Antibiotic Resistance Profiles and Genomic Analysis of Endophytic Bacteria Isolates from Wild Edible Fungi in Yunnan

The use of antibiotics has led to the emergence of antibiotic resistance, posing significant challenges in the prevention, control, and treatment of microbial diseases, while threatening public health, the environment, and food safety. In this study, the antibiotic resistance phenotypes and genotypes of 56 endophytic bacteria isolates from three species of wild edible fungi in Yunnan were analyzed using the Kirby-Bauer disk diffusion method and PCR amplification. The results revealed that all isolates were sensitive to ofloxacin, but resistance was observed against 17 other antibiotics. Specifically, 55, 53, and 51 isolates exhibited resistance to amoxicillin, penicillin, and vancomycin, respectively. Antibiotic resistance gene (ARG) detection indicated that the sulfonamide <i>sul1</i> gene had the highest detection rate (53.57%). Excluding the ARG that was not detected, the lowest detection rates were the sulfonamide <i>sul2</i> and <i>sul3</i> genes, both at 1.79%. Among six tetracycline resistance genes, only <i>tetK</i> and <i>tetM</i> were detected. For β-lactam antibiotics, <i>blaTEM</i>, <i>blaVIM</i>, and <i>blaSHV</i> genes were present, while <i>blaOXA</i> was absent. In aminoglycoside resistance genes, <i>aadB</i> was not detected, while detection rates for <i>aac(3')-IIa</i>, <i>acrB</i>, and <i>aadA1</i> were 3.57%, 1.79%, and 37.5%, respectively. The chloramphenicol <i>Cat</i> gene was detected at a rate of 14.29%, whereas <i>floR</i> was absent. For polypeptide resistance, <i>VanC</i> was detected at 3.57%, with <i>EmgrB</i> not detected. All three quinolone genes were detected, with detection rates of 8.92% for <i>GyrA</i>, 39.29% for <i>GyrB</i>, and 37.5% for <i>ParC</i>. Through phylogenetic analysis, 12 isolates that are closely related to ten common foodborne pathogenic bacteria were further selected for whole-genome sequencing and assembly. Gene annotations revealed that each isolate contained more than 15 ARGs and over 30 virulence factors. Notably, the detection rate of antibiotic resistance phenotypes was higher than that of genotypes, highlighting the importance of studying phenotypic antibiotic resistance that lacks identifiable ARGs. This study enriches the research on endophytes in wild edible fungi and provides new data for microbial ecology and antibiotic resistance research. It also offers critical insights for monitoring microbial antibiotic resistance in wild edible fungi and potentially other food sources, contributing to more effective strategies for ecological protection, sustainable agricultural development, and public health security.