Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysi...
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2022.807610/full |
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| author | Yang Song Xinmin Xu Zhenzhou Huang Yue Xiao Keyi Yu Mengnan Jiang Shangqi Yin Mei Zheng Huan Meng Ying Han Yajie Wang Duochun Wang Qiang Wei |
| author_facet | Yang Song Xinmin Xu Zhenzhou Huang Yue Xiao Keyi Yu Mengnan Jiang Shangqi Yin Mei Zheng Huan Meng Ying Han Yajie Wang Duochun Wang Qiang Wei |
| author_sort | Yang Song |
| collection | DOAJ |
| description | Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi 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 R. equi 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 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi 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, R. equi 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. |
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| language | English |
| last_indexed | 2024-04-13T02:57:39Z |
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| spelling | doaj.art-4b5046421ec44099b1989414a08406202022-12-22T03:05:35ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882022-02-011210.3389/fcimb.2022.807610807610Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equiYang Song0Xinmin Xu1Zhenzhou Huang2Yue Xiao3Keyi Yu4Mengnan Jiang5Shangqi Yin6Mei Zheng7Huan Meng8Ying Han9Yajie Wang10Duochun Wang11Qiang Wei12National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaCenter for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, ChinaCenter for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, ChinaCenter for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, ChinaNational Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaDepartment of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, ChinaCenter for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, ChinaNational Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, ChinaRhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi 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 R. equi 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 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi 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, R. equi 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.https://www.frontiersin.org/articles/10.3389/fcimb.2022.807610/fullgenomic characteristicsplasmid-mediated pathogenicityrifamycin resistanceRhodococcus equipan-genome |
| spellingShingle | Yang Song Xinmin Xu Zhenzhou Huang Yue Xiao Keyi Yu Mengnan Jiang Shangqi Yin Mei Zheng Huan Meng Ying Han Yajie Wang Duochun Wang Qiang Wei Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi Frontiers in Cellular and Infection Microbiology genomic characteristics plasmid-mediated pathogenicity rifamycin resistance Rhodococcus equi pan-genome |
| title | Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi |
| title_full | Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi |
| title_fullStr | Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi |
| title_full_unstemmed | Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi |
| title_short | Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi |
| title_sort | genomic characteristics and pan genome analysis of rhodococcus equi |
| topic | genomic characteristics plasmid-mediated pathogenicity rifamycin resistance Rhodococcus equi pan-genome |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2022.807610/full |
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