scholarly journals Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires

2021 ◽  
Author(s):  
Eugen Pfeifer ◽  
Jorge A Moura de Sousa ◽  
Marie Touchon ◽  
Eduardo P C Rocha
Keyword(s):  
Mobile Genetic Elements ◽  
Bacterial Evolution ◽  
Bacterial Phyla ◽  
Genetic Organization ◽  
Plasmid Gene ◽  
Genetic Elements ◽  
Accessory Genes ◽  
Number Distribution ◽  
Sizeable Fraction ◽  
Large Groups

Abstract Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage–plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage–plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage–plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage–plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage–plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage–plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

scholarly journals Bacteria have numerous phage-plasmid families with conserved phage and variable plasmid gene repertoires

2020 ◽  
Author(s):  
Eugen Pfeifer ◽  
Jorge A. Moura de Sousa ◽  
Marie Touchon ◽  
Eduardo P.C. Rocha
Keyword(s):  
Mobile Genetic Elements ◽  
Bacterial Evolution ◽  
Bacterial Phyla ◽  
Genetic Organization ◽  
Plasmid Gene ◽  
Genetic Elements ◽  
Accessory Genes ◽  
Number Distribution ◽  
Sizeable Fraction ◽  
Large Groups

ABSTRACTPlasmids and temperate phages are mobile genetic elements driving bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage-plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage-plasmids are poorly known. Here, we screened for these elements among ca. 14000 phages and plasmids and identified 780 phage-plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to define 8 families and 18 other broader communities of elements. The existence of these large groups suggests that phage-plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage-plasmids and found the key phage genes to be conserved and co-localized within families, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage-plasmids are a sizeable fraction of all phages and plasmids and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.

scholarly journals Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

2018 ◽  
Author(s):  
Chrispin Chaguza ◽  
Ellen Heinsbroek ◽  
Rebecca A. Gladstone ◽  
Terence Tafatatha ◽  
Maaike Alaerts ◽  
...  
Keyword(s):  
Population Structure ◽  
Mobile Genetic Elements ◽  
Post Vaccination ◽  
Accessory Genome ◽  
Genetic Elements ◽  
Genomic Level ◽  
Accessory Genes ◽  
Serotype Replacement ◽  
Vaccine Type ◽  
Genome Level

AbstractPneumococcal conjugate vaccines (PCV) have reduced pneumococcal diseases globally. Despite this, much remains to be learned about their effect on pathogen population structure. Here we undertook whole genome sequencing of 660 pneumococcal strains from asymptomatic carriers to investigate population restructuring in pneumococcal strains sampled before and after PCV13 introduction in a previously vaccine-naïve setting. We show substantial decreasing frequency of vaccine-type (VT) strains and their strain diversity post-vaccination in the vaccinated but not unvaccinated age groups indicative of direct but limited or delayed indirect effect of vaccination. Clearance of identical VT serotypes associated with multiple lineages occurred regardless of their genetic background. Interestingly, despite the increasing frequency of non-vaccine type (NVT) strains through serotype replacement, the serotype diversity was not fully restored to the levels observed prior to vaccination implying limited serotype replacement. The frequency of antibiotic resistant strains was low and remained largely unchanged post-vaccination but intermediate-penicillin-resistant lineages were reduced in the post vaccine population. Significant perturbations marked by changing frequency of accessory genes associated with diverse functions especially mobile genetic elements and bacteriocin activity were detected. This phylogenomic analysis demonstrates early vaccine-induced pneumococcal population restructuring not only at serotype but also accessory genome level.Author summaryDifferent formulations of PCVs have been effective in reducing the invasive pneumococcal disease burden globally. Clinical trials have started to indicate high impact and effectiveness of PCV13 in Sub Saharan Africa (SSA) but there is limited understanding of how the introduction of PCVs alters the population structure of pneumococcal strains at serotype and genomic level. Here we investigated this using pneumococcal strains sampled pre‐ and post-PCV13 introduction from a previously vaccine naïve setting in Northern Malawi. Our findings reveal decrease in frequency of VT serotypes and their associated lineages in the largely vaccinated under-five population but not older individuals indicating a direct but limited or delayed indirect protection. The diversity of serotypes also decreased post-vaccination in VT strains in the under-fives but there was no change in NVT strains suggesting incomplete serotype replacement. At the genomic level, logistic regression revealed changing frequency of accessory genes largely associated with mobile genetic elements but such changes did not include any antibiotic resistance genes. These findings show significant perturbations at serotype and accessory genome level in carried pneumococcal population after two years from PCV13 introduction but the pneumococcal population was still perturbed and had not returned to a new equilibrium state.

scholarly journals Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

2020 ◽  
Vol 117 (27) ◽  
pp. 15755-15762
Author(s):  
Jerónimo Rodríguez-Beltrán ◽  
Vidar Sørum ◽  
Macarena Toll-Riera ◽  
Carmen de la Vega ◽  
Rafael Peña-Miller ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mobile Genetic Elements ◽  
Model System ◽  
Host Bacterium ◽  
Wild Type ◽  
Bacterial Evolution ◽  
Human Interest ◽  
Genetic Dominance ◽  
Genetic Elements

Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.

scholarly journals Expanding the type IIB DNA topoisomerase family: identification of new topoisomerase and topoisomerase-like proteins in mobile genetic elements

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Tomio S Takahashi ◽  
Violette Da Cunha ◽  
Mart Krupovic ◽  
Claudine Mayer ◽  
Patrick Forterre ◽  
...  
Keyword(s):  
Mobile Genetic Elements ◽  
Dna Topology ◽  
Rapid Expansion ◽  
Dna Topoisomerase ◽  
Dna Topoisomerases ◽  
Origin And Evolution ◽  
Bacterial Phyla ◽  
Genetic Elements ◽  
Archaeal Viruses

Abstract The control of DNA topology by DNA topoisomerases is essential for virtually all DNA transactions in the cell. These enzymes, present in every organism, exist as several non-homologous families. We previously identified a small group of atypical type IIB topoisomerases, called Topo VIII, mainly encoded by plasmids. Here, taking advantage of the rapid expansion of sequence databases, we identified new putative Topo VIII homologs. Our analyses confirm the exclusivity of the corresponding genes to mobile genetic elements (MGE) and extend their distribution to nine different bacterial phyla and one archaeal superphylum. Notably, we discovered another subfamily of topoisomerases, dubbed ‘Mini-A’, including distant homologs of type IIB topoisomerases and encoded by extrachromosomal and integrated bacterial and archaeal viruses. Interestingly, a short, functionally uncharacterized motif at the C-terminal extremity of type IIB topoisomerases appears sufficient to discriminate between Mini-A, Topo VI and Topo VIII subfamilies. This motif could be a key element for understanding the differences between the three subfamilies. Collectively, this work leads to an updated model for the origin and evolution of the type IIB topoisomerase family and raises questions regarding the role of topoisomerases during replication of MGE in bacteria and archaea.

scholarly journals Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements

2020 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Heiko Liesegang ◽  
Olivia Roth ◽  
Carolin Charlotte Wendling
Keyword(s):  
Clonal Expansion ◽  
Mobile Genetic Elements ◽  
Vibrio Alginolyticus ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Kiel Fjord ◽  
Genetic Elements ◽  
Genomic Signatures ◽  
Accessory Genes ◽  
Niche Adaptation

Abstract Background Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate (1) those genomic signatures that characterize a habitat-specific ecotype and (2) the source of genomic variation within this ecotype. Results We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. Conclusion We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.

scholarly journals Evolution of Staphylococcus aureus by Large Chromosomal Replacements

2004 ◽  
Vol 186 (4) ◽  
pp. 1060-1064 ◽  
Author(s):  
D. Ashley Robinson ◽  
Mark C. Enright
Keyword(s):  
Staphylococcus Aureus ◽  
Natural Populations ◽  
Mobile Genetic Elements ◽  
Conjugative Transfer ◽  
Bacterial Evolution ◽  
Genetic Elements ◽  
Unique Structure ◽  
Large Size ◽  
Order Of Magnitude

ABSTRACT Conjugative transfer and replacement of hundreds of kilobases of a bacterial chromosome can occur in vitro, but replacements in nature are either an order of magnitude smaller or involve the movement of mobile genetic elements. We discovered that two lineages of Staphylococcus aureus, including a pandemic methicillin-resistant lineage, were founded by single chromosomal replacements of at least ∼244 and ∼557 kb representing ∼10 and ∼20% of the chromosome, respectively, without the obvious involvement of mobile genetic elements. The replacements are unprecedented in natural populations of bacteria because of their large size and unique structure and may have a dramatic impact on bacterial evolution.

scholarly journals Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements

2020 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Olivia Roth ◽  
Heiko Liesegang ◽  
Carolin Charlotte Wendling
Keyword(s):  
Clonal Expansion ◽  
Mobile Genetic Elements ◽  
Vibrio Alginolyticus ◽  
Genomic Variation ◽  
Comparative Genomic ◽  
Kiel Fjord ◽  
Genetic Elements ◽  
Genomic Signatures ◽  
Accessory Genes ◽  
Niche Adaptation

Abstract Background Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate (1) those genomic signatures that characterize a habitat-specific ecotype and (2) the source of genomic variation within this ecotype.Results We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. Conclusion We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.

scholarly journals Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria

2019 ◽  
Author(s):  
Jerónimo Rodríguez-Beltrán ◽  
Vidar Sørum ◽  
Macarena Toll-Riera ◽  
Carmen de la Vega ◽  
Rafael Peña-Miller ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Horizontal Gene Transfer ◽  
Mobile Genetic Elements ◽  
Model System ◽  
Host Bacterium ◽  
Wild Type ◽  
Bacterial Evolution ◽  
Genetic Dominance ◽  
Genetic Elements

AbstractMobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium and, as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. Moreover, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalogue of genes encoded on MGEs, dictating bacterial evolution through HGT.

scholarly journals Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Anil Poudel ◽  
Yuan Kang ◽  
Rabindra K Mandal ◽  
Anwar Kalalah ◽  
Patrick Butaye ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Mobile Genetic Elements ◽  
Fecal Samples ◽  
Bacterial Phyla ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes ◽  
Microbial Analysis ◽  
Qpcr Array ◽  
Curtis Dissimilarity

ABSTRACT Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray–Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.

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