Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

Abstract Background Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines. Here, we aimed to identify novel immunogenic Shigella antigens that could serve as Shigella vaccine candidates, either alone, or when conjugated to Shigella O-antigen. Methods Using a reverse vaccinology approach, where genomic analysis informed the Shigella immunome via an antigen microarray, we aimed to identify novel immunogenic Shigella antigens. A core genome analysis of Shigella species, pathogenic and non-pathogenic Escherichia coli, led to the selection of 234 predicted immunogenic Shigella antigens. These antigens were expressed and probed with acute and convalescent serum from microbiologically confirmed Shigella infections. Results Several Shigella antigens displayed IgG and IgA seroconversion, with no difference in sero-reactivity across by sex or age. IgG sero-reactivity to key Shigella antigens was observed at birth, indicating transplacental antibody transfer. Six antigens (FepA, EmrK, FhuA, MdtA, NlpB, and CjrA) were identified in in vivo testing as capable of producing binding IgG and complement-mediated bactericidal antibody. Conclusions These findings provide six novel immunogenic Shigella proteins that could serve as candidate vaccine antigens, species-specific carrier proteins, or targeted adjuvants.

Download Full-text

Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

Scientific Reports ◽

10.1038/s41598-020-80690-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongru Su ◽

Eri Onoda ◽

Hitoshi Tai ◽

Hiromi Fujita ◽

Shigetoshi Sakabe ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Core Genome ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Housekeeping Genes ◽

Pcr Screening ◽

Taxonomic Profiling ◽

Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

Download Full-text

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.

Download Full-text

Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.

Infection Genetics and Evolution ◽

10.1016/j.meegid.2018.10.021 ◽

2019 ◽

Vol 67 ◽

pp. 38-43 ◽

Cited By ~ 4

Author(s):

Jagadesan Sankarasubramanian ◽

Udayakumar S. Vishnu ◽

Paramasamy Gunasekaran ◽

Jeyaprakash Rajendhran

Keyword(s):

Multilocus Sequence Typing ◽

Core Genome

Download Full-text

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Genome Biology ◽

10.1186/s13059-021-02473-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Rachel M. Colquhoun ◽

Michael B. Hall ◽

Leandro Lima ◽

Leah W. Roberts ◽

Kerri M. Malone ◽

...

Keyword(s):

Core Genome ◽

Graph Structure ◽

Rare Snps ◽

Pan Genome ◽

Nucleotide Resolution ◽

Reference Bias ◽

Multiple Samples ◽

Reference Graph ◽

Genome Graph ◽

Better Than

AbstractWe present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.

Download Full-text

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer

Microorganisms ◽

10.3390/microorganisms9081761 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1761

Author(s):

Gaurav Agarwal ◽

Ronald D. Gitaitis ◽

Bhabesh Dutta

Keyword(s):

Gene Transfer ◽

Core Genome ◽

Foxtail Millet ◽

Gene Clusters ◽

Evaluation Study ◽

Full Spectrum ◽

Pan Genome ◽

Pantoea Stewartii ◽

Comparative Phylogenetic Analysis ◽

Core Genes

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.

Download Full-text

Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis

Microbial Genomics ◽

10.1099/mgen.0.000347 ◽

2020 ◽

Vol 6 (4) ◽

Cited By ~ 2

Author(s):

Floriana Gona ◽

Francesco Comandatore ◽

Simone Battaglia ◽

Aurora Piazza ◽

Alberto Trovato ◽

...

Keyword(s):

Cluster Analysis ◽

Klebsiella Pneumoniae ◽

Core Genome

Download Full-text

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

10.1101/173146 ◽

2017 ◽

Cited By ~ 5

Author(s):

Mickael Silva ◽

Miguel Machado ◽

Diogo N. Silva ◽

Mirko Rossi ◽

Jacob Moran-Gilad ◽

...

Keyword(s):

Open Source ◽

Core Genome ◽

Bacterial Species ◽

Outbreak Detection ◽

Strain Identification ◽

List Type ◽

Whole Genome ◽

Link Type ◽

The Creation ◽

Allele Calling

ABSTRACTGene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available athttps://github.com/B-UMMI/chewBBACAor as a docker image athttps://hub.docker.com/r/ummidock/chewbbaca/.DATA SUMMARYAssembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted asStreptococcus agalactiaetaxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare (https://figshare.com/s/9cbe1d422805db54cd52), where a file with the original ftp link for each NCBI directory is also available.Code for the chewBBACA suite is available athttps://github.com/B-UMMI/chewBBACAwhile the tutorial example is found athttps://github.com/B-UMMI/chewBBACA_tutorial.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠IMPACT STATEMENTThe chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability. The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.

Download Full-text