In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i>
As the mobile cassette carrier of the methicillin resistance gene <i>mecA</i> that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>)—and in particular, the composition of <i>...
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| author | Huawei Wang Jinxing He |
| author_facet | Huawei Wang Jinxing He |
| author_sort | Huawei Wang |
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| description | As the mobile cassette carrier of the methicillin resistance gene <i>mecA</i> that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>)—and in particular, the composition of <i>mecA</i> and SCC<i>mec</i>—have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCC<i>mec</i>. Herein, the cassette chromosome recombinase genes <i>ccrAB/C</i>, as essential components of SCC<i>mec</i>, were employed to explore the evolution of SCC<i>mec</i>. This work established the basic taxonomy of 33 staphylococci species. The CUB of <i>mecA</i>, <i>ccrAB/C</i> of 12 SCC<i>mec</i> types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of <i>ccrAB/C</i> was observed via SCC<i>mec</i> typing on a temporal and geographical scale; and the duplicate appearance of <i>ccrAB/C</i> was illustrated by comparing SCC<i>mec</i> compositions. The results highlighted a deviation in the CUB of <i>mecA</i> and <i>ccrAB/C</i>, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of <i>ccrAB/C</i> as representative of SCC<i>mec</i>. Importantly, the phylogenetic relationship of <i>ccrAB/C</i> did not exhibit centralization over time; instead, similarly to <i>mecA</i>, <i>ccrAB/C</i> with similar identities had close clades across decades and geographical limits and different SCC<i>mec</i> types, which enabled us to discriminate SCC<i>mec</i> based on the sequence identity of <i>ccrAB/C</i>. In addition, the duplicate appearance of <i>ccrAB/C</i> and fixed composition of the <i>ccrAB/C</i> complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCC<i>mec</i>. |
| format | Article |
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| institution | Kabale University |
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| spelling | doaj-art-76feabec6e8e4c8c9f9754966b3d0afd2025-01-24T13:42:50ZengMDPI AGMicroorganisms2076-26072025-01-0113115310.3390/microorganisms13010153In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i>Huawei Wang0Jinxing He1College of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, ChinaCollege of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, ChinaAs the mobile cassette carrier of the methicillin resistance gene <i>mecA</i> that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>)—and in particular, the composition of <i>mecA</i> and SCC<i>mec</i>—have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCC<i>mec</i>. Herein, the cassette chromosome recombinase genes <i>ccrAB/C</i>, as essential components of SCC<i>mec</i>, were employed to explore the evolution of SCC<i>mec</i>. This work established the basic taxonomy of 33 staphylococci species. The CUB of <i>mecA</i>, <i>ccrAB/C</i> of 12 SCC<i>mec</i> types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of <i>ccrAB/C</i> was observed via SCC<i>mec</i> typing on a temporal and geographical scale; and the duplicate appearance of <i>ccrAB/C</i> was illustrated by comparing SCC<i>mec</i> compositions. The results highlighted a deviation in the CUB of <i>mecA</i> and <i>ccrAB/C</i>, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of <i>ccrAB/C</i> as representative of SCC<i>mec</i>. Importantly, the phylogenetic relationship of <i>ccrAB/C</i> did not exhibit centralization over time; instead, similarly to <i>mecA</i>, <i>ccrAB/C</i> with similar identities had close clades across decades and geographical limits and different SCC<i>mec</i> types, which enabled us to discriminate SCC<i>mec</i> based on the sequence identity of <i>ccrAB/C</i>. In addition, the duplicate appearance of <i>ccrAB/C</i> and fixed composition of the <i>ccrAB/C</i> complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCC<i>mec</i>.https://www.mdpi.com/2076-2607/13/1/153<i>ccrAB/C</i>evolutionstaphylococciin silico |
| spellingShingle | Huawei Wang Jinxing He In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> Microorganisms <i>ccrAB/C</i> evolution staphylococci in silico |
| title | In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> |
| title_full | In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> |
| title_fullStr | In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> |
| title_full_unstemmed | In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> |
| title_short | In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> |
| title_sort | in silico exploration of staphylococcal cassette chromosome i mec i scc i mec i evolution based on phylogenetic relationship of i ccrab c i |
| topic | <i>ccrAB/C</i> evolution staphylococci in silico |
| url | https://www.mdpi.com/2076-2607/13/1/153 |
| work_keys_str_mv | AT huaweiwang insilicoexplorationofstaphylococcalcassettechromosomeimecisccimecievolutionbasedonphylogeneticrelationshipoficcrabci AT jinxinghe insilicoexplorationofstaphylococcalcassettechromosomeimecisccimecievolutionbasedonphylogeneticrelationshipoficcrabci |