Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum

Wafa A Alshehri; Aala A Abulfaraj; Mashael D Alqahtani; Maryam M Alomran; Nahaa M Alotaibi; Khairiah Alwutayd; Abeer S Aloufi; Fatimah M Alshehrei; Khulood F Alabbosh; Sahar A Alshareef; Ruba A Ashy; Mohammed Y Refai; Rewaa S Jalal

doi:10.1186/s13568-023-01597-w

Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum

AMB Express. 2023 Aug 30;13(1):92. doi: 10.1186/s13568-023-01597-w.

Affiliations

¹ Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
² Biological Sciences Department, College of Science & Arts, King Abdulaziz University, 21911, Rabigh, Saudi Arabia.
³ Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O.Box 84428, 11671, Riyadh, Saudi Arabia.
⁴ Department of Biology, Jumum College University, Umm Al-Qura University, P.O. Box 7388, 21955, Makkah, Saudi Arabia.
⁵ Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia.
⁶ Department of Biology, College of Science and Arts at Khulis, University of Jeddah, 21921, Jeddah, Saudi Arabia.
⁷ Department of Biochemistry, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
⁸ Department of Biology, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia. rsjalal@uj.edu.sa.

Abstract

A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers (commensal) included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump (for mtrA, soxR and golS genes), major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine.

Keywords: AMR; ARG; Antibiotic resistance mechanism; HGT; MGEs; Microbiome; Prevalence; Rhizosphere; mWGS.

Grants and funding

PNURSP2023R355/Deanship of Scientific Research, Princess Nourah Bint Abdulrahman University