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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Olivia Roth ◽  
Heiko Liesegang ◽  
Carolin Charlotte Wendling
Keyword(s):  
Mobile Genetic Elements ◽  
Vibrio Alginolyticus ◽  
Genomic Variation ◽  
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 High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages inClostridioides difficile

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Julian R. Garneau ◽  
Ognjen Sekulovic ◽  
Bruno Dupuy ◽  
Olga Soutourina ◽  
Marc Monot ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mobile Genetic Elements ◽  
Large Chromosome ◽  
Comparative Genomic ◽  
Content Type ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
A Genome ◽  
Depth Analysis ◽  
High Prevalence

ABSTRACTClostridioides difficile(formerlyClostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified inC. difficileso far, with a genome of 131 kbp. It shares morphological and genomic similarity with other large siphophages, like phage 949, infectingLactococcus lactis, and phage c-st, infectingClostridium botulinum. A PhageTerm analysis indicated the presence of 378-bp direct terminal repeats at the phiCD211 genome termini. Among striking features of phiCD211, the presence of several transposase and integrase genes suggests past recombination events with other mobile genetic elements. Several gene products potentially influence the bacterial lifestyle and fitness, including a putative AcrB/AcrD/AcrF multidrug resistance protein, an EzrA septation ring formation regulator, and a spore protease. We also identified a CRISPR locus and acas3gene. We screened 2,584C. difficilegenomes available and detected 149 prophages sharing ≥80% nucleotide identity with phiCD211 (5% prevalence). Overall, phiCD211-like phages were detected inC. difficilestrains corresponding to 21 different multilocus sequence type groups, showing their high prevalence. Comparative genomic analyses revealed the existence of several clusters of highly similar phiCD211-like phages. Of note, large chromosome inversions were observed in some members, as well as multiple gene insertions and module exchanges. This highlights the great plasticity and gene coding potential of the phiCD211/phiCDIF1296T genome. Our analyses also suggest active evolution involving recombination with other mobile genetic elements.IMPORTANCEClostridioides difficileis a clinically important pathogen representing a serious threat to human health. Our hypothesis is that genetic differences between strains caused by the presence of integrated prophages could explain the apparent differences observed in the virulence of differentC. difficilestrains. In this study, we provide a full characterization of phiCD211, also known as phiCDIF1296T, the largest phage known to infectC. difficileso far. Screening 2,584C. difficilegenomes revealed the presence of highly similar phiCD211-like phages in 5% of the strains analyzed, showing their high prevalence. Multiple-genome comparisons suggest that evolution of the phiCD211-like phage community is dynamic, and some members have acquired genes that could influence bacterial biology and fitness. Our study further supports the relevance of studying phages inC. difficileto better understand the epidemiology of this clinically important human pathogen.

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 Foodborne Pathogenic Vibrios: Antimicrobial Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Dipanjan Dutta ◽  
Anupam Kaushik ◽  
Dhirendra Kumar ◽  
Satyabrata Bag
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Vibrio Vulnificus ◽  
Mobile Genetic Elements ◽  
Generation Cephalosporin ◽  
Watery Diarrhea ◽  
Comparative Genomic ◽  
Freshwater Environment ◽  
Genetic Elements ◽  
Pathogenic Vibrios

Foodborne illness caused by pathogenic Vibrios is generally associated with the consumption of raw or undercooked seafood. Fish and other seafood can be contaminated with Vibrio species, natural inhabitants of the marine, estuarine, and freshwater environment. Pathogenic Vibrios of major public health concerns are Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. Common symptoms of foodborne Vibrio infection include watery diarrhea, stomach cramping, nausea, vomiting, fever, and chills. Administration of oral or intravenous rehydration salts solution is the mainstay for the management of cholera, and antibiotics are also used to shorten the duration of diarrhea and to limit further transmission of the disease. Currently, doxycycline, azithromycin, or ciprofloxacin are commonly used for V. cholerae, and doxycycline or quinolone are administered for V. parahaemolyticus, whereas doxycycline and a third-generation cephalosporin are recommended for V. vulnificus as initial treatment regimen. The emergence of antimicrobial resistance (AMR) in Vibrios is increasingly common across the globe and a decrease in the effectiveness of commonly available antibiotics poses a global threat to public health. Recent progress in comparative genomic studies suggests that the genomes of the drug-resistant Vibrios harbor mobile genetic elements like plasmids, integrating conjugative elements, superintegron, transposable elements, and insertion sequences, which are the major carriers of genetic determinants encoding antimicrobial resistance. These mobile genetic elements are highly dynamic and could potentially propagate to other bacteria through horizontal gene transfer (HGT). To combat the serious threat of rising AMR, it is crucial to develop strategies for robust surveillance, use of new/novel pharmaceuticals, and prevention of antibiotic misuse.

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.

Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India

2021 ◽  
Author(s):  
Chaitra Shankar ◽  
Jobin John Jacob ◽  
Suganya Gopal Sugumar ◽  
Lavanya Natarajan ◽  
Camilla Rodrigues ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Clonal Expansion ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Carbapenem Resistant
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