Longitudinal Monitoring of Abscess Microbiota in a Wild California Sea Lion (Zalophus californianus) Using Next-Generation Sequencing.

Antimicrobial resistance is a growing threat to human and animal health and is recognized as a global One Health issue. Strategies to reduce its impact include judicious usage of antibiotics guided by accurate bacterial identification and antimicrobial susceptibility. Next-generation sequencing (NGS) offers a DNA-based diagnostic approach that profiles the bacteria microbiota and can help support more informed antibiotic selection. We utilized NGS to identify Fusobacterium gonidiaformans in the neck abscess of a wild California sea lion (Zalophus californianus) undergoing rehabilitation. Initially, NGS revealed that the microbial population was dominated by F. gonidiaformans. Following treatment, the microbial profile shifted over the following eight weeks, during which 13 other bacterial species were detected, demonstrating the need for repeated testing to monitor changes in persistent lesions. Despite effective treatment to eliminate F. gonidiaformans from the abscess, the patient died during treatment due to suspected unrelated causes. Necropsy and histopathology identified bacterial pneumonia and sepsis associated with a large squamous cell carcinoma of the oropharynx and neck, all contributing to a deadly outcome. To our knowledge, this is the first case report of the use of longitudinal NGS sampling with the identification of Fusobacterium gonidiaformans associated with an abscess in the neck in a California sea lion. These findings support the utility of NGS in monitoring microbial dynamics to allow informed decision-making in antimicrobial selection in complex infections.