Novel Antibiotic Resistance Genes Identified by Functional Gene Library Screening in Stenotrophomonas maltophilia and Chryseobacterium spp. Bacteria of Soil Origin

As one of the most diverse habitats of microorganisms, soil has been recognised as a reservoir of both antibiotics and the antibiotic resistance genes (ARGs). Bacteria naturally inhabiting soil or water often possess innate ARGs to counteract the chemical compounds produced by competitors living in the same environment. When such bacteria are able to cause infections in immunocompromised patients, their strong innate antibiotic resistance mechanisms make treatment difficult. We generated functional gene libraries using antibiotic-resistant Stenotrophomonas maltophilia and Chryseobacterium spp. bacteria isolated from agricultural soils in Lithuania to select for the genetic determinants responsible for their resistance. We were able to find novel variants of aminoglycoside and beta-lactam resistance genes, with beta-lactamases isolated from the Chryseobacterium spp. functional gene library, one of which is a variant of IND-like metallo-beta-lactamase (MBL) IND-17 and the other of which is a previously uncharacterised MBL we named CHM (Chryseobacterium metallo beta-lactamase). Our results indicate that soil microorganisms possess a diversity of ARG variants, which could potentially be transferred to the clinical setting.

Automated summary

Soil, as a diverse habitat for microorganisms, contains both antibiotics and antibiotic resistance genes (ARGs). Bacteria naturally present in soil or water have innate ARGs to counteract the chemical compounds produced by competitors, making treatment difficult when these bacteria cause infections. By creating functional gene libraries using antibiotic-resistant bacteria from agricultural soils in Lithuania, we discovered novel variants of aminoglycoside and beta-lactam resistance genes. Our findings suggest that soil microorganisms possess a range of ARG variants that could potentially spread to clinical settings.