Empyema: the use of broad range 16S rDNA PCR for pathogen detection

Liver abscess and septic shock due to Clostridium perfringens infection: a case report and literature review

Clostridium perfringens causes liver abscesses with a low incidence, rapid progression, and high mortality. Within a few days or even within 24 h, patients may progress from a liver abscess to sepsis, multi-organ failure, and potentially death. Diagnosing Clostridium perfringens infection by routine microbiological testing (CMT) is often challenging. Here, we present a patient with negative blood cultures who was ultimately diagnosed with a liver abscess due to Clostridium perfringens infection, confirmed by metagenomic next-generation sequencing (mNGS). The patient initially presented with fever only, and his blood cultures were negative. Subsequently, the patient's condition progressed rapidly, and he developed signs of septic shock. Immediately after admission to the ICU, he received combined anti-infective therapy with meropenem and tigecycline, as well as urgent ultrasound-guided puncture and drainage. Blood mNGS identified Clostridium perfringens and a variety of anaerobic bacteria, confirming that the pathogen had been covered by empirical antibiotics. Continued anti-infective therapy and drainage improved the patient's symptoms, and he was eventually discharged from the hospital. Clinicians should be highly suspicious of liver abscesses with negative blood cultures. The use of mNGS to identify the pathogen, appropriate antibiotics, and abscess aspiration and drainage are key to patient survival.

Epidemiology and Management of Pediatric Group A Streptococcal Pneumonia With Parapneumonic Effusion: An Observational Study

BACKGROUND

During autumn/winter 2022, UK pediatricians reported an unseasonal increase in invasive group A streptococcal infections; a striking proportion presenting with pneumonia with parapneumonic effusion.

METHODS

Clinicians across the United Kingdom were requested to submit pseudonymized clinical data using a standardized report form for children (<16 years) admitted between September 30, 2022 and February 17, 2023, with microbiologically confirmed group A streptococcal pneumonia with parapneumonic effusion.

RESULTS

From 185 cases submitted, the median patient age was 4.4 years, and 163 (88.1%) were previously healthy. Respiratory viral coinfection was detected on admission for 101/153 (66.0%) children using extended respiratory pathogen polymerase chain reaction panel. Molecular testing was the primary method of detecting group A streptococcus on pleural fluid (86/171; 50.3% samples). Primary surgical management was undertaken in 171 (92.4%) children; 153/171 (89.4%) had pleural drain inserted (96 with fibrinolytic agent), 14/171 (8.2%) had video-assisted thoracoscopic surgery. Fever duration after admission was prolonged (median, 12 days; interquartile range, 9-16). Intravenous antibiotic courses varied in length (median, 14 days; interquartile range, 12-21), with many children receiving multiple broad-spectrum antibiotics, although evidence for additional bacterial infection was limited.

CONCLUSIONS

Most cases occurred with viral coinfection, a previously well-recognized risk with influenza and varicella zoster, highlighting the need to ensure routine vaccination coverage and progress on vaccines for other common viruses (eg, respiratory syncytial virus, human metapneumovirus) and for group A streptococcus. Molecular testing is valuable to detect viral coinfection and confirm invasive group A streptococcal diagnosis, expediting the incorporation of cases into national reporting systems. Range and duration of intravenous antibiotics administered demonstrated the need for research on the optimal duration of antimicrobials and improved stewardship.

Severe pneumonia with empyema due to multiple anaerobic infections: case report and literature review

Background

Cases of severe pneumonia complicated by empyema due to normal anaerobic flora from the oral cavity are infrequent. Diagnosing anaerobic infections through conventional microbiological test (CMT) is often challenging.

Case presentation

This study describes the case of a 67-year-old man, bedridden long-term, who developed severe pneumonia with empyema caused by multiple anaerobic bacterial infections. The patient was hospitalized with a 5-day history of cough, sputum and fever, accompanied by a 2-day history of dyspnea. Despite CMT, the specific etiology remained elusive. However, metagenomic next-generation sequencing (mNGS) identified various anaerobic bacteria in bronchoalveolar lavage fluid (BALF), blood and pleural effusion. The patient was diagnosed with a polymicrobial infection involving multiple anaerobic bacteria. Following treatment with metronidazole and moxifloxacin, the patient's pulmonary symptoms improved.

Conclusion

mNGS serves as a valuable adjunctive tool for diagnosting and managing patients whose etiology remains unidentified following CMT.

Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection

Introduction

The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI.

Methods

In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR).

Results

The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases.

Conclusion

The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.

Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms

Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.

A challenging case of thoracic empyema caused by Prevotella spp

We report here the case of a 49-year-old man admitted for a diagnostic work-up of bilateral lung nodules. Empyema rapidly developed after a chest computed-tomodensitometry guided lung puncture. Despite the lack of obvious aetiology after two biopsies, the diagnosis was reached by performing 16S ribosomal DNA (rDNA) sequence analysis, which identified Prevotella spp in the pleural liquid. The empyema and lung nodules resolved after appropriate antibiotic therapy.

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.

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.

Effect of Prehospital Antibiotic Therapy on Clinical Outcome and Pathogen Detection in Children With Parapneumonic Pleural Effusion/Pleural Empyema

BACKGROUND

Parapneumonic pleural effusion and pleural empyema (PPE/PE) are complications of community-acquired pneumonia. The objective of this study was to analyze prehospital antibiotic therapy (PH-ABT) of children with PPE/PE and investigate its effects on clinical outcome and pathogen detection.

METHODS

Prospective nationwide active surveillance in Germany between October 2010 and June 2018. Children and adolescents <18 years of age with pneumonia-associated PE or PPE requiring drainage or with persistence of PPE/PE >7 days were included.

RESULTS

A total of 1724 children with PPE/PE were reported, of whom 556 children (32.3% of 1719 with available data) received PH-ABT. Children with PH-ABT had a shorter median hospital length of stay (15 vs. 18 days, P < 0.001), a longer time from onset of symptoms until hospital discharge (25 vs. 23 days, P = 0.002), a lower rate of intensive care unit admission (58.3% vs. 64.4%, P = 0.015) and fewer infectious complications (5.9% vs. 10.0%; P = 0.005). Bacterial pathogens in blood or pleural fluid culture were detected in 597 (34.5%) of 1513 children. Positive culture results were less frequent in children with than without PH-ABT (81/466 [17.4%] vs. 299/1005 [29.8%]; P < 0.001), whereas detection rates in pleural fluid samples by polymerase chain reaction were similar (91/181 [50.3%] vs. 220/398 [55.3%]; P = 0.263).

CONCLUSIONS

In children with PPE/PE, PH-ABT significantly reduced the overall rate of bacterial pathogen detection by culture, but not by polymerase chain reaction. PH-ABT was associated with a lower rate of infectious complications but did not affect the overall duration of disease. We therefore speculate that the duration of PPE/PE is mainly a consequence of an infection-induced inflammatory process, which can only partially be influenced by antibiotic treatment.

Multiplex bacterial polymerase chain reaction in a cohort of patients with pleural effusion

Background

The identification of the pathogens in pleural effusion has mainly relied on conventional bacterial culture or single species polymerase chain reaction (PCR), both with relatively low sensitivity. We investigated the efficacy of a commercially available multiplex bacterial PCR assay developed for pneumonia to identify the pathogens involved in pleural infection, particularly empyema.

Methods

A prospective, monocentric, observational study including 194 patients with pleural effusion. Patients were evaluated based on imaging, laboratory values, pleura ultrasound and results of thoracentesis including conventional microbiology studies during hospitalisation. Multiplex bacterial PCR (Curetis Unyvero p55) was performed in batch and had no influence on therapeutic decisions.

Results

Overall, there were 51/197 cases with transudate and 146/197 with exudate. In 42% (n = 90/214) there was a clinical suspicion of parapneumonic effusion and the final clinical diagnosis of empyema was made in 29% (n = 61/214) of all cases. The most common microorganisms identified in the cases diagnosed with empyema were anaerobes [31] followed by gram-positive cocci [10] and gram-negative rods [4]. The multiplex PCR assay identified more of the pathogens on the panel than the conventional methods (23.3% (7/30) vs. 6.7% (2/30), p = 0.008).

Conclusion

The multiplex PCR-based assay had a higher sensitivity and specificity than conventional microbiology when only the pathogens on the pneumonia panel were taken into account. A dedicated pleural empyema multiplex PCR panel including anaerobes would be needed to cover most common pathogens involved in pleural infection.

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.

An unusual case of seronegative, 16S PCR positive Brucella infection

Introduction:

Brucella is a zoonotic infection commonly diagnosed by isolation of the organism from blood culture or positive serological testing. It is an uncommon cause of a pyrexia of unknown origin in the United Kingdom.

Case presentation:

We describe the case of a 14-year-old girl with no history of travel who presented with pyrexia, weight loss, arthralgia, multiple splenic abscesses and a subsequent pleural effusion, the latter of which isolated a Brucella species on 16S rRNA PCR. The patient responded well to initiation of treatment for brucellosis and on repeat imaging, after 3 months, the splenic abscesses had resolved.

Conclusion:

This unique case demonstrates uncommon complications of brucellosis and the challenges of diagnosing the organism, the latter of which can be alleviated by the utilization of molecularbased technologies. This patient had a negative serology result for brucellosis, which highlights the need to interpret serology results with caution in non-endemic regions for brucellosis.

Pleural infection: past, present, and future directions

Pleural space infections are increasing in incidence and continue to have high associated morbidity, mortality, and need for invasive treatments such as thoracic surgery. The mechanisms of progression from a non-infected, pneumonia-related effusion to a confirmed pleural infection have been well described in the scientific literature, but the route by which pathogenic organisms access the pleural space is poorly understood. Data suggests that not all pleural infections can be related to lung parenchymal infection. Studies examining the microbiological profile of pleural infection inform antibiotic choice and can help to delineate the source and pathogenesis of infection. The development of radiological methods and use of clinical indices to predict which patients with pleural infection will have a poor outcome, as well as inform patient selection for more invasive treatments, is particularly important. Randomised clinical trial and case series data have shown that the combination of an intrapleural tissue plasminogen activator and deoxyribonuclease therapy can potentially improve outcomes, but the use of this treatment as compared with surgical options has not been precisely defined, particularly in terms of when and in which patients it should be used.

A two-stage microresistive pulse immunosensor for pathogen detection

We present a two-stage immunosensor for pathogen detection in a mixed population. In this approach, antibody-conjugated microparticles were used to functionalize the surface of the capture chamber via a convenient magnetic method and a two-stage resistive pulse sensor was used to detect and quantify pathogen cells. We firstly tested the capture efficiency of the functionalized capture chamber. The specific capture efficiency of S. cerevisiae is greater than 94.8%, while the non-specific capture efficiency is 3.4%. We showed that the device can accurately measure pure S. cerevisiae at concentrations ranging from 1.0 to 8.0 × 10(3) cells per μL. We performed S. cerevisiae measurements in a mixture with Chlorella. Both cells have similar sizes. For S. cerevisiae to Chlorella ratios ranging from 1.0 to 2.0, the measurement error was less than 7%, while the error became 20% to 32% for lower ratios ranging from 0.1 to 0.5 caused by nonspecific attachment. We demonstrated that this device is able to isolate target cells and quantitatively measure the cell population in a short time. This device can be potentially used for pathogen detection in the food industry, biological research and clinical applications.

Etiology and Incidence of Pleural Empyema in South African Children

BACKGROUND

South Africa introduced the 7-valent pneumococcal conjugate vaccine (PCV7) in 2009 and PCV13 in 2011. The etiology and incidence of childhood empyema in an 8-year period overlapping the introduction of PCV was investigated.

METHODS

Children younger than 12 years admitted with empyema at a tertiary pediatric hospital in Cape Town, South Africa, from December 2006 to December 2011 (cohort A) and January 2012 to December 2014 (cohort B) were investigated. Pathogens were identified by culture of pleural fluid and blood. In addition, polymerase chain reaction targeting bacterial pathogens and Streptococcus pneumoniae serotypes was conducted on pleural fluid in a subset of patients enrolled 2009-2011.

RESULTS

Cohort A: 142 children were prospectively enrolled, with a median age of 17 months (interquartile range 8-43). Most (92%) children were unimmunized with PCV. S. pneumoniae and Staphylococcus aureus were the most common culture-identified pathogens (each 25 of 142; 18%); polymerase chain reaction of pleural fluid increased yield of S. pneumoniae detection by 31% [26 of 54 (48%) vs. 9 of 54 (17%), P < 0.001]. Serotypes were identified for 24 of 26 (92%) patients with S. pneumoniae, of which 22 of 24 (92%) were included in PCV13. Cohort B: 22 patients were retrospectively identified. No pathogen was found in 12 of 22 (54.5%) patients and S. pneumoniae in 1 patient (4.5%). Empyema incidence declined by 50% in cohort B compared with that of cohort A (4.2 vs. 10.4 cases per 1000 pneumonia admissions; risk ratio: 0.5; 95% confidence incidence: 0.3-0.7).

CONCLUSION

S. pneumoniae is the commonest cause of childhood empyema in South Africa. PCV has been highly effective at reducing empyema incidence in South African children.

What to expect from molecular tools for non-documented pediatric infectious diseases

OBJECTIVE

Evaluation of the contribution of molecular tools to the overall diagnosis of infectious diseases in children.

METHODS

Results of 16S rDNA analysis (179 children; 228 specimens), combined to specific amplification of Kingella kingae (126 children; 166 osteoarticular specimens), were retrospectively analyzed for samples with inconclusive cultures.

RESULT

The overall positive yield in diagnosis was 12.8% of the patients for 16S rDNA PCR, 40.5% for K. kingae PCR and 45.2% for combined use of both methods. Results were related to clinical and biological data (direct examination, certainty/uncertainty of clinical diagnosis, fever, biological markers, previous antibiotics), and to the number of samples analyzed per patient, allowing the identification of specific situations with significant contribution of PCR methods.

CONCLUSION

Molecular techniques constitute valuable tools to improve the bacterial infection diagnosis in children; however, specific indications, dedicated samples, and number of analyzed samples per patient are key points to optimize their contribution.

The role of latex agglutination test for the etiological diagnosis of pleural effusion in children and adolescents

INTRODUCTION

The etiological diagnosis of pleural effusion is a difficult task because the diagnostic tools can only establish a definitive etiological diagnosis in at most 76% of cases.

OBJECTIVES

To verify the diagnostic accuracy of the latex agglutination test (LAT) for the etiological diagnosis of pleural effusions caused by Streptococcus pneumoniae and Haemophilus influenzae type b.

METHODS

After thoracocentesis, paired fresh samples of pleural fluid from 418 children and adolescents were included in this investigation. They were tested blindly and simultaneously through counterimmunoelectrophoresis (CIE) and LAT for both bacteria. Sensitivity, specificity, predictive values and likelihood ratios (LR) were calculated taking CIE as a reference standard.

RESULTS

The sensitivity and specificity of LAT was 100% (95% confidence interval, 94.4%-100%) and 83.3% (95% confidence interval, 79.0%-87.0%), respectively, whereas the positive (calculated from Bayes' theorem) and negative predictive values were, respectively, lower than 1% and 100% (95% confidence interval, 98.8%-100%). Positive and negative LR were 6.0 (95% confidence interval, 4.7-7.6) and zero, respectively.

CONCLUSIONS

Our results suggest that LAT is a useful tool for the etiological diagnosis of pleural effusion. It is a reliable, rapid, simple to perform and shows an excellent yield in our studied population, helping to prescribe appropriate antibiotics for this clinical condition.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.

[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.

Real-time polymerase chain reaction for microbiological diagnosis of parapneumonic effusions in Canadian children

Community-acquired pneumonia with parapneumonic effusion/empyema is not uncommon in children and can cause serious illness; there -fore, the timely optimization of antimicrobial therapy is essential in this situation. The aim of this study was to determine whether using real-time polymerase chain reaction of pleural fluids to identify the causative organism improves the process of microbiological diagnosis in the context of community-acquired pneumonia with parapneumonic effusion/empyema. This technique was compared with traditional culture methods for microbiological diagnosis.

BACKGROUND:

Community-acquired pneumonia (CAP) complicated by parapneumonic effusion/empyema is an infectious syndrome commonly encountered by physicians caring for children in Canada.

OBJECTIVE:

To investigate the incremental benefit of novel molecular testing for the microbiological diagnosis of pediatric CAP complicated by parapneumonic effusion/empyema in Canada.

METHODS:

A convenience sample of pleural fluid from 56 children who had been admitted to hospital in Ontario with CAP complicated by parapneumonic effusion between 2009 and 2011 was examined. Multiple uniplex real-time polymerase chain reaction (PCR) testing was performed on these pleural fluids and compared with traditional culture-based testing of blood and pleural fluid samples.

RESULTS:

Molecular methods detected a pathogen in 82% of cases, whereas traditional cultures of blood and pleural fluids detected a pathogen in only 25%. The majority of parapneumonic effusions were associated with pneumococcal infection; Streptococcus pneumoniae was detected in 62% of the samples using molecular methods but in only 14% of samples using culture-based methods. Streptococcus pyogenes, detected in 16% of samples using PCR, was the second most common pathogen found. No patients were found to have empyema caused by Staphylococcus aureus.

DISCUSSION:

The results showed that multiple uniplex real-time PCR performed substantially better than traditional culture methods for microbiological diagnosis of CAP complicated by effusion/ empyema. S pneumoniae and S pyogenes were found to be responsible for the majority of infections. The approach detected pathogens in a similar proportion of pleural fluid samples as previously reported nested PCR assays; furthermore, the real-time closed-well approach also minimized the risk of nonspecificity due to cross-contamination relative to nested PCR.

CONCLUSIONS:

Real-time PCR for the detection of bacterial DNA in pleural fluids has the potential to better define the microbiological cause of pediatric CAP. This approach could help clinicians provide targeted antimicrobial therapy.

Necrotising pneumonia in children

Necrotising pneumonia remains an uncommon complication of pneumonia in children but its incidence is increasing. Pneumococcal infection is the predominant cause in children but Methicillin resistant Staphylococcus aureus (MRSA) and Panton-Valentine leukocidin (PVL) staphylococcal infection are also important causes of severe necrotising pneumonia. Clinical features of necrotic pneumonia are similar to those of an uncomplicated pneumonia except that the patient is clinically much more unwell and has usually failed to respond adequately to what would normally be considered as appropriate antibiotics. Pleural involvement is frequent. Initial management is similar to that for non-complicated pneumonia with careful attention to fluid balance and adequate analgesia required. Some patients will need intensive care support, particularly those with PVL-positive staphylococcal infection. Broad-spectrum antibiotics should be given intravenously, with the exact choice of agent informed by local resistance patterns. Pleural drainage is often required. Despite the severity of the illness, outcomes remain excellent with the majority of children making a full recovery.

Pediatric Pleural Empyema in the Province of Quebec: Analysis of a 10-Fold Increase Between 1990 and 2007

BACKGROUND

Although the frequency of pneumonia has decreased over time, an increase in pleural empyema has been observed in different settings worldwide. This study assessed the epidemiology of community-acquired pediatric pleural empyema in the province of Quebec through validation of cases found in a hospitalization discharge database.

METHODS

We used the national administrative database of hospitalization to identify children (6 months-14 years) hospitalized for pleural empyema or pleural effusion with drainage from January 1990 until December 2007 and reviewed their medical charts. Patients with pleural effusion secondary to chest trauma, thoracic surgery, malignancies, cardiac failure, or metabolic disorders were excluded.

RESULTS

Predictive positive value (PPV) of empyema code in any position among discharge diagnostics in the administrative database was 86.5% (95% confidence interval: 81.9%-90.3%). After chart revision, 292 met the inclusion criteria. Age-adjusted incidence of pleural empyema in the pediatric population increased from 0.23 in 1990 to 4.01/100,000 person-years in 2007. A bacterial pathogen was identified in 46.5%; Streptococcus pneumoniae (Sp) (42%) and S pyogenes (30%) were most frequent. There was no obvious change in the PPV and proportions of children with chronic disease or asthma and in identified pathogens over time, but an increase in pre-admission respiratory symptoms duration (from 3.8 days to 5.7) and nonsteroidal anti-inflammatory drug use (from 0% to 19%) was observed.

CONCLUSIONS

From 1990 to 2007, we observed a 10-fold increase in the incidence of pediatric hospitalizations associated with pleural empyema. This increase preceded the introduction of a pneumococcal conjugated vaccine program in Quebec. Sp remained the major pathogen identified.

Nested polymerase chain reaction (PCR) targeting 16S rDNA for bacterial identification in empyema

BACKGROUND

Empyema in children causes significant morbidity and mortality. However, identification of organisms is a major concern.

OBJECTIVE

To detect bacterial pathogens in pus specimens of children with empyema by 16S rDNA nested polymerase chain reaction (PCR) and correlate it with culture and sensitivity.

METHOD

Sixty-six children admitted to the paediatric ward with a diagnosis of empyema were enrolled prospectively. Aspirated pus was subjected to cytochemical examination, culture and sensitivity, and nested PCR targeting 16S rDNA using a universal eubacterial primer.

RESULTS

Mean (SD) age was 5·8 (1·8) years (range 1-13). Analysis of aspirated pus demonstrated total leucocyte count >1000×10(6)/L, elevated protein (≧20 g/L) and decreased glucose (≤2·2 mmol/L) in 80·3%, 98·5% and 100%, respectively. Gram-positive cocci were detected in 29 (43·9%) and Gram-negative bacilli in two patients. Nested PCR for the presence of bacterial pathogens was positive in 50·0%, compared with 36·3% for culture.

CONCLUSION

16S rDNA PCR improves rates of detection of bacteria in pleural fluid, and can detect bacterial species in a single assay as well as identifying unusual and unexpected causal agents.

The increasing incidence of empyema

PURPOSE OF REVIEW

The aim of this review is to highlight recent changes concerning the incidence of empyema. In this article we have focused on community-acquired empyema

RECENT FINDINGS

The incidence of empyema seems to have been increasing both in children and adults worldwide in the past decades, mainly in healthy young adults and in older patients. The bacteriology of pleural infection is changing as well. In children, the most common microorganism that causes empyema continues to be Streptococcus pneumoniae. Interestingly, the widespread use of the seven valent conjugate vaccine has produced a replacement phenomenon with the emergence of some pneumococcal serotypes such as serotypes 1, 3 and 19A, which have a higher propensity to cause empyema. Moreover increases in the incidence of empyema due to Staphylococcus aureus have also been observed. In adults, increases in the rate of empyema due to Streptococcus milleri group and S. aureus have been reported.

SUMMARY

Continued surveillance in the epidemiology of empyema is needed. Progress in new strategies of prevention, such as a new generation of conjugate pneumococcal vaccines and protein-based vaccines, could become an important step in the control of this important complication.

Respiratory viral infections among children with community-acquired pneumonia and pleural effusion

Pleural effusion (PE), a complication of community-acquired pneumonia (CAP), is usually attributed to a bacterial infection. Nonetheless, viral infections have not been investigated routinely. We searched for bacterial and viral infections among 277 children hospitalized with CAP. Among these children 206 (74%) had radiographic confirmation, of whom 25 (12%) had PE. The aetiology was established in 18 (72%) PE cases: bacterial (n = 5; 28%), viral (n = 9; 50%), and viral-bacterial (n = 4; 22%) infections were found. Infection by rhinovirus (n = 3), enterovirus, Streptococcus pneumoniae (n = 2 each), Haemophilus influenzae, Moraxella catarrhalis, Mycoplasma pneumoniae, influenza A virus, and respiratory syncytial virus (RSV) (n = 1 each) were detected as probable sole infections. Parainfluenza virus 1/3 + influenza A virus and RSV + influenza A virus (n = 1 each) were identified as mixed viral-viral infections. Probable viral non-bacterial infection was identified in a third of the cases with CAP and PE. It is advisable to investigate viral as well as bacterial infections among children with CAP and PE.

Community-Acquired Pneumonia in the Conjugate Vaccine Era

Community-acquired pneumonia (CAP) remains one of the most common serious infections encountered among children worldwide. In this review, we highlight important literature and recent scientific discoveries that have contributed to our current understanding of pediatric CAP. We review the current epidemiology of childhood CAP in the developed world, appraise the state of diagnostic testing for etiology and prognosis, and discuss disease management and areas for future research in the context of recent national guidelines.

Pleural fluid nucleic acid testing enhances pneumococcal surveillance in children

BACKGROUND AND OBJECTIVE

National surveillance of invasive pneumococcal disease (IPD) includes serotyping Streptococcus pneumoniae (SP) isolates from sterile site cultures. PCR is more sensitive and can identify more SP serotypes (STs) in culture-negative samples. The aim of this study was to determine whether enhanced surveillance of childhood empyema, using PCR, provides additional serotype information compared with conventional surveillance.

METHODS

Pleural fluid (PF) from children with empyema were cultured and tested by PCR to identify SP, targeting the autolysin gene (lytA). Multiplex PCR-based reverse line blot assay was used to identify SP STs. Corresponding IPD surveillance and serotype data were obtained from the National Notifiable Diseases Surveillance System (NNDSS).

RESULTS

Eighty-nine children with empyema, aged ≤16 years, were recruited between April 2008 and March 2009, inclusive. SP was isolated from 5/84 (5.9%) PF cultures and by PCR in 43/79 (54.4%) PF samples. Serotypes were unidentifiable in 15 samples. The frequency of six serotypes (or serotype pairs) identified in 28 samples, including one with two serotypes, were: ST1, n = 4/29 (13.8%); ST3, n = 9/29 (31.0%); ST19A, n = 12/29 (41.4%); ST7F/7A, n = 1/29 (3.4%); ST9V/9A, n = 1/29 (3.4%); ST22F/22A, n = 2/29 (6.9%). Over the same period, 361 IPD patients, aged 16 years or less, were notified to NNDSS. Among 331 serotypeable NNDSS isolates (71.5% from blood), the frequencies of ST1 and 3 were significantly lower than in PF samples: ST1, n = 8/331 (2.4%; P < 0.05); ST3, n = 13/331 (3.9%; P < 0.0001).

CONCLUSIONS

The use of PCR to identify and serotype SP in culture-negative specimens provides additive information.

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

Conventional culture of pleural fluid samples frequently provides false-negative results. Universal polymerase chain reaction (PCR) of the 16S ribosomal ribonucleic acid (rRNA) gene (16S PCR) has proven useful in the diagnosis of various bacterial infections. We conducted a prospective study to assess the value of 16S PCR in the etiologic diagnosis of pleural effusion. All pleural fluid samples received for culture were also studied using 16S PCR. Positive samples were sequenced for identification. Clinical records and conventional culture results were analyzed to classify pleural fluid samples as infected or not infected. We studied 723 samples. We excluded 188 samples because they were obtained from a long-term chest tube, there was a diagnosis of mycobacterial infection, or there were insufficient data to classify the episode. Finally, 535 pleural fluid samples were analyzed. According to our criteria, 82 (15.3%) were infected and 453 (84.7%) were not infected. In the infected samples, 16S PCR was positive in 67 samples (81.7%) while conventional culture was positive in 45 (54.9%). There were 4 false positives with 16S PCR (0.9%) and 12 with culture (2.6%). The values for the etiologic diagnosis of bacterial pleural effusion of conventional culture compared with 16S PCR were as follows: sensitivity, 54.9%/81.7%; specificity, 97.4%/99.1%; positive predictive value, 76.3%/94.4%; negative predictive value, 92.6%/96.8%; and accuracy, 90.8%/96.5%.When compared with conventional culture, 16S PCR plus sequencing substantially improves the etiologic diagnosis of infectious pleural effusion. In our opinion, this technique should be added to the routine diagnostic armamentarium of clinical microbiology laboratories.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

Broad-range bacterial polymerase chain reaction in the microbiologic diagnosis of complicated pneumonia

BACKGROUND

A bacterial cause is not frequently identified in children with pneumonia complicated by parapneumonic effusion (ie, complicated pneumonia).

OBJECTIVES

To determine the frequency of positive blood and pleural fluid cultures in children with complicated pneumonia and to determine whether broad-range 16S rRNA polymerase chain reaction (PCR) improves identification of a microbiologic cause.

METHODS

This prospective cohort study included children 1-18 years of age hospitalized with complicated pneumonia.

RESULTS

Pleural fluid drainage was performed in 64 (51.6%) of 124 children with complicated pneumonia. A microbiologic cause was identified in 11 of 64 patients (17.2%; 95% confidence interval [CI]: 8.9%-28.7%). Bacteria were isolated from pleural fluid culture in 6 of 64 patients (9.4 %; 95% CI: 3.5%-19.3%) undergoing pleural drainage; the causative bacteria were Staphylococcus aureus (n = 5) and Streptococcus pneumoniae (n = 1). Blood culture identified a bacterial cause in 3 of 44 cases (6.8%; 95% CI: 1.4%-18.7%) undergoing pleural fluid drainage; S. pneumoniae (n = 1), Haemophilus influenzae (n = 1), and S. aureus (n = 1) were isolated. Only 3 of the 19 pleural fluid samples (15.8%; 95% CI: 3.4%-39.6%) analyzed with 16S rRNA PCR were positive. S. pneumoniae was the only organism detected in all three samples; two of these three had negative pleural fluid cultures and absence of bacteria on Gram stain. S. aureus was isolated from pleural fluid culture in one patient with a negative 16S rRNA PCR test.

CONCLUSIONS

Causative bacteria were infrequently identified in children with complicated pneumonia. Broad-range 16S rRNA PCR only modestly improved the microbiologic yield over conventional culture methods.

Diagnosis of fulminant pneumonia caused by Legionella pneumophila serogroup 8 with the sequence analysis of the 16S rRNA gene

Pneumonia is the fourth leading cause of death in Japan. Accurate and rapid detection of the causative pathogen(s) is necessary and important for appropriate antimicrobial treatment, especially in patients with rapidly progressive pneumonia or immunocompromised patients. Conventional methods, such as cultivations, detection of urinary antigens or PCR amplification of specific genes, inevitably require the precise presumption of potential pathogens in each case, and pneumonia caused by unanticipated microorganisms might lead to inadequate antimicrobial treatments and unfortunate consequences. We herein report an immunocompromised female patient (69 years old) with fulminant pneumonia caused by Legionella (L.) pneumophila serogroup 8. Ordinary cultivation methods and urinary antigen detection failed to identify the causative organisms. Accordingly, DNA was extracted from the bronchoalveolar lavage fluid and used for the PCR-based cloning of the bacterial 16S rRNA gene. Sequencing analysis of the isolated clones revealed the predominance of L. pneumophila. Based on this information, the patient received an appropriate and successful antimicrobial treatment. In addition, L. pneumophila serogroup 8 was identified with culturing the bronchoalveolar lavage fluid and serotyping with L. pneumophila antisera. The 16S rRNA gene sequencing analysis can reveal the potential pathogens without any presumption about the organism, and can evaluate the kinds and ratio of bacterial species in each specimen. In conclusion, this cultivation-independent method is a potential diagnostic modality for pneumonia, especially in patients with rapidly progressive pneumonia or those who are immunocompromised.

Sustained high prevalence of pneumococcal serotype 1 in paediatric parapneumonic empyema in southern Spain from 2005 to 2009

The epidemiology and microbiological characteristics of paediatric parapneumonic empyema (PPE) before the introduction of the new generation of conjugate pneumococcal vaccines (10-valent and 13-valent) are described. All patients <14 years old admitted to a tertiary paediatric hospital with a diagnosis of PPE were prospectively enrolled from January 2005 to December 2009. Pneumococcal serotyping of culture-negative pleural fluid samples was performed using a multiplex real-time PCR assay. Overall, 219 patients had PPE. Incidence rates for PPE remained stable during the study period with a not significant increase in 2009 compared with 2005 (p 0.13), and were temporally associated with higher circulation of pandemic influenza A H1N1 during the last quarter in our population (p 0.001). Pneumococci were detected in 72% of culture-positive and 79% of culture-negative samples. Serotypes were determined in 104 PPE cases. Serotype 1 was the most prevalent serotype identified (42%) followed by serotypes 7F (20%), 3 (16%), 19A (8%) and 5 (7%). Serotype distribution remained similar during all time periods. Pneumococcal serotype 1 remained the most common cause of PPE during the 5-year study. The new generation of pneumococcal conjugate vaccines offers potential serotype coverage of 73% (10-valent) and 99% (13-valent) in the population studied suffering from PPE. Continuous epidemiological and molecular studies are paramount to monitor the impact of pneumococcal vaccines on the epidemiology of PPE.

Pleural infection: changing bacteriology and its implications

The incidence of pleural infection continues to rise worldwide. Identifying the causative organism(s) is important to guide antimicrobial therapy. The bacteriology of pleural infection is complex and has changed over time. Recent data suggest that the bacterial causes of empyema are significantly different between adult and paediatric patients, between community-acquired and nosocomial empyemas and can vary among geographical regions of the world. Since the introduction of pneumococcal vaccines, a change has been observed in the distribution of the serotypes of Streptococcus pneumoniae in empyema. These observations have implications on therapy and vaccine strategies. Clinicians need to be aware of the local bacteriology of empyema in order to guide antibiotic treatment.

Molecular analysis improves pathogen identification and epidemiologic study of pediatric parapneumonic empyema

BACKGROUND

Parapneumonic empyema (PPE) is an increasingly common complication of bacterial pneumonia. Epidemiologic study is complicated by the low frequency of positive cultures. We sought to describe the epidemiology of PPE in children using molecular analysis of pleural fluid.

METHODS

We performed molecular testing for bacterial pathogens using archived pleural fluid from children hospitalized in 2009 with PPE. Real-time polymerase chain reaction (PCR) to detect Streptococcus pneumoniae, Staphylococcus aureus (including methicillin-resistant), Streptococcus pyogenes, Haemophilus influenzae, and Mycoplasma pneumoniae as well as PCR-based serotyping of S. pneumoniae was performed. Demographic, laboratory, and microbiologic data were abstracted.

RESULTS

Pleural fluid specimens from 63 children were available for PCR. By culture, a pathogen was isolated from blood and/or pleural fluid in 22 (35%) patients, with S. pneumoniae in 15 (24%), S. pyogenes in 3 (5%), and methicillin-resistant Staphylococcus aureus in 4 (6%). By PCR, a pathogen was detected in 53 (84%), including S. pneumoniae in 45 (71%). Compared with culture, PCR testing significantly increased detection of any pathogen (35% vs. 84%; P < 0.001) and of S. pneumoniae (24% vs. 71%; P < 0.001). Serotype 7F was the most common pneumococcal serotype detected. Comparison of culture-negative to culture-positive disease showed differences in both the pathogen profile and clinical outcomes.

CONCLUSIONS

Molecular analysis of pleural fluid more than doubled the detection of pathogens causing PPE. S. pneumoniae was the most common cause of both culture-positive and culture-negative PPE, although serotype distribution and outcomes differed.

A bedside assay to detect streptococcus pneumoniae in children with empyema

BACKGROUND

Empyema is a complication of pneumonia, commonly caused by Streptococcus pneumoniae.

AIMS

To validate the utility of an immunochromatographic test for the detection of S. pneumoniae antigen in the pleural fluid of children with empyema.

METHODS

Empyema patients had blood and pleural fluid cultured, and polymerase chain reaction (PCR) to detect the S. pneumoniae autolysin gene, lytA, in pleural fluid. Pleural fluid was tested using the Binax NOW S. pneumoniae antigen detection assay and compared with lytA PCR results and/or culture in blood or pleural fluid.

RESULTS

S. pneumoniae was detected by PCR in pleural fluid of 68 of 137 (49.6%) patients, by culture in 11 of 135 (8.1%) pleural specimens and 16 of 120 (13.3%) blood specimens. Pleural fluid Binax NOW testing from 130 patients demonstrated a sensitivity of 83.8% and specificity of 93.5% (positive predictive value of 93.4% and negative predictive value of 84.1%).

CONCLUSIONS

In pediatric empyema, high predictive values of pleural fluid Binax NOW S. pneumoniae antigen test suggest that this test may help rationalize antibiotic choice in these patients.

Usefulness of pneumococcal antigen detection in pleural effusion for the rapid diagnosis of infection by Streptococcus pneumoniae

Pleural effusion is increasingly reported in children. Standard culture of blood or pleural fluid is frequently negative and molecular diagnosis by polymerase chain reaction is not available in all hospitals. The Binax NOW Streptococcus pneumoniae Antigen test (Binax, Portland, USA) is a rapid immunochromatographic test (ICT) for the detection of the C polysaccharide antigen. We evaluated the Binax NOW test on the pleural fluid of 73 children hospitalized with pleural effusion over a period of 4 years. In our sample, the sensitivity and specificity of ICT were high (88% and 71%, respectively), with a positive predictive value of 96%. Detection of the pneumococcal antigen in pleural fluid by ICT is easy and quick, and enables us to identify the pneumococcal origin of the effusion, thus, making the treatment of complicated pneumonia suitably and early.

Pediatric parapneumonic pleural effusion: epidemiology, clinical characteristics, and microbiological diagnosis

BACKGROUND

In recent years an increase in the incidence and severity of parapneumonic pleural effusion (PPE) in pediatric populations has been observed. Streptococcus pneumoniae remains the main causal agent. New molecular and antigen techniques have increased the microbiological diagnosis of this pathology.

OBJECTIVES

To describe the epidemiology and clinical characteristics of PPE in our population.

PATIENTS AND METHODS

Prospective study of patients under the age of 18 years admitted for PPE in a tertiary-care pediatric hospital in Barcelona (Spain) between September 2003 and December 2006.

RESULTS

One hundred ninety cases of PPE were diagnosed. The annual incidence of PPE in the population under 18 years of age increased from 19.9 cases per 100,000 in 2004 to 35.2 per 100,000 in 2006. S. pneumoniae was the main causal agent identified: 82.9% of the 21.6% patients with positive culture. Non-vaccine serotypes (NVS) predominated (81.5%), and serotype 1 was responsible for 38.5% of cases. The use of polymerase chain reaction (PCR) test to detect S. pneumoniae increased etiological diagnosis from 21.6% to 42.1%. Antigen assays used to detect pneumococcus in pleural fluid demonstrated 87.9% sensitivity and 100% specificity when PCR was used as the gold standard.

CONCLUSIONS

There has been an increase in the incidence of PPE that parallels the increase in CAP. S. pneumoniae remains the principal causal agent, and NVS clearly predominate. The use of PCR to detect S. pneumoniae substantially increases etiologic diagnosis. The use of antigen assays to detect pneumococcus in pleural fluid is a quick and sensitive diagnostic method, and thus a valid alternative to PCR.

Assessment of the burden of paediatric empyema in Australia

AIMS

To investigate the change in incidence of childhood empyema and pneumonia in Australia, and ascertain the management trends in all hospitals caring for children with empyema.

METHODS

The incidences of empyema and pneumonia were calculated for each year between 1993/1994 and 2004/2005 using retrospective primary diagnostic coding from ICD-9 and 10 comprising the Australian National Hospital Morbidity Database for five age groups in patients less than 20 years of age. Hospitals with allocated paediatric beds were surveyed on referral pattern and treatment preferences.

RESULTS

In this study, 145 562 patients with pneumonia were admitted with a mean (range) incidence of 2306 (1846-2652) per million. The trend towards an overall increase was not statistically significant. Only the 1-4 years old age group demonstrated a significant increase (P < 0.01, r2 = 0.61). A total of 469 cases of empyema were identified with a mean incidence of 7.35 (4-10.2) per million. There was an overall increase in incidence (P < 0.05, r2 = 0.51) reflecting an increase in the 1- to 4-year-olds (P < 0.005, r2 = 0.60) and 15- to 19-year-olds (P < 0.05, r2 = 0.37). The overall percentage of empyema as a proportion of pneumonia increased from 0.27 to 0.70% (0.48% (0.27-0.70%), P < 0.05, r2 = 0.38). The survey response rate was 75%. Ninety-nine of 121 (82%) hospitals referred children with empyema to a more appropriate centre with wide variations in treatments provided.

CONCLUSIONS

The rise in incidence of empyema reflects that seen in other countries. Furthermore, there are diverse management practices suggesting a clear need for national guidelines.