scholarly journals Different evolutionary trends form the twilight zone of the bacterial pan-genome

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Gal Horesh ◽  
Alyce Taylor-Brown ◽  
Stephanie McGimpsey ◽  
Florent Lassalle ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Population Structure ◽  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Resistance Mechanisms ◽  
Content Type ◽  
Pan Genome ◽  
Metabolic Versatility ◽  
Species Population ◽  
Genome Analyses ◽  
Uneven Sampling

The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.

scholarly journals Different evolutionary trends form the twilight zone of the bacterial pan-genome

2021 ◽  
Author(s):  
Gal Horesh ◽  
Alyce Taylor-Brown ◽  
Stephanie McGimpsey ◽  
Florent Lassalle ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Population Structure ◽  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Resistance Mechanisms ◽  
E Coli ◽  
Pan Genome ◽  
Metabolic Versatility ◽  
Species Population ◽  
Genome Analyses ◽  
Uneven Sampling

AbstractThe pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialised bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7,500 E. coli genomes, one of the most-studied bacterial species used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

scholarly journals Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Virulence Factors ◽  
Evolutionary Dynamics ◽  
Content Type ◽  
Pan Genome ◽  
Gastrointestinal Pathogen ◽  
High Level ◽  
Core Genes ◽  
Isolated Species

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

scholarly journals Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Daniel Castillo ◽  
Paul D. Alvise ◽  
Ruiqi Xu ◽  
Faxing Zhang ◽  
Mathias Middelboe ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Bacterial Species ◽  
Vibrio Anguillarum ◽  
Genomic Diversity ◽  
Comparative Genome ◽  
Accessory Genome ◽  
Pan Genome ◽  
Virulent Strains ◽  
Genome Analyses ◽  
Unique Core

ABSTRACT Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.

scholarly journals Distinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Cooper J. Park ◽  
Cheryl P. Andam
Keyword(s):  
Salmonella Enterica ◽  
Bacterial Species ◽  
Foodborne Pathogen ◽  
Disease Outbreaks ◽  
Thiamine Pyrophosphate ◽  
Data Set ◽  
Content Type ◽  
Pan Genome ◽  
Environmental Selection ◽  
The Impact

ABSTRACT Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in Salmonella is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of S. enterica subspecies. Using a data set of previously published 926 Salmonella genomes representing the 10 S. enterica subspecies and Salmonella bongori, we calculated a genus-wide pan-genome composed of 84,041 genes and the S. enterica pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in S. enterica subsp. arizonae (subsp. IIIa) to 33,257 genes in S. enterica subsp. enterica (subsp. I). A total of 12,136 genes in the Salmonella pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure. Certain lineages, such as the more uncommon non-enterica subspecies (non-S. enterica subsp. enterica), may also act as a major reservoir of genetic diversity for the wider population. IMPORTANCE S. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.

scholarly journals Burkholderia cepacia Complex Bacteria: a Feared Contamination Risk in Water-Based Pharmaceutical Products

2020 ◽  
Vol 33 (3) ◽  
Author(s):  
Mariana Tavares ◽  
Mariya Kozak ◽  
Alexandra Balola ◽  
Isabel Sá-Correia
Keyword(s):  
Burkholderia Cepacia ◽  
Bacterial Species ◽  
Public Health Problem ◽  
Pharmaceutical Products ◽  
Health Care Facilities ◽  
Burkholderia Cepacia Complex ◽  
Pseudomonas Cepacia ◽  
Environmental Distribution ◽  
Content Type ◽  
Metabolic Versatility

SUMMARY Burkholderia cepacia (formerly Pseudomonas cepacia) was once thought to be a single bacterial species but has expanded to the Burkholderia cepacia complex (Bcc), comprising 24 closely related opportunistic pathogenic species. These bacteria have a widespread environmental distribution, an extraordinary metabolic versatility, a complex genome with three chromosomes, and a high capacity for rapid mutation and adaptation. Additionally, they present an inherent resistance to antibiotics and antiseptics, as well as the abilities to survive under nutrient-limited conditions and to metabolize the organic matter present in oligotrophic aquatic environments, even using certain antimicrobials as carbon sources. These traits constitute the reason that Bcc bacteria are considered feared contaminants of aqueous pharmaceutical and personal care products and the frequent reason behind nonsterile product recalls. Contamination with Bcc has caused numerous nosocomial outbreaks in health care facilities, presenting a health threat, particularly for patients with cystic fibrosis and chronic granulomatous disease and for immunocompromised individuals. This review addresses the role of Bcc bacteria as a potential public health problem, the mechanisms behind their success as contaminants of pharmaceutical products, particularly in the presence of biocides, the difficulties encountered in their detection, and the preventive measures applied during manufacturing processes to control contamination with these objectionable microorganisms. A summary of Bcc-related outbreaks in different clinical settings, due to contamination of diverse types of pharmaceutical products, is provided.

scholarly journals Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Marina Muñoz ◽  
Enzo Guerrero-Araya ◽  
Catalina Cortés-Tapia ◽  
Angela Plaza-Garrido ◽  
Trevor D. Lawley ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Intestinal Homeostasis ◽  
Content Type ◽  
Link Type ◽  
Potential Biomarker ◽  
Antimicrobial Resistance Genes ◽  
Genome Analyses

Sellimonas intestinalis is a Gram-positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who have recovered from intestinal homeostasis after dysbiosis events. In this context, the aim of the present study was to take advantage of a massive in vitro culture protocol that allowed the recovery of extremely oxygen-sensitive species from faecal samples, which led to isolation of S. intestinalis . Whole genome analyses of 11  S . intestinalis genomes revealed that this species has a highly conserved genome with 99.7 % 16S rRNA gene sequence similarity, average nucleotide polymorphism results >95, and 50.1 % of its coding potential being part of the core genome. Despite this, the variable portion of its genome was informative enough to reveal the existence of three lineages (lineage-I including isolates from Chile and France, lineage-II from South Korea and Finland, and lineage-III from China and one isolate from the USA) and evidence of some recombination signals. The identification of a cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for microbiota from healthy individuals. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in lineage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about the potential of S. intestinalis as a bioindicator of intestinal homeostasis recovery and contribute to advancing the characterization of gut microbiota members with beneficial potential.

scholarly journals Remodeling of pSK1 Family Plasmids and Enhanced Chlorhexidine Tolerance in a Dominant Hospital Lineage of Methicillin-ResistantStaphylococcus aureus

2019 ◽  
Vol 63 (5) ◽  
Author(s):  
Sarah L. Baines ◽  
Slade O. Jensen ◽  
Neville Firth ◽  
Anders Gonçalves da Silva ◽  
Torsten Seemann ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Resistance Mechanisms ◽  
Structural Variants ◽  
Content Type ◽  
Susceptibility Data ◽  
Enhanced Resistance ◽  
Evolutionary Response ◽  
Global Spread ◽  
Gentamicin Resistance ◽  
Phenotypic Susceptibility

ABSTRACTStaphylococcus aureusis a significant human pathogen whose evolution and adaptation have been shaped in part by mobile genetic elements (MGEs), facilitating the global spread of extensive antimicrobial resistance. However, our understanding of the evolutionary dynamics surrounding MGEs, in particular, how changes in the structure of multidrug resistance (MDR) plasmids may influence important staphylococcal phenotypes, is incomplete. Here, we undertook a population and functional genomics study of 212 methicillin-resistantS. aureus(MRSA) sequence type 239 (ST239) isolates collected over 32 years to explore the evolution of the pSK1 family of MDR plasmids, illustrating how these plasmids have coevolved with and contributed to the successful adaptation of this persistent MRSA lineage. Using complete genomes and temporal phylogenomics, we reconstructed the evolution of the pSK1 family lineage from its emergence in the late 1970s and found that multiple structural variants have arisen. Plasmid maintenance and stability were linked to IS256- and IS257-mediated chromosomal integration and disruption of the plasmid replication machinery. Overlaying genomic comparisons with phenotypic susceptibility data for gentamicin, trimethoprim, and chlorhexidine, it appeared that pSK1 has contributed to enhanced resistance in ST239 MRSA isolates through two mechanisms: (i) acquisition of plasmid-borne resistance mechanisms increasing the rates of gentamicin resistance and reduced chlorhexidine susceptibility and (ii) changes in the plasmid configuration linked with further enhancement of chlorhexidine tolerance. While the exact mechanism of enhanced tolerance remains elusive, this research has uncovered a potential evolutionary response of ST239 MRSA to biocides, one of which may contribute to the ongoing persistence and adaptation of this lineage within health care institutions.

scholarly journals Genetic Contexts ofblaNDM-1in Patients Carrying Multiple NDM-Producing Strains

2015 ◽  
Vol 59 (12) ◽  
pp. 7405-7410 ◽  
Author(s):  
Alexander M. Wailan ◽  
Anna L. Sartor ◽  
Hosam M. Zowawi ◽  
John D. Perry ◽  
David L. Paterson ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Species ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Gram Negative ◽  
Content Type ◽  
Novel Approach ◽  
Plasmid Replicon ◽  
Underlying Mechanisms ◽  
Genetic Context

ABSTRACTThe carbapenem resistance determinantblaNDM-1has been found in various Gram-negative bacteria and upon different plasmid replicon types (Inc). Here, we present four patients within two hospitals in Pakistan harboring between two and four NDM-1-producing Gram-negative bacilli of different species coresident in their stool samples. We characterize theblaNDM-1genetic contexts of these 11 NDM-1-producing Gram-negative bacilli in addition to other antimicrobial resistance mechanisms, plasmid replicon profiles, and sequence types (STs) in order to understand the underlying acquisition mechanisms of carbapenem resistance within these bacteria. Two common plasmid types (IncN2 and IncA/C) were identified to carryblaNDM-1among the six different bacterial species isolated from the four patients. Two of these strains were novelCitrobacter freundiiST 20 and ST 21. The same IncN2-typeblaNDM-1genetic context was found in all four patients and within four different species. The IncA/C-typeblaNDM-1genetic context was found in two different species and in two of the four patients. Combining genetic context characterization with other molecular epidemiology methods, we were able to establish the molecular epidemiological links between genetically unrelated bacterial species by linking their acquisition of an IncN2 or IncA/C plasmid carryingblaNDM-1for carbapenem resistance. By combining plasmid characterization and in-depth genetic context assessment, this analysis highlights the importance of plasmids in antimicrobial resistance. It also provides a novel approach for investigating the underlying mechanisms ofblaNDM-1-related spread between bacterial species and genera via plasmids.

scholarly journals Urease Activity Represents an Alternative Pathway for Mycobacterium tuberculosis Nitrogen Metabolism

2012 ◽  
Vol 80 (8) ◽  
pp. 2771-2779 ◽  
Author(s):  
Wenwei Lin ◽  
Vanessa Mathys ◽  
Emily Lei Yin Ang ◽  
Vanessa Hui Qi Koh ◽  
Julia María Martínez Gómez ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Urease Activity ◽  
Alternative Pathway ◽  
Bacterial Species ◽  
Deficient Mutant ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTUrease represents a critical virulence factor for some bacterial species through its alkalizing effect, which helps neutralize the acidic microenvironment of the pathogen. In addition, urease serves as a nitrogen source provider for bacterial growth. Pathogenic mycobacteria express a functional urease, but its role during infection has yet to be characterized. In this study, we constructed a urease-deficientMycobacterium tuberculosisstrain and confirmed the alkalizing effect of the urease activity within the mycobacterium-containing vacuole in resting macrophages but not in the more acidic phagolysosomal compartment of activated macrophages. However, the urease-mediated alkalizing effect did not confer any growth advantage onM. tuberculosisin macrophages, as evidenced by comparable growth profiles for the mutant, wild-type (WT), and complemented strains. In contrast, the urease-deficient mutant exhibited impairedin vitrogrowth compared to the WT and complemented strains when urea was the sole source of nitrogen. Substantial amounts of ammonia were produced by the WT and complemented strains, but not with the urease-deficient mutant, which represents the actual nitrogen source for mycobacterial growth. However, the urease-deficient mutant displayed parental colonization profiles in the lungs, spleen, and liver in mice. Together, our data demonstrate a role for the urease activity inM. tuberculosisnitrogen metabolism that could be crucial for the pathogen's survival in nutrient-limited microenvironments where urea is the sole nitrogen source. Our work supports the notion thatM. tuberculosisvirulence correlates with its unique metabolic versatility and ability to utilize virtually any carbon and nitrogen sources available in its environment.

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