Whole-genome analysis showed the promotion of genetic diversity and coevolution in Staphylococcus aureus lytic bacteriophages and their hosts mediated by prophages via worldwide recombination events
Prophages as a part of genome contribute to the genetic diversity as well as survival strategies of their host. Some prophages also have an imminent risk of host cell lysis and become a lytic phage. Nonetheless, interactions among prophages, lytic phages, and their hosts, as well as the genetic dive...
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| Published in: | Frontiers in microbiology Vol. 14; p. 1088125 |
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| Main Authors: | , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
Switzerland
Frontiers Media S.A
10-03-2023
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| Subjects: | |
| Online Access: | Get full text |
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| Summary: | Prophages as a part of
genome contribute to the genetic diversity as well as survival strategies of their host. Some
prophages also have an imminent risk of host cell lysis and become a lytic phage. Nonetheless, interactions among
prophages, lytic phages, and their hosts, as well as the genetic diversity of
prophages, remain unclear. We identified 579 intact and 1,389 incomplete prophages in the genomes of 493
isolates obtained from the NCBI database. The structural diversity and gene content of intact and incomplete prophages were investigated and compared with 188 lytic phages. Mosaic structure comparison, ortholog group clustering, phylogenetic analysis, and recombination network analysis were performed to estimate genetic relatedness among
intact prophages, incomplete prophages, and lytic phages. The intact and incomplete prophages harbored 148 and 522 distinct mosaic structures, respectively. The major difference between lytic phages and prophages was the lack of functional modules and genes. Compared to the lytic phages, both the
intact and incomplete prophages harbored multiple antimicrobial resistance (AMR) and virulence factor (VF) genes. Several functional modules of lytic phages 3_AJ_2017 and 23MRA shared more than 99% nucleotide sequence identity with
intact (ST20130943_p1 and UTSW_ MRSA_55_ip3) and incomplete prophages (SA3_LAU_ip3 and MRSA_FKTN_ip4); other modules showed little nucleotide sequence similarity. Ortholog and phylogenetic analyses revealed a common gene pool shared between the prophages and lytic Siphoviridae phages. Moreover, most shared sequences existed within intact (43428/137294, 31.6%) and incomplete prophages (41248/137294, 30.0%). Therefore, the maintenance or loss of functional modules in intact and incomplete prophages is key to balance the costs and benefits of large prophages harboring various AMR and VF genes in the bacterial host. The shared identical functional modules between
lytic phages and prophages are likely to result in the exchange, acquisition, and loss of functional modules, and therefore contribute to their genetic diversity. Moreover, constant recombination events within prophages globally were responsible for the coevolution of lytic phages and their bacterial hosts. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Reviewed by: Haiyan Zeng, Guangdong University of Technology, China; Jens Andre Hammerl, Bundesinstitut für Risikobewertung, Germany Edited by: Antony T. Vincent, Laval University, Canada This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology |
| ISSN: | 1664-302X 1664-302X |
| DOI: | 10.3389/fmicb.2023.1088125 |