information

Whoever comes in this website may find a hint

Phage therapy is influenced by:

Phage therapy is influenced by:

Country :
the epidemiological situation is different from country to country in terms of circulating bacteria and bacteriophages. Example: a lytic phages from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.
Chronolability
Mutation rate
Phenotypical delay
Phage cocktail
My point of view

From Wikipedia


If the target host* of a phage therapy treatment is not
an animal the term "
biocontrol" (as in phage-mediated biocontrol of bacteria) is usually employed, rather than "phage therapy".

"In silico"

From:"Genomics,Proteomics and Clinical Bacteriology", N.Woodford and Alan P.Johnson

Phrase that emphasizes the fact that many molecular biologists spend increasing amounts of their time in front of a computer screen, generating hypotheses that can subsequently be tested and (hopefully) confirmed in the laboratory.

Showing posts with label Mycobacterium ulcerans. Show all posts
Showing posts with label Mycobacterium ulcerans. Show all posts

Tuesday, 22 July 2014

Buruli ulcer disease and the best stage for the therapy


The clinical feature of the pre-ulcerative stage of the disease are painless nodules, usually occurring singly on the legs or forearms and in theory they are the best target for all therapies.
Nodule
The lesion starts as a small subcutaneous swelling which is barely palpable but not visible. It gradually increases in size until the skin is slightly raised. The nodule is firm with a regular margin and is attached to skin but is not attached to the deep fascia.

As the lesion enlarges it involves the deep fascia and then extends in this layer . At this stage the edges are less distinct owing to an intervening layer of normal tissue. The skin overlying the lesion tends to desquamate,leaving a shiny surface which often appears darker than normal. Later the skin over the centre of the lesion loses its pigmentation, becomes necrotic, and eventually ulcerates. In some lesions a small central vesicle develops, which may be broken to exude a small amount of clear fluid. The burst vesicle may progress to an ulcer or it may heal.

BURULI: In this disease it is important to recognize the right moment for starting with a Phage Therapy treatment.




Top: Early nodular lesion.
Center/bottom:Deep and undermined ulcerative lesion with necrotic borders, before and after medical treatment plus local surgery including skin grafting.

This figure appears in color here

Are there Mycobacteriophages utilizable for Phage Therapy in Buruli ulcer?



Comment: I am happy about this work but not for mycobacteriophage choice. The same phages are used in all works with mycobacteria (the host range for D29 is very large and includes both slow and fast-growing species). This aspect ( this is my opinion) is not a favourable point for phage therapy in Buruli: we must wait  for a specific phage for Mycobacterium ulcerans strain that is isolated together in the same country.
This work supports the timeliness of phage therapy before the infection to become chronic (33 days) and confirms my working hypothesis: a, b, c



At the moment my answer to this question is negative.






Mostly well-known mycobacteriopages are isolated and multiplied by growth on Mycobacterium smegmatis lawn and are also lysogenic phages,
example:

Mycobacterium phage 244
Mycobacterium phage Adjutor
Mycobacterium phage Angel
Mycobacterium phage BPs
Mycobacterium phage Barnyard
Mycobacterium phage Bethlehem
Mycobacterium phage Boomer
Mycobacterium phage Brujita
Mycobacterium phage Butterscotch
Mycobacterium phage Bxb1
Mycobacterium phage Bxz1
Mycobacterium phage Bxz2
Mycobacterium phage Cali
Mycobacterium phage Catera
Mycobacterium phage Chah
Mycobacterium phage Che12
Mycobacterium phage Che8
Mycobacterium phage Che9c
Mycobacterium phage Che9d
Mycobacterium phage Cjw1
Mycobacterium phage Cooper
Mycobacterium phage Corndog
Mycobacterium phage D29
Mycobacterium phage DD5
Mycobacterium phage Fruitloop
Mycobacterium phage Giles
Mycobacterium phage Gumball
Mycobacterium phage Halo
Mycobacterium phage Jasper
Mycobacterium phage KBG
Mycobacterium phage Konstantine
Mycobacterium phage Kostya
Mycobacterium phage L5
Mycobacterium phage Llij
Mycobacterium phage Lockley
Mycobacterium phage Myrna
Mycobacterium phage Nigel
Mycobacterium phage Omega
Mycobacterium phage Orion
Mycobacterium phage PBI1
Mycobacterium phage PG1
Mycobacterium phage PLot
Mycobacterium phage PMC
Mycobacterium phage Pacc40
Mycobacterium phage Phaedrus
Mycobacterium phage Phlyer
Mycobacterium phage Pipefish
Mycobacterium phage Porky
Mycobacterium phage Predator
Mycobacterium phage Pukovnik
Mycobacterium phage Qyrzula
Mycobacterium phage Ramsey
Mycobacterium phage Rizal
Mycobacterium phage Rosebush
Mycobacterium phage ScottMcG
Mycobacterium phage Solon
Mycobacterium phage Spud
Mycobacterium phage TM4
Mycobacterium phage Troll4
Mycobacterium phage Tweety
Mycobacterium phage U2
Mycobacterium phage Wildcat



 
To find "genuine" lytic mycobacteriophages is not easy and it seems to me that it is also rare .

D29 is a lytic phage but I can not consider this phage
a "genuine " lytic phage by genome analysis.

These mycobacteriophages have a broad Host range and this feature is not favourable when they are used in Phage therapy.

I am of the opinion that Mycobacterium marinum may be the valid alternative to Mycobacterium smegmatis for growing and isolating phages with a potential action on Mycobacterium ulcerans but until now there is little information about growing phages on Mycobacterium marinum.

 

It is indispensable to work on
this virgin ground.

Monday, 21 July 2014

In silico 2D-SDS-PAGE:M.marinum,M.ulcerans and M.smegmatis


In silico 2D-SDS-PAGE



Mycobacterium marinum
Proteome



Mycobacterium ulcerans Proteome




Mycobacterium smegmatis
Proteome



superimposing of pictures of Mycobacterium ulcerans Proteome with Mycobacterium marinum Proteome



superimposing of pictures
of Mycobacterium ulcerans
Proteome with Mycobacterium smegmatis Proteome



Short Database about Mycobacterium ulcerans


From WHO
 
"Buruli ulcer is caused by a germ that mainly affects the skin but which can also affect the bone. The causative organism is called Mycobacterium ulcerans, which although different, belongs to the same family of organisms that cause leprosy and tuberculosis.

Buruli ulcer has been reported in over 30 countries with tropical and subtropical climates but it may also occur in some countries where it has not yet been recognized. Limited knowledge of the disease, its focal distribution and the fact that it affects mainly poor rural communities contribute to low reporting of cases. Progress is being made now to develop tools for early diagnosis, to understand exactly how infection is transmitted and to improve treatment".



From:

Wikipedia

WHO publications on Buruli ulcer

 Buruli

 Mycobacterium ulcerans Infection(CDC)


 Mycobacterium ulcerans infection(MJA)

Buruli ulcer research

Stop buruli

Morphology of Mature Mycobacterium ulcerans Colonies


From A.S.M


Fig. 1

Three-month-old Mycobacterium ulcerans colonies growing on Middlebrook 7H10 agar supplemented with 10% oleic acid, albumin, dextrose, and catalase (OADC). 

Scale bar = 1 mm








Fig. 2

Five-month-old Mycobacterium ulcerans colonies growing on  

Middlebrook 7H10 agar supplemented with 10% OADC. Scale bar = 1 mm.




Introduction

Macroscopic examination reveals the presence of large and small Mycobacterium ulcerans colonies after 3 (Fig. 1) and 5 months (Fig. 2) of growth at 30°C on Middlebrook 7H10 agar supplemented with 10% oleic acid, albumin, dextrose, and catalase (OADC). The buff-colored M. ulcerans colonies on supplemented Middlebrook 7H10 medium appear dry, waxy, wrinkled, and rough with irregular edges. Buff-colored colonies qualitatively indicate absence of mycolactone toxin production. Colonies of M. ulcerans on OADC-supplemented Middlebrook 7H10 agar are variable in size and have elevated, condensed centers which gradually flatten toward the irregular, undulating periphery (Fig. 1 and 2). Compared to the younger M. ulcerans colonies in Fig. 1, the mature M. ulcerans colonies are slightly larger and raised, exhibiting more compacted, dense colony growth (Fig. 2).



 Methods

Prior to imaging, cultures were inoculated onto Middlebrook 7H10 agar supplemented with 10% OADC from frozen stock cultures stored at -70°C. Plates were wrapped with parafilm and incubated at 30°C for 3 or 5 months. Images for Fig. 1 and 2 were taken on a Fisher Scientific Stereomaster zoom microscope equipped with a 1.3 megapixel color digital camera head for direct real-time viewing via a computer monitor.

 Discussion

Mycobacterium sp. are classified as either slow or rapid growers.  By definition, slow growers require more than 7 days to observe visible colonies on a solid medium, while rapid growers form colonies within 7 days.  Similar to Mycobacterium tuberculosis, M. ulcerans is a member of the slow-growing group of mycobacteria.  However, M. ulcerans is considered extremely slow-growing as cultures must be incubated for 6 to 8 weeks (or longer) under appropriate laboratory conditions prior to forming distinct colonies. Figures 1 and 2 are images of mature M. ulcerans colonies that were grown for approximately 4 to 5 months, respectively.  M. ulcerans grows optimally on mycobacteriological media (e.g., Löwenstein-Jensen medium, Middlebrook 7H10 medium, etc.) under the same conditions as M. tuberculosis (which generally forms colonies on solid media in 3 to 4 weeks), except the M. ulcerans optimal growth temperature is 30 to 32°C (9).

M. ulcerans, the causative agent of a human disease known as Buruli ulcer, is an  environmental mycobacterium of which the natural reservoir is unknown (2). Worldwide, Buruli ulcer is the third most common mycobacterial disease of immunocompetent humans, after tuberculosis and leprosy (14). Human transmission is believed to occur via skin transmission by direct inoculation or an insect vector (10, 14).

Most individuals infected with M. ulcerans initially develop a small, painless, preulcerative skin nodule with larger areas of indurated skin and edema (13).  As the disease progresses over 1 to 2 months, the infected skin begins to ulcerate with characteristic necrosis of the subcutaneous fatty tissues, deeply undermined edges, and vascular blockage. Because

M. ulcerans is a very slow-growing mycobacterium, more serious and advanced ulcerative disease manifests over several months.  The necrotic ulcers can lead to: extensive skin loss; damage to nerves, blood vessels, and appendages; and deformity and disability, particularly in children (13, 14).  One study reported that 26% of patients with healed Buruli ulcers suffered from chronic functional disability (8).

In contrast to other pathogenic mycobacteria, M. ulcerans is an extracellular pathogen that produces a secreted toxin known as mycolactone (4, 5, 12).  Mycolactone has both cytotoxic (ability to damage or kill certain types of human cells) and immunosuppressive (reduces the activation or responsiveness of the human immune system) properties and is most likely responsible for tissue necrosis observed in patients, as injection of purified toxin into experimental animals causes disease characteristics similar to Buruli ulcer (6).  Although secondary bacterial infections can further complicate the extensive ulcerative lesions, death from an M. ulcerans infection is rare (7).

Currently, no vaccine is available for the prevention of Buruli ulcer (11).  Although antibiotic treatment has been shown to be effective in vitro and in animal models (1), success in the clinical environment has been limited, especially in the case of advanced ulcerative disease.  Accordingly, surgical excision, combined with antibiotic therapy, prevails as an accepted remedy for these difficult-to-treat infections (3, 15).

Sunday, 20 July 2014

KEGG: Mycobacterium ulcerans

KEGG Mycobacterium ulcerans

Genome information

T numberT00435
Org codemul
AliasesMYCUA, 362242
Full nameMycobacterium ulcerans
DefinitionMycobacterium ulcerans Agy99
Annotationmanual
TaxonomyTAX: 362242
    LineageBacteria; Actinobacteria; Actinobacteridae;                                                                                  Actinomycetales;Corynebacterineae;                                                                                 Mycobacteriaceae; Mycobacterium
Data sourceRefSeq (Assembly:GCA_000013925.1)
Original DBPasteur
KeywordsHuman pathogen
DiseaseH00285 Blau syndrome
H01042 Buruli ulcer
CommentIsolated from an ulcerative lesion on the right elbow                                                                    of a female patient from the Ga district of Ghana in 1999
ChromosomeCircular
    SequenceRS: NC_008611
    Length5631606
PlasmidpMUM001; Circular
    SequenceRS: NC_005916
    Length174155
StatisticsNumber of nucleotides: 5805761
Number of protein genes: 4241
Number of RNA genes: 50
ReferencePMID: 17210928
    AuthorsStinear TP, et al.
    TitleReductive evolution and niche adaptation inferred from                                                               the genome of Mycobacterium ulcerans, the causative                                                         agent of Buruli ulcer.
    JournalGenome Res 17:192-200 (2007)





Summary of Mycobacterium ulcerans, Strain Agy99

From: BioCyc Database Collection



RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)

Chromosome 149814931507715,631,606
Plasmid 1818100174,155

Total:50625012507715,805,761


Pathways:193
Enzymatic Reactions:1209
Transport Reactions:53

Polypeptides:4241
Protein Complexes:11
Enzymes:841
Transporters:67

Compounds:806

Transcription Units:3542
tRNAs:51

Saturday, 19 July 2014

Mycobacterium ulcerans Harvey

        Browse Genome         BLAST Genome        
About Genome

Overview


Proposal Name Mycobacterium ulcerans Harvey
Organism Name Mycobacterium ulcerans Harvey
Taxon ID 2565956790
IMG Submission ID 36722
NCBI Taxon ID 1299332
GOLD ID in IMG Database Project ID: Gi0041622  
External Links NCBI/RefSeq:JAOL01000001; NCBI/RefSeq:JAOL01000002; NCBI/RefSeq:JAOL01000003; NCBI/RefSeq:JAOL01000004; NCBI/RefSeq:JAOL01000005; NCBI/RefSeq:JAOL01000006 
Lineage Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; Mycobacteriaceae; Mycobacterium; ulcerans
Sequencing Status Permanent Draft
IMG Release  
Comment  
Release Date 2014-04-28
Add Date 2014-04-28
Modified Date
Distance Matrix Calc. Date
High Quality No
IMG Product Flag No
Is Public Yes
Project Information  
Cultured Yes
Culture Type Isolate
GOLD ID Gi0041622
Isolation Country USA
NCBI Project ID 191796
Publication Journal Unpublished
GOLD Sequencing Status Complete
Project Sequencing Method Pacbio
Sequencing Center Institute for Genome Sciences
Metadata  
Assembly Method SMRT HGAP v. 2.0.1
Gram Staining Gram+
Phenotypes/Metabolism from Pathway Assertion  
Metabolism Auxotroph (L-lysine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-alanine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-aspartate auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Prototrophic (L-glutamate prototroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-phenylalanine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-tyrosine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-tryptophan auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-histidine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (Glycine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-arginine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-asparagine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-cysteine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-glutamine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-isoleucine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-leucine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-proline auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-serine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-threonine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (L-valine auxotroph) (IMG_PIPELINE; 2014-05-01)
Metabolism (Non-selenocysteine synthesizer) (IMG_PIPELINE; 2014-05-01)
Metabolism (Non-biotin synthesizer) (IMG_PIPELINE; 2014-05-01)
Metabolism Auxotroph (Incomplete Coenyzme A biosynthesis) (IMG_PIPELINE; 2014-05-01)

Genome Statistics



Hint To view rows that are zero, go to MyIMG preferences
and set "Hide Zeroes in Genome Statistics" to "No".


Number % of Total
DNA, total number of bases 6247430 100.00%
        DNA coding number of bases 5084742 81.39%
        DNA G+C number of bases 4072505 65.19% 1
                       
DNA scaffolds 209 100.00%
                       
Genes total number 9228 100.00%
        Protein coding genes 9178 99.46%
        Pseudo Genes 1 0.01%2
        RNA genes 50 0.54%
                rRNA genes 2 0.02%
                        5S rRNA 1 0.01%
                        23S rRNA 1 0.01%
                tRNA genes 48 0.52%
        Protein coding genes with function prediction 6911 74.89%
                without function prediction 2267 24.57%
        Protein coding genes with enzymes 637 6.90%
        w/o enzymes but with candidate KO based enzymes 1394 15.11%
        Protein coding genes connected to Transporter Classification 363 3.93%
        Protein coding genes connected to KEGG pathways3 684 7.41%
                not connected to KEGG pathways 8494 92.05%
        Protein coding genes connected to KEGG Orthology (KO) 1141 12.36%
                not connected to KEGG Orthology (KO) 8037 87.09%
        Protein coding genes connected to MetaCyc pathways 625 6.77%
                not connected to MetaCyc pathways 8553 92.69%
        Protein coding genes with COGs3 1793 19.43%
                with KOGs3 2217 24.02%
                with Pfam3 5548 60.12%
                with TIGRfam3 1028 11.14%
                with InterPro 3058 33.14%
                with IMG Terms 295 3.20%
                with IMG Pathways 117 1.27%
                with IMG Parts List 133 1.44%
                in paralog clusters 7002 75.88%
                in Chromosomal Cassette 9228 100.00%
        Chromosomal Cassettes 1159 -
        Biosynthetic Clusters 115 -
                Genes in Biosynthetic Clusters 1780 19.29%
        Fused Protein coding genes 73 0.79%
        Protein coding genes coding signal peptides 343 3.72%
        Protein coding genes coding transmembrane proteins 1305 14.14%
COG clusters 997 55.61%
KOG clusters 728 40.60%
Pfam clusters 1795 32.35%
TIGRfam clusters 755 73.44%
Notes:
1 - GC percentage shown as count of G's and C's divided by the total number of bases.
      The total number of bases is not necessarily synonymous with a total number of G's, C's, A's, and T's.
2 - Pseudogenes may also be counted as protein coding or RNA genes, so is not additive under total gene count. 3 - Graphical view available.

Browse Genome




Phylogenetic Distribution of Genes



Putative Horizontally Transferred Genes




Compare Gene Annotations


Gene annotation values are precomputed and stored in a tab delimited file
also viewable in Excel.

Scaffold Consistency Check


Export Gene Information


Gene information is precomputed and stored in a tab delimited file
also viewable in Excel.

Export Genome Data

Scaffold Search


Scaffold search allows for seaching for all scaffolds within an organism or microbiome.
Please enter a search term or matching substring for scaffold name or read ID.


or enter low and high range for
-