First Case of Acute Pleural Empyema Caused by Mediterraneibacter gnavus

ABSTRACT

Mediterraneibacter gnavus (M. gnavus) is an obligately anaerobic, gram‐positive coccus that is a major constituent of the human gut microbiota. Although it has been implicated in inflammatory bowel disease and sporadic invasive infections in immunocompromised hosts, respiratory infections caused by M. gnavus have not been reported. We herein describe the first case of acute pleural empyema caused by M. gnavus in a 78‐year‐old man with multiple comorbidities, including diabetes mellitus, severe malnutrition and pre‐existing loculated pleural effusion. Aerobic cultures of blood and pleural fluid were negative, whereas an anaerobic culture of pleural fluid yielded bacterial growth. The organism was initially identified as M. gnavus by matrix‐assisted laser desorption ionisation time‐of‐flight mass spectrometry and subsequently confirmed by 16S rRNA gene sequencing. The patient was successfully treated with beta‐lactam antibiotics and pleural drainage. This case highlights M. gnavus as a potential causative pathogen of pleural infections and underscores the importance of comprehensive microbiological evaluation, including anaerobic culture and advanced microbial identification techniques.

We report the first case of acute pleural empyema caused by Mediterraneibacter gnavus, a gut commensal organism, identified by anaerobic culture in combination with MALDI‐TOF mass spectrometry and 16S rRNA gene sequencing. This case suggests that M. gnavus can act as an opportunistic pathogen in patients with significant comorbidities and highlights the importance of a comprehensive microbiological evaluation.

1. Introduction

Mediterraneibacter gnavus (formerly Ruminococcus gnavus ; hereafter, M. gnavus) is an obligately anaerobic, gram‐positive coccus belonging to the Lachnospiraceae family of the phylum Firmicutes, first identified in 1974 [1]. It is a major constituent of the human gut microbiota and has been increasingly recognised to be associated with inflammatory bowel disease and mucosal immune dysregulation [1]. Although M. gnavus is generally regarded as a commensal organism, sporadic cases of invasive infections, such as bacteraemia, intra‐abdominal infections and septic arthritis, have been reported, particularly in immunocompromised hosts [2, 3]. To date, however, there have been no reports of M. gnavus as a causative pathogen of respiratory infections, including pleural infections. Here, we report the first case of acute pleural empyema caused by M. gnavus.

2. Case Report

A 78‐year‐old Japanese man presented to the emergency department of our hospital in November 2025 with a 3‐day history of general fatigue and anorexia, followed by a fever on the day of admission. His medical history included laparoscopic resection and adjuvant chemotherapy for colon cancer in 2011, with no evidence of recurrence. He had type 2 diabetes mellitus complicated by diabetic nephropathy and was being treated with insulin. In March 2025, he developed necrotising fasciitis of the lower extremity due to group A Streptococcus, requiring a six‐month prolonged hospitalisation, which resulted in marked functional decline. In July 2025, a right‐sided loculated pleural effusion was incidentally identified on a computed tomography (CT). Diagnostic thoracentesis revealed no evidence of infection or malignancy; therefore, the effusion was managed conservatively.

On admission, he was alert, with a temperature of 39.8°C, a heart rate of 112 beats/min, a blood pressure of 123/73 mmHg, a respiratory rate of 12 breaths/min and an oxygen saturation of 98% while receiving oxygen at 6 L/min via a face mask. His body mass index was 15 kg/m², indicating severe undernutrition. Laboratory tests revealed a white blood cell count of 11,400/μL with 90% segmented neutrophils, a serum creatinine level of 1.90 mg/dL, a blood glucose level of 179 mg/dL, a haemoglobin A1c level of 7.0% and a C‐reactive protein level of 18.2 mg/dL. Chest CT revealed an increased attenuation in the right lower lobe, suggesting passive atelectasis and/or inflammatory infiltration (Figure 1A). Additionally, an increase in the right‐sided loculated pleural effusion with multiple intrapleural air bubbles was observed (Figure 1B). Thoracentesis was performed under ultrasound guidance at the right 8th intercostal space along the midaxillary line using a standard aseptic technique, yielding a reddish‐brown, turbid pleural fluid. Gram staining demonstrated clusters of chain‐forming Gram‐positive cocci (Figure 2A). Based on these findings, acute pleural empyema was diagnosed.

FIGURE 1.

Chest computed tomography of the patient on admission. (A) An increased attenuation in the right lower lobe, suggesting passive atelectasis and/or inflammatory infiltration. (B) A right‐sided loculated pleural effusion with multiple intrapleural air bubbles (arrowheads).

FIGURE 2.

Microbiological findings of pleural fluid. (A) Gram staining of pleural fluid obtained by thoracentesis showing clusters of chain‐forming Gram‐positive cocci (×1000, oil immersion). (B) Anaerobic culture of pleural fluid on Brucella HK (RS) agar incubated under anaerobic conditions, yielding white colonies.

A 16‐Fr double‐lumen trocar catheter was inserted, and empirical antimicrobial therapy with piperacillin‐tazobactam was initiated. Both aerobic and anaerobic blood cultures were negative. Aerobic cultures of pleural fluid were also negative. In contrast, anaerobic cultures performed on Chocolate II agar (Becton Dickinson, Franklin Lakes, NJ, USA) and Brucella HK (RS) agar (Kyokuto Pharmaceutical Industrial Co. Ltd., Tokyo, Japan) at 37°C for 48 h using AnaeroPack Anaero (Mitsubishi Gas Chemical Company Inc., Tokyo, Japan) yielded white colonies (Figure 2B). For species identification, matrix‐assisted laser desorption ionisation time‐of‐flight mass spectrometry (MALDI‐TOF MS; Bruker MALDI Biotyper, Bruker Daltonics GmbH, Bremen, Germany) was performed. Colonies were applied to a target plate, treated with 70% formic acid prior to matrix application and subsequently analysed. The isolate was initially identified as M. gnavus, with the top two MALDI‐TOF MS scores of 2.16 (M. gnavus ENR_0100) and 2.12 (M. gnavus DSM 108212), indicating reliable genus‐level identification with probable species‐level assignment. To further confirm species identification, 16S rRNA gene sequencing was conducted. PCR amplification of the 16S rRNA gene was conducted, and the amplified products were purified using the FastGene Gel/PCR Extraction Kit and subjected to Sanger sequencing. The resulting sequence showed 98.9% similarity to M. gnavus ATCC 29149 (GenBank accession number: AB910745), whereas the similarity to a closely related species, Sporofaciens musculi (GenBank accession number: MN756014), was 93.7%. These findings confirmed the identification of the isolate as M. gnavus. Antimicrobial susceptibility testing demonstrated susceptibility to penicillin‐class antibiotics, and antimicrobial therapy was de‐escalated to ampicillin‐sulbactam. Gram staining and cultures of pleural fluid obtained on day 15 of hospitalisation were negative, and the chest drain was removed on day 22. The patient was transferred to another hospital on day 36 for rehabilitation and nutritional support.

3. Discussion

To our knowledge, this is the first reported case of acute pleural empyema in which M. gnavus was identified as the causative pathogen.

Traditionally, pleural infections have been most commonly attributed to the Streptococcus anginosus group and oral anaerobes [4]. However, advances in microbiological identification techniques, including MALDI‐TOF MS, 16S rRNA gene sequencing and metagenomic analyses, have revealed a broader spectrum of obligate anaerobes and previously unrecognised organisms involved in empyema pathogenesis [5]. In the present case, aerobic cultures were negative, and the causative pathogen was detected only by anaerobic culture. According to the manufacturer's criteria for the Bruker MALDI Biotyper system, scores of 2.0–2.299 indicate reliable genus‐level identification with probable species‐level assignment; the score of 2.12 obtained in this case fell within this range. To further confirm species identification, 16S rRNA gene sequencing was performed using the preserved isolate, which was consistent with M. gnavus.

Recent studies suggest that M. gnavus can cause invasive infections in immunosuppressed patients or those with significant comorbidities [2, 3]. Although blood cultures were negative, bacterial translocation from the gastrointestinal tract is a plausible route of infection, particularly given the patient's history of colorectal cancer surgery. Additionally, the presence of multiple comorbidities, including diabetes mellitus and severe malnutrition, may have contributed to impaired mucosal barrier function and increased susceptibility to bacterial translocation. The pre‐existing loculated pleural effusion may have provided a favourable environment for secondary infection. From a therapeutic perspective, management of this case was consistent with standard treatment strategies for empyema, combining appropriate antimicrobial therapy with early pleural drainage. M. gnavus is generally susceptible to penicillin‐class antibiotics, with reported resistance primarily to fluoroquinolones [2, 3], and the patient showed a favourable clinical response to beta‐lactam therapy.

In conclusion, this case highlights M. gnavus, a gut commensal organism, as a potential causative pathogen of empyema, particularly in patients with significant comorbidities or pre‐existing pleural disease. A comprehensive microbiological evaluation, including anaerobic culture and advanced identification methods such as mass spectrometry, may facilitate accurate diagnosis and optimal management of pleural infections.

Author Contributions

M.S. contributed to the conceptualisation of the work and to the collection, analysis and interpretation of the data, and drafted the manuscript. M.T. contributed to the conceptualisation of the work and critically revised the manuscript for important intellectual content. All authors approved the final version of the manuscript.

Consent

The authors declare that written informed consent was obtained from the patient for the publication of this manuscript and accompanying images using the consent form provided by the journal.

Conflicts of Interest

The authors declare no conflicts of interest.

Shirata M. and Tsuchiya M., “First Case of Acute Pleural Empyema Caused by Mediterraneibacter gnavus ,” Respirology Case Reports 14, no. 6 (2026): e70643, 10.1002/rcr2.70643.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.