Systematic use of universal 16S rRNA gene polymerase chain reaction (PCR) and sequencing for processing pleural effusions improves conventional culture techniques

Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis

Pleural infections are common and associated with substantial healthcare costs, morbidity, and mortality. Accurate diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Here, we undertook a prospective study examining the feasibility and performance of molecular methods for diagnosing suspected pleural infection. We prospectively characterized 26 consecutive clinically suspected pleural infections, and 10 consecutive patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14 out of 26) positive cases among the pleural infection cohort, versus 38% (10 out of 26) with culture. Metagenomics and bacterial metataxonomics unveiled complex polymicrobial infections that were not captured by culture. Dominant microbes included streptococci (Streptococcus intermedius, Streptococcus pyogenes, and Streptococcus mitis), Prevotella spp. (Prevotella oris and Prevotella pleuritidis), staphylococci (S. aureus and S. saprophyticus), and Klebsiella pneumoniae. However, we encountered challenges that complicated pleural infection interpretation, including: (i) uncertainties regarding microbial pathogenicity and the impact of prior antibiotic therapy on diagnostic performance; (ii) lack of a clinical diagnostic gold-standard for molecular performance comparisons; (iii) potential microbial contamination during specimen collection or processing; and (iv) difficulties distinguishing background microbial noise from true microbial signal in low-biomass specimens. This pilot study demonstrates the potential utility and value of molecular methods in diagnosing pleural infection and highlights key concepts and challenges that should be addressed when designing larger prospective trials.IMPORTANCEConfident pleural infection diagnosis is often challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Limitations of conventional diagnostic tests result in prolonged and inappropriately broad-spectrum antimicrobial use, encouraging antimicrobial resistance and leading to avoidable adverse effects. Here, we demonstrate the feasibility, utility, and challenges associated with the use of culture-independent molecular techniques for accurate pleural infection diagnosis in a real-world clinical setting. These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome before next-generation sequencing technologies can be integrated into routine clinical practice.

Pleural space infection microbiology as assessed using a clinical sequencing-based assay: Fusobacterium nucleatum group, Streptococcus intermedius, and other oral normal microbiota are the most common bacteria identified in community-acquired pleural space infections

The definition of the microbiology of pleural space infection has been challenging due to the poor yield of conventional culture. Here, the results of a 16S ribosomal RNA gene PCR/sequencing assay performed on pleural fluid in routine clinical practice between August 2020 and January 2023 were evaluated. Amplified 16S rRNA gene DNA was submitted to Sanger sequencing and/or next-generation sequencing or results were reported as negative, depending on PCR crossing threshold value. In all, 496 pleural fluids were tested at Mayo Clinic Laboratories, with 227 positive results, including 57 from Mayo Clinic patients. Among the 57 Mayo Clinic patients, pleural space infection was community acquired in 48 (84%); Fusobacterium nucleatum group and/or Streptococcus intermedius were detected in 31/57 (54%) cases [including 28/48 (58%) community-acquired cases], with additional facultative and/or anaerobic species also found in various combinations in 17/31 (55%). Results of this study suggest that the most frequent microorganism profile involved in community-acquired pleural space infection may be a combination of F. nucleatum group and/or S. intermedius, with or without other normal microbiota.

IMPORTANCE

We describe here the most frequent microorganisms detected in community-acquired pleural space infection using a clinically performed sequencing-based assay. We found that the most common detection was the Fusobacterium nucleatum group and/or Streptococcus intermedius, with or without other normal microbiota. We propose the term e-FuSion (effusion with Fusobacterium nucleatum group, Streptococcus intermedius, and other oral normal microbiota) for this entity.

Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes

IMPORTANCE

Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.

Diagnosis and management of pleural infection

Pleural infection remains a medical challenge. Although closed tube drainage revolutionised treatment in the 19th century, pleural infection still poses a significant health burden with increasing incidence. Diagnosis presents challenges due to non-specific clinical presenting features. Imaging techniques such as chest radiographs, thoracic ultrasound and computed tomography scans aid diagnosis. Pleural fluid analysis, the gold standard, involves assessing gross appearance, biochemical markers and microbiology. Novel biomarkers such as suPAR (soluble urokinase plasminogen activator receptor) and PAI-1 (plasminogen activator inhibitor-1) show promise in diagnosis and prognosis, and microbiology demonstrates complex microbial diversity and is associated with outcomes. The management of pleural infection involves antibiotic therapy, chest drain insertion, intrapleural fibrinolytic therapy and surgery. Antibiotic therapy relies on empirical broad-spectrum antibiotics based on local policies, infection setting and resistance patterns. Chest drain insertion is the mainstay of management, and use of intrapleural fibrinolytics facilitates effective drainage. Surgical interventions such as video-assisted thoracoscopic surgery and decortication are considered in cases not responding to medical therapy. Risk stratification tools such as the RAPID (renal, age, purulence, infection source and dietary factors) score may help guide tailored management. The roles of other modalities such as local anaesthetic medical thoracoscopy and intrapleural antibiotics are debated. Ongoing research aims to improve outcomes by matching interventions with risk profile and to better understand the development of disease.

Diagnostic Yield of 16S Ribosomal Ribonucleic Acid Gene-Based Targeted Metagenomic Sequencing for Evaluation of Pleural Space Infection: A Prospective Study

Objective

To better understand the microbial profile of complicated parapneumonic effusions and empyema, and to evaluate whether antimicrobial selection would differ if guided by targeted metagenomic sequencing (tMGS) vs conventional cultures (CCs) alone.

Patients and Methods

We analyzed the pleural fluid of a cohort of 47 patients undergoing thoracentesis from January 1, 2017 to August 31, 2019, to characterize their microbial profile. All samples underwent 16S ribosomal ribonucleic acid gene polymerase chain reaction, followed by tMGS.

Results

Pleural space infection was deemed clinically present in 20 of the 47 (43%) participants. Of those, n=7 (35%) had positive pleural fluid cultures and n=14 (70%) had positive tMGS results. The organisms identified by tMGS were concordant with CCs; however, tMGS detected additional bacterial species over CCs alone. Streptococcus and Staphylococcus species were the most common organisms identified, with Streptococcus intermedius/constellatus identified in 5 patients. Polymicrobial infections were found in 6 of the 20 patients, with anaerobes being the most common organisms identified in these cases.

Conclusion

Streptococci and staphylococci were the most common organisms identified in infected pleural fluid. Anaerobes were common in polymicrobial infections. When compared with CCs, tMGS had higher sensitivity than CCs. Targeted metagenomic sequencing identified additional organisms, not identified by CCs, with associated potential management implications.

Development and performance of a multiplex PCR assay for the detection of bacteria in sterile body fluids

Aim: To assess the performance characteristics of a lab-developed multiplex PCR assay for the detection of common bacterial pathogens associated with infections in pediatric patients from normally sterile sites, such as cerebrospinal fluid, synovial and pleural fluids. Materials & methods: A total of 272 specimens were tested by PCR and traditional culture methods to assess the presence of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, methicillin-sensitive and methicillin-resistant Staphylococcus aureus, and Kingella kingae. Results: Compared with culture, the overall positive and negative percentage agreement of the PCR were 95.9% and 74.1%, respectively. Conclusion: This sterile body fluid PCR affords a rapid and sensitive alternative for bacterial detection, allowing for more timely pathogen-directed antimicrobial therapy.

Clinical relevance of molecular testing methods in the diagnosis and guidance of therapy in patients with staphylococcal empyema: a systematic review and meta-analysis

Background

Efficient detection tools for determining staphylococcal pleural infection are critical for its eradication. The objective of this meta-analysis was to assess the diagnostic utility of nucleic acid amplification tests (NAAT) in suspected empyema cases to identify staphylococcal strains and avoid unnecessary empiric methicillin-resistant Staphylococcus aureus (MRSA) therapy.

Methods

From inception to July 24, 2021, relevant records were retrieved from PubMed, Embase, Scopus, Web of Science, and the Cochrane Library. The quality of studies was determined using the QUADAS-2 tool. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and hierarchical summary receiver operating characteristic (HSROC) curve for NAAT's diagnostic performance were evaluated using an HSROC model.

Results

Eight studies comprising 424 samples evaluated NAAT accuracy for Staphylococcus aureus (SA) identification, while four studies comprising 317 samples evaluated methicillin-resistant Staphylococcus aureus (MRSA) identification. The pooled NAAT summary estimates for detection of both SA (sensitivity: 0.35 (95% CI 0.19-0.55), specificity: 0.95 (95% CI 0.92-0.97), PLR: 7.92 (95% CI 4.98-12.59), NLR: 0.44 (95% CI 0.14-1.46), and DOR: 24.0 (95% CI 6.59-87.61) ) and MRSA (sensitivity: 0.45 (95% CI 0.15-0.78), specificity: 0.93 (95% CI 0.89-0.95), PLR: 10.06 (95% CI 1.49-67.69), NLR: 0.69 (95% CI 0.41-1.15), and DOR: 27.18 (95% CI 2.97-248.6) ) were comparable. The I2 statistical scores for MRSA and SA identification sensitivity were 13.7% and 74.9%, respectively, indicating mild to substantial heterogeneity. PCR was frequently used among NAA tests, and its diagnostic accuracy coincided well with the overall summary estimates. A meta-regression and subgroup analysis of country, setting, study design, patient selection, and sample condition could not explain the heterogeneity (meta-regression P = 0.66, P = 0.46, P = 0.98, P = 0.68, and P = 0.79, respectively) in diagnostic effectiveness.

Conclusions

Our study suggested that the diagnostic accuracy of NAA tests is currently inadequate to substitute culture as a principal screening test. NAAT could be used in conjunction with microbiological culture due to the advantage of faster results and in situations where culture tests are not doable.

Parapneumonic Effusion and Empyema

The rising incidence and high morbidity of pleural infection remain a significant challenge to health care systems worldwide. With distinct microbiology and treatment paradigms from pneumonia, pleural infection is an area in which the evidence base has been rapidly evolving. Progress in recent years has revolved around characterizing the microbiome of pleural infection and the addition of new strategies such as intrapleural enzyme therapy to the established treatment pathway of drainage and antibiotics. The future of improving outcomes lies with personalizing treatment, establishing optimal timing of intrapleural agents and surgery, alongside wider use of risk stratification to guide treatment.

16S rRNA is a valuable tool in finding bacterial aetiology of community-acquired pleural empyema-a population-based observational study in South Sweden

BACKGROUND

The incidence of community-acquired pleural empyema is increasing. Knowledge of the bacterial aetiology is important in order to base recommendations on empirical antimicrobial treatment. The primary aim of the present study was to describe the bacterial aetiology of adult patients with culture proven and/or 16S rRNA-positive community-acquired pleural infection.

METHODS

We performed a retrospective, population-based observational cohort study in Skåne County, south of Sweden. We included all patients with pleural samples obtained between 1st of January 2011 to 31st of December 2017 in Skåne, south of Sweden, with a positive culture and/or 16S rRNA result. Exclusion criteria were patients with culture-negative and/or 16S rRNA-negative pleural samples, age < 18 years, pleural empyema caused by trauma or iatrogenesis, pleural infection caused by tuberculosis or fungi, simultaneous lung- or abscess of the abdomen and bacterial species considered to be contaminants.

RESULTS

A total of 291 patients were included in the study, of which 63% were men and the median age was 69 years. The dominating bacterial aetiology was viridans streptococci (36%), followed by Streptococcus pneumoniae (14%) and anaerobic bacteria (12%). 16S rRNA added information of bacterial aetiology in addition to standard culturing methods in 63% of the patients.

CONCLUSION

We found that the aetiology of adult patients with culture proven and/or 16S rRNA-positive community-acquired pleural empyema is dominated by viridans streptococci, S. pneumoniae and anaerobic bacteria. Our study shows that 16S rRNA is a valuable tool in finding the bacterial aetiology of community-acquired pleural empyema.

Recent Insights into the Management of Pleural Infection

Pleural infection in adults has considerable morbidity and continues to be a life-threatening condition. The term “pleural infection” encompasses complicated parapneumonic effusions and primary pleural infections, and includes but is not limited to empyema, which refers to collection of pus in the pleural cavity. The incidence of pleural infection in adults has been continuously increasing over the past two decades, particularly in older adults, and most of such patients have comorbidities. Management of pleural infection requires prolonged duration of hospitalization (average 14 days). There are recognized differences in microbial etiology of pleural infection depending on whether the infection was acquired in the community or in a health-care setting. Anaerobic bacteria are acknowledged as a major cause of pleural infection, and thus anaerobic coverage in antibiotic regimens for pleural infection is mandatory. The key components of managing pleural infection are appropriate antimicrobial therapy and chest-tube drainage. In patients who fail medical therapy by manifesting persistent sepsis despite standard measures, surgical intervention to clear the infected space or intrapleural fibrinolytic therapy (in poor surgical candidates) are recommended. Recent studies have explored the role of early intrapleural fibrinolytics or first-line surgery, but due to considerable costs of such interventions and the lack of convincing evidence of improved outcomes with early use, early intervention cannot be recommended, and further evidence is awaited from ongoing studies. Other areas of research include the role of routine molecular testing of infected pleural fluid in improving the rate of identification of causative organisms. Other research topics include the benefit of such interventions as medical thoracoscopy, high-volume pleural irrigation with saline/antiseptic solution, and repeated thoracentesis (as opposed to chest-tube drainage) in reducing morbidity and improving outcomes of pleural infection. This review summarizes current knowledge and practice in managing pleural infection and future research directions.

Octenidine dihydrochloride treatment of a meticillin-resistant Staphylococcus aureus biofilm-infected mouse wound

OBJECTIVE

This study sought to estimate the effect of a liquid octenidine dihydrochloride (OCT)-impregnated gauze dressing in the treatment of meticillin-resistant Staphylococcus aureus (MRSA) biofilm-infected wounds.

METHOD

In this animal study, a six-millimetre punch full-thickness wound on each mouse back was inoculated with MRSA suspension, and then covered with a Tegaderm (3M Health Care, US) dressing for an established biofilm model. Animals were divided into three groups for topical application: control group (treated with phosphate-buffered saline, PBS); mupirocin group (treated with 2% mupirocin); and OCT group (treated with OCT). All applications were administrated once 24 hours post-wounding. The bioburden was determined by counting colony-forming units (cfus) and the biofilm architecture was viewed using fluorescent staining and scanning electron microscopy (SEM) on day two. The tissue repair was evaluated histologically and the related genes were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) on day 15.

RESULTS

The results suggested OCT accelerated healing and reduced by >3.6 log cfu/g bacterial counts on the wounds relative to the PBS-treated control (p<0.05). Histological analysis showed OCT-treated tissue exhibited lower burden of the inflammatory cells, more mature collagen fibres and well-defined epithelialisation. LIVE/DEAD fluorescent staining and SEM confirmed OCT induced a substantial destruction to biofilm structure. RT-qPCR further demonstrated that OCT therapy could inhibit the expression of MRSA and its biofilm genes by nearly 100% (p<0.05).

CONCLUSION

This investigation provides a rare in vivo experimental basis for OCT improvement on MRSA-infected wound healing and the superior efficacy implies OCT topical application may represent an ideal choice to address established bacterial biofilm in hard-to-heal wounds.

Clinical utility of 16S rRNA PCR in pleural infection

Pleural infections cause major morbidity and mortality, particularly amongst paediatric and elderly populations. The aetiology is broad, but pleural culture fails to yield a causative pathogen in approximately 40 % of cases. Alternative pathogen identification methods are therefore required. The aim of the study was to investigate the yield from and impact on patient care when performing 16S rRNA PCR on culture-negative pleural fluid specimens and to determine whether any individual laboratory parameters were associated with a positive 16S rRNA PCR result. We conducted a study on 90 patients with suspected pleural infection, who had a culture-negative pleural fluid specimen, which underwent 16S rRNA PCR analysis between August 2017 and June 2019. This study was undertaken at a large NHS Trust in London, UK. Thirty-one per cent of culture-negative pleural fluid specimens tested by 16S rRNA PCR yielded a positive PCR result. Our data demonstrated that 16S rRNA PCR detected a significantly higher proportion of Streptococcus pneumoniae (P<0.0001) and fastidious, slow-growing and anaerobic pathogens (P=0.0025) compared with culture-based methods. Of the 25 16S rRNA PCR results that were positive for a causative pathogen, 76 % had a direct impact on clinical management. No single laboratory variable was found to be associated with a positive 16S rRNA PCR result. The findings from our real-world evaluation highlight the importance of 16S rRNA PCR in confirming pleural infection when the aetiology is unknown, and its direct, positive impact on clinical management.

Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study

Background

PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types.

Methods

From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive.

Results

Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001).

Conclusion

In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05892-4.

Pleural Effusion in Adults-Etiology, Diagnosis, and Treatment

BACKGROUND

Pleural effusion is common in routine medical practice and can be due to many different underlying diseases. Precise differential diagnostic categorization is essential, as the treatment and prognosis of pleural effusion largely depend on its cause.

METHODS

This review is based on pertinent publications retrieved by a selective search in PubMed and on the authors' personal experience.

RESULTS

The most common causes of pleural effusion are congestive heart failure, cancer, pneumonia, and pulmonary embolism. Pleural fluid puncture (pleural tap) enables the differentiation of a transudate from an exudate, which remains, at present, the foundation of the further diagnostic work-up. When a pleural effusion arises in the setting of pneumonia, the potential devel- opment of an empyema must not be overlooked. Lung cancer is the most common cause of malignant pleural effusion, followed by breast cancer. Alongside the treatment of the underlying disease, the specific treatment of pleural effusion ranges from pleurodesis, to thoracoscopy and video-assisted thoracoscopy (with early consultation of a thoracic surgeon), to the placement of a permanently indwelling pleural catheter.

CONCLUSION

The proper treatment of pleural effusion can be determined only after meticulous differential diagnosis. The range of therapeutic options has recently become much wider. More data can be expected in the near future concerning diagnostic test- ing for the etiology of the effusion, better pleurodetic agents, the development of interventional techniques, and the genetic background of the affected patients.

Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases

BACKGROUND

Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection.

METHODS

Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned.

RESULTS

There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ).

CONCLUSIONS

In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.

Pleural infection: a closer look at the etiopathogenesis, microbiology and role of antibiotics

INTRODUCTION

Pleural infection is a condition that continues to pose a significant challenge to respiratory physicians. We hypothesize that the main barriers to progress include limited understanding of the etiopathogenesis, microbiology,and role of antibiotics in the pleural space. Areas covered: PubMed was searched for articles related to adult pleural infection using the terms 'pleural infection', 'empyema' and 'parapneumonic'. The search focused on relevant literature within the last 10 years, with any older citations used only to display context or lack of progress. Tuberculous pleural infection was excluded. We chose to give specific attention to the etiopathogenesis of pleural infection, including recent advances in diagnostics and biomarkers. We discuss our understanding of the pleural microbiome and rationalize the current use of antibiotics in treating this condition. Expert commentary: Understanding of key events in the development of this condition remains limited. The microbiology is unique compared to the lung, and highly variable. Higher culture yields from pleural biopsy may add new insights into the etiopathogenesis. There is little evidence into achievable effective antibiotic concentration within the pleura. Research into issues including the relevance of biofilm formation and significance of pleural thickening is necessary for treatment progress.

Detection of the major bacterial pathogens among children suffering from empyema in Ahvaz city, Iran

Introduction

Empyema is one of the important causes of pediatric hospital admissions.

Aim

In this study, we had investigated the frequency rates of S aureus, S pneumoniae, H influenzae, and P aeruginosa using PCR and bacterial culture among children suffering from empyema in Ahvaz city, Iran.

Methods

This was a descriptive study conducted on the patients hospitalized in ICUs of two teaching Hospitals of Ahvaz, Iran, between March and September 2018 on 105 pleural fluid (PF) samples of the children less than 16 years of age with the diagnosis of empyema thoracis. These specimens were inoculated on the bacterial culture media and identified using biochemical characteristics. Then, the existence of the four pathogens mentioned above was evaluated using PCR method.

Result

In this study, these bacteria agents were identified in 81 (77.14%) and 30 (28.57%) cases using the PCR assay and bacterial culture, respectively. Moreover, the PCR assay identified the infectious agents in 51 (68%) of PFs where the culture method failed. S pneumoniae (63 cases) was recognized as the most common pathogen, followed by P aeruginosa(19 cases), S aureus(15 cases), and H influenzae (9 cases) using the bacterial culture and PCR. Co‐infections were detected in 21 samples (20%) using PCR and one sample using the bacterial culture (P aeruginosa and S pneumoniae).

Conclusion

In this study, we found the higher frequencies of these microorganisms using PCR than culture. In addition, we showed that PCR was a sensitive and accurate method that unaffected by antibiotic therapy and could detect well co‐infections.

The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method

The aim of this study was to use a 16S rDNA sequencing method in combination with conventional culture in patients with parapneumonic effusions (PPE) to evaluate the methods, study the microbiological spectrum, and examine the presence of bacteria within the different stages of PPE. Adults with community-acquired pneumonia (CAP) and PPE (n = 197) admitted to the Departments of Infectious Diseases at four hospitals in Stockholm County during 2011-2014 were prospectively studied. All patients underwent thoracentesis. Twenty-seven non-infectious pleural effusions were used as controls. The pleural samples were analyzed with culture, 16S rDNA sequencing, pH, glucose, and lactate dehydrogenase. Microbiological etiology was found in 99/197 (50%) of the patients with mixed infections in 20 cases. The most common pathogens were viridans streptococci (n = 37) and anaerobic bacteria (n = 40). Among the 152 patients with both methods performed, 26/152 (17%) and 94/152 (62%) had bacteria identified with culture and 16S rDNA sequencing respectively (p < 0.001). In 24/26 (92%) culture-positive cases, the same organism was identified by 16S rDNA. All controls were negative in both methods. Among the patients with complicated PPE and complete sampling, bacteria were found in 69/74 patients (93%), all detected with 16S rDNA sequencing, compared to 23/74 (31%) culture-positive samples (p < 0.001). Compared with culture, 16S rDNA sequencing substantially improved the microbiological yield, a microbiological diagnosis was achieved in almost all patients with complicated PPE, and the specificity seemed to be high. 16S rDNA sequencing should be used together with culture in patients with PPE to guide antibiotic therapy.

Conventional culture method and qPCR using 16S rDNA for tissue bank: a comparison using a model of cardiac tissue contamination

Real-time polymerase chain reaction (qPCR) using 16S rDNA is an alternative to conventional culture-based tests. The aim of this study was to compare the conventional culture method with qPCR using 16S rDNA in a model of cardiac tissue contamination. Samples of cardiac tissue for artificial contamination with Escherichia coli and control samples were submitted for DNA extraction, which was conducted by selective and alkaline lysis and purification steps. A standard curve for 16S rDNA was constructed to determine the efficiency and analytical sensitivity of the assay in concentrations from 10⁶ to 10² c.f.u. ml^-1 using TaqMan Master Mix. 16S rDNA was detected in all contaminated samples; however, it was not detected in the the final washing step solution of the sample with a bioburden of 10² c.f.u. ml^-1. Using qPCR is a potential alternative to conventional culture for microbiological safety testing of allograft tissues for biobanking, reducing the time and labour input required.

Molecular analysis of endotracheal tube biofilms and tracheal aspirates in the pediatric intensive care unit

BACKGROUND

Ventilator-associated pneumonia (VAP) is a known complication of mechanically ventilated children in the pediatric intensive care unit (PICU). Endotracheal tube (ETT) biofilms are often implicated in the development of VAP by providing a conduit for pathogens to the lower respiratory tract.

METHODS

A prospective cohort study from April 2010-March 2011 of children 4 weeks to 18 years of age ventilated for greater than 72 hours to determine the microbiota of ETT biofilms and tracheal aspirates.

RESULTS

Thirty-three patients were included with a mean age of 6.1 years (SD ± 5.1 years) and average length of intubation of 8.8 days (SD ± 5.0 days). Bacterial communities from tracheal aspirates and the proximal and distal ends of ETTs were determined using 16S rRNA gene libraries. Statistical analysis utilized two-part statistics and the Wilcoxon signed rank sum test for comparison of bacterial communities. Sequencing revealed a predominance of oropharyngeal microbiota including Prevotella and Streptococcus spp. Pathogenic bacterial genera including Staphylococcus, Burkholderia, Moraxella, and Haemophilus were also represented. Bacterial load was greatest at the proximal aspect of the ETT. Duration of intubation did not significantly impact bacterial load. Morisita Horn analysis across sites showed similar communities in 24/33 (72%) of patients.

CONCLUSIONS

ETT biofilms and tracheal aspirates of intubated patients in the PICU primarily consisted of oropharyngeal microbiota, but had a significant representation of potentially pathogenic genera. While the majority of patients had similar microbiota when comparing their ETT biofilms and tracheal aspirates, a subset of patients showed a divergence between communities that requires further investigation.

Ribosomal PCR assay of excised intervertebral discs from patients undergoing single-level primary lumbar microdiscectomy

PURPOSE

To determine the presence of infectious microorganisms in the herniated discs of immunocompetent patients, using methodology that we hoped would be of higher sensitivity and specificity than has been reported in the past. Recent studies have demonstrated a significant rate of positive cultures for low virulent organisms in excised HNP samples (range 19-53%). These studies have served as the theoretical basis for a pilot trial, and then, a well done prospective randomized trial that demonstrated that systemic treatment with antibiotics may yield lasting improvements in a subset of patients with axial back pain. Whether the reported positive cultures in discectomy specimens represent true positives is as yet not proven, and critically important if underlying the basis of therapeutic approaches for chronic low back pain.

METHODS

This consecutive case series from a single academic center included 44 patients with radiculopathy and MRI findings of lumbar HNP. Patients elected for lumbar microdiscectomy after failure of conservative management. All patients received primary surgery at a single spinal level in the absence of immune compromise. Excised disc material was analyzed with a real-time PCR assay targeting the 16S ribosomal RNA gene followed by amplicon sequencing. No concurrent cultures were performed. Inclusion criteria were as follows: sensory or motor symptoms in a single lumbar nerve distribution; positive physical examination findings including positive straight leg raise test, distributional weakness, and/or a diminished deep tendon reflexes; and magnetic resonance imaging of the lumbar spine positive for HNP in a distribution correlating with the radicular complaint.

RESULTS

The PCR assay for the 16S rRNA sequence was negative in all 44 patients (100%). 95% CI 0-8%.

CONCLUSIONS

Based on the data presented here, there does not appear to be a significant underlying rate of bacterial disc infection in immunocompetent patients presenting with radiculopathy from disc herniation.

Distinguishing complicated from uncomplicated parapneumonic effusions

PURPOSE OF REVIEW

Treatment of parapneumonic effusions (PPEs) is challenged by the decision of whether or not to insert chest tubes. This review focuses on the factors that may aid in determining which patients require an immediate drainage of the pleural space, that is, have a complicated PPE.

RECENT FINDINGS

Clinical guidelines advocate the evaluation of radiological (large effusion or loculation), bacteriological (Gram-positive stain or culture), biochemical (pH < 7.20 or glucose <60 mg/dl), and macroscopic (pus) characteristics of the pleural fluid to assist in the identification of complicated PPEs. In the past few years, a number of new pleural fluid biomarkers have been tested for the same purpose, but with the exception of C-reactive protein (CRP), they should be considered investigative. A pleural fluid CRP higher than 100 mg/l or a serum CRP higher than 200 mg/l, when combined with pleural fluid pH or glucose, may greatly increase our capability to predict the need for instituting tube thoracostomy. Although some ultrasonographic and computed tomography features favor the diagnosis of pleural infection, their role in uncomplicated-complicated PPE discrimination has not been systematically evaluated.

SUMMARY

No pleural fluid tests, other than pH or glucose, have gained wide acceptance for the assessment of patients with PPE. However, if corroborated with further studies, the measurement of pleural fluid or serum CRP, in combination with the classical fluid parameters, may have the potential to be incorporated into medical decision making.

The diagnosis of pleural effusions

Pleural effusions arise from a variety of systemic, inflammatory, infectious and malignant conditions. Their precise etiological diagnosis depends on a combination of medical history, physical examination, imaging tests and pertinent pleural fluid analyses; including specific biomarkers (e.g., natriuretic peptides for heart failure, adenosine deaminase for tuberculosis, or mesothelin for mesothelioma). Invasive procedures, such as pleuroscopic biopsies, may be required for persistently symptomatic effusions which remain undiagnosed after the analysis of one or more pleural fluid samples. However, whenever parietal pleural nodularity or thickening exist, image-guided biopsies should first be attempted. This review addresses the current diagnostic approach to pleural effusions secondary to heart failure, pneumonia, cancer, tuberculosis and other less frequent conditions.

Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

Relative microorganism abundance is a parameter describing biodiversity, referring to how common a bacterial species is within the total bacterial flora. Anal, rectal, skin, mucal, and respiratory swabs are typical clinical samples where knowledge of relative bacterial abundance might make distinction between asymptomatic carriers and symptomatic cases. Assays trying to measure total bacterial load are usually based on the amplification of universal segments of 16S rRNA genes. Previous assays were not adoptable to "direct" PCR protocols, and/or they were not compatible with hydrolysis-based detection. Using the latest summary of universal 16S sequence motifs present in literature and testing our design with 500 liquid and 50 formed stool samples, we illustrate the performance characteristics of a new 16S quantitative PCR (qPCR) assay, which addresses well-known technical problems, including a) positive priming reaction in the absence of intended target due to self-priming and/or mispriming of unintended targets; b) amplification bias due to nonoptimal primer/probe coverage; and c) too large amplicons for clinical qPCR. Stool swabs ranked into bins of different bacterial loads show significant correlation with threshold cycle values of our new assay. To the best of our knowledge, this is the first description of qPCR assay measuring individual differences of total bacterial load present in human stool.

[Parapneumonic pleural effusions: Epidemiology, diagnosis, classification and management]

Parapneumonic pleural effusions represent the main cause of pleural infections. Their incidence is constantly increasing. Although by definition they are considered to be a "parapneumonic" phenomenon, the microbial epidemiology of these effusions differs from pneumonia with a higher prevalence of anaerobic bacteria. The first thoracentesis is the most important diagnostic stage because it allows for a distinction between complicated and non-complicated parapneumonic effusions. Only complicated parapneumonic effusions need to be drained. Therapeutic evacuation modalities include repeated therapeutic thoracentesis, chest tube drainage or thoracic surgery. The choice of the first-line evacuation treatment is still controversial and there are few prospective controlled studies. The effectiveness of fibrinolytic agents is not established except when they are combined with DNase. Antibiotics are mandatory; they should be initiated as quickly as possible and should be active against anaerobic bacteria except for in the context of pneumococcal infections. There are few data on the use of chest physiotherapy, which remains widely used. Mortality is still high and is influenced by underlying comorbidities.

European perspective and update on the management of nosocomial pneumonia due to methicillin-resistant Staphylococcus aureus after more than 10 years of experience with linezolid

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of antimicrobial-resistant hospital-acquired infections worldwide and remains a public health priority in Europe. Nosocomial pneumonia (NP) involving MRSA often affects patients in intensive care units with substantial morbidity, mortality and associated costs. A guideline-based approach to empirical treatment with an antibacterial agent active against MRSA can improve the outcome of patients with MRSA NP, including those with ventilator-associated pneumonia. New methods may allow more rapid or sensitive diagnosis of NP or microbiological confirmation in patients with MRSA NP, allowing early de-escalation of treatment once the pathogen is known. In Europe, available antibacterial agents for the treatment of MRSA NP include the glycopeptides (vancomycin and teicoplanin) and linezolid (available as an intravenous or oral treatment). Vancomycin has remained a standard of care in many European hospitals; however, there is evidence that it may be a suboptimal therapeutic option in critically ill patients with NP because of concerns about its limited intrapulmonary penetration, increased nephrotoxicity with higher doses, as well as the emergence of resistant strains that may result in increased clinical failure. Linezolid has demonstrated high penetration into the epithelial lining fluid of patients with ventilator-associated pneumonia and shown statistically superior clinical efficacy versus vancomycin in the treatment of MRSA NP in a phase IV, randomized, controlled study. This review focuses on the disease burden and clinical management of MRSA NP, and the use of linezolid after more than 10 years of clinical experience.

Detecting the presence of bacterial DNA by PCR can be useful in diagnosing culture-negative cases of infection, especially in patients with suspected infection and antibiotic therapy

Failing in bacteria isolation in a significant number of infections might be due to the involvement of microorganisms nonrecoverable in culture media. The presence cannot be ruled out of nondividing cells or even bacterial products still capable of promoting a host immunological response. Antibiotic therapy, for example, might induce a block of bacterial division and the impossibility of recovering cells in culture media. In these cases, a molecular method targeting DNA should be used. In this study, 230 clinical samples with a culture-negative report obtained from 182 patients were examined with a protocol of PCR targeting the bacterial 16S rRNA gene to evaluate the usefulness of molecular methods in differencing culture-negative infections from other pathologies. Amplicons were obtained in 14% of the samples, although this percentage increased (27%) in a subgroup of patients with presumptive diagnosis of infection and ongoing antibiotic therapy. By multiplex PCR, it was shown that detected DNA belonged mostly to Enterobacteriaceae and enterococcal species. Multiple culture-negative, PCR-positive samples and isolation of the same bacterial species in culture in additional samples from the same patient support the clinical significance of the data obtained and highlight the complementary role and usefulness of applying molecular methods in diagnostic microbiology.

Etiology of pleural effusions: analysis of more than 3,000 consecutive thoracenteses

OBJECTIVE

To investigate the etiology of pleural effusions (PE) in adults and the accuracy of pleural fluid (PF) cytology and cultures in malignant and infectious PE, respectively.

PATIENTS AND METHODS

Retrospective analysis of all consecutive patients with PE undergoing diagnostic thoracentesis during the last 19 years in a university hospital.

RESULTS

The leading causes of PE among the 3,077 patients were: cancer (27%), heart failure (21%), pneumonia (19%), tuberculosis (9%), abdominal surgery (4%), pericardial diseases (4%) and cirrhosis (3%). Tuberculosis was the most common etiology in patients <34 years of age (52%), whereas heart failure predominated in octogenarians (45%). The most common primary tumors in malignant PE were lung (37%) and breast (16%). The overall accuracy of PF cytology was 59%, although it was significantly lower in mesotheliomas (27%) and squamous cell lung cancer (25%). In infectious PE, only 30% of cultures yielded positive results, a percentage which increased two-fold (66%) in purulent fluids (empyemas). Viridans streptococci were the most commonly isolated pathogens (25.5%). The sensitivity of solid media cultures of PF for Mycobacterium tuberculosis was low (18.5%).

CONCLUSIONS

Three-quarters of patients with PE in whom a diagnostic thoracentesis was indicated had cancer, heart failure, pneumonia or tuberculosis. PF cytology and cultures give false negative results in a significant number of cases.

Advances in the management of pleural disease

Pleural disease affects over 3000 people per million population annually. Consequently, it represents a significant proportion of the respiratory physician's workload and can present to clinicians of all backgrounds in primary and secondary care. Pleural effusions have been reported in association with over 50 different conditions; some related to specific pulmonary pathologies, but many being manifestations of multisystem disease. The burden that conditions such as pleural infection; malignant pleural disease; and pneumothorax impose on patients and health care systems is enormous and growing. As such, a clear understanding of these key conditions is crucial to any physician regardless of the specialty. This article addresses a number of areas relating to pleural disease, providing an overview of the diagnostic and therapeutic advances that have been made in our understanding of pleural pathology in recent years. The directions that future research in this important area of respiratory medicine might take will also be discussed.

New therapeutic approaches to pleural infection

PURPOSE OF REVIEW

Pleural infection is a common and serious clinical problem that because of its high morbidity and mortality imposes a significant burden on clinicians, healthcare resources and patients of all ages. Defining the optimal management strategy for pleural infection remains a cause for research and debate. This review considers the areas of interest including bacteriology and antibiotic selection, intrapleural fibrinolytics and the role of surgery.

RECENT FINDINGS

Pleural infection is increasing in the adult and paediatric populations without clear explanation and with clinical and financial consequences. The bacteriology of pleural infection is recognized as being unique from parenchymal lung infection with implications for its treatment. Although established in paediatric management, intrapleural fibrinolytics remain of uncertain benefit in adults, though the novel combination of tissue plasminogen activator and deoxyribonuclease used in the MIST2 study offers cause for optimism. Surgery remains a key intervention in pleural infection, but its precise role is unclear with no robust evidence to show when and in whom it should be optimally utilized.

SUMMARY

The high mortality in adults from pleural infection despite advances in clinical knowledge, diagnostics and therapeutics highlights the need for ongoing research. Future studies are required to focus on improving the clinical outcomes, with the identification of those patients at greatest risk of poor outcomes at presentation and most likely to benefit from more radical treatment a priority to allow the delivery of individualized care.

Use of universal 16S rRNA gene PCR as a diagnostic tool for venous access port-related bloodstream infections

Amplification of the universal 16S rRNA gene using PCR has improved the diagnostic yield of microbiological samples. However, no data have been reported on the reliability of this technique with venous access ports (VAPs). We assessed the utility of 16S rRNA PCR for the prediction of VAP-related bloodstream infection (VAP-RBSI). During a 2-year period, we prospectively received all VAPs removed by interventional radiologists. PCR and conventional cultures were performed using samples from the different VAP sites. We compared the results of PCR with those of conventional culture for patients with confirmed VAP-RBSI. We collected 219 VAPs from 219 patients. Conventional VAP culture revealed 15 episodes of VAP-RBSI. PCR revealed a further 4 episodes in patients undergoing antibiotic therapy which would have gone undetected using conventional culture. Moreover, it had a negative predictive value of 97.8% for the prediction of VAP-RBSI when it was performed using biofilm from the internal surface of the port. In conclusion, universal 16S rRNA PCR performed with samples from the inside of VAPs proved to be a useful tool for the diagnosis of VAP-RBSI. It increased detection of VAP-RBSI episodes by 21.1% in patients undergoing antibiotic therapy whose episodes would have gone undetected using conventional culture. Therefore, we propose a new application of 16S rRNA PCR as a useful tool for the diagnosis of VAP-RBSI in patients receiving antibiotic therapy.