scholarly journals To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Jorge A. Moura de Sousa ◽  
Eduardo P. C. Rocha
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Abundance Distribution ◽  
Theme Issue ◽  
Genetic Elements ◽  
The Core ◽  
Antagonistic Interactions ◽  
Variable Genes

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli , sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

scholarly journals To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites

2021 ◽  
Author(s):  
Jorge Moura de Sousa ◽  
Eduardo P. C. Rocha
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Molecular Evolution ◽  
Molecular Mechanisms ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Abundance Distribution ◽  
The Core ◽  
Antagonistic Interactions ◽  
Variable Genes

Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution, and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 10% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding co-evolution. They also reveal broad host ranges in P4-like elements, since almost identical elements can be found in distinct bacterial genuses. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites.

scholarly journals Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

2021 ◽  
Author(s):  
Rebecca J Hall ◽  
Fiona J Whelan ◽  
Elizabeth A Cummins ◽  
Christopher Connor ◽  
Alan McNally ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complex Network ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Dynamic Nature ◽  
Accessory Genome ◽  
Genetic Elements ◽  
The Core ◽  
Sequence Types

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene, suggesting that cooperation is more common than conflict in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

scholarly journals Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Rebecca J. Hall ◽  
Fiona J. Whelan ◽  
Elizabeth A. Cummins ◽  
Christopher Connor ◽  
Alan McNally ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complex Network ◽  
Type Species ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Dynamic Nature ◽  
Content Type ◽  
Accessory Genome ◽  
The Core ◽  
Sequence Types

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

scholarly journals Comparative genomics of Xylella fastidiosa suggests determinants of host-specificity and expands its mobile genetic elements repertoire

2021 ◽  
Author(s):  
Guillermo Uceda-Campos ◽  
Oseias R. Feitosa-Junior ◽  
Caio R.N. Santiago ◽  
Paulo M. Pierry ◽  
Paulo A. Zaini ◽  
...  
Keyword(s):  
Host Specificity ◽  
Plant Species ◽  
Core Genome ◽  
Xylella Fastidiosa ◽  
Mobile Genetic Elements ◽  
Plant Host ◽  
Genetic Elements ◽  
The Core ◽  
Plant Hosts ◽  
Specificity Determinants

The Gram-negative bacterium Xylella fastidiosa colonizes plant xylem vessels and is obligately vectored by xylem sap-feeding hemipteran insects. X. fastidiosa causes diseases in many plant species but in a variety of its plant hosts this bacterium behaves as a commensal endophyte. Originally confined to the Americas, infecting mainly grapevine, citrus and coffee plants, X. fastidiosa has spread to several plant species in Europe, causing devastating crop diseases. Although many pathogenicity and virulence factors have been identified in X. fastidiosa which enable the bacterium to successfully establish in the xylem tissue, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in specific plant hosts have not been fully elucidated. Here we present comparative analyses of 94 publicly available whole-genome sequences of X. fastidiosa strains with the goal of providing insights into plant host specificity determinants for this phytopathogen as well as of expanding the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results revealed a pangenome of 4,549 protein coding sequences (CDSs) which is still open. The core- and accessory genomes comprise 954 and 2,219 CDSs, respectively. Phylogenetic tree construction using all core genome CDSs grouped the strains in three major clades of subspecies fastidiosa, multiplex and pauca, with subclades related to the strains sequence type (ST) obtained from multi-locus sequence typing (MLST). The geographic region where the strains were collected showed stronger association with the clades of X. fastidiosa strains rather than the plant species from which they were isolated. Among the CDSs related to virulence and pathogenicity found in the core genome, those related to lipopolysaccharide (LPS) synthesis and trimeric autotransporter adhesins (TAA) are somewhat related with the plant host of a given strain according to phylogenetic inference. The X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, which includes a diversity of prophage regions. In summary, the genome comparisons reported here will enable a better understanding of the diversity of phylogenetically close genomes and warrant further investigation of LPS and TAAs as potential X. fastidiosa host-specificity determinants.

scholarly journals Genomic evolution of antimicrobial resistance in Escherichia coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Markus Hans Kristofer Johansson ◽  
Patrick Munk ◽  
Burkhard Malorny ◽  
Magdalena Skarżyńska ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Mobile Genetic Elements ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Fecal Samples ◽  
E Coli ◽  
Genetic Elements

AbstractThe emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

scholarly journals Escherichia coli ST131: a multidrug-resistant clone primed for global domination

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 195 ◽  
Author(s):  
Johann D.D. Pitout ◽  
Rebekah DeVinney
Keyword(s):  
Escherichia Coli ◽  
Core Genome ◽  
Multidrug Resistant ◽  
Accessory Gene ◽  
The Core ◽  
Gene Profiles ◽  
Clade C ◽  
Compensatory Mutations ◽  
The 1960S ◽  
Sequential Acquisition

A single extra-intestinal pathogenic Escherichia coli (ExPEC) clone, named sequence type (ST) 131, is responsible for millions of global antimicrobial-resistant (AMR) infections annually. Population genetics indicate that ST131 consists of different clades (i.e. A, B, and C); however, clade C is the most dominant globally. A ST131 subclade, named C1-M27, is emerging in Japan and has been responsible for the recent increase in AMR ExPEC in that country. The sequential acquisition of several virulence and AMR genes associated with mobile genetic elements during the 1960s to 1980s primed clade C (and its subclades C1 and C2) for success in the 1990s to 2000s. IncF plasmids with F1:A2:B20 and F2:A1:B replicons have shaped the evolution of the C1 and C2 subclades. It is possible that ST131 is a host generalist with different accessory gene profiles. Compensatory mutations within the core genome of this clone have counterbalanced the fitness cost associated with IncF plasmids. ST131 clade C had dramatically changed the population structure of ExPEC, but it still remains unclear which features of this clade resulted in one of the most unprecedented AMR successes of the 2000s.

scholarly journals Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Nicole Stoesser ◽  
Anna E. Sheppard ◽  
Louise Pankhurst ◽  
Nicola De Maio ◽  
Catrin E. Moore ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Evolutionary History ◽  
Mobile Genetic Elements ◽  
The United States ◽  
Sequence Type ◽  
E Coli ◽  
Genetic Elements ◽  
Extended Spectrum ◽  
History Of

ABSTRACT Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection ( n = 215) of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/ H 30R and C2/ H 30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/ H 30Rx clade driven by the acquisition of a bla CTX-M-15 -containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of bla CTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the bla CTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli . These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. IMPORTANCE Escherichia coli , perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specific E. coli lineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.

CTX-M- and pAmpC-Encoding Genes Are Associated with Similar Mobile Genetic Elements in Escherichia coli Isolated from Different Brands of Brazilian Chicken Meat

2020 ◽  
Vol 26 (1) ◽  
pp. 14-20 ◽  
Author(s):  
Larissa Alvarenga Batista Botelho ◽  
Gabriela Bergiante Kraychete ◽  
Patrícia Batista Rocha ◽  
Ana Paula de Souza da-Silva ◽  
Renata Cristina Picão ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Mobile Genetic Elements ◽  
Chicken Meat ◽  
Genetic Elements ◽  
Encoding Genes

Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria

2021 ◽  
Vol 377 (1842) ◽  
Author(s):  
Alexandra J. Weisberg ◽  
Marilyn Miller ◽  
Walt Ream ◽  
Niklaus J. Grünwald ◽  
Jeff H. Chang
Keyword(s):  
Mobile Genetic Elements ◽  
Nitrogen Fixing ◽  
Genome Sequences ◽  
Theme Issue ◽  
Nitrogen Fixing Bacteria ◽  
Disease Symptoms ◽  
Genetic Elements ◽  
Virulence Plasmids ◽  
Evolution Of Genomes

Members of the agrobacteria–rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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