Comparative Genomic Analysis of <i>Rhodococcus equi</i>: An Insight into Genomic Diversity and Genome Evolution

Ying, Jianchao; Ye, Jun; Xu, Teng; Wang, Qian; Bao, Qiyu; Li, Aifang

doi:10.1155/2019/8987436

Cited by 7 publications

(5 citation statements)

References 65 publications

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“…The genus Rhodococcus , a group of facultative aerobic Gram-positive bacteria, belongs to nocardiaceae, Corynebacterium suborder, and is widely distributed in rocks, groundwater, soil, marine sediments, insects, animals and plants ( Gao and Gupta, 2012 ; Vazquez-Boland et al., 2020 ). Among the 57 species in the genus Rhodococcus , at least six species ( R. equi , R. erythropolis , R. ruber , R. gordoniae R. fascians and R.defluvii ) have been proved to be related to animal and plant pathogenicity ( Sangal et al., 2015 ; Anastasi et al., 2016 ; Canetti et al., 2019 ; Ying et al., 2019 ). Among these six species, R. equi is the main pathogen of human infection.…”

Section: Introductionmentioning

confidence: 99%

Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

Song

Huang

et al. 2022

Front. Cell. Infect. Microbiol.

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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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Section: Introductionmentioning

confidence: 99%

Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

Song

Huang

et al. 2022

Front. Cell. Infect. Microbiol.

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“…The phylogenetic analyses have shown that “ R. equi ” has a high degree of core genome (conserved gene set) similarity with non-pathogenic environmental rhodococcal species [ 96 ]. There are genes involved in protein biosynthesis, metabolism, transport, and signal transduction, which can be associated with both adaptation and virulence.…”

Section: Ubiquity Of Rhodococcus and Existence Of Pathogenic Speciesmentioning

confidence: 99%

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

et al. 2021

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Under conditions of increasing environmental pollution, true saprophytes are capable of changing their survival strategies and demonstrating certain pathogenicity factors. Actinobacteria of the genus Rhodococcus, typical soil and aquatic biotope inhabitants, are characterized by high ecological plasticity and a wide range of oxidized organic substrates, including hydrocarbons and their derivatives. Their cell adaptations, such as the ability of adhering and colonizing surfaces, a complex life cycle, formation of resting cells and capsule-like structures, diauxotrophy, and a rigid cell wall, developed against the negative effects of anthropogenic pollutants are discussed and the risks of possible pathogenization of free-living saprotrophic Rhodococcus species are proposed. Due to universal adaptation features, Rhodococcus species are among the candidates, if further anthropogenic pressure increases, to move into the group of potentially pathogenic organisms with “unprofessional” parasitism, and to join an expanding list of infectious agents as facultative or occasional parasites.

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“…In contrast, the transcription (K, 936 genes), carbohydrate transport and metabolism (G, 655 genes), and inorganic ion transport and metabolism (P, 645 genes) categories occurred more frequently in the accessory genome. These COG categories are fundamental for niche adaptation because they represent functions that induce the activation of related internal systems and introduce various external sources [ 57 ]. The unique genome showed high ratios of genes in the mobilome (X, 69 genes) and defence mechanism (V, 58 genes) categories (Table S6), which can be mediated by rapid sequence evolution or HGT [ 58 ].…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities

Jung,

Lee,

Lee

et al. 2023

Microbial Genomics

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Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein–protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR–Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.

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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

Cited by 7 publications

References 65 publications

Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

Genomic Characteristics and Pan-Genome Analysis of Rhodococcus equi

Responses to Ecopollutants and Pathogenization Risks of Saprotrophic Rhodococcus Species

Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities

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