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

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.

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.

Rapid and Sensitive Identification of Bacterial Infection and Bacteria Gram Types in Pleural Fluid of Children

Real-time polymerase chain reaction (RT-PCR) techniques have been increasingly used to detect microbial DNA in clinic for the diagnosis of bacterial infection. This study aims to developing an RT-PCR method to detect bacteria in pleural fluid (PF). We performed a method to simultaneously detect and classify the clinically relevant bacterial pathogens in hydrothorax with Gram probe RT-PCR (GRT-PCR), which targets the conserved region of the 16S rRNA gene. Our results showed this method could specifically and correctly identify 14 clinically important bacterial strains in hydrothorax including 7 gram-positive and 7 gram-negative bacteria. And the sensitivity of this GRT-PCR method in serial dilution can reach 10 CFU/mL. In clinical trial, 180 PF samples from children who were clinically suspected to suffer from bacterial pneumonia and empyema were collected. These samples were detected by GRT-PCR, standard culture, and biochemical routine analysis. The positive rate of the GRT-PCR array was 17.78% (32/180), significantly higher than that of PF culture (11.67%; 21/180; P = .003). When PF culture was used as control, the sensitivity of GRT-PCR was 95.24% (95% confidence interval = 74.13-99.75), and the specificity was 92.45% (95% confidence interval = 86.89-95.86). Our study showed that GRT-PCR is a more effective method for rapid, sensitive, and specific diagnosis of bacterial infection in hydrothorax compared with other traditional methods.

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.

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.

Bacterial causes of empyema in children, Australia, 2007-2009

An increase in the incidence of empyema worldwide could be related to invasive pneumococcal disease caused by emergent nonvaccine replacement serotypes. To determine bacterial pathogens and pneumococcal serotypes that cause empyema in children in Australia, we conducted a 2-year study of 174 children with empyema. Blood and pleural fluid samples were cultured, and pleural fluid was tested by PCR. Thirty-two (21.0%) of 152 blood and 53 (33.1%) of 160 pleural fluid cultures were positive for bacteria; Streptococcus pneumoniae was the most common organism identified. PCR identified S. pneumoniae in 74 (51.7%) and other bacteria in 19 (13.1%) of 145 pleural fluid specimens. Of 53 samples in which S. pneumoniae serotypes were identified, 2 (3.8%) had vaccine-related and 51 (96.2%) had nonvaccine serotypes; 19A (n = 20; 36.4%), 3 (n = 18; 32.7%), and 1 (n = 8; 14.5%) were the most common. High proportions of nonvaccine serotypes suggest the need to broaden vaccine coverage.

Identification of bacterial DNA in noninfectious pleural fluid with a highly sensitive PCR method

BACKGROUND

Bacterial DNA due to bacterial translocation has been identified in noninfectious ascitic fluid samples.

OBJECTIVE

This study investigated the possible presence of bacterial DNA in the pleural fluid of patients with pleural effusions of noninfectious origin, using a highly sensitive PCR-based method.

METHODS

Pleural fluid samples from 175 patients (average age ± SD: 69 ± 14 years) with noninfectious pleural effusion (62 transudates, 113 exudates) were analyzed. Bacterial DNA was detected using nested PCR with amplification of a fragment of the gene r16S, with 2 amplification protocols, i.e. low sensitivity (10 and 40 cycles) and high sensitivity (40 and 40 cycles).

RESULTS

With the less sensitive amplification process, only 1 sample was positive (Haemophilus parainfluenzae in a patient with hepatic hydrothorax). With the highly sensitive nested PCR method, bacterial DNA was identified in the pleural fluid, of both transudative and exudative origin, of 75 of the 175 patients (43%). In cases of isolation of a single bacterium, the more frequent were Escherichia coli, Salmonella enterica and Streptococcus pneumoniae.

CONCLUSIONS

Regardless of its origin, bacterial DNA can be identified in almost half of noninfectious pleural effusions by using a highly sensitive PCR-based method. The possible clinical significance or prognostic value of these findings deserves to be evaluated.

Factors associated with the outcome of life-threatening necrotizing pneumonia due to community-acquired Staphylococcus aureus in adult and adolescent patients

BACKGROUND

Although community-acquired Staphylococcus aureus pneumonia with highly virulent Panton-Valentine leukocidin (PVL)-positive strains, a severe disease with significant lethality, is rare, especially in adult and adolescent patients, recent reports highlight that these infections are on the rise.

OBJECTIVES

To describe the demographic and clinical features of reported cases of life-threatening community-acquired S. aureus pneumonia with usually PVL-positive strains in adult and adolescent patients, to evaluate the variables related to death, and to select a more appropriate antimicrobial treatment for this potentially deadly disease.

METHODS

We summarized all of the 92 reported cases and our case. The effect of 5 variables on mortality was measured using logistic regression.

RESULTS

S. aureus community-acquired pneumonia (CAP) with usually PVL-positive strains is a severe disease with significant lethality, i.e. 42.9%; a short duration of the time from the onset of symptoms to death, i.e. 5.5 ± 10.1 days, and prolonged hospital admissions, i.e. 33.2 ± 29.5 days. Seventy-three cases have been tested for the gene for PVL, and 71 strains have been found to carry the PVL gene. Logistic regression analysis showed that leucopenia (p = 0.002), influenza-like symptoms or laboratory-confirmed influenza (p = 0.011), and hemoptysis (p = 0.024) were the factors associated with death. Antibiotic therapies inhibiting toxin production were associated with an improved outcome in these cases (p = 0.007).

CONCLUSIONS

Physicians should pay special attention to those patients who acquired severe CAP during influenza season and have flu-like symptoms, hemoptysis, and leucopenia, and they should consider S. aureus more frequently among the possible pathogens of severe CAP. Empiric therapy for severe CAP with this distinct clinical picture should include coverage for S. aureus. Targeted treatment with antimicrobials inhibiting toxin production appears to be a more appropriate selection.

Pneumonia due to methicillin-resistant Staphylococcus aureus: clinical features, diagnosis and management

PURPOSE OF REVIEW

The review highlights the clinical findings and the management of community-acquired, health-care associated and nosocomial pneumonia due to methicillin-resistant Staphylococcus aureus (MRSA).

RECENT FINDINGS

Although previously considered as a purely nosocomial event, community-acquired MRSA pneumonia is underestimated and is spreading worldwide. A retrospective study showed that almost half of patients with nonnosocomial MRSA pneumonia admitted to a large teaching hospital did not present established criteria for healthcare-associated infections. Recent data show that MRSA ventilator-associated pneumonia is associated with significantly higher mortality than ventilator-associated pneumonia caused by methicillin-susceptible Staphylococcus aureus. Therefore, prompt and appropriate therapy is essential. The optimal therapy for MRSA pneumonia has not been fully elucidated. Although vancomycin has been considered the gold standard for the treatment of MRSA infections, clinical failures have also been reported in the presence of in-vitro susceptibility. Linezolid may provide improved outcomes compared with vancomycin in patients with MRSA pneumonia, but validation in a prospective trial is currently lacking. Recently licensed tigecycline and dalbavancin, a drug in phase III trial, look promising. Animal models showed that immunization against a cytolytic toxin secreted by most Staphylococcus aureus strains protects against lethal pneumonia.

SUMMARY

Rapid recognition of possible staphylococcal infection in patients with severe pneumonia is essential. The treatment of MRSA pneumonia must be prompt and effective in order to allow a fast microbiological clearance and to successfully manage the infection.

Clinical practice: treatment of childhood empyema

INTRODUCTION

The incidence of empyema in children is increasing. Adequate knowledge of treatment modalities is therefore essential for every pediatrician. At the university hospital of Leuven, the incidence per 100,000 admissions increased from 40 in 1993 to 120 in 2005. The treatment of choice, however, is still a matter of debate. This is mainly due to the scarcity of prospective randomized trials in children but is further complicated by the absence of uniform terminology. This review starts with clarifying definitions of empyema and complicated versus noncomplicated parapneumonic effusion. The place of different imaging techniques--ultrasound, chest X-ray, computerized tomography and magnetic resonance imaging--is illustrated. All treatment steps are evaluated starting with antibiotic choices, duration of i.v. and oral antibiotics, pleural fluid analysis, indications for chest drain placement, and fibrinolysis. As to the surgical interventions, there is at present insufficient evidence that early surgery is superior to noninvasive medical treatment. Therefore, video-assisted thoracoscopy cannot be advised as general first-line therapy.

CONCLUSION

Since the pathogenicity of empyema is a dynamic process, therapeutic strategy must be decided based on empyema stage and clinical experience. Each referral center should agree on a diagnostic and therapeutic flowchart based on current evidence and local expertise. The flow chart outlined for our center is presented.