Microbial spectrum and resistance of odontogenic abscesses - microbiological analysis using next generation sequencing

OBJECTIVES: This study aimed to map the microbiome of odontogenic abscesses using next-generation sequencing (NGS) to identify bacterial and fungal species, as well as antibiotic resistances. MATERIALS AND METHODS: Wound swabs were taken from patients treated for odontogenic abscesses at the Department of Oral and Maxillofacial Plastic Surgery, University Hospital Bonn. NGS was used to analyze the swabs, and bioinformatic analysis assigned the genetic material to microorganism profiles and identified antibiotic resistances. RESULTS: Bacteria were detected in all samples from 51 patients. Anaerobes were found in 50 swabs, while aerobic bacteria were detected in 30. Four of the five most common bacterial genera were anaerobes (Fusobacterium, Prevotella, Parvimonas, Porphyromonas). A median of eight genera were identified per swab. Infections were mostly polymicrobial; only one case was a monoinfection with Streptococcus. Aerobic bacteria were less frequent in patients who had prior antibiotic therapy (p = 0.015). Fungi were present in 52.9% of cases, with Malassezia (33.3%), Aspergillus (9.8%), and Candida (3.9%) being the most common. Antibiotic resistance was detected in 66.7% of patients, mainly against lincosamides, macrolides and tetracyclines. Fusobacterium showed a 25.9% resistance rate to clindamycin. CONCLUSIONS: The microbiome of odontogenic abscesses is polymicrobial, dominated by anaerobic bacteria, and more extensive than indicated by traditional cultural diagnostics. NGS provides detailed pathogen diagnostics, aiding in precise and individualized antibiotic therapy. CLINICAL RELEVANCE: Improved understanding of the bacterial and fungal spectrum, along with current resistance patterns of odontogenic abscesses, is crucial for optimizing treatment outcomes. NGS offers rapid, accurate and detailed microbiome analysis, enhancing patient-specific therapeutic strategies.