Clinical Trial Details
— Status: Recruiting
Administrative data
| NCT number |
NCT05394220 |
| Other study ID # |
PPE_Metagenomic |
| Secondary ID |
|
| Status |
Recruiting |
| Phase |
|
| First received |
|
| Last updated |
|
| Start date |
June 1, 2023 |
| Est. completion date |
May 31, 2027 |
Study information
| Verified date |
June 2023 |
| Source |
Chinese University of Hong Kong |
| Contact |
Ka Pang Chan, MBChB |
| Phone |
35052211 |
| Email |
chankapang[@]gmail.com |
| Is FDA regulated |
No |
| Health authority |
|
| Study type |
Observational
|
Clinical Trial Summary
Objective: To identify known and unknown bacterial pathogens in patients with pleural
infections using a combination of conventional culture and next-generation sequencing
approaches.
Hypothesis to be tested: The investigators hypothesize that next-generation sequencing will
serve as a comprehensive approach to identify culturable and unculturable bacterial pathogens
in patients with pleural infections compared to the conventional culture.
Design and subjects: This is a prospective cohort study to be conducted in the medical
department of a tertiary care hospital in Hong Kong involving patients with pleural
infection. Patients will be recruited if a pleural infection is suspected, with pleural fluid
sampled and a 6-month follow-up. The clinical management by the medical team will not be
interfered.
Study instruments: Pleural fluid will be collected for conventional culture, 16S amplicon and
shotgun metagenomic sequencing in parallel. The clinical information will be collected to
clarify the causative correlation between symptoms, clinical outcomes and pathogen
infections.
Main outcome measures: The full spectrum of causative bacteria in pleural infection will be
characterized. The diagnostic performance of identifying causative bacteria in pleural
infection will be compared between the studied methods. The antimicrobial resistance pattern,
clinical outcomes of pleural infection will also be compared between groups as categorized by
the pattern of bacteriology identified by different methods.
Data analysis: With reference to the conventional culture as the gold standard, sensitivity,
specificity, positive predictive values and negative predictive values of 16S ribosomal
ribonucleic acid (rRNA) gene amplicon and shotgun metagenomic sequencing will be calculated.
Description:
Parapneumonic effusion (PPE) is a common and serious clinical problem. Among patients
suffering from community-acquired pneumonia, up to 57% of them would develop parapneumonic
effusion (PPE), and 7.2% would develop complicated parapneumonic effusion (CPPE) and empyema.
The latter two, collectively known as pleural infection, are associated with long hospital
stay, high Intensive Care Unit admission rates, serious morbidity and mortality.
The cornerstone of treating pleural infection is the timely administration of appropriate
antibiotics and adequate pleural fluid drainage. However, the initial choice of antibiotics
is almost always empirical, and only able to be adjusted upon the return of positive
microbiological results from the pleural fluid or relevant specimens. Indeed, the inadequate
understanding of local bacteriology, drug resistance pattern and the lack of local guidance
on empirical antibiotic coverage for pleural infection have led to heterogeneous prescription
behaviour of antibiotics, which is a significant risk factor of the emergence of drug
resistance (e.g., increasing incidence of methicillin-resistant Staphylococcus aureus),
complications of antibiotic therapies (e.g., Clostridium difficile infections) and adverse
patient outcomes.
Conventional culture of pleural effusion has been considered as an essential part of the
treatment algorithm, but it carries two critical disadvantages that may limit clinical care:
1. Long turnaround time Although the Gram stain results can usually be available within one
day, the final culture results and antimicrobial sensitivity pattern only return after
up to five days. In case the pleural infection is not under control while waiting for
the culture results, physicians would blindly escalate the coverage of antibiotics or
proceed to additional pleural interventions, which may be avoidable if the
microbiological results can be available early. The delayed return of drug sensitivity
pattern may lead to the initial use of discordant antibiotics, which happened in 17 to
24% of patients in two local cohorts
2. Negative pleural fluid culture is common in pleural infection Up to 40% of pleural fluid
in pleural infection failed to reveal any microorganism by conventional culture, due to
a failure to culture fastidious organisms and antibiotics treatment before pleural fluid
sampling. Our study group has found that 88% of patients with empyema received empirical
antibiotics before any pleural intervention, which reflected the real-world practice.
Although inoculating pleural fluid into a blood culture bottle may increase the culture
yield in pleural infection by 20%, it is still far from satisfactory in clinical
practice. In addition, the microbiological workup of non-respiratory specimens is
frequently not informative. Thus, the use of antibiotics throughout the treatment course
is purely empirical in those patients with culture-negative pleural infection. To
overcome this problem and the often polymicrobial nature of the infections, very
broad-spectrum agents are currently advocated. On the contrary, a lack of bacterial
culture information with inadequate antibiotic coverage has been associated with an
increased mortality rate.
Non-culture molecular studies have been applied to overcome the insufficiencies of
conventional culture in the past decade, to characterize the spectrum of bacteria in pleural
infection and the antibiotic resistance pattern within a short period of time and inform
correct clinical decisions. Multiplex PCR (polymerase chain reaction) sequencing with a
pneumonia panel is able to identify bacteria that are commonly involved in pneumonia.
However, the aetiology of pleural infection is not completely a replicate of
community-acquired pneumonia, and thus limit its utility. 16S ribosomal ribonucleic acid
(rRNA) gene sequencing outperforms the conventional culture method by identifying more
bacteria, especially anaerobes, in the pleural fluid. It provides a high-throughput and
cost-efficient solution to screen the microbiota community for clinical samples with low
bacterial biomass and/or high host genomic contamination. However, it has a limitation in
detecting microbiome at the species level and may introduce PCR-biases that mask the true
community composition. Dyrhovden R et al performed the first metagenomic sequencing analysis
in Norway to understand the spectrum of bacteriology in confirmed empyema. They identified
385 bacterial detections, whereas culture detected 38 (10%) and 16S rRNA gene
PCR/Sanger-based sequencing detected 87 (23%) in 64 patients with empyema. Such findings
confirmed the disadvantage of the conventional culture method and broader coverage of
antibiotics is required for the treatment of pleural infection. However, this metagenomic
study was retrospective in nature, covered patients with empyema only and did not reflect the
full spectrum of pleural infection. Chen et al employed a metagenomic sequencing study with
functional analysis and identified two distinct microbiome clusters in pleural infection,
Staphylococcus aureus as the core species (HA-SA type) and a more diverse microbial community
(LA-SA type), which is different from the usual bacteriology pattern found in Hong Kong
studies. They also identified the resistome of bacteria, including tetracycline and
beta-lactam resistance, which is important to guide the appropriate antibiotic regimen in the
initial treatment phase. The interpretation of these two studies was limited because the
authors did not correlate the microbiological results with patient clinical outcomes.
Recently, Kanellakis et al confirmed the predominantly polymicrobial nature of pleural
infection by 16S rRNA metagenomic sequencing analysis, with a diverse bacterial spectrum.
They also identified a distinct bacteriology spectrum in polymicrobial and monomicrobial
cases and correlated the bacteriology with clinical outcomes.
Given the fact that geographical differences in bacteriology of pleural infection may exist
and previous studies did not translate the modern molecular sequencing technologies in
refining the initial antibiotic use, a local prospective study linking the laboratory and
clinical findings using broader metagenomic sequencing methods is desired. We hypothesize
that the 16S rRNA gene amplicon and shotgun metagenomic sequencing has a higher detection
rate of bacteria in the pleural fluid and identification of antibiotic resistance patterns
than conventional culture in patients with pleural infection. The results from the two
molecular sequencing methods are complementary and can guide the initial antibiotic
treatment, minimize the emergence of drug resistance, correlate the microbiological spectrum
with the clinical outcomes and prepare for a large-scale territory-wide study by
incorporating molecular technology into the management of pleural infection. The short
turnaround time also makes this technology attractive to physicians and ultimately benefits
the patient by improving the quality of care. As the diagnostic performance, technical
requirements and cost of the two molecular sequencing methods are different, this study will
provide fundamental information and guide their use in clinical settings.
The pathogenesis of community-acquired pleural infection is controversial. The conventional
belief of transmigration of bacterial through the lung parenchyma to the pleural cavity was
challenged by (1) different spectrum of causative pathogens for pneumonia and pleural
infection, (2) the absence of radiological evidence of pneumonia, and (3) anaerobes are
frequently found in pleural fluid culture but are uncommon in normal lung parenchyma because
of high oxygen tension. Therefore, understanding the ultimate source of pathogens and
understand their route of entering the pleural space is a critical step in preventing and
treating pleural infection. Currently, there is very limited evidence associating the
microbiota in pleural fluid of pleural infection, and those in the oral cavity and
gastrointestinal tract.
The aim of the study is to characterize the full spectrum of causative bacteria in pleural
infection and compare the diagnostic performance of identifying the pathogens between
conventional culture, 16S rRNA gene amplicon and shotgun metagenomic sequencing. The
antimicrobial resistance pattern of causative bacteria, clinical outcomes of pleural
infection will also be compared between groups as categorized by the pattern of bacteriology
identified by different methods.
