Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.

Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.