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.

Wednesday, 17 September 2014

Main steps in Phage therapy procedure

In a Country

The epidemiological situation is different from country to country in terms of circulating bacteria and bacteriophages. Example: a lytic phage from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.


1.
2.


3.









 Commercial phage preparations


Friday, 12 September 2014

Monday, 8 September 2014

Two rivals: Mycobacterium ulcerans and Mycobacteriophage D29


 From this scientific work:



I quote meticulously  from this scientific work :

"The genomes of Mycobacterium ulcerans and Mycobacterium marinum are closely related, sharing >97% overall nucleotide identity [1], but cause very different kinds of infections in humans.
M. marinum causes minor skin infections, characterised by intracellular bacteria and the granulomatous lesions that are features of infection with many mycobacterial pathogens, notably Mycobacterium tuberculosis[2]. In contrast, M. ulcerans causes Buruli ulcer (BU), a slowly progressing, ulcerative disease characterized by necrosis of subcutaneous tissue. BU has a characteristic histopathology with large numbers of extracellular bacteria during the acute phase of the infection, with a marked lack of inflammatory response in advanced infection."

 "This unusual pathology is principally mediated by an immunosuppressive polyketide called mycolactone, which is not produced by M. marinum or M. tuberculosis. In BU patients, mycolactone is present in cutaneous lesions but also diffuses and can be detected in serum [3,4]."

" Two main features differentiate the genomes of M. ulcerans and M. marinum. The first is the pMUM megaplasmid, found in M. ulcerans but absent from M. marinum[5,6]. This plasmid harbours three large genes (mlsA1: 51 kb, mlsA2: 7.2 kb, mlsB: 43 kb) that encode the polyketide synthases (PKSs) required for mycolactone synthesis [2]. The second is the insertion sequence (IS) IS2404 that is absent from M. marinum but present in high copy number (>200) in M. ulcerans genomes. IS2404 expansion in the M. ulcerans genome has led to the inactivation of many genes through disruption of coding and promoter sequences and has mediated the deletion of approximately 1 Mbp of DNA from M. ulcerans compared with M. marinum[1]."

My contribution:

 By Gepard Dot plot software: 
 M.ulcerans versus M.ulcerans

     M.marinum versus M.marinum
 

M.marinum versus M.ulcerans



"Together with loss of DNA, there is also evidence of extensive loss of gene function in M. ulcerans - the genome of M. ulcerans isolate Agy99 harbours 771 pseudogenes (inactivated genes), while the M. marinum genome harbours only 65. Acquisition of foreign DNA, IS expansion, pseudogene accumulation and genome reduction are features in common with bacterial populations that have passed through an evolutionary bottleneck [7-12], suggesting there has been constriction of population size during adaptation to a new, niche environment."

"Analysis of the M. ulcerans Agy99 genome showed deletion or inactivation of genes expressing potent T-cell antigens, and genes required for pigment biosynthesis, anaerobiosis, and intracellular growth [1]. This profile suggested a bacterium that has adapted to a dark, extracellular environment where slow growth, loss of immunogens and production of an immunosuppressive molecule provide a selective advantage [1,13]. In contrast, its progenitor, M. marinum, has the characteristics of both a specialist bacterium that can persist within an intracellular environment as well as a generalist that can survive in extracellular conditions. A niche environment for M. ulcerans has not yet been demonstrated although the recent discovery that Australian native possums inhabiting BU endemic areas appear to harbour the bacteria in their gastrointestinal tracts raises some interesting possibilities [14]."
........After there is the  discussion  of the results.


My question:
Why these phage are non capable to growth on Mycobacterium marinum?




Growth:

-Photochromogens (Group I)
    Produce nonpigmented colonies when grown in the dark and pigmented colonies only after exposure to light and reincubation.

 
        Ex: M. kansasii, M. marinum, M. simiae.

On primary isolation M. marinum grows on LJ slants at 30-33°C in 7–21 days.

-Non-chromogens (Groups III & IV)
    Nonpigmented in the light and dark or have only a pale yellow, buff or tan pigment that does not intensify after light exposure.

        Ex: M. tuberculosis, M. avium-intra-cellulare, M. bovis, M. ulcerans
        Ex: M. fortuitum, M. chelonae

M. ulcerans can be cultured from many lesions, either from exudates or tissue fragments, but visible growth often requires 6 to 8 weeks incubation at 33 °C.

Saturday, 6 September 2014

Two rivals: Mycobacteriophage D29 and Mycobacterium ulcerans

From this scientific work:
 

I quote meticulously from this scientific work :

"Phage therapy presents several potential advantages for the treatment of BU patients, namely phages present lytic activity against extracellular bacteria which predominate in advanced lesions; phages may be used for the treatment of ulcerative lesions where the necrotic infection site would be accessible; and phages may be administered topically [28]."

"In the present study, following the screening of the lytic activity of several mycobacteriophages, the therapeutic effect of the selected mycobacteriophage D29 was evaluated against M. ulcerans in the mouse footpad model of infection. The progression of macroscopic/microscopic pathology and bacterial load, as well as the cytokine profile, in both the footpad and the draining lymph node (DLN), were evaluated after mycobacteriophage D29 administration."

"In order to select mycobacteriophages active against M. ulcerans strains, we first selected representative isolates of M. ulcerans from endemic BU areas, based on their genetic and phenotypic characteristics, including the type of mycolactone produced [3], [32], [33] and their virulence in mice [7], [34] (see Table 1). The strains were obtained from the collection of the Institute of Tropical Medicine (ITM), Antwerp, Belgium."


Table 1. Characteristics of M. ulcerans isolates used.

"This host-range determination was done by adapting a spot-test technique described elsewhere [35], [36]. Briefly, M. ulcerans was grown to an OD600 of 1.0 and clumps were dispersed by passing the bacterial suspension several times through a 25-gauge needle. The suspension was plated on Middlebrook 7H9 agar medium (Becton, Dickinson and Company). For each mycobacteriophage, serial dilutions were prepared in phage buffer (MPB) (10 mM Tris, pH 7.5, 1 mM MgSO4, 70 mM NaCl) and were plated onto the M. ulcerans lawn and the spots were allowed to dry completely. Plates were incubated at 32°C for approximately 6–8 weeks. "

 Animals

"A total of 120 (per experience) eight-week-old female BALB/c mice were obtained from Charles River (Barcelona, Spain) and were housed under specific-pathogen-free conditions with food and water ad libitum."

 Footpad mouse model of M. ulcerans infection

"M. ulcerans 1615 is a mycolactone A/B producing strain isolated in Malaysia from an ulcerative case [7]. The isolate was grown on Middlebrook 7H9 agar medium at 32°C for approximately 6–8 weeks. For the preparation of inoculum, M. ulcerans was recovered, diluted in phosphate-buffered saline (PBS) and vortexed using glass beads. The number of acid-fast bacilli (AFB) in inocula were determined as described previously using Ziehl-Neelsen (ZN) staining [37]. Mice were infected in the left hind footpad with 0.03 ml of M. ulcerans suspension containing 5.5 log10 AFB."

Treatment of M. ulcerans-infected mice with mycobacteriophage D29 

  " D29 particles were propagated in Mycobacterium smegmatis mc2155 (ATCC), as described elsewhere [36]. In brief, approximately 105 phage particles and 250 µl of M. smegmatis mc2155 (ATCC) (OD600 of 1.0) were plated on Middlebrook 7H9 overlays (0.6% agar) and incubated at 37°C overnight. Phage particles were extracted with 3 ml of MPB and harvested filtering through a 0.2 µm pore-size filter. Phages were concentrated through polyethylene glycol (PEG) precipitation and purified using a CsCl equilibrium density gradient centrifugation. Phage titers (PFU/ml) were determined by serial dilution and plaque assays by the soft overlay technique with some modifications [35]. Briefly, phage dilutions were spotted onto Middlebrook 7H9 overlays (0.6% agar) with M. smegmatis mc2155 (ATCC) and incubated at 37°C overnight.

The treatment was initiated at day 33 post-infection, when the footpad of mice were swollen to 3.0 mm, and was performed by subcutaneous injection in the infected footpad with a single dose of mycobacteriophage D29 containing 8 log10 PFU. MPB was given to control (non-treated) mice."

Assessment of footpad swelling 

"Footpad swelling was monitored throughout the experiment, as an index of lesion development, by using a caliper to measure the diameter of the frontal area of the footpad. For ethical reasons, the non-treated mice were sacrificed after the emergence of ulceration at day 68 post-infection, and no further parameters were evaluated for this group."

Bacterial and phage growth

"M. ulcerans growth and phage proliferation were evaluated in footpad tissues and in the DLN. Briefly, footpad tissue specimens were minced, resuspended in PBS (Sigma) and vortexed with glass beads to obtain homogenized suspensions. DLN were homogenized, the cell numbers were counted and then suspensions were lysed with saponin 0.1%. Serial dilutions of the footpad and DLN homogenates were plated on Middlebrook 7H9 agar medium. M. ulcerans numbers were counted after 6 to 8 weeks of incubation at 32°C and expressed as colony forming units (CFU/ml). Homogenized samples were also centrifuged for 10 min at 5000 rpm, supernatant was used for phage determination by the soft overlay technique [35] and expressed as plaque forming units (PFU/ml). Phage dissemination was also investigated by detecting phages in the spleen and sera of mice."

Detection of cytokines

"The levels of the cytokines tumor necrosis factor (TNF), interleukin (IL)-6, gamma interferon (IFN-γ) and IL-10 in the supernatant of homogenized suspensions from DLN and footpad tissues of control-infected and mycobacteriophage D29 treated mice were quantified by using a Quantikine Murine ELISA kit (eBioscience Inc), according to the manufacturer's instructions."

Histological studies

"Mouse footpads and DLN were harvested, fixed in 10% phosphate-buffered formalin and embedded in paraffin. Light microscopy studies were performed on tissue sections stained with hematoxylin and eosin (HE) or Ziehl-Neelsen (ZN). Images were obtained with an Olympus BX61 microscope."

Statistical analysis

"Differences between the means of experimental groups were analyzed with the two-tailed Student t test. Differences with a P value of ≤0.05 were considered significant."

Mycobacteriophage D29 shows a broad lytic activity against M. ulcerans isolates in vitro

"We first tested the lytic activity of different mycobacteriophages against several M. ulcerans isolates. The results for the plaque formation on the tested M. ulcerans strains are given in Table 2. We observed that some phages were more strain-specific, such as the phages Adjutor, Kostya and Brujita, and others presented a more narrow lytic host range spectrum (L5, Chah and Phaedrus). A cluster of three phages, namely D29, Bxz2 and Tweety, displayed the broadest lytic host range spectrum and highest lytic activity against representative strains of M. ulcerans. In line with a previous report [36], D29 phage showed the broadest lytic host range spectrum amongst the tested mycobacteriophages, affecting M. ulcerans isolates with genetic heterogeneity, variable phenotypic characteristics and from different geographic origins (Table 1). Based on these results, we selected mycobacteriophage D29 for in vivo therapeutic studies against infection with M. ulcerans 1615, a well characterized and stable strain that presents a mycolactone profile identical to that of African strains [32]."

 Table 2. Sensitivity of phages to M. ulcerans isolates.

........After there is the  discussion  of the results.

My contribution:

-This scientific work is good but I should have remember to the authors what is the objective of Phage therapy in Buruli: it is the lysis of M.ulcerans in the lesion.

-This scientific work shows for different phage a problem about  the host range spectrum.

 

There are for L5 and Bxz2  contrary results if I compare the table above with the table below from this scientific work :

 
 
 I have the confirmation about the presence of the problem in host range spectrum.

- Why there is not  a list and a table with only lytic mycobacteriophages?  
-lysogenic mycobacteriophages   must be eliminated.
- In theory I should have used  a mini cocktail with two lytic phage: ( D29 + ?) but in the table is  there another lytic phage?
- I should have used 240 (per experience) eight-week-old female BALB/c mice divided like this: 120 for M. ulcerans 1615 and 120 for M. ulcerans 94-1327 and I should have used the cocktail in both.

-When  two different infections (two groups) by different M. ulcerans strains are controlled by the same cocktail in both groups it would have been the best result.
 

Wednesday, 3 September 2014

Mycobacterium ulcerans strain Agy99 and its 174-kb pMUM001 plasmid


I quote the passages from:

Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans

"...MU contains a 174-kb plasmid, pMUM001, bearing a cluster of genes encoding giant polyketide synthases (PKSs), and polyketide-modifying enzymes, and demonstrate that these are necessary and sufficient for mycolactone synthesis."

"...reflects the acquisition of pMUM001 by horizontal transfer."

"...The 12-membered core of mycolactone is produced by two giant, modular PKSs,
MLSA1 (1.8 MDa) and MLSA2 (0.26 MDa), whereas its side chain is synthesized by MLSB (1.2 MDa), a third modular PKS highly related to MLSA1."

"...There is an extreme level of sequence identity within the different domains of the MLS cluster (>97% amino acid identity), so much so that the 16 ketosynthase domains seem functionally identical."

"..confirming the existence in MU of a circular plasmid, designated pMUM001, comprising 174,155 bp, with a GC content of 62.8% and carrying 81 protein-coding DNA sequences."

"..Replication seems to be initiated by the predicted product of repA, which shares
68.3% amino acid identity with RepA from the cryptic Mycobacterium fortuitum plasmid, pJAZ38 (10)"

"..Two different direct repeat regions were identified 500–1,000 bp upstream of repA, suggesting possible replication origins (ori). GC-skew plots [(G - C) (G+ C)], which highlight compositional biases between leading and lagging DNA strands, displayed a random pattern and did not help pinpoint a possible ori (Fig. 2)."

"..Approximately 2 kb downstream of repA is parA, a gene encoding a chromosome partitioning protein, required for plasmid segregation on cell division. In this region, there is also a potential regulatory gene cluster composed of a serine threonine protein kinase (mup008), a gene encoding a protein of unknown function(mup018) but containing a phosphopeptide recognition domain,a domain found in many regulatory proteins (11), and a WhiB like transcriptional regulator (mup021)."

"...The plasmid is rich in insertion sequences (IS), with 26 examples, including
4 copies of IS2404 and 8 copies of IS2606 (13)."

Circular presentation of pMUM001:





 

My contribution for pMUM001 plasmid seen from a new perspective by Dot-plot analysis :


by virtual 2G gel:

PKS,polyketide synthase
KS, ketosynthase
TE, thioesterase

by UGENE

Monday, 1 September 2014

D29p04



CDS :   2354-2650, 297 bp,  gp4 predicted 11.1 kD protein (98 Aa)
misc_feature: 2405-2569, 165 bp,HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and...; Region: HNHc; cd00085
misc_feature:2486-2569,active site


By Snapgen software:



By Artemis software:



Aa sequence (98Aa):


misc_feature  HNH nucleases, Aa sequence ( 55Aa):





 misc_feature ;active site,Aa sequence :DDHKPNLCRHS


misc-features: start and end:



 HNH nucleases




HNH motifs:







 consensus: e-x-h-H-i-x-p-x(2,4)-g-x(5,6)-N-l-x(3)-t-p-x(2,3)-H-x(3)-h ; capitalized letters are most conserved.


Scientific works: 





My contribution
By mJemboss software 

Statistics on the protein properties:

  
 one signal cleavage site in  the protein sequence:
 

Poor Pest motif:



Virtual 2G-gel:





In the sequence there are two motifs:

-DVDHK ( D/E X)K


-HSRSNLQAICRVCH


consensus:e-x-h-H-i-x-p-x(2,4)-g-x(5,6)-N-l-x(3)-t-p-x(2,3)-H-x(3)-h