Diversity of antibiotic resistance genes and mobile genetic elements of Sof Umer Cave microbiomes, Ethiopia.

Abstract

Antibiotic resistance is a major global health concern that caused by the overuse and misuse of antibiotics. Mobile genetic elements have a roles in the transmission of antibiotic resistance genes. The distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave have yet to be explored. To map the distribution and diversity of antibiotic resistance genes and mobile genetic elements in the microbiome of Sof Umer Cave using high-throughput shotgun sequencing. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit. Purified environmental DNA was sequenced using a NovaSeq PE150. Analysis of the pathogen host interaction database revealed the predominance of pathogenic organisms such as Xanthomonas oryzae, Acinetobacter baumannii, Erwinia amylovora, and Mycobacterium tuberculosis. Similarly, analysis of the virulence factor database confirmed the presence of Type IV pili (VF1240), lipopolysaccharides, capsules, heme biosynthesis (VF0758), and alginate. More than 800 antibiotic resistance genes were identified, with 50% related to glycopeptide resistance, followed by antibiotic resistance genes associated with multidrug efflux pumps (30%), aminoglycoside resistance genes (10%), and unknown genes. A variety of mobile genetic elements were also identified, highlighting their importance in the genetic diversity and adaptation of the microbiome of Sof Umer Cave. These findings underscore the importance of the Sof Umer Cave habitat as a reservoir for antibiotic resistance, emphasizing the need for ongoing monitoring to enhance the understanding and control of antibiotic resistance genes.