Draft genomes of 12 host-adapted and environmental isolates ofPseudomonas aeruginosaand their positions in the core genome phylogeny

Abstract Purpose Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens. KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.

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Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw129 ◽

2016 ◽

Vol 3 (3) ◽

Cited By ~ 31

Author(s):

James R. Johnson ◽

Gregg Davis ◽

Connie Clabots ◽

Brian D. Johnston ◽

Stephen Porter ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Core Genome ◽

Sequence Type ◽

Whole Genome Sequence ◽

Whole Genome ◽

The Core ◽

Genome Phylogeny ◽

Genome Level ◽

Repeated Infections

Abstract Background. Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods. Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results. In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member. Conclusions. Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.

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A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Journal of Bacteriology ◽

10.1128/jb.01202-08 ◽

2008 ◽

Vol 191 (1) ◽

pp. 91-99 ◽

Cited By ~ 115

Author(s):

Marc Deloger ◽

Meriem El Karoui ◽

Marie-Agnès Petit

Keyword(s):

Dna Sequences ◽

Dna Content ◽

Core Genome ◽

Biological Diversity ◽

Bacterial Species ◽

Genomic Distance ◽

The Core ◽

Intraspecies Diversity ◽

Genome Level ◽

Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0475 ◽

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’.

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The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis

BMC Genomics ◽

10.1186/s12864-020-06817-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Áron B. Kovács ◽

Zsuzsa Kreizinger ◽

Barbara Forró ◽

Dénes Grózner ◽

Alexa Mitter ◽

...

Keyword(s):

Core Genome ◽

Multi Locus Sequence Typing ◽

The Core

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Revisiting Bap Multidomain Protein: More Than Sticking Bacteria Together

Frontiers in Microbiology ◽

10.3389/fmicb.2020.613581 ◽

2020 ◽

Vol 11 ◽

Author(s):

Jaione Valle ◽

Xianyang Fang ◽

Iñigo Lasa

Keyword(s):

Biofilm Formation ◽

Core Genome ◽

Current Knowledge ◽

Surface Proteins ◽

Structure And Properties ◽

Diverse Range ◽

The Core ◽

Self Assembling ◽

Abiotic Surfaces ◽

Range Of Functions

One of the major components of the staphylococcal biofilm is surface proteins that assemble as scaffold components of the biofilm matrix. Among the different surface proteins able to contribute to biofilm formation, this review is dedicated to the Biofilm Associated Protein (Bap). Bap is part of the accessory genome of Staphylococcus aureus but orthologs of Bap in other staphylococcal species belong to the core genome. When present, Bap promotes adhesion to abiotic surfaces and induces strong intercellular adhesion by self-assembling into amyloid like aggregates in response to the levels of calcium and the pH in the environment. During infection, Bap enhances the adhesion to epithelial cells where it binds directly to the host receptor Gp96 and inhibits the entry of the bacteria into the cells. To perform such diverse range of functions, Bap comprises several domains, and some of them include several motifs associated to distinct functions. Based on the knowledge accumulated with the Bap protein of S. aureus, this review aims to summarize the current knowledge of the structure and properties of each domain of Bap and their contribution to Bap functionality.

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Why? – Successful Pseudomonas aeruginosa clones with a focus on clone C

FEMS Microbiology Reviews ◽

10.1093/femsre/fuaa029 ◽

2020 ◽

Vol 44 (6) ◽

pp. 740-762

Author(s):

Changhan Lee ◽

Jens Klockgether ◽

Sebastian Fischer ◽

Janja Trcek ◽

Burkhard Tümmler ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Core Genome ◽

Genomic Island ◽

Protein Quality ◽

Temperature Tolerance ◽

Protein Homeostasis ◽

Gene Products ◽

Accessory Genome ◽

The Core ◽

Conserved Core

ABSTRACT The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.

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Core Genome Allelic Profiles of Clinical Klebsiella pneumoniae Strains Using a Random Forest Algorithm Based on Multilocus Sequence Typing Scheme for Hypervirulence Analysis

The Journal of Infectious Diseases ◽

10.1093/infdis/jiz562 ◽

2020 ◽

Vol 221 (Supplement_2) ◽

pp. S263-S271 ◽

Cited By ~ 1

Author(s):

Peng Lan ◽

Qiucheng Shi ◽

Ping Zhang ◽

Yan Chen ◽

Rushuang Yan ◽

...

Keyword(s):

Random Forest ◽

Klebsiella Pneumoniae ◽

Multilocus Sequence Typing ◽

Operating Characteristic ◽

Core Genome ◽

Characteristic Curve ◽

Random Forest Algorithm ◽

The Core ◽

Model Based ◽

Operating Characteristic Curve

Abstract Background Hypervirulent Klebsiella pneumoniae (hvKP) infections can have high morbidity and mortality rates owing to their invasiveness and virulence. However, there are no effective tools or biomarkers to discriminate between hvKP and nonhypervirulent K. pneumoniae (nhvKP) strains. We aimed to use a random forest algorithm to predict hvKP based on core-genome data. Methods In total, 272 K. pneumoniae strains were collected from 20 tertiary hospitals in China and divided into hvKP and nhvKP groups according to clinical criteria. Clinical data comparisons, whole-genome sequencing, virulence profile analysis, and core genome multilocus sequence typing (cgMLST) were performed. We then established a random forest predictive model based on the cgMLST scheme to prospectively identify hvKP. The random forest is an ensemble learning method that generates multiple decision trees during the training process and each decision tree will output its own prediction results corresponding to the input. The predictive ability of the model was assessed by means of area under the receiver operating characteristic curve. Results Patients in the hvKP group were younger than those in the nhvKP group (median age, 58.0 and 68.0 years, respectively; P < .001). More patients in the hvKP group had underlying diabetes mellitus (43.1% vs 20.1%; P < .001). Clinically, carbapenem-resistant K. pneumoniae was less common in the hvKP group (4.1% vs 63.8%; P < .001), whereas the K1/K2 serotype, sequence type (ST) 23, and positive string tests were significantly higher in the hvKP group. A cgMLST-based minimal spanning tree revealed that hvKP strains were scattered sporadically within nhvKP clusters. ST23 showed greater genome diversification than did ST11, according to cgMLST-based allelic differences. Primary virulence factors (rmpA, iucA, positive string test result, and the presence of virulence plasmid pLVPK) were poor predictors of the hypervirulence phenotype. The random forest model based on the core genome allelic profile presented excellent predictive power, both in the training and validating sets (area under receiver operating characteristic curve, 0.987 and 0.999 in the training and validating sets, respectively). Conclusions A random forest algorithm predictive model based on the core genome allelic profiles of K. pneumoniae was accurate to identify the hypervirulent isolates.

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Transmission of Vancomycin-Resistant Enterococci in the Hospital Setting: Uncovering the Patient–Environment Interplay

Microorganisms ◽

10.3390/microorganisms8020203 ◽

2020 ◽

Vol 8 (2) ◽

pp. 203 ◽

Cited By ~ 3

Author(s):

Carlos L. Correa-Martinez ◽

Hauke Tönnies ◽

Neele J. Froböse ◽

Alexander Mellmann ◽

Stefanie Kampmeier

Keyword(s):

Core Genome ◽

Hospital Setting ◽

Hospital Environment ◽

Environmental Isolates ◽

Resistance Determinants ◽

Vancomycin Resistant Enterococci ◽

Vancomycin Resistant ◽

And Control ◽

Sequence Types

Vancomycin-resistant enterococci (VRE) are relevant nosocomial pathogens with an increasing incidence in the last decades. Their transmission is optimal in the hospital setting, as it offers two potential, large reservoirs that are closely related: susceptible patients and their environment. Here we investigate the role of the hospital environment in the nosocomial transmission of VRE by establishing concrete links between contaminated surfaces and colonized/infected patients in outbreak and non-outbreak settings. Environmental and patient VRE isolates were collected between 2013 and 2019 and analyzed by whole-genome sequencing (WGS), subsequent multilocus sequence typing (MLST), and core genome (cg) MLST. Pairs of isolates differing in <3 alleles were rated as closely related, making a transmission likely. Fifty-three environmental VRE isolates were analyzed. MLST sequence types (ST) ST203 (50.0%), ST192 (21.3%), ST117 (17.3%), ST721 (8.8%), ST80 (2%), and ST1489 (0.7%) were detected, carrying the resistance determinants vanA (72.7%), vanB (24%), or both (3.3%). Of the 53 environmental isolates, 51 were found to form five clusters with genetically related patient isolates (n = 97 isolates). WGS confirms the role of the environment in the transmission dynamics of VRE in both the outbreak and non-outbreak settings, highlighting the importance of prevention and control of VRE spread.

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Genome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551

Genome Biology and Evolution ◽

10.1093/gbe/evz189 ◽

2019 ◽

Vol 11 (9) ◽

pp. 2557-2562 ◽

Cited By ~ 2

Author(s):

Sarwar Azam ◽

Sunil Parthasarathy ◽

Chhaya Singh ◽

Shakti Kumar ◽

Dayananda Siddavattam

Keyword(s):

Core Genome ◽

Gc Content ◽

Mobile Element ◽

Membrane Receptors ◽

Harsh Environments ◽

Adaptive Potential ◽

Gene Encoding ◽

Organophosphate Hydrolase ◽

The Core ◽

Close Relationship

Abstract Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.

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