AUTHOR=Song Yang , Xu Xinmin , Huang Zhenzhou , Xiao Yue , Yu Keyi , Jiang Mengnan , Yin Shangqi , Zheng Mei , Meng Huan , Han Ying , Wang Yajie , Wang Duochun , Wei Qiang 

TITLE=Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.807610

DOI=10.3389/fcimb.2022.807610

ISSN=2235-2988

ABSTRACT=<p><italic>Rhodococcus equi</italic> is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of <italic>R. equi</italic> infection are not clear. This study characterized the genomes of 53 <italic>R. equi</italic> strains from different sources. Pan-genome analysis showed that all <italic>R. equi</italic> strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the <italic>R. equi</italic> strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 <italic>R. equi</italic> strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (<italic>RbpA, tetA (33), erm (46), sul1, qacEdelta 1</italic> and <italic>aadA9</italic>) were detected, and all strains carried <italic>RbpA</italic> related to rifamycin resistance. In addition, 28 plasmids were found in the 53 <italic>R. equi</italic> strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, <italic>R. equi</italic> strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.</p>