Phylogenomic analysis of vancomycin-resistant Pediococcus acidilactici and P. pentosaceus isolated from the environment

Abstract This study provides a phylogenomic analysis of P. acidilactici and P. pentosaceus highlighting antibiotic resistance genes, plasmids and pathogenicity. The whole genomes of isolates of P. acidilactici and P. pentosaceus isolates were sequenced. Additional P. acidilactici and P. pentosaceus genome sequences were downloaded from the National Center for Biotechnology Information (NCBI). The phylogenomic tree inferred through the CSI Phylogeny indicates two distinct species of P. acidilactici and P. pentosaceus. Resistome analysis revealed vancomycin resistance genes and aminoglycosides (aph(3′)-III and aac(6′)-Ii). Intrinsic vancomycin resistance operons VanL, vanRM and vanTG genes were present in 95.65% (n = 22) of all genomes, whereas the acquired vancomycin resistance gene vanHAX was only found in one isolated genome. In this study, we elucidated for the first time the resistome, plasmids and pathogenicity of complete genomes of Pediococcus acidilactici and P. pentosaceus from NCBI and our environmentally isolated strains (RS11, RS13, RW6 and RW12).