Diversity of L1/L2 genes and molecular epidemiology of high-level carbapenem resistance Stenotrophomonas maltophilia isolates from animal production environment in China

Stenotrophomonas maltophilia is emerging as a significant cause of human and animal disease worldwide. A total of 3400 samples were collected from animal farms and adjacent environments in China. The blaL1 and blaL2 genes were identified using whole genome sequence analyses and examined by phylogenetics. Isolates were also tested for susceptibility to 18 antibiotics. We isolated 118 strains of S. maltophilia from 3400 samples. The positive rates of blaL1 and blaL2 genes were 75% (89/118) and 22% (26/118) and we identified 11 L1 and 6 L2 amino acid sequence variants. S. maltophilia has at least two inducible β-lactamases (L1 and L2) that can hydrolyze almost all classes of β-lactams and these genes are suspected to confer carbapenem resistance. This represents a significant public health threat especially for hospitalized patients. We conducted a molecular surveillance study on the prevalence and characteristics of the blaL1 and blaL2 genes of S. maltophilia. •The strains of 118 S. maltophilia with high levels resistance to carbapenems.•Seventy-seven L1 and eighty L2 variants were discovered.•The 8 L1 and 1 L2 novel variants of S. maltophilia were isolated.•The cloning of novel variants MICs showed 0.125 to 32 μg/mL to MEM, IMP, ERT, CTX, CZA.•The MICs of cloned novel variants showed 2–2000-fold greater than the negative control strain.•The clonal S. maltophilia in human-animal-environment can pose a potential threat to public health.