Application of BALF combined with tNGS for detecting Chlamydia psittaci in resource-limited areas: lessons learned from the 2025 temporally associated case series investigation

Chlamydia psittaci (Cps) is a neglected zoonotic cause of community-acquired pneumonia (CAP), and its incidence may be underestimated in county-level hospitals lacking rapid diagnostic tools. We evaluated the potential utility of targeted next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF) for early Cps detection during a small group of temporally associated cases in rural southwestern China. We retrospectively analyzed four nonsevere Cps pneumonia patients admitted to Dafang County People’s Hospital between April 19 and May 6, 2025. Epidemiological exposure profiles, clinical data, laboratory results, and chest CT images were extracted. BALF samples were sent to a central reference laboratory for tNGS, covering 226 respiratory pathogens, including three Cps-specific amplicons. The time from symptom onset to appropriate antibiotic adjustment and clinical outcomes were recorded. Patients presented with high fever (39.5–39.6 °C), cough, dyspnea, and patchy ground‒glass opacities on CT. All had recent bird exposure: three through daily visits to live poultry markets or pigeon clubs within 500 m of their homes and one through household parrot breeding (within 3 km). The mean time from symptom onset to hospitalization was 5.25 days (range 3–7), and that from admission to Cps confirmation via tNGS was 2.75 days (range 2–3). Empirical β-lactam therapy failed; prompt switching to doxycycline or fluoroquinolones led to fever resolution within 3–5 days and complete radiographic resolution by 3 months. Outsourcing BALF-tNGS to central labs facilitated rapid Cps diagnosis in a county hospital and may have helped reduce the risk of severe disease. This case series suggests that it may be useful to incorporate bird exposure history and accessible molecular diagnostics into CAP care in similar settings.