Characterization of a novel class A carbapenemase PAD-1 from Paramesorhizobium desertii A-3-ET, a strain highly resistant to β-lactam antibiotics

Abstract

Although clinical antibiotic-resistant bacteria have attracted tremendous attention in the microbiology community, the resistant bacteria that persist in natural environments have been overlooked for a longtime. We previously proposed a new species Paramesorhizobium desertii, isolated from the soil of the Taklimakan Desert in China that is highly resistant to most β-lactam antibiotics. To identify potential β-lactamase(s) in this bacteria, we first confirmed the carbapenemase activity in the freeze–thawed supernatant of a P. desertii A-3-ET culture using the modified Hodge assay. We then identified a novel chromosome-encoded carbapenemase (PAD-1) in strain A-3-ET, using a shotgun proteomic analysis of the supernatant and genomic information. The bioinformatics analysis indicated that PAD-1 is a class A carbapenemase. Subsequent enzyme kinetic assays with purified PAD-1 confirmed its carbapenemase activity, which is similar to that of clinically significant class A carbapenemases, including BKC-1 and KPC-2. Because the location in which A-3-ET was isolated is not affected by human activity, PAD-1 is unlikely to be associated with the selection pressures exerted by modern antibiotics. This study confirmed the diversity of antibiotic-resistant determinants in the environmental resistome.

The Carbapenemase BKC-1 from Klebsiella pneumoniae Is Adapted for Translocation by Both the Tat and Sec Translocons

“…Initial studies on the signal peptides of b-lactamases revealed three putative Tattransported enzymes: BKC-1 and GPC-1, first identified in clinical isolates of K. pneumoniae and P. aeruginosa, respectively (59)(60)(61), as well as PAD-1 from the soil bacterium Paramesorhizobium desertii (60). Here, we show that these three proteins represent an isolated subfamily of b-lactamases with carbapenemase activity.…”

“…1B). Molecular phylogeny analysis in this global context demonstrated that BKC-1 is most closely related to GPC-1 from P. aeruginosa (61), and these two in turn are related to PAD-1 from the soil bacterium P. desertii (60). These proteins have a sequence identity of 66% (Fig.…”

“…Theoretically, there are a number of restrictions to the dissemination of AMR and virulence phenotypes in bacteria by LGT (4,5,7). Our initial interest in BKC-1 was piqued by the observation that two related enzymes, BKC-1and GPC-1, have each been identified only once and, despite being carried by highly transmissible plasmids, have not spread further by LGT or arisen more broadly than in the distinct countries where each was first found (59)(60)(61)71). With only a few related sequences available, it is difficult to trace the exact origins of this lineage of carbapenemases, but a very recent report suggested that the plasmid-encoded BKC-1 may have originated from Shinella, given the oddity of its sequence (72).…”