Characterization of a Novel Chromosomal Class C β-Lactamase, YOC-1, and Comparative Genomics Analysis of a Multidrug Resistance Plasmid in Yokenella regensburgei W13

Abstract

Yokenella regensburgei, a member of the family Enterobacteriaceae, is usually isolated from environmental samples and generally resistant to early generations of cephalosporins. To characterize the resistance mechanism of Y. regensburgei strain W13 isolated from the sewage of an animal farm, whole genome sequencing, comparative genomics analysis and molecular cloning were performed. The results showed that a novel chromosomally encoded class C β-lactamase gene with the ability to confer resistance to β-lactam antibiotics, designated bla YOC-1 , was identified in the genome of Y. regensburgei W13. Kinetic analysis revealed that the β-lactamase YOC-1 has a broad spectrum of substrates, including penicillins, cefazolin, cefoxitin and cefotaxime. The two functionally characterized β-lactamases with the highest amino acid identities to YOC-1 were CDA-1 (71.69%) and CMY-2 (70.65%). The genetic context of the bla YOC−1-ampR-encoding region was unique compared with the sequences in the NCBI nucleotide database. The plasmid pRYW13-125 of Y. regensburgei W13 harbored 11 resistance genes (bla OXA−10 , bla LAP-2 , dfrA14, tetA, tetR, cmlA5, floR, sul2, ant(3)-IIa, arr-2 and qnrS1) within an ∼34 kb multidrug resistance region; these genes were all related to mobile genetic elements. The multidrug resistance region of pYRW13-125 shared the highest identities with those of two plasmids from clinical Klebsiella pneumoniae isolates, indicating the possibility of horizontal transfer of these resistance genes between bacteria of various origins.

Characterization and identification of a novel chromosomal class C β-lactamase, LAQ-1, and comparative genomic analysis of a multidrug resistance plasmid in Lelliottia amnigena P13

“…The overnight culture was diluted 100-fold in 100 mL of LB medium and shaken at 37°C for 2–3 h until the OD 600 reached 0.6–0.8. Isopropyl-β-d-thiogalactopyranoside (IPTG; Sigma Chemicals Co., St. Louis, MO, United States) was added at a final concentration of 1 mM, and incubation was continued for an additional 4 h. According to the instructions for BeyoGold His tag Purification Resin (Beyotime, Shanghai, China), the protein was purified by affinity chromatography, followed by incubation with Enterokinase (GenScript, Nanjing, China) at 16°C for 36 h to remove the histidine tag ( Zhou et al, 2020 ).…”

In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria

“…In addition, the ESBL phenotype has been reported in other groups of β-lactamases such as CARB and L2. Additional minor ESBL types, such as FONA, BPU and YOC, have also been recently identified [9][10][11]. An interesting example of the minor ESBL group is SFO-1 encoded by a plasmid which includes the ampR regulatory gene, which allows for β-lactamase induction in a manner similar to class C β-lactamases.…”

Characterization of Beta-Lactam Resistome of Escherichia coli Causing Nosocomial Infections

“…The blaLAP gene was expressed in 6.88% of the isolated Escherichia coli strains, with only two detected isoforms: bla LAP-1 was the dominant gene expressed, accounting for 73.33% of all positive bla LAP strains, followed by the bla LAP-2 gene isoform, representing 26.67%. This gene, in combination with other beta-lactamases, contributes to the multi-drug resistance characteristics [ 74 ].…”