scholarly journals Genome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Kumaragurubaran Karthik ◽  
Subbaiyan Anbazhagan ◽  
Prasad Thomas ◽  
Murugesan Ananda Chitra ◽  
Tuticorin Maragatham Alagesan Senthilkumar ◽  
...  
Keyword(s):  
Tamil Nadu ◽  
Core Genome ◽  
Virulence Genes ◽  
Small Ruminant ◽  
Brucella Melitensis ◽  
Bootstrap Support ◽  
Specific Gene ◽  
Family Protein ◽  
Indian Isolates ◽  
Genome Phylogeny

Brucella melitensis causes small ruminant brucellosis and a zoonotic pathogen prevalent worldwide. Whole genome phylogeny of all available B. melitensis genomes (n = 355) revealed that all Indian isolates (n = 16) clustered in the East Mediterranean lineage except the ADMAS-GI strain. Pangenome analysis indicated the presence of limited accessory genomes with few clades showing specific gene presence/absence pattern. A total of 43 virulence genes were predicted in all the Indian strains of B. melitensis except 2007BM-1 (ricA and wbkA are absent). Multilocus sequence typing (MLST) analysis indicated all except one Indian strain (ADMAS-GI) falling into sequence type (ST 8). In comparison with MLST, core genome phylogeny indicated two major clusters (>70% bootstrap support values) among Indian strains. Clusters with <70% bootstrap support values represent strains with diverse evolutionary origins present among animal and human hosts. Genetic relatedness among animal (sheep and goats) and human strains with 100% bootstrap values shows its zoonotic transfer potentiality. SNP-based analysis indicated similar clustering to that of core genome phylogeny. Among the Indian strains, the highest number of unique SNPs (112 SNPs) were shared by a node that involved three strains from Tamil Nadu. The node SNPs involved several peptidase genes like U32, M16 inactive domain protein, clp protease family protein, and M23 family protein and mostly represented non-synonymous (NS) substitutions. Vaccination has been followed in several parts of the world to prevent small ruminant brucellosis but not in India. Comparison of Indian strains with vaccine strains showed that M5 is genetically closer to most of the Indian strains than Rev.1 strain. The presence of most of the virulence genes among all Indian strains and conserved core genome compositions suggest the use of any circulating strain/genotypes for the development of a vaccine candidate for small ruminant brucellosis in India.

scholarly journals Transcription of Candidate Virulence Genes ofHaemophilus ducreyi during Infection of Human Volunteers

2001 ◽  
Vol 69 (3) ◽  
pp. 1483-1487 ◽  
Author(s):  
Robert E. Throm ◽  
Stanley M. Spinola
Keyword(s):  
Experimental Infection ◽  
Virulence Genes ◽  
Human Model ◽  
Specific Gene ◽  
Gene Products ◽  
Virulence Determinants ◽  
Reverse Transcription Pcr ◽  
Human Volunteers

ABSTRACT Haemophilus ducreyi expresses several putative virulence factors in vitro. Isogenic mutant-to-parent comparisons have been performed in a human model of experimental infection to examine whether specific gene products are involved in pathogenesis. Several mutants (momp, ftpA, losB, lst, cdtC, and hhdB) were as virulent as the parent in the human model, suggesting that their gene products did not play a major role in pustule formation. However, we could not exclude the possibility that the gene of interest was not expressed during the initial stages of infection. Biopsies of pustules obtained from volunteers infected with H. ducreyiwere subjected to reverse transcription-PCR. Transcripts corresponding to momp, ftpA, losB, lst, cdtB, and hhdA were expressed in vivo. In addition, transcripts for other putative virulence determinants such as ompA2, tdhA, lspA1, andlspA2 were detected in the biopsies. These results indicate that although several candidate virulence determinants are expressed during experimental infection, they do not have a major role in the initial stages of pathogenesis.

scholarly journals Genomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 177 ◽  
Author(s):  
Yael Yagel ◽  
Stephanie Sestito ◽  
Yair Motro ◽  
Anat Shnaiderman-Torban ◽  
Boris Khalfin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Genes ◽  
Opportunistic Infections ◽  
Species Classification ◽  
Genome Phylogeny ◽  
Genomic Characterization ◽  
Specific Species ◽  
Lactamase Gene

Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.

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

2013 ◽  
Vol 71 (1) ◽  
pp. 20-25 ◽  
Author(s):  
Lewis Stewart ◽  
Amy Ford ◽  
Vartul Sangal ◽  
Julie Jeukens ◽  
Brian Boyle ◽  
...  
Keyword(s):  
Core Genome ◽  
Environmental Isolates ◽  
The Core ◽  
Genome Phylogeny

scholarly journals Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Anna Janowicz ◽  
Fabrizio De Massis ◽  
Massimo Ancora ◽  
Cesare Cammà ◽  
Claudio Patavino ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Brucella Melitensis ◽  
Reference Sequence ◽  
Snp Analysis ◽  
Phylogenetic Distance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACT The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome multilocus sequence typing (cgMLST) has not been explored so far. The current study developed an allele-based cgMLST method and compared its performance to that of the genome-wide SNP approach and the traditional multilocus variable-number tandem repeat analysis (MLVA) on a defined sample collection. The data set was comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 isolates with unknown epidemiological status, composed of human and animal samples collected in Italy. The cgMLST scheme generated in this study contained 2,704 targets of the B. melitensis 16M reference genome. We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤6 loci in the cgMLST and ≤7 in WGS SNP analysis. Higher phylogenetic distance resolution was achieved with cgMLST and SNP analysis than with MLVA, particularly for strains belonging to the same lineage, thereby allowing diverse and unrelated genotypes to be identified with greater confidence. The application of a cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen, and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

scholarly journals Cell Envelope Virulence Genes among Field Strains of Brucella melitensis Isolated in West Bank Part of Palestine

2015 ◽  
Vol 6 ◽  
pp. 281-286 ◽  
Author(s):  
Elena Awwad ◽  
Kamel Adwan ◽  
Mohammed Farraj ◽  
Tamer Essawi ◽  
Issa Rumi ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Brucella Melitensis ◽  
Cell Envelope ◽  
West Bank

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 Frequency of endoscopic findings of equine squamous gastric disease (ESGD) in rural horses and its association with Helicobacter pylori virulence genes

2021 ◽  
Author(s):  
F Rezazadeh ◽  
N Pourebrahimi ◽  
R Ghotaslou ◽  
M Golshani Nasab ◽  
MY Memar
Keyword(s):  
Helicobacter Pylori ◽  
Virulence Genes ◽  
Gastric Fluid ◽  
Gastric Disease ◽  
Specific Gene ◽  
Squamous Mucosa ◽  
Faecal Samples ◽  
Potential Risk Factors ◽  
H Pylori ◽  
Lesion Severity

Equine gastric ulcer syndrome (EGUS) is a multifactorial disorder and one of the most common diseases in horses. The objective of this research was to detect one of the potential risk factors of equine squamous gastric disease (ESGD), the Helicobacter pylori specific gene, and tracing the presence of the duodenal ulcer-promoting gene (dupA) as a possible virulence marker. Gastric fluid together with faecal samples were collected from twenty rural horses from around Tabriz, Iran. Throughout the endoscopic examinations, the type, numbers, severity, and the location of the lesions were documented. Nine of twenty horses exhibited macroscopic lesions in the squamous mucosa that were later classified into grades 1, 2, 3, and 4. Only three of these horses exhibited H. pylori in their gastric fluid samples, whereas all faecal samples were H. pylori-negative. All the H. pylori-positive cases manifested severe forms of ESGD (grades 3–4). The age and sex were both unrelated to the lesion severity and ESGD status in this study. Research is required to further discuss the virulence aspects of dupA regarding ESGD.

scholarly journals CAZymes in Maribacter dokdonensis 62–1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura A. Wolter ◽  
Maximilian Mitulla ◽  
Jovan Kalem ◽  
Rolf Daniel ◽  
Meinhard Simon ◽  
...  
Keyword(s):  
Core Genome ◽  
Ecological Specialization ◽  
Surface Attachment ◽  
Niche Specialization ◽  
Genomic Signatures ◽  
Host Interaction ◽  
Continental Shelves ◽  
Polysaccharide Lyases ◽  
Genome Phylogeny ◽  
Polysaccharide Utilization Loci

Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62–1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62–1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches.” Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.

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