Computational protocol: Antibody Production in Response to Staphylococcal MS-1 Phage Cocktail in Patients Undergoing Phage Therapy

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Protocol publication

[…] The MS-1 phage cocktail consists of three lytic S. aureus phages – 676/Z, A5/80 and P4/6409. Among 458 tested MSSA strains of S. aureus, 73.4% were susceptible to the MS-1 phage cocktail. Effectiveness was lower for MRSA strains (from 28 tested strains 53.6% of them were susceptible to MS-1 phage cocktail). Detailed analysis of susceptibility to the MS-1 phage cocktail is presented in Table . The phage components of MS-1 cocktail were chosen to achieve optimal (maximal) lytic range based on the theoretical statistical analysis of the results of the sensitivity of staphylococcal strains against individual staphylococcal phages from our collection. The results shown in Table are presented for new collection of staphylococcal strains isolated from patients after introduction of MS-1 phage cocktail. Therefore, they represent a real staphylococcal sensitivity to MS-1 as well as to its individual phages. We are working on new, more efficient composition of staphylococcal phage cocktail based on the results and experience obtained from using MS-1. All our patients are treated with targeted phage preparations, which means that in each case we use only phages or phage cocktail which are lytic against a pathogenic bacterial strain isolated from the patient. Therefore, in all our MRSA cases treated with MS-1, the bacteria were susceptible to the phage cocktail. Otherwise, our MRSA patients were treated with another single staphylococcal phage from our collection. If we were not able to identify an active phage, patients were not qualified to experimental phage treatment.Bacterial susceptibility to specific polyvalent staphylococcal phages from our collection was evaluated by spotting method (; ). The bacteria cultures were prepared in liquid broth medium. Next, the suspensions were spread on plates with solid agar medium. Plates were dried in incubator (37°C, 1.5 h). Drop of each phage lysate (107-109 pfu/ml of initial suspension) was spotted on plate surface, then plates were incubated (37°C, 6 h) and stored at 4°C until the following day. A positive result was recognized (under the therapeutic point of view) when confluent or semi-confluent lysis was observed. [...] The evaluation of statistical significance of differences between groups in the neutralization test was performed using Wilcoxon’s test (for dependent variables) and the Mann–Whitney U test (for independent variables).Results carried out by ELISA technique were analyzed using Wilcoxon’s test (for dependent variables). For independent variables, we used the Mann–Whitney’s U test and Student’s t-test. To choose the appropriate statistical test we confirmed whether in groups of IgG, IgA, and IgM antibodies distributions were normal and whether there were homogeneous variances. In case of normal distribution and homogeneous variances we applied parametric Student’s t-test. In remaining cases we used nonparametric Mann-Whitney’s U test.Significance was set at p < 0.05 and p < 0.001. Analysis was performed using the Statistica 10 software package. […]

Pipeline specifications

Software tools Fast H-DROP, Statistica
Applications Miscellaneous, Protein sequence analysis
Organisms Homo sapiens