HeaemoBase includes genome and clinical data on five Haemophilus haemolyticus (Hhae) strains and one non-typeable influenzae (NTHi) strain.

Haemophilus haemolyticusHaemophilus influenzae


While many strains within these species reside as commensal microflora in the back of the throat,various H. influenza strains are virulent and can cause disease including acute bacterial meningitis. Immunity to serotype B strainscan be conferred by the Hib vaccine. However, this does not prevent the emergence of hyper-virulent NTHi strains like the NTHi biogroup aegyptius strain responsible for the outbreak of Brazilian Purpuric Fever in the 1980s.

Recently, noncommensal Hhae strains have appeared in clinically derived blood and knee fluid cultures. Hhae strains have traditionally been distinguished from closely related NTHi strains by their beta hemolysis activity on blood agar. However, not all Hhae strains exhibit this activity. Distinguishing between pathogenic and commensal strains of Hhae and NTHi and documenting the genetic basis of virulence in these strains are crucial steps in developing public health initiatives to combat disease caused by these strains.

Summary of Strain Features

BRIG

      M19107

Haemophilus hemolyticus M19107

Biological Information
Assembly Information
Genome Size : 1,774,129
No. of Contigs : 129
Assembly Platform : Newbler+Mira
N50 Size : 25,914
 
Gene Prediction Information:
No. of Genes : 1,967
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
Gene_dist
Comparative Information:  
GC content %  39.39
HGT signals : 360
Pathogenic : No
Insertion Elements : 6
Hemolytic Activity : Y

      M19501

Haemophilus hemolyticus M19501

Biological Information
Assembly Information
Genome Size : 1,809,865
No. of Contigs : 19
Assembly Platform : Newbler+Mira
N50 Size : 284,900
 
Gene Prediction Information:
No. of Genes : 1,779
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
19501
Comparative Information:  
GC content %  38.23
HGT signals : 145
Pathogenic : No
Insertion Elements : 6
Hemolytic Activity : N

      M21127

Haemophilus hemolyticus M21127

Biological Information
Assembly Information
Genome Size : 2,029,793
No. of Contigs : 32
Assembly Platform : Newbler+Mira
N50 Size : 122,121
 
Gene Prediction Information:
No. of Genes : 2,075
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
Gene_dist
Comparative Information:  
GC content %  39.11
HGT signals : 225
Pathogenic : Yes
Insertion Elements : -
Hemolytic Activity : Y

      M21621

Haemophilus hemolyticus M21621

Biological Information
Assembly Information
Genome Size : 1,959,123
No. of Contigs : 27
Assembly Platform : Newbler+Mira
N50 Size : 139,238
 
Gene Prediction Information:
No. of Genes : 1,914
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
Gene_dist
Comparative Information:  
GC content %  39.11
HGT signals : 253
Pathogenic : Yes
Insertion Elements : -
Hemolytic Activity : Y

      M21396

Haemophilus hemolyticus M21639

Biological Information
Assembly Information
Genome Size : 2,397,847
No. of Contigs : 56
Assembly Platform : Newbler+Mira
N50 Size : 87,673
 
Gene Prediction Information:
No. of Genes : 2,667
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
Gene_dist
Comparative Information:  
GC content %  38.30
HGT signals : 108
Pathogenic : Yes
Insertion Elements : 15
Hemolytic Activity : N

      M21709

Haemophilus influenzae M21709

Biological Information
Assembly Information
Genome Size : 1,808,157
No. of Contigs : 28
Assembly Platform : Newbler+Mira
N50 Size : 140,484
 
Gene Prediction Information:
No. of Genes : 1,834
Gene Prediction Methods Prodigal + GeneMark + Glimmer + RAST


Functional Annotation Information
Gene_dist
Comparative Information:  
GC content %  38.81
HGT signals : 185
Pathogenic : No
Insertion Elements : -
Hemolytic Activity : N

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    Haemophilus haemolyticus
    ID Geographic Origin Date Received Source Disease Hemolysis omp2 hpda hpdb fucK H2S Strip NH Strip 16S rRNA Gene Download
    M19107 Minnesota, USA 2/12/2009 OP Swab ASYM + - - ND - + H. quentini Fasta GFF3 GenBank
    M19501 Minnesota, USA 2/19/2009 OP Swab ASYM - - + ND - - H. quentini Fasta GFF3 GenBank
    M21127 Georgia, USA 1/27/2010 Blood PATH + ND - - - + 3424 Hhae Fasta GFF3 GenBank
    M21621 Texas, USA 5/14/2010 Knee Fluid PATH + ND - - - + 3420 Hhae Fasta GFF3 GenBank
    M21639 Illinois, USA 5/21/2010 Blood PATH - ND - - - +/- 1420 Hhae Fasta GFF3 GenBank



    Haemophilus influenzae
    ID Geographic Origin Date Received Source Disease Hemolysis omp2 hpda hpdb fucK H2S Strip NH Strip 16S rRNA Gene Download
    M21709 New York, USA 6/17/2010 Blood PATH - ND - - + + 7424 Hi Fasta GFF3


    Disease Samples were determined to be asymptomatic (ASYM) or pathogenic (PATH) based on the source.
    Hemolysis Test for beta hemolysis activity of colonies grown on blood agar.
    omp2 (rtPCR) Real time PCR test for outer membrane protein P2.
    hpda (rtPCR) Real time PCR test for hod gene encoding Haemophilus protein D (a surface lipoprotein).
    hpdb (PCR) Conventional PCR test for hod gene encoding Haemophilus protein D (a surface lipoprotein).
    fucK (PCR) Conventional PCR test for fUCK gene encoding fuculose kinase.
    H2S strip Test for hydrogen sulfide production.
    NH strip Data code for API NH strip Ref. 10400 (bioMérieux) results.
    16S rRNA gene Strain as determined by 16S rRNA sequencing

    About this project

    Unassembled genome sequence data from the Centers for Disease Control and Prevention (CDC) is proceed through five distinct stages of analysis and interpretation of that data: genome assembly, gene prediction, functional annotation, comparative genomics, production of a genome browser. All public results from this project is available on this site, as well as the compgenomics2012 wiki page.


    Collaboration

     CompGenomics2012 at Georgia Tech

       Genome Assembly Group
       Gene Prediction Group
       Functional Annotation Group
       Comparative Genomics Group
       Genome Browser Group

     Meningitis Laboratory, CDC (Atlanta, GA)

    Developed by the Browser Group of CompGenomics 2012 @ Georgia Institute of Technology