Whole-genome analysis of a novel <i>Pandoraea sputorum</i> lineage causing high-mortality bloodstream infections

<b>Background.</b> <i>Pandoraea sputorum</i> is an emerging multidrug-resistant pathogen primarily associated with cystic fibrosis. Bloodstream infections (BSIs) are rare but linked to high mortality. The genomic characteristics and evolutionary history of <i>P. sputorum</i> lineages causing BSIs remain poorly understood.<b>Methods.</b> We performed whole-genome sequencing on 18 <i>P</i>. <i>sputorum</i> isolates recovered from patients with BSIs in China between June 2022 and March 2024. Phylogenetic relationships were determined by core-genome SNP analysis, and the pan-genome was characterized using Roary. Antimicrobial resistance and virulence genes were identified using the CARD and VFDB databases. Evolutionary timescales were estimated using Bayesian molecular clock analysis.<b>Results.</b> The case fatality rate among patients was 27.8% (5 out of 18). Common clinical manifestations included fever (83.3%, 15 out of 18), productive cough (77.8%, 14 out of 18) and dyspnoea (61.1%, 11 out of 18). All isolates formed a distinct monophyletic lineage, genetically distant (>2,000 SNPs) from known <i>P. sputorum</i> strains but with minimal intra-lineage diversity (15-98 SNPs), indicating recent clonal expansion. The pan-genome was highly conserved, with core genes comprising 94.6% of the gene repertoire. All strains harboured core genome-encoded <i>ceoB</i> (efflux pump) and <i>OXA-155</i> (β-lactamase) genes, conferring resistance to multiple antimicrobials but remaining susceptible to imipenem. Bayesian analysis estimated the origin of this lineage in 2004 (95% highest posterior density: 2003.2-2005.8), with major diversification occurring between 2007 and 2018.<b>Conclusion.</b> We identified a novel, recently emerged and highly clonal lineage of <i>P. sputorum</i> associated with high-mortality BSIs. Its stable reservoir of core genome-encoded resistance mechanisms poses a significant therapeutic challenge. This lineage represents an emerging multidrug-resistant threat to public health, necessitating enhanced surveillance and infection control measures.