Metagenomic next-generation sequencing–guided management of descending mediastinitis and empyema caused by Segatella baroniae: a case report

Abstract

Background

Deep neck infections can rapidly progress to descending mediastinitis and empyema, both of which are associated with high morbidity and mortality. Early diagnosis and timely intervention are essential but can be challenging, particularly in infections caused by rare anaerobic pathogens.

Case presentation

We report a case of a 63-year-old man presenting with fever and neck pain. Computed tomography revealed extensive cervical emphysema and pneumomediastinum with a large right-sided empyema. The patient developed respiratory failure requiring endotracheal intubation. Endoscopic examination identified a retropharyngeal fistula, and thoracoscopic exploration confirmed communication between the mediastinum and pleural cavity. Combined cervical, mediastinal, and thoracic drainage was performed. Metagenomic next-generation sequencing identified Segatella baroniae as the predominant pathogen, guiding targeted antimicrobial therapy. The patient showed gradual clinical and radiological improvement and was discharged in good condition.

Conclusion

This case highlights the importance of early recognition and aggressive surgical management in deep neck infections complicated by descending mediastinitis. Metagenomic next-generation sequencing may facilitate rapid pathogen identification and guide targeted therapy in complex anaerobic infections.

Background

Deep neck infections (DNI) typically originate from odontogenic or oropharyngeal sources and may rapidly spread along the cervical fascial planes, forming multi-space abscesses [1, 2]. Once the infection breaches the fascial barrier and extends into the thoracic cavity, it can progress to descending necrotizing mediastinitis (DNM) and empyema, with mortality rates reported as high as 40–76% [3–5]. Recent systematic reviews have confirmed that descending necrotizing mediastinitis remains associated with substantial morbidity and mortality despite advances in surgical and critical care management, highlighting the importance of early recognition and aggressive intervention [6, 7]. Early pathogen identification, timely source control, and effective drainage are therefore essential to improving patient outcomes.

The mediastinum is anatomically divided into anterior, middle, and posterior compartments, which contain vital structures including the heart, great vessels, trachea, and esophagus. These anatomical spaces provide potential pathways for the spread of infection from the deep cervical fascia into the thoracic cavity. Mediastinitis may arise from various etiologies, including esophageal perforation, postoperative complications, and descending infections from deep neck spaces [1, 11]. The retropharyngeal space and the so-called “danger space” are particularly important routes for the downward spread of infection into the mediastinum [1, 2]. Infections caused by anaerobic oral flora are commonly implicated in descending infections; however, cases specifically attributed to Segatella baroniae are exceedingly rare, with only limited reports available in the literature [13, 14].

Metagenomic next-generation sequencing (NGS) has recently gained traction in the diagnosis of infectious diseases, offering rapid and precise pathogen identification, particularly in cases with negative routine cultures or fastidious organisms [8, 9]. In patients with DNI complicated by DNM and empyema, early and adequate surgical debridement with drainage remains the cornerstone of therapy, whereas delayed intervention is strongly associated with increased mortality [10, 11].

Here, we describe a rare and severe case of DNI caused by an oral anaerobic pathogen that extended downward into the mediastinum and thoracic cavity. The pathogen was identified using NGS, and the patient achieved full recovery through combined multi-site surgical drainage and comprehensive management. This case adds to the limited literature and offers clinically meaningful insights into the diagnosis and treatment of rare pathogen-associated descending infections.

Case presentation

A 63-year-old man presented to the emergency department with a 9-day history of fever and progressively worsening neck pain, accompanied by mild cough. His medical history included hypertension and cholelithiasis. No history of diabetes mellitus, malignancy, chronic kidney disease, chronic liver disease, immunosuppressive therapy, or long-term corticosteroid use was documented. There was no documented history of recent dental procedures or oral trauma. Regular medication history was unremarkable except for antihypertensive therapy. He had been treated empirically for a presumed neck infection at a local hospital, but his symptoms progressively worsened and were later complicated by gastrointestinal bleeding. On admission, he appeared fatigued with cervical tenderness and erythema, tachypnea, and asymmetric breath sounds with marked reduction on the right. Laboratory investigations showed elevated inflammatory markers. Contrast-enhanced computed tomography of the neck and chest demonstrated extensive cervical emphysema and pneumomediastinum with a large right-sided pleural effusion (Figs. 1A and 2A and E). The patient developed progressive respiratory distress requiring endotracheal intubation and was admitted to the intensive care unit for airway compromise and sepsis management. Initial thoracic drainage yielded a large volume of purulent fluid (Fig. 3G), and empirical intravenous antimicrobial therapy was initiated.

Fig. 1.

Serial cervical CT scans demonstrating progressive improvement of deep neck infection. A (Day 0): Red arrow shows extensive gas accumulation in the retropharyngeal and deep neck spaces with marked soft-tissue swelling. B (Day 2): Red arrow indicates persistent but slightly reduced emphysema, suggesting ongoing infection spread. C (Day 7): Red arrow highlights significant reduction of gas and inflammatory edema. D (Day 21): Resolution of emphysema with near-normal soft tissue appearance, indicating controlled infection

Fig. 2.

Serial thoracic CT scans and chest radiographs showing improvement of mediastinal and pleural infection. A (Day 0): CT demonstrates massive right pleural effusion with pneumomediastinum and right lung atelectasis (red arrow). B (Day 2): Effusion persists with mild reduction (red arrow), indicating ongoing infection and exudation. C (Day 7): Marked decrease in pleural effusion (red arrow) with partial lung re-expansion. D (Day 21): Near-complete resolution of effusion (red arrow) and full lung re-expansion. E–H: Corresponding chest radiographs showing progressive recovery from Day 0 to Day 21

Fig. 3.

Endoscopic and intraoperative findings, drainage placement, and NGS pathogen identification. A Endoscopy revealed extensive purulent secretions and mucosal edema in the posterior pharyngeal wall. B Thoracoscopic view showing a mediastinal pleural perforation (blue arrow) with massive purulent discharge entering the thoracic cavity. C Post-debridement thoracoscopic field demonstrating exposed infection cavity with necrotic tissue removed. D Upper endoscopy showing a longitudinal retropharyngeal fistula (red arrow), providing an anatomical route for downward spread to the mediastinum and pleural cavity. E Bilateral drainage tubes placed in the right thoracic cavity and posterior mediastinum postoperatively. F Cervical incision with negative-pressure drainage tube and temporary tracheostomy in place. G Initial thoracic drainage collected approximately 1900 mL of thick yellow pus. H Metagenomic next-generation sequencing (mNGS) revealed significant reads corresponding to Segatella baroniae (coverage rate ≈ 0.4373%), confirming the primary anaerobic pathogen

Endoscopic examination revealed a longitudinal fistula on the right posterior pharyngeal wall with purulent discharge (Fig. 3D), suggesting extension of infection beyond the mucosal barrier into the deep neck space. The examination was advanced beyond the pharynx to systematically evaluate the esophagus, stomach, and duodenum. The esophageal and gastric mucosa were grossly unremarkable, while a duodenal bulb ulcer was identified without active bleeding. Given the endoscopic finding, the initial melena and hematochezia were considered most likely secondary to the duodenal ulcer. No further gastrointestinal bleeding was observed during hospitalization. Despite ongoing pleural drainage, the patient remained clinically unwell with persistent purulent output, and follow-up imaging demonstrated progression of infection into the mediastinum and thoracic cavity. Based on these findings, a multidisciplinary surgical approach was undertaken, including thoracoscopic drainage, mediastinal debridement, and cervical abscess drainage with airway protection. Intraoperative findings confirmed extensive purulent collections with communication between the mediastinum and pleural cavity (Fig. 3A–C). Drains were placed in the mediastinal, thoracic, and cervical compartments to ensure adequate drainage (Fig. 3E–F).Given the presence of extensive cervical emphysema and pneumomediastinum, esophageal perforation, malignancy-related fistulization, foreign body injury, polymicrobial deep neck infection, and atypical infections such as actinomycosis were considered in the initial differential diagnosis. Endoscopic evaluation showed a longitudinal retropharyngeal fistula with purulent discharge, while the esophageal and gastric mucosa were grossly unremarkable. No foreign body or tumor-like lesion was identified during transoral exploration. The acute clinical course, intraoperative findings of extensive purulent collections, and subsequent radiological resolution after drainage and antimicrobial therapy favored an infectious descending process rather than malignancy or noninfectious causes.

Following surgical intervention, the patient remained hemodynamically stable under tracheostomy ventilation, with ongoing thoracic, mediastinal, and cervical drainage. Although inflammatory markers remained elevated, no further clinical deterioration was observed. Metagenomic next-generation sequencing identified Segatella baroniae (formerly Prevotella baroniae) as the predominant pathogen (Fig. 3H). Antimicrobial therapy was continued to ensure adequate coverage against anaerobic oral flora, along with comprehensive supportive care including nutritional support and airway management. Follow-up computed tomography demonstrated a reduction in pleural effusion with appropriately positioned drains (Figs. 1B and 2B and F).

The patient was successfully weaned from mechanical ventilation and transitioned to high-flow oxygen therapy via tracheostomy, with stable respiratory status. Inflammatory markers gradually improved, accompanied by a marked reduction in drainage output from all compartments.Given the prolonged use of broad-spectrum antibiotics and metagenomic next-generation sequencing findings indicating anaerobic predominance, antimicrobial therapy was adjusted to optimize anaerobic coverage.Follow-up computed tomography demonstrated reduced cervical soft tissue edema, decreased pleural effusion, and improved lung re-expansion (Figs. 1C and 2C and G). The patient’s mental status improved, sputum production decreased, and airway patency was maintained.

The patient showed progressive clinical improvement, with reduced sputum production and minimal drainage output. Antimicrobial therapy was adjusted to optimize treatment and minimize resistance risk, while organ function remained stable. Follow-up imaging demonstrated near-complete resolution of pleural effusion, reduced cervical soft tissue swelling, and improved lung re-expansion (Figs. 1D and 2D and H).

The retropharyngeal fistula gradually closed, and the patient regained adequate airway protection and swallowing function, allowing successful removal of the tracheostomy. Remaining thoracic and cervical drains were subsequently removed, with well-healed incisions and no fluid reaccumulation. Repeat NGS or microbiological cultures were not performed during follow-up. However, effective infection control was supported by the patient’s favorable clinical course, including sustained resolution of fever, progressive normalization of inflammatory markers, absence of ongoing purulent drainage, and marked radiological improvement. The patient was discharged in stable condition with complete clinical recovery. During the hospital course, no recurrent melena or hematochezia occurred, and the patient remained hemodynamically stable without a decline in hemoglobin. Final imaging demonstrated complete lung re-expansion and resolution of mediastinal inflammation.

At 3-month follow-up, the patient remained asymptomatic with normal swallowing and no dyspnea. Follow-up imaging showed no evidence of residual disease or recurrence, and he returned to normal daily activity without complications. The full clinical timeline and treatment course are summarized in Fig. 4.

Fig. 4.

Patient’s treatment course

Discussion

This case highlights a rare but clinically significant presentation of deep neck infection complicated by descending necrotizing mediastinitis and pleural empyema. The disease progression reflects a typical but often underrecognized pathway of infection spreading from the oropharynx through the retropharyngeal space into the mediastinum and thoracic cavity. Such descending infections are associated with high morbidity and mortality, particularly when diagnosis and intervention are delayed. In this case, early identification of the infection pathway, prompt multidisciplinary surgical intervention, and effective source control were critical to preventing further deterioration. In addition, metagenomic next-generation sequencing enabled rapid identification of an uncommon anaerobic pathogen, facilitating targeted antimicrobial therapy. The integration of advanced diagnostic tools with timely surgical management contributed to the favorable clinical outcome observed in this patient.

DNI may spread inferiorly through the retropharyngeal, prevertebral, or “danger space” fascial pathways toward the mediastinum, promoted by gravity and negative intrathoracic pressure, eventually leading to DNM [10, 11]. Risk factors for downward extension include diabetes, treatment delay, anaerobic infection, and odontogenic or pharyngeal origin [12]. In our patient, gastroscopy demonstrated a clear longitudinal retropharyngeal fistula, and intraoperative exploration confirmed continuous pus tracking through a pleural defect into the mediastinum, providing direct anatomical evidence of extension. Early and adequate drainage remains fundamental to successful management. The multi-space debridement strategy implemented in this case–simultaneously addressing the neck, mediastinum, and pleural cavity–enabled rapid source control and effective abscess clearance. Combined with continuous irrigation and NGS-guided targeted therapy, systemic deterioration was prevented. This experience suggests that, in DNI complicated by retropharyngeal fistula and empyema, early multi-route drainage may be superior to limited single-site procedures.

Segatella baroniae (formerly Prevotella baroniae) is an oral anaerobe seldom implicated in clinical infections and more commonly associated with periodontal or apical abscesses [13, 14]. Due to its fastidious nature and oxygen sensitivity, culture positivity is typically low, often delaying pathogen identification. Deep neck infections are typically polymicrobial, frequently involving a mixture of aerobic and anaerobic organisms derived from oral and pharyngeal flora. NGS has increasingly enhanced diagnostic accuracy in complex or culture-negative infections by detecting microbial nucleic acids directly from clinical samples, even after antimicrobial exposure, thereby supporting precision antimicrobial therapy [8, 9, 15]. Recent systematic reviews have also demonstrated that metagenomic NGS significantly improves pathogen detection in deep-seated or culture-negative infections, particularly for anaerobic and fastidious organisms, thereby facilitating earlier targeted therapy and potentially improving clinical outcomes [8, 16]. In the present case, although polymicrobial infection could not be completely excluded, S. baroniae was considered the predominant pathogen based on several factors. First, metagenomic NGS demonstrated a relative predominance of S. baroniae among detected organisms. Second, the anatomical route of infection—via a retropharyngeal fistula—was consistent with an oropharyngeal source, supporting the biological plausibility of this anaerobic oral commensal as a causative pathogen. Third, the patient showed a favorable clinical response following surgical source control and antimicrobial therapy targeting anaerobic flora. The concordance between microbiological findings, anatomical pathway, and clinical response supports its likely pathogenic role in this case.

In this case, conventional culture was negative, whereas NGS rapidly identified S. baroniae, allowing timely antimicrobial adjustment in combination with surgical drainage. This highlights the value of NGS in diagnosing rapidly progressive anaerobic DNI and similar deep-space infections.

This case emphasizes that once the mucosal barrier is breached and a fistula forms, rapid inferior spread may occur, leading to necrotizing mediastinitis and empyema. Early recognition of disease progression, timely surgical source control, adequate drainage, and pathogen-directed therapy are key determinants of outcome. Our multidisciplinary approach–integrating early endoscopic and radiologic identification of the fistula, combined cervical–mediastinal–thoracic debridement and drainage, plus NGS-guided antimicrobial adjustment–achieved successful infection control. Clinicians should maintain vigilance when encountering rapidly progressive DNI with subcutaneous emphysema, mediastinal involvement, or empyema, particularly when anaerobic pathogens are suspected. The strategic model of “Early assessment, timely surgical intervention, adequate drainage, and dynamic optimization of antimicrobial therapy are essential for successful management.” may improve survival in similar cases.

Several limitations should be acknowledged. First, as S. baroniae remains rarely reported, its virulence features, mechanisms of pharyngeal penetration, and factors promoting downward dissemination are not well established. Second, antimicrobial selection in this case was guided by NGS and clinical judgment in the absence of standardized treatment protocols, highlighting the need for further evidence. Third, the relative contributions of extensive debridement, multi-cavity drainage, and antimicrobial adjustment to clinical recovery cannot be quantitatively separated. Moreover, Segatella taxonomy continues to evolve, and clinical recognition heavily relies on NGS due to low culture positivity, potentially leading to underdiagnosis. Nonetheless, this case adds valuable clinical insight into S. baroniae-associated DNI with DNM and empyema, and may support early decision-making in similar presentations.

Conclusion

This case represents a rare instance of DNI caused by Segatella baroniae progressing to descending mediastinitis and empyema. Rapid pathogen identification via NGS, together with early thoracoscopic and cervical debridement, adequate multi-site drainage, and targeted antimicrobial therapy, resulted in full recovery. This case underscores that in patients with cervical infection complicated by pneumomediastinum or empyema, early recognition of the infection pathway, timely and thorough surgical drainage, and NGS-assisted microbiological diagnosis are essential for improving clinical outcomes.

Abbreviations

DNM

Descending necrotizing mediastinitis

DNI

Deep neck infection

NGS

Next-generation sequencing

EICU

Emergency intensive care unit

Authors’ contributions

W.D. contributed to the conception and design of the study, collected and analyzed the clinical data, and drafted and revised the manuscript. F.P. participated in clinical data acquisition, conducted the literature review, and assisted in manuscript preparation. P.L. contributed to clinical data collection, patient management, and assisted in data interpretation. L.X. participated in patient monitoring and clinical management during hospitalization and assisted in case analysis. C.Z. performed thoracic and mediastinal surgery, contributed to perioperative decision-making and critical case management, and critically reviewed the manuscript. H.W. supervised the study, provided critical revisions for important intellectual content, and served as the corresponding author. All authors have read and approved the final manuscript.

Funding

This study received no specific funding from any public, commercial, or not-for-profit funding agencies.

Data availability

All data generated or analyzed during this study are included in this published article.

Declarations

Ethics approval and consent to participate

This study does not involve any experimental interventions on humans or animals. Ethical approval was waived by the Ethics Committee of Lishui Central Hospital due to the retrospective nature of this single case report. Written informed consent for participation was obtained from the patient prior to the use of clinical data.

Consent for publication

Written informed consent was obtained from the patient for the publication of this case report and all accompanying images.

Competing interests

The authors declare no competing interests.