The bacterial aetiology of pleural empyema. A descriptive and comparative metagenomic study

Clinical characteristics of community-acquired primary pleural infection compared to postpneumonic pleural infection: a retrospective study

BACKGROUND

Data on the clinical features and treatment outcomes in patients with primary pleural infection (PI) are limited. This study aimed to investigate the clinical characteristics of these patients.

PATIENTS AND METHODS

In this retrospective study, patients with community-acquired PI, diagnosed based on pleural fluid analysis, were classified into postpneumonic and primary PI groups according to computed tomography (CT) findings. Clinical variables, microbiological data, and CT findings were compared between the two groups.

RESULTS

Approximately 28 % of patients with community-acquired PI presented as primary PI. Treatment success rates and in-hospital or 30-day mortality were comparable between the two groups. However, compared to the postpneumonic PI group, the primary PI group was significantly younger and had lower proportions of patients with Pneumonia Severity Index classes 4-5 and RAPID (Renal, Age, Purulence, Infection source, and Dietary factors) score >3. On CT scans, subpleural abscesses were present in less than half of the patients in the primary PI group, compared to most patients in the postpneumonic PI group. Pleural enhancement and extrapleural fat proliferation were more frequently observed in patients with primary PI than in those with postpneumonic PI. In the primary PI group, Streptococcus anginosus group was the most common pathogen, accounting for nearly half of the causative organisms.

CONCLUSIONS

Patients with primary PI had similar treatment outcomes compared to those with postpneumonic PI. However, different causative pathogens and radiologic findings of primary PI suggest a distinct pathogenesis of PI independent of pneumonia.

Diversity in the composition of pleural cavity and oral cavity microbiota in different bacterial empyema

Introduction

Recent studies have proposed primary empyema and demonstrated a correlation between it and the microbial composition of the oral cavity. However, no study has systematically characterized the differences in microbial composition between primary and secondary empyema. Furthermore, the correlation between the characteristics of empyema and oral microbiota remains to be explored.

Methods

The study included forty-six patients diagnosed with empyema. Hydrothorax was collected from all patients, and mouthwash samples were collected from 24 patients. Both types of samples underwent amplification and sequencing using primer sets specific for the 16S rRNA gene.

Results and discussion

Compared with the primary empyema group, the pleural cavity microbial diversity of pneumonia complicated with empyema was significantly decreased (p < 0.05). At the phylum level, the relative abundance of Proteobacteria was significantly higher in the primary empyema group than pneumonia with empyema (p < 0.05). At the genus level, the abundance of Streptococcus, Escherichia-Shigella, and Corynebacterium increased in the primary empyema group, while the abundance of Campylobacter, Salmonella, Bacillus, and Staphylococcus decreased (p > 0.05). The shared sequences between the hydrothorax samples and mouthwash samples from the patients with empyema contributed to 94% of the total sequences used in these analyses. Correlation analysis indicated that the presence of Streptococcus constellatus in empyema is positively correlated with leukocytes and neutrophils, and negatively correlated with lymphocytes (p < 0.05).

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

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

Polymicrobial empyema in a patient with lung adenocarcinomacontaining Capnocytophaga sputigena

A man in his 60s with advanced COPD and lung adenocarcinoma presented with sepsis and acute hypoxaemic respiratory failure. Imaging revealed bilateral pleural effusions, and he was found to have a polymicrobial empyema which included Capnocytophaga sputigena Despite appropriate treatment, he continued to deteriorate and ultimately died of sepsis. Capnocytophaga species, typically benign constituents of the oral microbiota, rarely can instigate pleuropulmonary infections, especially in immunocompromised individuals. We highlight the difficulty in the identification and the optimal antimicrobial treatment of Capnocytophaga in the setting of growing antibiotic resistance.

Tunneled Pleural Catheters: An Effective Nonsurgical Alternative for Nonexpandable Lung in Chronic Pleural Infection

BACKGROUND

Open window thoracostomy (OTW) is the standard of care for debilitated patients with chronic pleural infection and nonexpandable lungs (NEL) who are not candidates for major surgical intervention. Tunneled pleural catheters (TPC) offer tremendous treatment potential in this setting based on their efficacy in malignant pleural effusion and NEL. We aim to assess the efficacy, safety, and health care utilization of TPC in this setting.

METHODS

We retrospectively evaluated patients who underwent TPC procedures for the long-term management of chronic pleural infection and NEL who were not candidates for major surgical intervention. Clinically, complete treatment success was defined as fever abatement, normalization of white cell count, and stoppage of antimicrobial therapy without requiring surgical intervention. It is deemed a partial success if chronic antimicrobial suppression is still needed.

RESULTS

There were 20 patients who had TPC placed for chronic pleural infection with NEL. Clinical and partial treatment success was achieved in 9/17 and 8/17 patients, respectively, excluding 3 patients who were placed on comfort measures only. The median change in pleural volume was -218 mL. The median length of stay after TPC placement was 4.5 days. TPC was removed in 8 patients due to successful obliteration of pleural space in a median duration of 46.5 days. Four patients passed away with TPCs in place, 7 retained TPCs at the last health care system contact, and 1 patient had OTW due to TPC failure.

CONCLUSION

This exploratory study suggests that TPC is an effective and safe intervention for the management of patients with chronic pleural infection and NEL lung who are not candidates for surgical intervention.

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

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

IMPORTANCE

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

Bilateral parapneumonic empyema caused by Fusobacterium necrophorum infection in a healthy individual

Pulmonary infection caused by Fusobacterium necrophorum, an obligate anaerobic gram-negative bacterium, most commonly occurs as a part of Lemierre's syndrome, i.e., pharyngotonsillitis complicated by septic thrombophlebitis of the internal jugular vein and secondary lung abscesses. A 51-year-old previously healthy man was admitted to our hospital with pleuritic right-sided chest pain. No sore throat, dysphagia, or neck pain was observed. Chest radiography and computed tomography (CT) revealed massive right pleural effusion and bilateral bronchopneumonia. Right thoracic drainage yielded purulent fluids, from which a pure culture of F. necrophorum was isolated. Blood culture and broad-range polymerase chain reaction for bacterial 16S ribosomal ribonucleic acid on blood samples were negative. CT scan showed no evidence of internal jugular vein thrombosis or peritonsillar abscess. The right thoracic tube was removed after the purulent fluids were no longer drained. Although the antibiotic treatment was continued with intravenous sulbactam/ampicillin, to which F. necrophorum was sensitive, left purulent pleural effusion emerged. The antibiotic was switched to clindamycin, cefazolin, cefotiam, and flomoxef. Although the left pleural effusion gradually decreased, the right purulent pleural fluid was reaccumulated. Thus, the patient underwent right-sided thoracoscopic decortication and debridement, followed by thoracic lavage through a chest tube with saline solution. After the surgery, the patient's condition improved, and no recurrence of pleural effusion was observed. This report presents the case of a previously healthy patient with bilateral parapneumonic empyema caused by F. necrophorum, without manifestations of pharyngotonsillitis, bacteremia, or Lemierre's syndrome. Extensive thoracic drainage, effective antibiotics, and timely surgical interventions are imperative.

Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology

The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.

Management of patient with Fusobacterim nucletum related pleural empyema: intrapleural antibiotic therapy can be considered for salvage therapy

Pleural empyema can lead to significant morbidity and mortality despite chest drainage and antibiotic treatment, necessitating novel and minimally invasive interventions. Fusobacterium nucleatum is an obligate anaerobe found in the human oral and gut microbiota. Advances in sequencing and puncture techniques have made it common to detect anaerobic bacteria in empyema cases. In this report, we describe the case of a 65-year-old man with hypertension who presented with a left-sided encapsulated pleural effusion. Initial fluid analysis using metagenomic next-generation sequencing (mNGS) revealed the presence of Fusobacterium nucleatum and Aspergillus chevalieri. Unfortunately, the patient experienced worsening pleural effusion despite drainage and antimicrobial therapy. Ultimately, successful treatment was achieved through intrapleural metronidazole therapy in conjunction with systemic antibiotics. The present case showed that intrapleural antibiotic therapy is a promising measure for pleural empyema.

Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel

Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.

Polymicrobial infections with specific Actinomyces and related organisms, using the current taxonomy

Actinomyces organisms reside on mucosal surfaces of the oropharynx and the genitourinary tract. Polymicrobial infections with Actinomyces organisms are increasingly being reported in the literature. Since these infections differ from classical actinomycosis, lacking of specific clinical and imaging findings, slow-growing Actinomyces organisms can be regarded as contaminants or insignificant findings. In addition, only limited knowledge is available about novel Actinomyces species and their clinical relevance. The recent reclassifications have resulted in the transfer of several Actinomyces species to novel genera Bowdeniella, Gleimia, Pauljensenia, Schaalia, or Winkia. The spectrum of diseases associated with specific members of Actinomyces and these related genera varies. In human infections, the most common species are Actinomyces israelii, Schaalia meyeri, and Schaalia odontolytica, which are typical inhabitants of the mouth, and Gleimia europaea, Schaalia turicensis, and Winkia neuii. In this narrative review, the purpose was to gather information on the emerging role of specific organisms within the Actinomyces and related genera in polymicrobial infections. These include Actinomyces graevenitzii in pulmonary infections, S. meyeri in brain abscesses and infections in the lower respiratory tract, S. turicensis in skin-related infections, G. europaea in necrotizing fasciitis and skin abscesses, and W. neuii in infected tissues around prostheses and devices. Increased understanding of the role of Actinomyces and related species in polymicrobial infections could provide improved outcomes for patient care. Key messages Due to the reclassification of the genus, many former Actinomyces species belong to novel genera Bowdeniella, Gleimia, Pauljensenia, Schaalia, or Winkia.Some of the species play emerging roles in specific infection types in humans.Increasing awareness of their clinical relevance as an established or a putative pathogen in polymicrobial infections brings about improved outcomes for patient care.

Fusobacterium nucleatum bacteremia complicated with intracranial Porphyromonas gingivalis and HSV-1 infection: a case report and literature review

BACKGROUND

Fusobacterium nucleatum (F. nucleatum) belongs to the genus Fusobacterium, which is a gram-negative obligate anaerobic bacterium. Bacteremia associated with F. nucleatum is a serious complication, which is not common in clinic, especially when it is combined with other intracranial pathogenic microorganism infection. We reported for the first time a case of F. nucleatum bacteremia combined with intracranial Porphyromonas gingivalis (P. gingivalis) and herpes simplex virus type 1(HSV-1) infection.

CASE PRESENTATION

A 60-year-old woman was admitted to our hospital with a headache for a week that worsened for 2 days. Combined with history, physical signs and examination, it was characterized as ischemic cerebrovascular disease (ICVD). F. nucleatum was detected in blood by matrix-assisted laser desorption/ionization time-offight mass spectrometry (MALDI-TOF-MS). Meanwhile, P. gingivalis and HSV-1 in cerebrospinal fluid (CSF) were identified by metagenome next generation sequencing (mNGS). After a quick diagnosis and a combination of antibiotics and antiviral treatment, the patient recovered and was discharged.

CONCLUSION

To our knowledge, this is the first report of intracranial P. gingivalis and HSV-1 infection combined with F. nucleatum bacteremia.

Rapid detection of S. pyogenes and S. pneumoniae in pleural fluid for diagnosis of parapneumonic empyema

The aim of this study was to assess the reliability of rapid antigen detection tests (RADT) for Streptococcus pyogenes (GAS) and Streptococcus pneumoniae on pleural fluid samples for diagnosis of parapneumonic effusion/empyema (PPE) and their potential for improving pathogen identification rates. Sixty-three pleural samples were included from 54 patients on which GAS and S. pneumoniae RADT (BinaxNOW), culture, 16S rRNA PCR, and S. pneumoniae-specific PCR were performed. GAS RADT showed a sensitivity of 95.2% and a specificity of 100%. Pneumococcal RADT showed a sensitivity of 100% and specificity of 88.6%. Both RADT increased the pathogen identification rate in PPE compared to culture.

Fusobacterium/Peptostreptococcus - A Case Report of Community- Acquired Empyema Resulting in Surgical Decortication with Prolonged Antibiotic Therapy: A Case Series and Review of the Literature

Background: Infections caused by anaerobic bacteria occur frequently and can be serious and life-threatening. Anaerobes are a rare cause of community-acquired pneumonia with Streptococcus pneumonia and respiratory viruses being the most frequently detected pathogens. We, herein, report a case of Fusobacterium/Peptostreptococcus parapneumonic effusion with empyema in a patient without risk factors for aspiration pneumonia. This case presents an opportunity to discuss an unusual case of community-acquired empyema secondary to anaerobic infection in a patient without the common risk factors for aspiration.

Case Presentation: A 59-year-old male patient without significant past medical history apart from a twenty-five-year history of smoking presented due to left flank pain and shortness of breath. Findings of a complicated parapneumonic effusion were found on imaging, resulting in surgical decortication and prolonged antibiotic therapy.

Discussion: Parapneumonic effusions and empyema are relatively common complications of pneumonia. It is important to note that the incidence of anaerobic empyema has been on the rise due to more modern culturing techniques.

Conclusion: This case highlights an unusual presentation of community-acquired empyema secondary to anaerobes without any risk factors for aspiration pneumonia. Therefore, clinicians should consider the possibility of anaerobic coverage in the treatment of community-acquired empyema in the appropriate setting.

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Diagnosis and management of pleural infection

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

Unilateral complicated pleural empyema in a patient with bronchial asthma due to clindamycin-resistant Prevotella buccae

Prevotella buccae (P. buccae) is a gram-negative obligate anaerobe mainly associated with infections of odontogenic origin. Non-oral monomicrobial infection by these obligate anaerobic bacteria is rare. Only a few cases of monomicrobial non-oral infections by P. buccae have been reported in the literature. We are reporting a case of unilateral complicated pleural empyema in a patient with bronchial asthma infected by P. buccae. Pleural fluid aerobic culture and blood culture reports were sterile. No acid-fast bacilli were detected by Acid Fast Bacilli (AFB) staining, and cartridge-based nucleic acid assay test (CBNAAT) reports were negative for Mycobacterium tuberculosis. The isolate, P. buccae was found susceptible to Metronidazole (MIC = 3 μg/ml) and resistant to Clindamycin (MIC = 256 μg/ml). In view of rising trends of antimicrobial resistance among anaerobes, it is recommended to perform anaerobic culture and sensitivity testing in clinically suspected cases of pleuropulmonary infection for appropriate diagnosis and optimal patient management. Clindamycin should be used with caution for empiric treatment.

Pleural Empyema Caused by Streptococcus intermedius and Fusobacterium nucleatum: A Distinct Entity of Pleural Infections

BACKGROUND

Many community-acquired pleural infections are caused by facultative and anaerobic bacteria from the human oral microbiota. The epidemiology, clinical characteristics, pathogenesis, and etiology of such infections are little studied. The aim of the present prospective multicenter cohort study was to provide a thorough microbiological and clinical characterization of such oral-type pleural infections and to improve our understanding of the underlying etiology and associated risk factors.

METHODS

Over a 2-year period, we included 77 patients with community-acquired pleural infection, whereof 63 (82%) represented oral-type pleural infections. Clinical and anamnestic data were systematically collected, and patients were offered a dental assessment by an oral surgeon. Microbial characterizations were done using next-generation sequencing. Obtained bacterial profiles were compared with microbiology data from previous investigations on odontogenic infections, bacteremia after extraction of infected teeth, and community-acquired brain abscesses.

RESULTS

From the oral-type pleural infections, we made 267 bacterial identifications representing 89 different species. Streptococcus intermedius and/or Fusobacterium nucleatum were identified as a dominant component in all infections. We found a high prevalence of dental infections among patients with oral-type pleural infection and demonstrate substantial similarities between the microbiology of such pleural infections and that of odontogenic infections, odontogenic bacteremia, and community-acquired brain abscesses.

CONCLUSIONS

Oral-type pleural infection is the most common type of community-acquired pleural infection. Current evidence supports hematogenous seeding of bacteria from a dental focus as the most important underlying etiology. Streptococcus intermedius and Fusobacterium nucleatum most likely represent key pathogens necessary for establishing the infection.

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

Objective

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

Patients and Methods

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

Results

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

Conclusion

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

Actinomycosis with Fusobacterium empyema

Actinomyces, are gram-positive, non-spore forming anaerobic or microaerophilic species. Empyema due to actinomycosis is relatively rare and can be difficult to diagnose as the presenting symptoms may be indolent and the micro-organism may be difficult to culture. This case report describes a patient presenting with dyspnoea, weight loss and lethargy. The chest radiograph, CT and thoracic ultrasound revealed a left-sided pleural effusion. A chest drain was inserted under ultrasound guidance. The pleural fluid was macroscopically consistent with pus and microbiology showed growth of gram-positive bacilli, Actinomyces meyeri as well as the Fusobacterium species. The patient was treated with a drainage of the pleural fluid, a prolonged course of antibiotics and made a good recovery. The awareness that the Actinomyces species and the Fusobacterium species through their synergistic interaction may cause empyema, may lead to a timely diagnosis and treatment.

Streptococcus intermedius Brain Abscess with Lung Abscess and Aortic Valve Endocarditis: A Case Report and Literature Review

Streptococcus intermedius is frequently associated with brain and liver abscesses, while pleuropulmonary infections are considered rarer. Even less frequent is the association of lung and brain abscesses due to this agent with infective endocarditis. We describe the case of a 40-year-old man complaining of cough, fever, and headache who was diagnosed with a brain abscess due to S. intermedius, a concomitant lung abscess, and aortic native valve endocarditis. He was treated with surgical drainage of the brain abscess and a 4-week course of intravenous ceftriaxone, followed by oral amoxicillin/clavulanate, obtaining healing of the lesions without relapse of the infection.

Clinical features of Streptococcus intermedius infection in children: a case series study

Introduction

Streptococcus intermedius is an opportunistic pathogen associated with prolonged hospital stays and high mortality rates in adults. However, little is currently known about the clinical features of Streptococcus intermedius infection in children.

Methods

This retrospective case series study included 40 children diagnosed with Streptococcus intermedius, confirmed through bacterial cultures or high-throughput sequencing. Antibiotic resistance was assessed through susceptibility testing. The site and clinical manifestations were evaluated for all patients.

Results

The common infection sites were the abdominal cavity, skin and soft tissue, intracranial, and invasive pulmonary, with the abdominal cavity being the most frequently affected. The drug susceptibility test showed 100% sensitivity to ceftriaxone, levofloxacin, chloramphenicol, vancomycin, and linezolid, 92.6% sensitivity to penicillin, 73.3% resistance to erythromycin, and 76.7% resistance to clindamycin. Besides antibiotic therapy, surgical intervention or pus drainage was often necessary. Lung imaging of four patients revealed pulmonary abscesses, nodules, or encapsulated pleura. Two cases yielded positive culture results, while three were identified as positive through high-throughput nucleotide sequencing of pleural effusion.

Discussion

In children with Streptococcus intermedius infection, emphasis should be placed on the risk of pus or abscess formation. In cases of pulmonary abscess and pleural effusion, especially in male children, Streptococcus intermedius should be suspected even if the culture is negative. Improvements in high-throughput nucleotide sequencing are required to reduce misdiagnosis rates.

Identification and characterization of pancreatic infections in severe and critical acute pancreatitis patients using 16S rRNA gene next generation sequencing

Objectives

This study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients.

Methods

A total of 78 pancreatic fluid samples were collected from 56 SAP and CAP patients and analyze using aerobic culture and 16S rRNA gene next-generation sequencing. The clinical data of the patients were obtained from the electronic medical records.

Results

Among the total 78 samples, 16S rRNA gene NGS identified a total of 660 bacterial taxa, belonging to 216 species in 123 genera. The dominant aerobic bacteria included Klebsiella pneumoniae, Acinetobacter baumannii, and Enterococcus faecium, while the dominant anaerobic bacteria included Bacteroides, Dialister invisus, and Olsenella uli. As compared to aerobic culturing, 95.96% (95/99) of the aerobic cultured bacteria were detected using the 16S rRNA gene NGS.

Conclusion

The pancreatic infections in SAP and CAP patients might originate not only from the gut but also from the oral cavity and airways as well as related environments. Dynamic analysis of bacterial profile and abundance showed that some bacteria with low abundance might become the main pathogenic bacteria. There were no significant differences in the bacterial diversity between SAP and CAP.

Clinical Implications of the Controlling Nutritional Status Score on Short-term Outcomes in Patients with Pleural Infection

Objective Pleural infection is a significant disease that continues to pose severe problems for respiratory physicians. However, prognostic factors of pleural infection remain poorly understood. The controlling nutritional status (CONUT) score represents the immune-nutrition status of patients with chronic infectious diseases. This study investigated its prognostic value in patients with pleural infections. Methods We retrospectively analyzed a collected database of 2,363 patients who underwent thoracentesis and pleural fluid analyses between January 2010 and December 2019. Of these, only 335 patients with complicated parapneumonic effusion and empyema defined as pleural infection were included. They were divided into two groups based on the dichotomized CONUT score (i.e. <6 for low scores and ≥6 for high scores). The primary outcome was all-cause mortality within 90 days from the time of pleural fluid collection. Results Overall mortality was 8.4% at 3 months (28 out of 335). The incidence of 90-day mortality was higher in patients with higher CONUT scores than in those with lower scores [25.3% (21/84) vs. 2.8% (7/251), p<0.001]. In addition, after adjusting for confounders, a high CONUT score was found to be an independent prognostic factor for 90-day mortality (hazard ratio, 9.30; 95% confidence interval, 3.96-21.87; p<0.001). Conclusion Our study indicated that a high CONUT score was associated with an increased risk of 90-day mortality in patients with pleural infection and can be considered for clinical evaluations in practice.

Empyema caused by Fusobacterium nucleatum with squamous cell carcinoma of the lung: a case report and literature review

Background

Fusobacterium nucleatum is a common oral symbiotic flora that can cause respiratory tract, oral nervous system, obstetric and skin infections. Fusobacterium nucleatum infections are mostly caused by aspiration. The clinical manifestations of pulmonary infections with Fusobacterium nucleatum can include simple pneumonia, lung abscesses, empyema, etc.

Case presentation

We described the case of a 49-year-old man with a 1-year history of intermittent cough and sputum production who had worsened over the last 4 days with fever and right chest pain. After thoracentesis and catheter drainage were performed, Fusobacterium nucleatum was detected in the pleural effusion by using next-generation sequencing. Meanwhile, a diagnosis of squamous cell carcinoma of the right lung was made by fiberoptic bronchoscopy. The patient's condition improved significantly after percutaneous drainage and long-term intravenous antibiotic treatment.

Conclusions

This is the first case reported of empyema due to Fusobacterium nucleatum infection in a patient with squamous cell carcinoma.

ERS/ESTS statement on the management of pleural infection in adults

Pleural infection is a common condition encountered by respiratory physicians and thoracic surgeons alike. The European Respiratory Society (ERS) and European Society of Thoracic Surgeons (ESTS) established a multidisciplinary collaboration of clinicians with expertise in managing pleural infection with the aim of producing a comprehensive review of the scientific literature. Six areas of interest were identified: 1) epidemiology of pleural infection, 2) optimal antibiotic strategy, 3) diagnostic parameters for chest tube drainage, 4) status of intrapleural therapies, 5) role of surgery and 6) current place of outcome prediction in management. The literature revealed that recently updated epidemiological data continue to show an overall upwards trend in incidence, but there is an urgent need for a more comprehensive characterisation of the burden of pleural infection in specific populations such as immunocompromised hosts. There is a sparsity of regular analyses and documentation of microbiological patterns at a local level to inform geographical variation, and ongoing research efforts are needed to improve antibiotic stewardship. The evidence remains in favour of a small-bore chest tube optimally placed under image guidance as an appropriate initial intervention for most cases of pleural infection. With a growing body of data suggesting delays to treatment are key contributors to poor outcomes, this suggests that earlier consideration of combination intrapleural enzyme therapy (IET) with concurrent surgical consultation should remain a priority. Since publication of the MIST-2 study, there has been considerable data supporting safety and efficacy of IET, but further studies are needed to optimise dosing using individualised biomarkers of treatment failure. Pending further prospective evaluation, the MIST-2 regimen remains the most evidence based. Several studies have externally validated the RAPID score, but it requires incorporating into prospective intervention studies prior to adopting into clinical practice.

Optimal diagnostic strategies for pleural diseases and identifying high-risk patients

INTRODUCTION

Pleural diseases encompass a broad range of conditions with diverse and heterogenous etiologies. Diagnostics in pleural diseases thus represents a challenging field with a wide array of available testing to distinguish between the numerous causes of pleural disease. Nonetheless, deploying best practice diagnostics in this area is essential in reducing both duration o the investigation pathway and symptom burden.

AREAS COVERED

This article critically appraises the optimal diagnostic strategies and pathway in patients with pleural disease, reviewing the latest evidence and key practice points in achieving a treatable diagnosis in patients with pleural disease. We also cover future and novel directions that are likely to influence pleural diagnostics in the near future. PubMed was searched for articles related to pleural diagnostics (search terms below), with the date ranges including June 2012 to June 2022.

EXPERT OPINION

No single test will ever be sufficient to provide a diagnosis in pleural conditions. The key to reducing procedure burden and duration to diagnosis lies in personalizing the investigation pathway to patients and deploying tests with the highest diagnostic yield early (such as pleural biopsy in infection and malignancy). Novel biomarkers may also allow earlier diagnostic precision in the near future.

Risk factors associated with length of hospital stay and medical expenses in pulmonary abscess patients: retrospective study

Background

Pulmonary abscess carries a high mortality and requires long-term managements. A better understanding of the risk factors associated with the prolonged hospital stay and high medical expenses in these patients can improve the management strategy in individual patient and optimize the overall healthcare resources.

Methods

We performed a retrospective study and reviewed the medical records on consecutive patients hospitalized at the Department of Respiratory Medicine of the General Hospital of Northern Theater Command, Shenyang, Liaoning, China, between January 1, 2015, and December 31, 2020. Demographics, comorbidity, clinical symptoms, laboratory tests, length of hospital stay, and medical expenses were recorded. Their relationships with the length of hospital stay and medical expenses in pulmonary abscess patients were analyzed.

Results

There were 190 patients with the pulmonary abscess and 12,189 patients without the pulmonary abscess. Compared with patients without the pulmonary abscess, patients with the pulmonary abscess had longer hospital stays (21.8 ± SD vs 12.8 ± SD, P < 0.01), In patients with the pulmonary abscess, the mean length of hospital stay was 5.3 days longer in male vs female patients (P = 0.025). Multivariate linear regression analyses showed that extrapulmonary disease and clinical symptoms were associated with the length of hospital stay and medical expenses, respectively. In addition, anemia was associated with both the length of hospital stay and medical expenses. Sex and hypoproteinemia were associated with the medical expenses.

Conclusions

The mean length of hospital stay was longer in patients with the pulmonary abscess than those without the pulmonary abscess. The length of hospital stay and medical expense were associated with sex, clinical symptoms, extrapulmonary disease, and abnormal laboratory tests in patients with the pulmonary abscess.

Relationship between oral health and prognosis in patients with empyema: Single center retrospective study with propensity score matching analysis

BACKGROUND

Empyema is a life-threatening infection often caused by oral microbiota. To the best of our knowledge, no reports have investigated the association between the objective assessment of oral health and prognosis in patients with empyema.

MATERIALS AND METHODS

A total of 63 patients with empyema who required hospitalization at a single institution were included in this retrospective study. We compared non-survivors and survivors to assess risk factors for death at three months, including the Renal, age, pus, infection, diet (RAPID) score, and Oral Health Assessment Tool (OHAT) score. Furthermore, to minimize the background bias of the OHAT high-score and low-score groups determined based on the cut-off value, we also analyzed the association between the OHAT score and death at 3 months using the propensity score matching method.

RESULTS

The 3-month mortality rate was 20.6% (13 patients). Multivariate analysis showed that a RAPID score ≥5 points (odds ratio (OR) 8.74) and an OHAT score ≥7 points (OR 13.91) were significantly associated with death at 3 months. In the propensity score analysis, a significant association was found between a high OHAT score (≥7 points) and death at 3 months (P = 0.019).

CONCLUSION

Our results indicated that oral health assessed using the OHAT score may be a potential independent prognostic factor in patients with empyema. Similar to the RAPID score, the OHAT score may become an important indicator for the treatment of empyema.

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.

Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples

While 16S rRNA PCR-Sanger sequencing has paved the way for the diagnosis of culture-negative bacterial infections, it does not provide the composition of polymicrobial infections. We aimed to evaluate the performance of the Nanopore-based 16S rRNA metagenomic approach, using both partial and full-length amplification of the gene, and to explore its feasibility and suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory. Thirty-one culture-negative clinical samples from mono- and polymicrobial infections based on Sanger-sequencing results were sequenced on MinION using both the in-house partial amplification and the Nanopore dedicated kit for the full-length amplification of the 16S rRNA gene. Contamination, background noise definition, bacterial identification, and time-effectiveness issues were addressed. Cost optimization was also investigated with the miniaturized version of the flow cell (Flongle). The partial 16S approach had a greater sensitivity compared to the full-length kit that detected bacterial DNA in only 24/31 (77.4%) samples. Setting a threshold of 1% of total reads overcame the background noise issue and eased the interpretation of clinical samples. Results were obtained within 1 day, discriminated polymicrobial samples, and gave accurate bacterial identifications compared to Sanger-based results. We also found that multiplexing and using Flongle flow cells was a cost-effective option. The results confirm that Nanopore technology is user-friendly as well as cost- and time-effective. They also indicate that 16S rRNA targeted metagenomics is a suitable approach to be implemented for the routine diagnosis of culture-negative samples in clinical laboratories.

Prevotella species as oral residents and infectious agents with potential impact on systemic conditions

Oral Prevotella are known as anaerobic commensals on oral mucosae and in dental plaques from early life onwards, including pigmented P. melaninogenica, P. nigrescens, and P. pallens and non-pigmented Prevotella species. Many Prevotella species contribute to oral inflammatory processes, being frequent findings in dysbiotic biofilms of periodontal diseases (P. intermedia, P. nigrescens), cariotic lesions (P. denticola, Alloprevotella (formerly Prevotella) tannerae), endodontic infections (P. baroniae, P. oris, P. multisaccharivorax), and other clinically relevant oral conditions. Over the years, several novel species have been recovered from the oral cavity without knowledge of their clinical relevance. Within this wide genus, virulence properties and other characteristics like biofilm formation seemingly vary in a species- and strain-dependent manner, as shown for the P. intermedia group organisms (P. aurantiaca, P. intermedia, P. nigrescens, and P. pallens). Oral Prevotella species are identified in various non-oral infections and chronic pathological conditions. Here, we have updated the knowledge of the genus Prevotella and the role of Prevotella species as residents and infectious agents of the oral cavity, as well as their detection in non-oral infections, but also gathered information on their potential link to cancers of the head and neck, and other systemic disorders.

Escherichia marmotae-a Human Pathogen Easily Misidentified as Escherichia coli

We hereby present the first descriptions of human-invasive infections caused by Escherichia marmotae, a recently described species that encompasses the former “Escherichia cryptic clade V.” We describe four cases, one acute sepsis of unknown origin, one postoperative sepsis after cholecystectomy, one spondylodiscitis, and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab over 6 months. Through genome sequencing of the causative strains combined with available genomes from elsewhere, we demonstrate Es. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of nonhuman sources in the phylogenetic analyses, thus indicating inherent virulence in multiple lineages. Pan genome analyses indicate that Es. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits, such as genes encoding antimicrobial resistance. Reliable identification might be possible by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), but relevant spectra are missing in commercial databases. It can be identified through 16S rRNA gene sequencing. Escherichia marmotae could represent a relatively common human pathogen, and improved diagnostics will provide a better understanding of its clinical importance.

IMPORTANCEEscherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes. We only recently have obtained methods to separate the two species, which means that possible differences in important clinical aspects, such as antimicrobial resistance rates, virulence, and phylogenetic structure, may exist. We believe that Es. marmotae as a common pathogen is new merely because we have not looked or bothered to distinguish between the thousands of invasive Escherichia passing through microbiological laboratories each day.

The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing

BACKGROUND

Pleural infection is a common and severe disease with high morbidity and mortality worldwide. The knowledge of pleural infection bacteriology remains incomplete, as pathogen detection methods based on culture have insufficient sensitivity and are biased to selected microbes. We designed a study with the aim to discover and investigate the total microbiome of pleural infection and assess the correlation between bacterial patterns and 1-year survival of patients.

METHODS

We assessed 243 pleural fluid samples from the PILOT study, a prospective observational study on pleural infection, with 16S rRNA next generation sequencing. 20 pleural fluid samples from patients with pleural effusion due to a non-infectious cause and ten PCR-grade water samples were used as controls. Downstream analysis was done with the DADA2 pipeline. We applied multivariate Cox regression analyses to investigate the association between bacterial patterns and 1-year survival of patients with pleural infection.

FINDINGS

Pleural infection was predominately polymicrobial (192 [79%] of 243 samples), with diverse bacterial frequencies observed in monomicrobial and polymicrobial disease and in both community-acquired and hospital-acquired infection. Mixed anaerobes and other Gram-negative bacteria predominated in community-acquired polymicrobial infection whereas Streptococcus pneumoniae prevailed in monomicrobial cases. The presence of anaerobes (hazard ratio 0·46, 95% CI 0·24-0·86, p=0·015) or bacteria of the Streptococcus anginosus group (0·43, 0·19-0·97, p=0·043) was associated with better patient survival, whereas the presence (5·80, 2·37-14·21, p<0·0001) or dominance (3·97, 1·20-13·08, p=0·024) of Staphylococcus aureus was linked with lower survival. Moreover, dominance of Enterobacteriaceae was associated with higher risk of death (2·26, 1·03-4·93, p=0·041).

INTERPRETATION

Pleural infection is a predominantly polymicrobial infection, explaining the requirement for broad spectrum antibiotic cover in most individuals. High mortality infection associated with S aureus and Enterobacteriaceae favours more aggressive, with a narrower spectrum, antibiotic strategies.

FUNDING

UK Medical Research Council, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust, Oxfordshire Health Services Research Committee, Chinese Academy of Medical Sciences, and John Fell Fund.

Targeted Metagenomic Sequencing-Based Approach Applied to 2,146 Tissue and Body Fluid Samples in Routine Clinical Practice

BACKGROUND

The yield of next generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene PCR assay was evaluated in clinical practice for diagnosis of bacterial infection.

METHODS

PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq), or reported as negative, depending on cycle threshold (Ct) value. 2,146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 subjects from whom clinical data was available.

RESULTS

Compared to Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay incorporating NGS was 53%, higher than culture (42%, p<0.001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup receiving antibiotics at sampling was 41% for culture and 63% for the sequencing assay (p<0.001).

CONCLUSION

Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, and especially so in patients who had received antibiotic therapy.

Pleural Peels Tissue Culture plus Pleural Fluid Culture Help to Improve Culture Rate for Empyema

Background: Empyema is known as a serious infection, and outcomes of empyema cases remain poor. Pleural fluid culture and blood culture have been reported to give unsatisfactory results. We introduce a novel pleural peels tissue culture during surgery and aim to improve the culture results of empyema. Methods: This was a retrospective study and was obtained from our institute. Patients with stage II or III empyema undergoing video-assisted thoracic surgery decortication from January 2019 to June 2021 were included in the study. Results: There were 239 patients that received a pleural peels tissue culture, a pleural fluid culture, and a blood culture concurrently during the perioperative period. Of these, 153 patients had at least one positive culture and 86 patients showed triple negative culture results. The positive culture rates were 46.9% for pleural peels tissue cultures, 46.0% for pleural fluid cultures, and 10% for blood cultures. The combination of pleural peels tissue culture and pleural fluid culture increased the positive rate to 62.7%. Streptococcus species and Staphylococcus species were the most common pathogens. Conclusion: The combination of pleural peels tissue culture and pleural fluid culture is an effective method to improve the positive culture rate in empyema.

Genetic Homology between Bacteria Isolated from Pulmonary Abscesses or Pyothorax and Bacteria from the Oral Cavity

Pulmonary abscesses and pyothorax are bacterial infections believed to be caused primarily by oral microbes. However, past reports addressing such infections have not provided genetic evidence and lack accuracy, as they used samples that had passed through the oral cavity. The aim of this study was to determine whether genetically identical bacterial strains exist in both the oral microbiota and pus specimens that were obtained percutaneously from pulmonary abscesses and pyothorax, without oral contamination. First, bacteria isolated from pus were identified by 16S rRNA gene sequencing. It was then determined by quantitative PCR using bacterial-species-specific primers that DNA extracted from paired patient oral swab sample suspensions contained the same species. This demonstrated sufficient levels of bacterial DNA of the targeted species to use for further analysis in 8 of 31 strains. Therefore, the whole-genome sequences of these eight strains were subsequently determined and compared against an open database of the same species. Five strain-specific primers were synthesized for each of the eight strains. DNA extracted from the paired oral swab sample suspensions of the corresponding patients was PCR amplified using five strain-specific primers. The results provided strong evidence that certain pus-derived bacterial strains were of oral origin. Furthermore, this two-step identification process provides a novel method that will contribute to the study of certain pathogens of the microbiota.

IMPORTANCE We present direct genetic evidence that some of the bacteria in pulmonary abscesses and pyothorax are derived from the oral flora. This is the first report describing the presence of genetically homologous strains both in pus from pulmonary abscesses and pyothorax and in swab samples from the mouth. We developed a new method incorporating quantitative PCR and next-generation sequencing and successfully prevented contamination of pus specimens with oral bacteria by percutaneous sample collection. The new genetic method would be useful for enabling investigations on other miscellaneous flora; for example, detection of pathogens from the intestinal flora at the strain level.

Investigating the human jejunal microbiota

Descriptions of the small intestinal microbiota are deficient and conflicting. We aimed to get a reliable description of the jejunal bacterial microbiota by investigating samples from two separate jejunal segments collected from the luminal mucosa during surgery. Sixty patients with morbid obesity selected for elective gastric bypass surgery were included in this survey. Samples collected by rubbing a swab against the mucosa of proximal and mid jejunal segments were characterized both quantitatively and qualitatively using a combination of microbial culture, a universal quantitative PCR and 16S deep sequencing. Within the inherent limitations of partial 16S sequencing, bacteria were assigned to the species level. By microbial culture, 53 patients (88.3%) had an estimated bacterial density of < 1600 cfu/ml in both segments whereof 31 (51.7%) were culture negative in both segments corresponding to a bacterial density below 160 cfu/ml. By quantitative PCR, 46 patients (76.7%) had less than 104 bacterial genomes/ml in both segments. The most abundant and frequently identified species by 16S deep sequencing were associated with the oral cavity, most often from the Streptococcus mitis group, the Streptococcus sanguinis group, Granulicatella adiacens/para-adiacens, the Schaalia odontolytica complex and Gemella haemolysans/taiwanensis. In general, few bacterial species were identified per sample and there was a low consistency both between the two investigated segments in each patient and between patients. The jejunal mucosa of fasting obese patients contains relatively few microorganisms and a core microbiota could not be established. The identified microbes are likely representatives of a transient microbiota and there is a high degree of overlap between the most frequently identified species in the jejunum and the recently described ileum core microbiota.

Oral Prevotella Species and Their Connection to Events of Clinical Relevance in Gastrointestinal and Respiratory Tracts

Prevotella is recognized as one of the core anaerobic genera in the oral microbiome. In addition, members of this genus belong to microbial communities of the gastrointestinal and respiratory tracts. Several novel Prevotella species, most of them of oral origin, have been described, but limited knowledge is still available of their clinical relevance. Prevotella melaninogenica is among the anaerobic commensals on oral mucosae from early months of life onward, and other early colonizing Prevotella species in the oral cavity include Prevotella nigrescens and Prevotella pallens. Oral Prevotella species get constant access to the gastrointestinal tract via saliva swallowing and to lower airways via microaspiration. At these extra-oral sites, they play a role as commensals but also as potentially harmful agents on mucosal surfaces. The aim of this narrative review is to give an updated overview on the involvement of oral Prevotella species in gastrointestinal and respiratory health and disease.

Parapneumonic Effusion and Empyema

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

An empyema caused by Streptococcus constellatus in an older immunocompetent patient: Case report

RATIONALE

Empyema caused by Streptococcus constellatus is rare in patients without underlying diseases. However, the importance of the Streptococcus anginosus group, which consists of S constellatus, S anginosus, and Streptococcus intermedius, as causative organisms of empyema has been increasing.

PATIENT CONCERNS

A 78-year-old man initially presented with dyspnea and chills for 4 days. He had no medical history.

DIAGNOSIS

Chest X-ray and chest computed tomography showed a large and multiloculated pleural effusion with an air bubble on the right side. Cultivation of the pleural effusion using clone library analysis of the 16S rRNA gene revealed S constellatus positivity.

INTERVENTIONS

The patient was treated by drainage of the pleural effusion and intravenous ceftriaxone and clindamycin for the possibility of anaerobes, followed by 10 weeks of oral antibiotics.

OUTCOMES

On the 11th day of admission, the thoracic drainage tube was removed. After 1 year of treatment, there were no sequelae of empyema.

LESSONS

Although S constellatus can cause serious infections in patients with underlying diseases and immunosuppression, physicians need to consider S constellatus infection in community-acquired empyema in elderly individuals. It should be treated with early pleural drainage and antibiotics to avoid surgical decortication and prolonged hospitalization.

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.

Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing

Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.

A unique case of Fusobacterium nucleatum spondylodiscitis communicating with a pleural empyema through a fistula

Species (spp.) belonging to the genus Fusobacterium are anaerobic commensals colonizing the upper respiratory tract, the gastrointestinal tract, and the genitals. Infections with Fusobacterium spp. have been reported at many anatomical sites, including pneumonias and pleural empyemas; however, there are very few published cases of Fusobacterium spp. causing spondylodiscitis or fistulas. Bone infections with Fusobacterium can spread directly to surrounding muscular tissue or by hematogenous transmission to any other tissue including pleurae and lungs. Similarly, pleural infections can spread Fusobacterium spp. to any other tissue including fistulas and bone. Concomitant pleural empyema and spondylodiscitis are rare; however, there are a few published cases with concomitant disease, although none caused by Fusobacterium spp. A 77-year-old female patient was assessed using computed tomography (CT) scanning of the thorax and abdomen, as well as analyses of fluid drained from the region affected by the pleural empyema. A diagnosis of Fusobacterium empyema, fistula, bacteremia, and spondylodiscitis was made, and the patient's condition improved significantly after drainage of the pleural empyema and relevant long-term antibiotic treatment. We describe the first confirmed case with concomitant infection with Fusobacterium nucleatum as spondylodiscitis and pleural empyema connected by a fistula.

Fusobacterium nucleatum Pleural Empyema in a Patient with Progressive Rheumatoid Arthritis and Immunosuppression

Fusobacterium nucleatum is an anaerobic oral commensal organism that is often associated with inflammatory bowel disease, adverse pregnancy outcomes, respiratory tract infections, and Lemierre's syndrome. Rheumatoid arthritis is often associated with pleuropulmonary manifestations including noninfectious pleural effusions and interstitial lung disease. We present a case of a 47-year-old man with progressive rheumatoid arthritis on immunosuppressive therapy who was found to have a left-sided pleural effusion, thought secondary to possible pneumonia, and was treated with levofloxacin and methylprednisolone. He presented a month later and was found to have a large left-sided thick-walled fluid collection found to be an empyema. A chest tube was placed, and fluid culture grew Fusobacterium nucleatum. The patient was successfully treated with intrapleural fibrinolytic therapy and amoxicillin-clavulanic acid.

Recent Insights into the Management of Pleural Infection

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

Managing Contamination and Diverse Bacterial Loads in 16S rRNA Deep Sequencing of Clinical Samples: Implications of the Law of Small Numbers

In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls. This process identified a few bacterial species dominating across all replicates but also a high intersample variability among low abundance contaminant species in replicates split before PCR amplification. Replicates split after PCR amplification yielded almost identical sequencing results. On the basis of these observations, we suggest using the abundance of the most dominant contaminant species to define a threshold in each clinical sample from where identifications with lower abundances possibly represent contamination. We evaluated this approach by sequencing of a diluted, staggered mock community and of bile samples from 41 patients with acute cholangitis and noninfectious bile duct stenosis. All clinical samples were sequenced twice using different sequencing depths. We were able to demonstrate the following: (i) The high intersample variability between sequencing replicates is caused by events occurring before or during the PCR amplification step. (ii) Knowledge about the most dominant contaminant species can be used to establish sample-specific cutoffs for reliable identifications. (iii) Below the level of the most abundant contaminant, it rapidly becomes very demanding to reliably discriminate between background and true findings. (iv) Adequate sequencing depth can be claimed only when the analysis also picks up background contamination.