Genomic characterization of clinical Burkholderia semiarida SYBS718, a Burkholderia cepacia complex strain isolated from an immunocompromised patient

Abstract

Burkholderia semiarida, a plant-pathogenic species within the Burkholderia cepacia complex (Bcc), has emerged as a worrying opportunistic pathogen causing serious respiratory infections in patients with cystic fibrosis (CF). In this study, strain SYBS718 was isolated from the blood and sputum of an immunocompromised patient. Conventional MALDI-TOF mass spectrometry and 16S rRNA sequencing misidentified this isolate as Burkholderia cenocepacia, whereas whole-genome sequencing enabled accurate species confirmation. Genomic analysis predicted a total of 569 virulence factors, 11 antibiotic resistance genes, and 1112 type III secretion system effector proteins related genes through the core databases of VFDB, CARD, and TS33. The virulence factors mainly include type VI secretion system (T6SS), type III secretion system (T3SS), iron uptake system, flagella, and type IV pili (TFP), which are associated with bacterial colonization, invasion, and pathogenicity. And the antibiotic resistance genes are primarily associated with fluoroquinolone, tetracycline, and aminoglycoside antibiotics. This study is the first to perform comprehensive genomic characterization of a clinical B. semiarida isolate. Our findings reveal the limitations of routine Bcc identification, and provide fundamental genomic data for further clinical and mechanistic research on this emerging opportunistic pathogen.