Sphingobacterium spp. as intrinsic producers of SPI Ambler class B metallo-β-lactamases

To characterize the intrinsic carbapenemase of Sphingobacterium spp.

Sphingobacterium spp. clinical isolates (n = 63) were collected in several French laboratories from 2012 to 2022. Antibiotic susceptibility was assessed by disc diffusion. MICs of last resort antimicrobials (including carbapenems, ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol) were determined by broth microdilution. WGS was performed on all isolates using the Illumina method. Cloning of the Sphingobacterium spiritivorum β-lactamase encoding gene, blaSPI-1, allowed expression of a novel metallo-β-lactamase (MBL), SPI-1, in Escherichia coli. Enzymatic kinetic parameters were determined with β-lactams as substrates.

Among the 64 Sphingobacterium isolates collected we identified six species, of which S. spiritivorum (n = 24) was the most prevalent followed by S. multivorum (n = 20), S. siyangense (n = 16), S. lactis (n = 2), S. thalpophilum (n = 1) and S. faecium (n = 1). Sphingobacterium isolates displayed a phenotype of multidrug resistance including resistance to last resort β-lactams and β-lactam-β-lactamase inhibitors (with MIC50 at 4, 4 and 2 mg/L for ceftazidime-avibactam, cefepime-enmetazobactam and cefiderocol, respectively). The most effective drugs were fluoroquinolones, tigecycline and eravacycline. All S. spiritivorum displayed a carbapenemase activity that correlated with the identification of SPI-1 encoding genes. SPI-like variants (n = 10) shared 93.7% amino-acid identity, but only 50.6% identity with the closest CGB-1 MBL intrinsic of Chryseobacterium gleum. Characterization of SPI-1 showed a strong hydrolytic activity towards most β-lactams including carbapenems.

S. spiritivorum was the most prevalent species of Sphingobacterium identified in clinical samples. All S. spiritivorum-like species produced a chromosomally encoded SPI-like MBL that might be challenging for the treatment of infections caused by this bacterial species.