Menu
July 7, 2019  |  

Complete genome of Vibrio parahaemolyticus FORC014 isolated from the toothfish.

Foodborne illness can occur due to various pathogenic bacteria such as Staphylococcus aureus, Escherichia coli and Vibrio parahaemolyticus, and can cause severe gastroenteritis symptoms. In this study, we completed the genome sequence of a foodborne pathogen V. parahaemolyticus FORC_014, which was isolated from suspected contaminated toothfish from South Korea. Additionally, we extended our knowledge of genomic characteristics of the FORC_014 strain through comparative analysis using the complete sequences of other V. parahaemolyticus strains whose complete genomes have previously been reported.The complete genome sequence of V. parahaemolyticus FORC_014 was generated using the PacBio RS platform with single molecule, real-time (SMRT) sequencing. The FORC_014 strain consists of two circular chromosomes (3,241,330 bp for chromosome 1 and 1,997,247 bp for chromosome 2), one plasmid (51,383 bp), and one putative phage sequence (96,896 bp). The genome contains a total of 4274 putative protein coding sequences, 126 tRNA genes and 34 rRNA genes. Furthermore, we found 33 type III secretion system 1 (T3SS1) related proteins and 15 type III secretion system 2 (T3SS2) related proteins on chromosome 1. This is the first reported result of Type III secretion system 2 located on chromosome 1 of V. parahaemolyticus without thermostable direct hemolysin (tdh) and thermostable direct hemolysin-related hemolysin (trh).Through investigation of the complete genome sequence of V. parahaemolyticus FORC_014, which differs from previously reported strains, we revealed two type III secretion systems (T3SS1, T3SS2) located on chromosome 1 which do not include tdh and trh genes. We also identified several virulence factors carried by our strain, including iron uptake system, hemolysin and secretion system. This result suggests that the FORC_014 strain may be one pathogen responsible for foodborne illness outbreak. Our results provide significant genomic clues which will assist in future understanding of virulence at the genomic level and help distinguish between clinical and non-clinical isolates.


July 7, 2019  |  

Genome sequence and comparative pathogenic determinants of multidrug resistant uropathogenic Escherichia coli O25b: H4, A clinical isolate from Saudi Arabia

Escherichia coli serotype O25b:H4 is involved in human urinary tract infections.In this study, we sequenced and analyzed E. coli O25b:H4 isolated from a patient sufferingfrom recurring UTI infections in an intensive care unit at Hera General Hospital inMakkah, Saudi Arabia. We aimed to determine the virulence genes for pathogenesis anddrug resistance of this isolate compared to other E. coli strains. We sequenced and analyzedthe E. coli O25b:H4 Saudi strain clinical isolate using next generation sequencing. Usingthe ERGO genome analysis platform, we performed annotations and identified virulenceand antibiotic resistance determinants of this clinical isolate. The E. coli O25b:H4 genomewas assembled into four contigs representing a total chromosome size of 5.28 Mb, andthree contigs were identified, including a 130.9 kb (virulence plasmid) contig bearing thebla-CTX gene and 32 kb and 29 kb contigs. In comparing this genome to otheruropathogenic E. coli genomes, we identified unique drug resistance and pathogenicityfactors. In this work, whole-genome sequencing and targeted comparative analysis of aclinical isolate of uropathogenic Escherichia coli O25b:H4 was performed. This strainencodes virulence genes linked with extraintestinal pathogenic E. coli (ExPEC) that areexpressed constitutively in E. coli ST131. We identified the genes responsible forpathogenesis and drug resistance and performed comparative analyses of the virulenceand antibiotic resistance determinants with those of other E. coli UPEC isolates. This isthe first report of genome sequencing and analysis of a UPEC strain from Saudi Arabia.


July 7, 2019  |  

Identification of a virulence determinant that is conserved in the Jawetz and Heyl biotypes of [Pasteurella] pneumotropica.

[Pasteurella] pneumotropica is a ubiquitous bacterium frequently isolated from laboratory rodents. Although this bacterium causes various diseases in immunosuppressed animals, little is known about major virulence factors and their roles in pathogenicity. To identify virulence factors, we sequenced the genome of [P.] pneumotropica biotype Heyl strain ATCC 12555, and compared the resulting non-contiguous draft genome sequence with the genome of biotype Jawetz strain ATCC 35149. Among a large number of genes encoding virulence-associated factors in both strains, four genes encoding for YadA-like proteins, which are known virulence factors that function in host cell adherence and invasion in many pathogens. In this study, we assessed YadA distribution and biological activity as an example of one of virulence-associated factor shared, with biotype Jawetz and Heyl. More than half of mouse isolates were found to have at least one of these genes; whereas, the majority of rat isolates did not. Autoagglutination activity, and ability to bind to mouse collagen type IV and mouse fibroblast cells, was significantly higher in YadA-positive than YadA-negative strains. To conclude, we identified a large number of candidate genes predicted to influence [P.] pneumotropica pathogenesis.© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.


July 7, 2019  |  

Genomic insights into Photobacterium damselae subsp. damselae strain KC-Na-1, isolated from the finless porpoise (Neophocaena asiaeorientalis)

Photobacterium damselae subsp. damselae (PDD) is a marine bacterium that can infect a variety of marine animals and humans. Although this bacterium has been isolated from several stranded dolphins and whales, its pathogenic role in cetaceans is still unclear. In this study, we report the complete genome of PDD strain KC-Na-1 isolated from a finless porpoise (Neophocaena asiaeorientalis) rescued from the South Sea (Republic of Korea). The sequenced genome comprised two chromosomes and four plasmids. Among the recently identified major virulence factors in PDD, only phospholipase (plpV) was found in strain KC-Na-1. Interestingly, two genes homologous to Vibrio thermostable direct hemolysin (tdh) and its transcriptional regulator toxR, which are known virulence factors associated with Vibrio parahaemolyticus, were encoded on the plasmid pPDD-Na-1-3. Based on these results, strain KC-Na-1 may have potential pathogenicity in humans and other marine animals and also could act as a potential virulent strain. To the best of our knowledge, this is the first report of the complete genome sequence of P. damselae.


July 7, 2019  |  

Assembly, annotation, and comparative genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.

In the “big data” era, research biologists are faced with analyzing new types that usually require some level of computational expertise. A number of programs and pipelines exist, but acquiring the expertise to run them, and then understanding the output can be a challenge.The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org ) has created an end-to-end analysis platform that allows researchers to take their raw reads, assemble a genome, annotate it, and then use a suite of user-friendly tools to compare it to any public data that is available in the repository. With close to 113,000 bacterial and more than 1000 archaeal genomes, PATRIC creates a unique research experience with “virtual integration” of private and public data. PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, but the main focus of this chapter is on assembly, annotation, and the downstream comparative analysis functionality that is freely available in the resource.


July 7, 2019  |  

Complete genome sequence of Lacinutrix venerupis DOK2-8 isolated from marine sediment from the East Sea, Republic of Korea.

Lacinutrix venerupis has recently been considered a potential fish pathogen. Here, we report the complete genome sequence of L. venerupis DOK2-8, which possesses several virulence-related genes. This strain may be potentially virulent to other marine organisms, and its genomic information will provide important insights into the biodiversity of the genus Lacinutrix. Copyright © 2018 Lim et al.


July 7, 2019  |  

Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05.

Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a bipartite genome consisting of a 3,930,849 bp chromosome and a 2,066,085 bp megaplasmid with 66.84% G+C content that harbors 5,427 coding sequences. Based on the whole genome, phylogenetic analysis showed that strain SEPPX05 is grouped with two phylotype I strains (EP1 and GMI1000). Pan-genomic analysis shows that R. solanacearum is a complex species with high biological diversity and was able to colonize various environments during evolution. Despite deletions, insertions, and inversions, most genes of strain SEPPX05 have relatively high levels of synteny compared with strain GMI1000. We identified 104 genes involved in virulence-related factors in the SEPPX05 genome and eight absent genes encoding T3Es of GMI1000. Comparing SEPPX05 with other species, we found highly conserved secretion systems central to modulating interactions of host bacteria. These data may provide important clues for understanding underlying pathogenic mechanisms of R. solanacearum and help in the control of sesame bacterial wilt.


July 7, 2019  |  

Complete genome sequence of multiple-antibiotic-resistant Streptococcus parauberis strain SPOF3K, isolated from diseased olive flounder (Paralichthys olivaceus).

Here, we report the complete genome sequence of multiple-antibiotic-resistant Streptococcus parauberis strain SPOF3K, isolated from the kidney of a diseased olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded a circular chromosome of 2,128,740?bp and a plasmid of 23,538?bp, harboring 2,123 and 24 protein-coding genes, respectively. Copyright © 2018 Lee et al.


July 7, 2019  |  

Complete genome sequence of Escherichia albertii strain 1551-2, a potential extracellular and intracellular pathogen.

Escherichia albertii has recently been recognized as an emerging human and bird enteric pathogen. Here, we report the complete chromosome sequence of a clinical isolate of E. albertii strain 1551-2, which may provide information about the pathogenic potential of this new species and the mechanisms of evolution of Escherichia species. Copyright © 2018 Romão et al.


July 7, 2019  |  

Whole genome sequence and phenotypic characterization of a Cbm+ serotype e strain of Streptococcus mutans.

We report the whole genome sequence of the serotype e Cbm+ strain LAR01 of Streptococcus mutans, a dental pathogen frequently associated with extra-oral infections. The LAR01 genome is a single circular chromosome of 2.1 Mb with a GC content of 36.96%. The genome contains 15 phosphotransferase system gene clusters, seven cell wall-anchored (LPxTG) proteins, all genes required for the development of natural competence and genes coding for mutacins VI and K8. Interestingly, the cbm gene is genetically linked to a putative type VII secretion system that has been found in Mycobacteria and few other Gram-positive bacteria. When compared with the UA159 type strain, phenotypic characterization of LAR01 revealed increased biofilm formation in the presence of either glucose or sucrose but similar abilities to withstand acid and oxidative stresses. LAR01 was unable to inhibit the growth of Strpetococcus gordonii, which is consistent with the genomic data that indicate absence of mutacins that can kill mitis streptococci. On the other hand, LAR01 effectively inhibited growth of other S. mutans strains, suggesting that it may be specialized to outcompete strains from its own species. In vitro and in vivo studies using mutational and heterologous expression approaches revealed that Cbm is a virulence factor of S. mutans by mediating binding to extracellular matrix proteins and intracellular invasion. Collectively, the whole genome sequence analysis and phenotypic characterization of LAR01 provides new insights on the virulence properties of S. mutans and grants further opportunities to understand the genomic fluidity of this important human pathogen.© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.


July 7, 2019  |  

Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic Rhizobia.

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with plant immunity constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Additional studies with a tripartite gnotobiotic plant system reveal that these traits operate in a modular fashion and thus might be relevant to microbial homeostasis in healthy roots. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.


July 7, 2019  |  

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.

Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci.We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system.We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci.


July 7, 2019  |  

Complete genome sequence of Agrobacterium pusense VsBac-Y9, a bacterial symbiont of the dark septate endophytic fungus Veronaeopsis simplex Y34 with potential for improving fungal colonization in roots.

A Rhizobium-related bacterium (Rhizobium sp. VsBac-Y9) is a symbiont living with the dark septate endophytic (DSE) fungus Veronaeopsis simplex Y34. Co-inoculation of Rhizobium sp. VsBac-Y9 with V. simplex Y34 improves the fungal colonization of tomato roots, resulting in a significant increase in aboveground biomass. This study sequenced the complete genome of this V. simplex-helper bacterium using the PacBio and Illumina MiSeq platforms. Hybrid assembly using SPAdes outputted a circular chromosome, a linear chromid, and a circular plasmid for a total genome 5,321,211 bp in size with a G?+?C content of 59.2%. Analysis of concatenated housekeeping genes (atpD-dnaK-groEL-lepA-recA-rpoB-thrE) and calculation of average nucleotide identity, showed that VsBac-Y9 was affiliated with the species Agrobacterium pusense (syn. Rhizobium pusense). Genome analysis revealed that A. pusense VsBac-Y9 contains a series of genes responsible for the host interactions with both fungus and plant. Such genomic information will provide new insights into developing co-inoculants of endophytic fungus and its symbiotic bacterium in future agricultural innovation. Copyright © 2018 Elsevier B.V. All rights reserved.


July 7, 2019  |  

Complete genome sequence of soil actinobacteria Streptomyces cavourensis TJ430.

A new actinobacteria Streptomyces cavourensis TJ430 was isolated from the mountain soil collected from the southwest of China. In previous study, TJ430 showed striking bactericidal activities and strong ability of antibiotic production. Here, we report complete genome of this bacterium, consisting of 7.6?Mb linear chromosome and 0.2?Mb plasmids. It was predicted 6450 genes in chromosome and 225 genes in plasmids, as well as 12 gene islands in chromosome. Abundant genes have predicted functions in antibiotic metabolism and stress resistance. A whole-genome comparison of S. cavourensis TJ430, S. coelicolor A3(2), and S. lividans 66 indicates that TJ430 has a relatively high degree of strain specificity. The 16S rRNA phylogenetic tree shows the high identities (99.79%) of TJ430 with S. cavourensis DSM40300. TJ430 is a new and rare Streptomyces species, and analysis of its genome helps us to better understand primary metabolism mechanism of this isolate, as well as the evolutionary biology.© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.