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

Abstract

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 β-lactam resistance genes, with β-lactamases isolated from the Chryseobacterium spp. functional gene library, one of which is a variant of IND-like metallo-β-lactamase (MBL) IND-17 and the other of which is a previously uncharacterised MBL we named CHM (Chryseobacterium metallo β-lactamase). Our results indicate that soil microorganisms possess a diversity of ARG variants, which could potentially be transferred to the clinical setting.

Chryseobacterium herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau

“…Antibiotic resistance gene predictions showed that herbae pc1-10 T contained two antibiotic resistance genes: IND-4, which is a beta-lactamase found in Chryseobacterium indologenes, and AdeF, which is the membrane fusion protein of the multidrug efflux complex AdeFGH; the proteincoding information is provided by CARD [59] (https://card.mcmaster.ca/ accessed on 21 May 2023). According to a study, bacteria that live in soil or water naturally have ARGs that they can use to compete with other organisms that share the same habitat [60]. We used CRISPRCasFinder [61] to identify CRISPR (clustered regularly interspaced short palindromic repeats) arrays; 5 of the 23 analysis sequences were found to contain CRISPR but no Cas genes were found in the vicinity of CRISPRs.…”