Phylogenetic relationships and antimicrobial susceptibility of human- and parrot-derived Chlamydia psittaci isolates in Shenzhen, China

Introduction: Chlamydia psittaci is an important zoonotic pathogen mainly transmitted to humans through exposure to infected birds or contaminated bird excreta, and infection may range from mild respiratory illness to severe systemic disease. Method: Between 2023 and 2024, 114 samples were collected in Shenzhen, China, including bronchoalveolar lavage fluid (BALF) samples from four laboratory-confirmed psittacosis patients, five tissue samples from one suspected infected parrot, and 105 oropharyngeal and cloacal swabs from parrots in a local bird market. C. psittaci was detected by conventional PCR targeting ompA. Positive samples were subjected to targeted capture sequencing, isolation in McCoy cells, ompA-based genotyping, whole-genome SNP phylogenetic analysis, and intracellular antibiotic inhibition assays. Results: C. psittaci DNA was detected in 42 samples, of which 19 yielded high-quality genomic sequence data. Three isolates were successfully cultured: SZ1 from parrot trachea, SZ2 from parrot small-intestinal mucosa, and SZ3 from BALF from Case 1. Phylogenetic analyses based on ompA and genome-wide SNPs showed that all three isolates belonged to genotype A and clarified their relationships with previously reported strains. No known acquired antimicrobial resistance genes were identified, but nucleotide substitutions were detected at selected loci previously reported to be potentially associated with antimicrobial susceptibility. Comparative intracellular inhibition assays showed different antibiotic response patterns between the parrot-derived isolate SZ1 and the human-derived isolate SZ3; SZ1 showed a less pronounced inhibitory response to doxycycline under the present in vitro conditions, suggesting reduced doxycycline susceptibility rather than confirmed resistance. Discussion: These findings highlight the value of genomic surveillance and antimicrobial susceptibility monitoring of C. psittaci isolates from both avian reservoirs and human infections, which may support risk assessment and clinical management of psittacosis.