BackgroundChlamydia psittaciis a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains ofC. psittacirespond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes ofC. psittacihave relatively stable hosts and different pathogenicity.MethodsMacrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients’ alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of theC. psittaci ompAgene were used, and a phylogenetic tree was constructed withC. psittacigenotypic sequences from other sources, including Chinese published sources. TheC. psittacifound in each patient were genotyped by comparingompAgene sequences. In addition, to better illustrate the relationship between genotype and host ofC. psittaci, 60 bird fecal samples were collected from bird-selling stores for screening andC. psittacityping.ResultsMacrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, includingC. psittaciresistance gene sequences from two patients that matched those previously published on NCBI. Based onompAgenotyping, two patients were infected withC. psittacigenotype A and one patient was infected with genotype B. All fiveC. psittaci-positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of theC. psittacigenotype A in this study were derived from parrots, while genotype B was probably derived from chickens.ConclusionThe presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes ofC. psittacimay help prevent transmission to humans.