Role of Next-Generation Sequencing in Excluding the Nosocomial Origin of a Case of Legionnaires’ Disease Integrating Environmental Surveillance and Clinical Diagnosis

Legionella pneumophila (Lp) remains one of the major causes of community- and hospital-acquired pneumonia, yet its diagnosis and source attribution continue to pose significant challenges. Here, we describe the case of an immunocompromised patient who developed Legionnaires’ disease during hospitalization. Following activation of the hospital’s internal surveillance system, Lp and Legionella anisa (L. anisa) were recovered from multiple water distribution points using a simplified culture-based protocol. Whole-genome sequencing (WGS) demonstrated that all environmental isolates belonged to a single clonal strain, whereas the clinical isolate was genetically unrelated, thereby excluding the hospital water system as the source of infection. Although not implicated in the patient’s disease, the detection of both Lp and L. anisa within the plumbing system highlighted underlying structural contamination and the potential masking effect of non-L. pneumophila species during culture-based surveillance. These findings support the integration of conventional microbiological methods with high-resolution genomic tools to enhance surveillance accuracy, support outbreak investigations, and strengthen public health responses. Overall, this case underscores the value of WGS as a decisive tool for source attribution, including the robust exclusion of a suspected nosocomial source, in complex clinical and environmental scenarios.