Diagnosis of parapneumonic pleural effusion by polymerase chain reaction in children

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.

Which Current and Novel Diagnostic Avenues for Bacterial Respiratory Diseases?

Bacterial acute pneumonia is responsible for an extremely large burden of death worldwide and diagnosis is paramount in the management of patients. While multidrug-resistant bacteria is one of the biggest health threats in the coming decades, clinicians urgently need access to novel diagnostic technologies. In this review, we will first present the already existing and largely used techniques that allow identifying pathogen-associated pneumonia. Then, we will discuss the latest and most promising technological advances that are based on connected technologies (artificial intelligence-based and Omics-based) or rapid tests, to improve the management of lung infections caused by pathogenic bacteria. We also aim to highlight the mutual benefits of fundamental and clinical studies for a better understanding of lung infections and their more efficient diagnostic management.

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.

Identifying pneumococci in parapneumonic pleural effusion: Is there a role for culture-independent methods?

OBJECTIVE

To evaluate culture-independent procedures (immunochromatography and quantitative polymerase chain reaction [qPCR]) in the detection and susceptibility of Streptococcus pneumoniae directly from culture-negative pleural fluid (PF) in children.

METHOD

Detection of S. pneumoniae in PF of children with parapneumonic effusion and/or empyema by using two culture-independent methods: an immunochromatographic membrane test (IMT) which identifies the pneumococcal C antigen, and a real-time PCR test to detect pneumococcal genes lytA and pbp2b, a marker of susceptibility of β-lactam agents, in PF samples.

RESULTS

We tested 36 PF specimens and recorded the previous use of antimicrobials. In the final analysis, 34 samples were included. IMT and qPCR presented positive results in 23 (67.6%) and 24 (70.6%) of the samples, respectively, showing a moderate agreement (k = 0.518) between the two methods. From the 36 children included, 34 (94.4%) had antibiotic data available by the time when PFs were collected. Thirty-four (100%) children had been given treatment before PF sampling, with 33 (97%) receiving β-lactam antibiotics administered empirically. Of the 24 lytA real-time positive samples, 21 (87.5%) were also positive for pbp2b, a marker of β-lactam susceptibility.

CONCLUSION

The reduced sensitivity of culture for pneumococcal detection can be improved through the addition of IMT and qPCR analysis. The utility of qPCR combining detection of lytA and a marker of β-lactam susceptibility should be explored further.

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.

Pleural effusion with negative culture: a challenge for pneumococcal diagnosis in children

BACKGROUND

Pneumococcal parapneumonic effusion seems to be increasing in children in the postvaccine era and is frequently associated with negative culture. Due to the low yield of culture, culture-independent tools are evaluated.

METHODS

Culture-negative pleural fluid specimens from 38 children with parapneumonic effusion were examined for pneumococcal lytA by quantitative polymerase chain reaction (qPCR) and soluble antigen (C-polysaccharide) using an immunochromatographic test (BinaxNow Streptococcus pneumoniae).

RESULTS

In 81% (30/37) and 63% (24/38) of the specimens, a positive result was obtained by qPCR and antigen detection, respectively. Most mismatches were observed in specimens with low quantities of pneumococcal DNA and a negative antigen test.

CONCLUSIONS

Our results suggest an imperfect relationship between the 2 described methods. The immunochromatographic assay is a simple diagnostic tool, which can be used when resources are limited, and even after antibiotic use, but negative results may require confirmation through a more sensitive test, such as qPCR.

Specimen collection for the diagnosis of pediatric pneumonia

Diagnosing the etiologic agent of pneumonia has an essential role in ensuring the most appropriate and effective therapy for individual patients and is critical to guiding the development of treatment and prevention strategies. However, establishing the etiology of pneumonia remains challenging because of the relative inaccessibility of the infected tissue and the difficulty in obtaining samples without contamination by upper respiratory tract secretions. Here, we review the published and unpublished literature on various specimens available for the diagnosis of pediatric pneumonia. We discuss the advantages and limitations of each specimen, and discuss the rationale for the specimens to be collected for the Pneumonia Etiology Research for Child Health study.

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.

A multiplex polymerase chain reaction method for rapid pneumococcal serotype determination in childhood empyema

Nonvaccine serotypes are increasingly responsible for pneumococcal empyema. We developed a one-step polymerase chain reaction for identifying all serotypes covered by the 13-valent conjugate vaccine. Over 1 year, we identified serotypes 19A (n = 6), 1 (n = 2), 3 (n = 1) and 7F/A (n = 2), both in culture-positive and culture-negative pleural fluid from 11 children with empyema.

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.

Pleural Fluid PCR Method for Detection of Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae in Pediatric Parapneumonic Effusions

BACKGROUND

Parapneumonic effusions cause significant morbidity and mortality despite current developments in diagnostic and therapeutic approaches. Causative microorganisms may remain unidentified in a significant number of patients by cultures and Gram smears. Polymerase chain reaction (PCR) is a molecular technique for the detection of causative bacteria; however, its efficiency in pleural fluids is less known.

OBJECTIVES

The present study was performed to compare the efficiency of PCR in the detection of the three most common organisms (Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae) with conventional methods.

METHODS

Twenty-eight consecutive patients with parapneumonic pleural effusions were studied. On admission, pleural fluid samples were obtained for Gram staining, routine culture and PCR analysis for S. aureus, S. pneumoniae and H. influenzae.

RESULTS

PCR analysis allowed detection of 11 microorganisms in 10 patients (35.7%), whereas pleural fluid cultures detected the etiological agent in only 2 (7.1%). S. pneumoniae was the most frequent agent.

CONCLUSIONS

Pleural fluid cultures may have low diagnostic yields, partly due to prior antibiotic use. Pleural fluid PCR analysis may improve the etiologic diagnosis in parapneumonic pleural effusions, with technical advances leading to higher yields than obtained in this study.

Bacteriology of complicated parapneumonic effusions

PURPOSE OF REVIEW

The bacteriology of complicated parapneumonic effusions has changed in recent decades, but the causative organisms often remain obscure in up to 40% of cases. Recently, new molecular methods have become available which might help clinical management and improve our understanding of this condition. In this review, we will consider the current bacteriological spectrum of pleural infection and look at some of the new molecular methods.

RECENT FINDINGS

Hospital-acquired pleural infection exhibits a different bacteriology than pleural infection originating in the community. It carries a significantly higher mortality and requires different antibiotics at presentation. Streptococcal and anaerobic infections have low associated mortalities whereas staphylococcal, enterobacterial and mixed aerobic infections carry a worse prognosis. The yield of causative organisms can be significantly increased by the use of bacterial nucleic acid amplification and this may have a role in routine clinical practice in the near future.

SUMMARY

The bacteriology of pleural infection has changed markedly in recent years. Mortality is highest with hospital-acquired pleural infection and infections caused by staphylococci, Enterobacteriacae and mixed aerobes. New molecular microbiological methods substantially increase bacterial yield in pleural fluid.

Streptococcus pneumoniae virulence factors and their clinical impact: An update

The morbidity and mortality rates associated with Streptococcus pneumoniae remain very high worldwide. The virulence of this bacterium is largely dependent on its polysaccharide capsule, which is quite heterogeneous and represents a serious obstacle for designing effective vaccines. However, it has been demonstrated that numerous protein virulence factors are involved in the pathogenesis of pneumococcal disease. An important related finding from experimental animal models is that non-capsulated strains of pneumococci are protective against capsulated ones. Hence, new vaccine designs are focused on the surface proteins (e. g., PspA and PspC) and on the cytolysin, pneumolysin. Moreover, several virulence factors have potential value for pneumococcal diagnosis by urinalysis. In this paper, we review the virulence factors involved in bacteria-host interactions, and the new developments in vaccines and diagnostic methods.