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BACKGROUND: The taxonomic ambiguity caused by species complexes (closely related species with overlapping phenotypic traits but distinct genetic profiles) has increasingly garnered attention. Cupriavidus species hold environmental, industrial, and clinical relevance, yet unresolved species complexes within this genus may limit insights into their pathogenesis. RESULTS: Six species (C. alkaliphilus, C. basilensis, C. gilardii, C. oxalaticus, C. necator, and C. taiwanensis) were identified as species complexes, comprising 36 correctly classified strains and 42 mislabeled strains. More importantly, C. alkaliphilus and a subset of C. taiwanensis are phylogenetically grouped together. We, therefore, propose a genome-based taxonomic framework to reclassify these species. For mislabeled strains, the 10 strains labeled as C. taiwanensis were reassigned to C. alkaliphilus; the remaining 32 strains were classified as 11 unnominated genomic groups. C. metallidurans and C. pauculus retained current classifications. The open pan-genome and prevalence of mobile genetic elements indicated high genetic variation in Cupriavidus. We identified 47 genes related to virulence factors. Virulence factors in almost all Cupriavidus strains were related to the antimicrobial activity (acrB), biofilm (adeG, algU), stress survival (clpP, katA, sodB, ureA, ureB, and ureG), adherence (htpB, kdsA), and others (icl); the opportunistic pathogens C. gilardii and C. metallidurans contained extra virulence genes (plc-2). Furthermore, six types of secretion systems (T1SS-T6SS) were identified in Cupriavidus. T2SS was conserved across all eight species; the other secretion systems presented diverse distribution. Interestingly, C. gilardii possesses two divergent T3SS clusters. Finally, emre, responsible for the efflux pump of aminoglycoside antibiotics, is a major antibiotic resistance gene of Cupriavidus strains. Other genes related to aminoglycosides, β-lactam, fosfomycin, and multidrug resistance are species-specific among opportunistic pathogens individually. CONCLUSIONS: This study addresses the taxonomic ambiguities arising from species complexes within 97 strains of Cupriavidus and proposes a genome-based taxonomic framework based on phylogenomic analysis. Beyond classification, we advance insights into the genus's pathogenesis by delineating virulence-related genetic profiles, including conserved and species-specific virulence factors, secretion systems, and antibiotic resistance genes. Collectively, this work establishes a genomic foundation for understanding phylogenetic relationships and a comparative framework to explore pathogenicity across 97 strains of Cupriavidus.
Chen et al. (Mon,) studied this question.