A new class A beta-lactamase gene bla(CAE-1) coexists with bla(AFM-1) in a novel untypable plasmid in Comamonas aquatica

Antimicrobial resistance, especially carbapenem resistance, poses a serious threat to global public health. Here, a carbapenem-resistant Comamonas aquatica isolate SCLZS63 was recovered from hospital sewage. Whole-genome sequencing showed that SCLZS63 has a 4,048,791-bp circular chromosome and three plasmids. The carbapenemase gene bla(AFM-1) is located on the 143,067-bp untypable plasmid p1_SCLZS63, which is a novel type of plasmid with two multidrug-resistant (MDR) regions. Notably, a novel class A serine β-lactamase gene, bla(CAE-1), coexists with bla(AFM-1) in the mosaic MDR2 region. Cloning assay showed that CAE-1 confers resistance to ampicillin, piperacillin, cefazolin, cefuroxime, and ceftriaxone, and elevates the MIC of ampicillin-sulbactam two-fold in Escherichia coli DH5α, suggesting that CAE-1 functions as a broad-spectrum β-lactamase. Amino acid sequences analysis suggested that bla(CAE-1) may originate from Comamonadaceae. The bla(AFM-1) in p1_SCLZS63 is located in a conserved structure of ISCR29-ΔgroL-bla(AFM-1)-ble-ΔtrpF-ΔISCR27-msrB-msrA-yfcG-corA. Comprehensive analysis of the bla(AFM)-bearing sequences revealed important roles of ISCR29 and ΔISCR27 in the mobilization and truncation of the core module of bla(AFM) alleles, respectively. The diverse passenger contents of class 1 integrons flanking the bla(AFM) core module make the complexity of genetic contexts for bla(AFM). In conclusion, this study reveals that Comamonas may act as an important reservoir for antibiotics-resistance genes and plasmids in the environment. Continuous monitoring for the environmental emergence of antimicrobial-resistant bacteria is needed to control the spread of antimicrobial resistance.