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Updated: May 4, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Thoracic empyema caused by Prevotella spp. diagnosed using 16S rDNA sequence analysis
Hua Zhou1, Yihong Shen, Qian Shen
1Department of Respiratory, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
Abstract:
We describe a case of thoracic empyema in a 76-year-old male with complication of diabetes mellitus and hypertension. His chief complaints were fever and chest pain. The patient was diagnosed as pleural infection according to the pulmonary computed tomography (CT) scan and laboratory results. The patient had persistent fever after the treatment of continuous percutaneous drainage and 1 week of intravenous moxifloxacin. He was then misdiagnosed as tuberculous pleuritis and still had fever after the treatment of 2 weeks' antituberculosis drugs. Repeated cultures of sputum, blood, bronchoalveolar lavage fluid and pleural fluid were all negative. A gram-negative bacillus was found in the pleural pus Gram stain, and it was identified as Prevotella spp. by 16S ribosomal DNA (rDNA) sequence analysis. The patient recovered after further treatment, including CT-induced pleural drain and intravenous imipenem. Totally, he received 2-week imipenem and 1-month metronidazole therapy from the day he was diagnosed with empyema to the termination of treatment. On the subsequent 2-month and 6-month follow-up visits, no recurrence has been reported for this patient. Routine microbiological methods are important in diagnosis of pleural infection, but they have limitations in some cases, especially for anaerobe. Molecular assay based on 16S rDNA is helpful in detecting causative organisms of thoracic empyema.
Insights
A challenging thoracic empyema case highlights the limitations of routine diagnostics for anaerobic bacteria. Molecular assays like 16S ribosomal DNA sequencing are crucial for accurate identification and effective treatment of pleural infections.
Area of Science:
- Infectious Diseases
- Microbiology
- Pulmonology
Background:
- Thoracic empyema, a serious pleural infection, can be challenging to diagnose and treat.
- Comorbidities such as diabetes mellitus and hypertension can complicate patient management.
Observation:
- A 76-year-old male with diabetes and hypertension presented with fever and chest pain, diagnosed with pleural infection.
- Initial treatment with drainage and moxifloxacin, followed by anti-tuberculosis drugs for suspected tuberculous pleuritis, failed to resolve persistent fever.
Findings:
- Gram stain of pleural pus revealed a gram-negative bacillus, identified as Prevotella spp. via 16S ribosomal DNA sequencing.
- Standard cultures of various samples were negative, underscoring the limitations of conventional methods for anaerobic organisms.
Implications:
- This case emphasizes the importance of considering anaerobic Prevotella species in refractory pleural infections.
- Molecular diagnostic techniques, such as 16S rDNA sequencing, are vital for identifying difficult-to-culture pathogens in thoracic empyema.
- Accurate identification led to effective treatment with imipenem and metronidazole, resulting in patient recovery and no recurrence.
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