Unravelling the interplay of antimicrobial resistance and stress response in the saline desert metagenomes of Gujarat, India

The metagenomic analysis of the present study states the intricate community of salt-tolerant bugs living in saline soils from Kutch, Gujarat. Metagenomics sequencing has already been explored in this region for community analysis. However, we analyzed the metagenome of a saline desert and compared it with publicly available published metagenomes to identify common antimicrobial resistance found in the saline desert. The bioinformatics-based analysis revealed the presence of various antibiotic resistance (AMR) genes in Escherichia coli EF-Tu mutants, which confer resistance to several compounds, including Pulvomycin, FosG, rsmA, qacJ, and qacG. Additionally, the vanW gene in the vanI cluster and the vanY gene in the vanM cluster were identified. These mutants exhibit different resistance mechanisms, such as antibiotic inactivation (VanA — VIM-VIA), alteration of antibiotic targets (cfr and VanB), and the involvement of antibiotic efflux pumps, etc. The prevalence of AMR genes related to efflux pump indicates the importance of this genes (copR, bcrA, cesC, merA, narA, tetA, trxLHR and yfeB) toward salt tolerance and antibiotic resistance. This effect was robust even when human impacts were not substantial, illustrating the overwhelming adaptability of these organisms. The variable presence of these genes throughout the samples highlights an environmental effect on their distribution, suggesting a resistance mechanism. This work paves the way to understanding antimicrobial resistance genes produced in these pristine, human-untouched places.