scholarly journals Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

2020 ◽  
Vol 59 (1) ◽  
pp. e02198-20
Author(s):  
N. Effelsberg ◽  
M. Stegger ◽  
L. Peitzmann ◽  
O. Altinok ◽  
G. W. Coombs ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
De Novo ◽  
Clinical Symptoms ◽  
Phylogenetic Analyses ◽  
Invasive Disease ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Global Epidemiology ◽  
History Of

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.

scholarly journals Human Origin for Livestock-Associated Methicillin-Resistant Staphylococcus aureus

mBio ◽  
2012 ◽  
Vol 3 (2) ◽  
Author(s):  
J. Ross Fitzgerald
Keyword(s):  
Staphylococcus Aureus ◽  
Evolutionary History ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Agricultural Practices ◽  
Methicillin Resistant ◽  
Content Type ◽  
Zoonotic Infections ◽  
Ancestral Origin ◽  
Important Study ◽  
History Of

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of human morbidity and mortality worldwide. The emergence in the last decade of a livestock-associated MRSA (LA-MRSA) clone which also has the capacity to cause zoonotic infections in humans has raised important questions regarding its origin and its potential to cause human epidemics. An important study by L. B. Price et al. [mBio 3(1):e00305-11, 2012] provides evidence for a human ancestral origin for LA-MRSA, raising concerns about agricultural practices that may have contributed to its emergence and expansion. The study highlights the potential for comparative whole-genome sequencing of closely related strains to provide valuable insights into the evolutionary history of bacterial pathogens.

scholarly journals Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

2018 ◽  
Author(s):  
Yuuhiko Tanabe ◽  
Haruyo Yamaguchi
Keyword(s):  
Evolutionary History ◽  
Core Genome ◽  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Green Light ◽  
Water Bloom ◽  
Phylogenetic Groups ◽  
Genome Phylogeny ◽  
History Of ◽  
Genomic Basis

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.

scholarly journals The evolutionary history of Shigella flexneri serotype 6 in Asia

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Si-Nguyen T. Mai ◽  
Ladaporn Bodhidatta ◽  
Paul Turner ◽  
Sonam Wangchuk ◽  
Tuyen Ha Thanh ◽  
...  
Keyword(s):  
Type Species ◽  
Evolutionary History ◽  
Vaccine Development ◽  
Phylogenetic Analyses ◽  
Shigella Flexneri ◽  
Epidemiological Studies ◽  
Genomic Research ◽  
Phylogenetic Groups ◽  
Content Type ◽  
Link Type

Shigella flexneri serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as S. flexneri , Shigella flexneri serotype 6 is phylogenetically distinct from other S. flexneri serotypes and more closely related to S. boydii . This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of Shigella flexneri serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian Shigella flexneri serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian S. flexneri serotype 6 could be traced back to an inferred common ancestor arising in the 18th century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian S. flexneri serotypes. Similar to other S. flexneri serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied Shigella flexneri serotype 6, providing a new piece in the puzzle of Shigella epidemiology and evolution.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

Craniopharyngioma arising de novo in middle age

1997 ◽  
Vol 86 (6) ◽  
pp. 1046-1048 ◽  
Author(s):  
Marc S. Arginteanu ◽  
Karin Hague ◽  
Robert Zimmerman ◽  
Mark J. Kupersmith ◽  
John H. Shaiu ◽  
...  
Keyword(s):  
Magnetic Resonance Image ◽  
De Novo ◽  
Middle Age ◽  
Benign Tumors ◽  
Fetal Life ◽  
Content Type ◽  
Steady Growth ◽  
History Of ◽  
Sixth Decade ◽  
Fine Print

✓ The authors report the case of a 55-year-old woman who developed a symptomatic craniopharyngioma within 2 years of obtaining a normal magnetic resonance image of her brain. Craniopharyngiomas are histologically benign tumors. They are thought to arise from embryonic remnants of Rathke's pouch and sac and to manifest themselves clinically after a steady growth that commences in fetal life. To the authors' knowlege, this is the first report that documents a tumor arising de novo in the sixth decade of life. This report appears to challenge the concept of the origin and natural history of craniopharyngiomas.

scholarly journals Masking of β(1-3)-Glucan in the Cell Wall of Candida albicans from Detection by Innate Immune Cells Depends on Phosphatidylserine

2014 ◽  
Vol 82 (10) ◽  
pp. 4405-4413 ◽  
Author(s):  
Sarah E. Davis ◽  
Alex Hopke ◽  
Steven C. Minkin ◽  
Anthony E. Montedonico ◽  
Robert T. Wheeler ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candida Albicans ◽  
De Novo ◽  
Invasive Disease ◽  
Innate Immune ◽  
Dependent Manner ◽  
Content Type ◽  
Immune Effector ◽  
Host Interactions ◽  
Innate Immune Effector

ABSTRACTThe virulence ofCandida albicansin a mouse model of invasive candidiasis is dependent on the phospholipids phosphatidylserine (PS) and phosphatidylethanolamine (PE). Disruption of the PS synthase geneCHO1(i.e.,cho1Δ/Δ) eliminates PS and blocks thede novopathway for PE biosynthesis. In addition, thecho1Δ/Δ mutant's ability to cause invasive disease is severely compromised. Thecho1Δ/Δ mutant also exhibits cell wall defects, and in this study, it was determined that loss of PS results in decreased masking of cell wall β(1-3)-glucan from the immune system. In wild-typeC. albicans, the outer mannan layer of the wall masks the inner layer of β(1-3)-glucan from exposure and detection by innate immune effector molecules like the C-type signaling lectin Dectin-1, which is found on macrophages, neutrophils, and dendritic cells. Thecho1Δ/Δ mutant exhibits increases in exposure of β(1-3)-glucan, which leads to greater binding by Dectin-1 in both yeast and hyphal forms. The unmasking of β(1-3)-glucan also results in increased elicitation of TNF-α from macrophages in a Dectin-1-dependent manner. The role of phospholipids in fungal pathogenesis is an emerging field, and this is the first study showing that loss of PS inC. albicansresults in decreased masking of β(1-3)-glucan, which may contribute to our understanding of fungus-host interactions.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

scholarly journals Draft Genome Sequence of the Community-Associated Staphylococcus aureus Sequence Type 88 Strain LVP-7, Isolated from an Ocular Infection

2021 ◽  
Vol 10 (7) ◽  
Author(s):  
Savitha Nadig ◽  
Sneha Murthy ◽  
Muralidharan Vandanashree ◽  
Hosahalli S. Subramanya ◽  
Balasubramanian Gopal ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Sequence Type ◽  
Draft Genome Sequence ◽  
Ocular Infection ◽  
Content Type ◽  
Type V ◽  
Panton Valentine Leukocidin

ABSTRACT We report a de novo-assembled draft genome sequence of the Indian Staphylococcus aureus sequence type 88 (ST88) strain LVP-7, isolated from an ocular infection. The genome harbors a Panton-Valentine leukocidin phage, a type V staphylococcal cassette chromosome mec element, the delta-hemolysin-converting Newman phage ΦNM3, and the pathogenicity island SaPI3, encoding the superantigen enterotoxin B.

Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

2021 ◽  
Author(s):  
Keerthic Aswin ◽  
Srinivasan Ramachandran ◽  
Vivek T Natarajan
Keyword(s):  
Convergent Evolution ◽  
Genome Stability ◽  
Evolutionary History ◽  
Rna Binding ◽  
Phylogenetic Analyses ◽  
Comparative Genome Analysis ◽  
The Family ◽  
History Of ◽  
Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

scholarly journals Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
Author(s):  
Elena A. Ritschard ◽  
Robert R. Fitak ◽  
Oleg Simakov ◽  
Sönke Johnsen
Keyword(s):  
Signal Transduction ◽  
Positive Selection ◽  
G Protein ◽  
Evolutionary History ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Signatures ◽  
History Of ◽  
G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

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