY gained. Results were robust in sensitivity analyses and alternative scenarios, except when low PCV13 effectiveness against nonbacteremic pneumococcal pneumonia was assumed or when greater childhood vaccination indirect effects were modeled. In these cases, PPSV23 as currently recommended was favored.

CONCLUSION

Overall, PCV13 vaccination was favored compared with PPSV23, but the analysis was sensitive to assumptions about PCV13 effectiveness against nonbacteremic pneumococcal pneumonia and the magnitude of potential indirect effects from childhood PCV13 on pneumococcal serotype distribution.

Rapid clinical diagnosis of Legionnaires' disease during the "herald wave" of the swine influenza (H1N1) pandemic: the Legionnaires' disease triad

BACKGROUND

In adults hospitalized with atypical community-acquired pneumonia (CAP), Legionnaires' disease is not uncommon. Legionnaire's disease can be differentiated from typical CAPs and from other atypical CAPs based on its characteristic pattern of extrapulmonary organ involvement. The first clinically useful diagnostic weighted point score system for the clinical diagnosis of Legionnaires' disease was developed by the Infectious Disease Division at Winthrop-University Hospital in the 1980s. It has proven to be diagnostically accurate and useful for more than two decades, but was time-consuming. Because Legionella spp. diagnostic tests are time-dependent and problematic, a need was perceived for a rapid, simple way to render a clinical, syndromic diagnosis of Legionnaires' disease pending Legionella test results. During the "herald wave" of the swine influenza (H1N1) pandemic in the New York area, our hospital, like others, was inundated with patients who presented to the Emergency Department with influenza-like illnesses (ILIs) for H1N1 testing/evaluation. Most patients with ILIs did not have swine influenza. Hospitalized patients with ILIs who tested positive with rapid influenza diagnostic tests (RIDTs) were placed on influenza precautions and treated with oseltamivir. Unfortunately, approximately 30% of adult patients admitted with an ILI had negative RIDTs. Because the definitive laboratory diagnosis of H1N1 pneumonia by reverse transcription-polymerase chain reaction(RT-PCR), testing was restricted by health departments, resulted in clinical and infection control dilemmas in determining which RIDT-negative patients did, in fact, have H1N1 pneumonia.

OBJECTIVE

Accordingly, a diagnostic weighted point score system was developed for H1N1 pneumonia patients, based on RT-PCR positivity by the Infectious Disease Division at Winthrop-University Hospital. This diagnostic point score system for hospitalized adults with negative RIDTs was time-consuming. As the pandemic progressed, a simplified diagnostic swine influenza (H1N1) triad was developed for the rapid clinical diagnosis of probable H1N1 pneumonia, which also differentiated it from its mimics as well as from bacterial pneumonia, eg, Legionnaires' disease. During the "herald wave" of the H1N1 pandemic, we noticed an unexplained increase in Legionnaires' disease CAPs. Because clinical resources were stressed to the maximum during the pandemic, it was critically important to rapidly identify patients rapidly with Legionnaire's disease who did not require influenza precautions or oseltamivir, but who did require anti-Legionella antimicrobial therapy.

METHODS

Based on the Winthrop-University Hospital Infectious Disease Division's diagnostic weighted point score system for Legionnaires' disease (modified), key indicators were identified and became the basis for the diagnostic Legionnaires' disease triad. The diagnostic Legionnaires' disease triad was used to make a clinical diagnosis of Legionnaires' disease until the results of Legionella diagnostic tests were reported. The diagnostic Legionnaires' disease triad diagnosed Legionnaires' disease in hospitalized adults with CAPs with extrapulmonary findings (atypical CAP) and relative bradycardia, accompanied by any three (ie, a triad) of the following: otherwise unexplained relative lymphopenia, early/mildly elevated serum transaminases (SGOT/SGPT), highly increased ferritin levels (> or =2 x n), or hypophosphatemia. The diagnostic Legionnaires' disease triad provides clinicians with a rapid way to clinically diagnose Legionnaires' disease, pending Legionella test results.

RESULTS

The accuracy of the diagnostic Legionnaires' disease triad was confirmed in our 9 cases of Legionnaires' disease by subsequent Legionella diagnostic testing.

CONCLUSIONS

The diagnostic Legionnaires' disease triad is particularly useful in situations where a rapid clinical syndromic diagnosis is needed, ie, during an H1N1 pandemic.

A prospective study of urinary pneumococcal antigen detection in healthy Karen mothers with high rates of pneumococcal nasopharyngeal carriage

Background

Detection of Streptococcus pneumoniae C-polysaccharide in urine is a useful rapid diagnostic test for pneumococcal infections in adults. In young children, high rates of false positive results have been documented due to detection of concurrent nasopharyngeal pneumococcal carriage. The relationship between pneumococcal carriage and urinary antigen detection in adults from developing countries with high pneumococcal carriage prevalence has not been well established.

Methods

We nested an evaluation of the BinaxNOW S. pneumoniae test within a longitudinal mother-infant pneumococcal carriage study in Karen refugees on the Thailand-Myanmar border. Paired urine and nasopharyngeal swab specimens were collected from 98 asymptomatic women at a routine study follow-up visit. The urine specimens were analyzed with the BinaxNOW test and the nasopharyngeal swabs were semi-quantitatively cultured to identify pneumococcal colonization.

Results

24/98 (25%) women were colonized by S. pneumoniae but only three (3%) had a positive BinaxNOW urine test. The sensitivity of the BinaxNOW test for detection of pneumococcal colonization was 4.2% (95% CI: 0.1 - 21.1%) with a specificity of 97.3% (95% CI: 90.6 - 99.7%). Pneumococcal colonization was not associated with having a positive BinaxNOW test (odds ratio 1.6; 95% CI: 0.0 - 12.7; p = 0.7).

Conclusions

Significant numbers of false positive results are unlikely to be encountered when using the BinaxNOW test to diagnose pneumococcal infection in adults from countries with moderate to high rates of pneumococcal colonization.

Comparative antibiotic failure rates in the treatment of community-acquired pneumonia: Results from a claims analysis

INTRODUCTION

Antibiotic treatment failure contributes to the economic and humanistic burdens of community-acquired pneumonia (CAP) by increasing morbidity, mortality, and healthcare costs. This study compared treatment failure rates of levofloxacin with those of other antibiotics in a large US sample.

METHODS

Medical and pharmacy claims in the nationally representative SDI database were used to identify adults with a new outpatient diagnosis of CAP receiving a study antibiotic (levofloxacin, amoxicillin/clavulanate, azithromycin, moxifloxacin) between September 1, 2005 and March 31, 2008. Treatment failure was defined as ≥1 of the following events ≤30 days after index date: a refill for the index antibiotic after completed days of therapy, a different antibiotic dispensed >1 day after the index prescription, or hospitalization with a pneumonia diagnosis or emergency department visit >3 days postindex. Cohorts were propensity score matched for demographic and clinical characteristics. Treatment failure rates were compared between pairs of cohorts for the full sample and for high-risk patients (age ≥65 and/or on Medicaid).

RESULTS

Among the 3994 study patients, the numbers of dispensed index prescriptions were 268 for amoxicillin/clavulanate, 1609 for azithromycin, 1460 for levofloxacin, and 657 for moxifloxacin. Unadjusted treatment failure rates for the sample were 20.8% for levofloxacin, 23.9% for amoxicillin/clavulanate, 23.9% for azithromycin, and 19.9% for moxifloxacin. For high-risk patients, unadjusted treatment failure rates were 19.1% for levofloxacin, 26.1% for amoxicillin/clavulanate, 26.3% for azithromycin, and 24.3% for moxifloxacin. Propensity score-matched treatment failure rates were significantly lower with levofloxacin than azithromycin (19.8% vs. 24.5%, odds ratio [OR] comparator vs. levofloxacin 1.38; 95% CI: 1.14, 1.67), a difference amplified in high-risk patients (19.0% vs. 26.4%, OR 1.61; 95% CI: 1.22, 2.13). No significant differences were observed for other paired comparisons.

CONCLUSION

In a large US sample, treatment failure in CAP appeared to be less likely with quinolones (such as levofloxacin) than azithromycin, an effect particularly marked in high-risk patients (age ≥65 and/or on Medicaid).

Efficacy and safety of nemonoxacin versus levofloxacin for community-acquired pneumonia

Nemonoxacin, a novel nonfluorinated quinolone, exhibits potent in vitro and in vivo activities against community-acquired pneumonia (CAP) pathogens, including multidrug-resistant Streptococcus pneumoniae. Patients with mild to moderate CAP (n = 265) were randomized to receive oral nemonoxacin (750 mg or 500 mg) or levofloxacin (500 mg) once daily for 7 days. Clinical responses were determined at the test-of-cure visit in intent-to-treat (ITT), clinical per protocol (PPc), evaluable-ITT, and evaluable-PPc populations. The clinical cure rates for 750 mg nemonoxacin, 500 mg nemonoxacin, and levofloxacin were 89.9%, 87.0%, and 91.1%, respectively, in the evaluable-ITT population; 91.7%, 87.7%, and 90.3%, respectively, in the evaluable-PPc population; 82.6%, 75.3%, and 80.0%, respectively, in the ITT population; and 83.5%, 78.0%, and 82.3%, respectively, in the PPc population. Noninferiority to levofloxacin was demonstrated in both the 750-mg and 500-mg nemonoxacin groups for the evaluable-ITT and evaluable-PPc populations, and also in the 750 mg nemonoxacin group for the ITT and PPc populations. Overall bacteriological success rates were high for all treatment groups in the evaluable-bacteriological ITT population (90.2% in the 750 mg nemonoxacin group, 84.8% in the 500 mg nemonoxacin group, and 92.0% in the levofloxacin group). All three treatments were well tolerated, and no drug-related serious adverse events were observed. Overall, oral nemonoxacin (both 750 mg and 500 mg) administered for 7 days resulted in high clinical and bacteriological success rates in CAP patients. Further, good tolerability and excellent activity against common causative pathogens were demonstrated. Nemonoxacin (750 mg and 500 mg) once daily is as effective and safe as levofloxacin (500 mg) once daily for the treatment of CAP.

Determining the optimal pneumococcal vaccination strategy for adults: is there a role for the pneumococcal conjugate vaccine?

On February 24, 2010, the US Food and Drug Administration approved a 13-valent pneumococcal protein conjugate vaccine (PCV13) for use in children. Currently, the only pneumococcal vaccine approved for use in adults in the United States is the 23-valent pneumococcal polysaccharide vaccine (PPV23). Although PPV23 provides partial protection against invasive pneumococcal disease, it does not appear to impact the risk of pneumonia in elderly patients or younger adults with comorbidities. Experience with PCV7 in children and studies of the immunogenicity of PCV7 in high-risk adults suggest that PCV13 may be effective in adults. However, prior receipt of PPV23 may blunt the antibody response to protein conjugate vaccination; thus, receipt of PPV23 could potentially diminish the benefit of subsequent pneumococcal conjugate vaccination. The approval of PCV13 for children has created a unique dilemma for physicians seeking to provide optimum protection for their high-risk adult patients. Potential options could include use of the PCV13 "off-label," perhaps followed by PPV23; withholding pneumococcal vaccination of adults while awaiting approval of PCV13; or continuing to use the PPV23. Although there are limited data on PCVs in adults, the availability of PCV13 for children will likely cause uncertainty for some physicians until there is updated official guidance regarding the optimum strategies for prevention of pneumococcal infection in adults.