Implementation
Our proposed end users are patients who are suffering from sepsis. With the phage therapy, the genetically engineered phage will be intravenously injected into the patients, serving as a treatment for sepsis. It will insert its genome into the cell and be incorporated into the host cell. As a result, the desired protein will then be made and influence the lipid-A molecules in the cell membrane, to avoid cytokine storms and treat sepsis. In addition, we developed a phage database with all the necessary information about the phages that can infect sepsis-related bacteria. We envision others, who are doing research on sepsis and phage therapy, being able to easily find needed information through Phage Database.
Next Step - Further Wetlab Research
After getting positive results from the lab, we can continue on with animal trials. Animal models of phage therapy are a critical approach to verify the efficiency of the phage therapy in vivo and search for potential adverse effects1. However, there are several challenges of the animal trials. The amount of liquid volume is limited for animals, such as mice, especially when the liquid is administered intravenously or intranasally. As a result, the concentration of the phage needs to accommodate. Also, because of the effects of the laboratory environment and other variables during the trials, the animal experiments may fail to ensure the reliability of administration on humans. The species differences in physiology and genetics between humans and animals can explain the unreliability and limitations of the animal trials as well2. Besides, there is one possibility that our fully developed phages continue to replicate and infect E.coli strains outside of the source of sepsis for a patient. This could lead to complications down the line for the patient after the threat of sepsis. This could be possibly mitigated by mutating certain genes that are involved in the lytic cycle.
Next Step - Phage Therapy
In the long run, we plan to have phage therapy on sepsis approved by the FDA and start on human trials. Also the phage database we created can be updated as more phages or information are discovered. To implement phage therapy on patients diagnosed with sepsis, the first step is to determine the type of phage that is going to be used in the phage therapy. Since phages only infect specific bacteria strain, it’s critical to find the specific phage that can infect the sepsis-causing bacteria for the patient. Our phage database plays a critical role at this step. By going through the phage list, instead of reviewing all the literature, doctors and researchers can save a lot of time to find the phage right for different patients. A list of potential phages would be helpful in case that some of them don’t work as planned in the following steps. Next, multiple anti-lipid A proteins and their pathways will be researched into. The proteins can be either binding to lipid A or altering the structures of lipid A in order to neutralize lipid A. The lipid-A neutralizing proteins will be inserted into the chosen phage. After successful insertion of the anti-lipid A proteins, the phage with the protein will be mass produced for administration. There are several companies commercializing bacteriophages or phage-based products for therapeutic purposes. However, an effective, constant and controllable process has yet to be developed. The processes in the laboratories are well defined but they’re difficult to scale up. Because of the biological nature of the system and the diverse types of interactions that occur between phages and bacteria, there are still many challenges along the way and further studies on it are needed3. Then delivery of the therapeutic phages between labs and hospitals is also critical. Dry formulations of embedded phage are one of the approaches to store bacteriophages for long-term. The drying of phages formulations can be achieved through ambient air drying, spray drying, lyophilization or spray freeze-drying4. After the engineered phages arrive at the hospitals, they can be intravenously administered into the patient to treat sepsis. It can be done orally, locally or by applying drops of phage suspension to the eye, middle ear or nasal mucosa. At the same time, the etiologic agents are monitored for phage susceptibility. The treatment can be 1 to 16 weeks and can be applied for up to 14 days after negative cultures are obtained5.
Phage Database
Phage Name | Locus | Genome (bp) | GC% | Linear/Circular DNA | Lytic/Lysogenic | Date | Genome |
---|---|---|---|---|---|---|---|
PT1028 | NC_007045 | 15,603 | 31.40 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_007045.1 | |
66 | AY954949 | 18,199 | 29.30 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954949 | |
44AHJD | NC_004678 | 16,784 | 29.70 | linear | lytic | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/29565721 |
P68 | 18,221 | 29.30 | lytic | ||||
187 | AY954950 | 39,620 | 34.30 | linear | lytic | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954950 |
69 | AY954951 | 42,732 | 34.30 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954951 | |
53 | AY954952 | 43,883 | 34.10 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954952 | |
85 | AY954953 | 44,283 | 34.60 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954953 | |
2638A | AY954954 | 41,318 | 36.90 | linear | lytic | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954954 |
77 | NC_005356 | 41,708 | 33.50 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/41189515 | |
42e | AY954955 | 45,861 | 33.70 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954955 | |
3A | AY954956 | 43,095 | 33.50 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954956 | |
47 | AY954957 | 44,777 | 33.50 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954957 | |
37 | AY954958 | 43,681 | 35.10 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954958 | |
EW | AY954959 | 45,286 | 38.00 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954959 | |
96 | AY954960 | 43,576 | 35.00 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954960 | |
ROSA | AY954961 | 43155 | 35.10 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954961 | |
71 | AY954962 | 43,114 | 35.20 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954962 | |
55 | AY954963 | 41,902 | 35.70 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954963 | |
29 | AY954964 | 42,802 | 35.40 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954964 | |
52A | AY954965 | 41,690 | 35.50 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954965 | |
88 | AY954966 | 43,231 | 35.50 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954966 | |
92 | AY954967 | 42,431 | 35.70 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954967 | |
X2 | AY954968 | 43,440 | 36.00 | linear | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/AY954968 | |
K | NC_005880 | 148,317 | 30.60 | linear | lytic | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_005880.2 |
G1 | NC_007066 | 138,715 | 30.40 | linear | lytic | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/NC_007066.1 |
Twort | NC_007021 | 130,706 | 30.30 | linear | lytic | 4/15/2005 | https://www.ncbi.nlm.nih.gov/nuccore/NC_007021.1 |
JD007 | NC_019726 | 141,836 | 30.37 | circular | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019726.1 | |
vB_SauM_Remus | NC_022090 | 134,643 | 29.97 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_022090.1 | |
vB_SauM_Romulus | NC_020877 | 131,332 | 30.01 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_020877.1 | |
MSA6 | JX080304 | 148,243 | 30.24 | linear | 3/31/2014 | https://www.ncbi.nlm.nih.gov/nuccore/JX080304.2 | |
B1 | MG656408 | 148,884 | 30.25 | linear | lytic | 4/27/2018 | https://www.ncbi.nlm.nih.gov/nuccore/1327516593 |
JA1 | MF405094 | 147,135 | 30.25 | linear | 4/27/2018 | https://www.ncbi.nlm.nih.gov/nuccore/1227560290 | |
Staph1N | JX080300 | 145,647 | 30.41 | linear | 3/28/2014 | https://www.ncbi.nlm.nih.gov/nuccore/JX080300.2 | |
A5W | EU418428 | 145,542 | 30.42 | linear | 3/12/2014 | https://www.ncbi.nlm.nih.gov/nuccore/EU418428.2 | |
Fi200W | JX080303 | 148,481 | 30.39 | linear | 3/28/2014 | https://www.ncbi.nlm.nih.gov/nuccore/JX080303.2 | |
676Z | JX080302 | 148,564 | 30.41 | linear | 3/26/2020 | https://www.ncbi.nlm.nih.gov/nuccore/JX080302.2 | |
P4W | JX080305 | 147,590 | 30.39 | linear | 3/28/2014 | https://www.ncbi.nlm.nih.gov/nuccore/JX080305.2 | |
A3R | JX080301 | 141,018 | 30.50 | linear | 3/26/2020 | https://www.ncbi.nlm.nih.gov/nuccore/JX080301.2 | |
812 | NC_029080 | 142,096 | 30.40 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/985759046 | |
IME-SA1 | KP687431 | 140,218 | 30.33 | circular | 4/15/2015 | https://www.ncbi.nlm.nih.gov/nuccore/KP687431.1 | |
IME-SA2 | KP687432 | 140,906 | 30.33 | circular | 4/15/2015 | https://www.ncbi.nlm.nih.gov/nuccore/KP687432.1 | |
IME-SA118 | KR902361 | 139,750 | 30.32 | linear | 7/15/2015 | https://www.ncbi.nlm.nih.gov/nuccore/KR902361.1 | |
IME-SA119 | KR908644 | 141,028 | 30.33 | linear | 7/15/2015 | https://www.ncbi.nlm.nih.gov/nuccore/KR908644.1 | |
Team1 | NC_025417 | 140,903 | 30.33 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_025417.1 | |
SA5 | JX875065 | 137,031 | 30.42 | linear | 12/7/2012 | https://www.ncbi.nlm.nih.gov/nuccore/JX875065.1 | |
GH15 | NC_019448 | 139,806 | 30.23 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019448.1 | |
ISP | FR852584 | 138,339 | 30.42 | linear | 9/19/2011 | https://www.ncbi.nlm.nih.gov/nuccore/FR852584.1 | |
MCE-2014 | NC_025416 | 141,907 | 30.38 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_025416.1 | |
P108 | NC_025426 | 140,807 | 30.22 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_025426.1 | |
phiP68 | NC_004679 | 18,227 | 29.32 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/29565743 | |
philPLA-C1C | NC_028962 | 140,961 | 27.96 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_028962.1 | |
philPLA-RODI | NC_028765 | 142,348 | 30.42 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_028765.1 | |
phiSA012 | NC_023573 | 142,094 | 30.31 | linear | lytic | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_023573.1 |
S25-3 | NC_022920 | 139,738 | 30.22 | circular | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_022920.1 | |
S25-4 | NC_022918 | 132,123 | 30.31 | circular | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_022918.1 | |
Sb-1 | NC_023009 | 127,188 | 30.48 | linear | lytic | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_023009.1 |
Stau2 | KP881332 | 133,798 | 29.97 | linear | lytic | 5/26/2016 | https://www.ncbi.nlm.nih.gov/nuccore/KP881332.1 |
phiPVL | NC_002321 | 41,401 | 33.55 | linear | 6/7/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_002321.1 | |
phiSLT | AB045978 | 42,942 | 33.31 | linear | 6/26/2008 | https://www.ncbi.nlm.nih.gov/nuccore/AB045978.2 | |
phiPV83-pro | NC_002486 | 45,636 | 33.48 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_002486.1 | |
108-PVL | 44,107 | ||||||
Sa2mw | 45,924 | ||||||
Sa2958 | 46,046 | ||||||
Sa2usa | 43,062 | ||||||
phi7247PVL | NC_048624 | 42,481 | 33.31 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_048624.1 | |
phi5967PVL | NC_019921 | 42,146 | 33.31 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019921.1 | |
phiETA | NC_003288 | 43,081 | 35.43 | circular | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_003288.1 | |
phiN315 | NC_004740 | 44,082 | 32.78 | linear | 6/29/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_004740.1 | |
Mu50A | 43,053 | ||||||
Mu50B | 44,391 | ||||||
Sa3mw | lytic | ||||||
Sa3ms | 42,612 | lysogenic | |||||
Sa3 (OC8) | LC129040 | 42,984 | 33.09 | linear | 10/19/2016 | https://www.ncbi.nlm.nih.gov/nuccore/LC129040.1 | |
phi 11 | AF424781 | 43,604 | 34.50 | linear | lytic | 01/06/2020 | https://www.ncbi.nlm.nih.gov/nuccore/AF424781.1 |
phi 12 | AF424782 | 44,970 | 33.35 | linear | 06/10/2020 | https://www.ncbi.nlm.nih.gov/nuccore/AF424782.1 | |
13 | 42,774 | ||||||
L54a | temperate | ||||||
phiNM1 | NC_008583 | 43,128 | 34.16 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_008583.1 | |
phiNM2 | NC_028913 | 43,145 | 34.59 | linear | temperate | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_028913.1 |
phiNM3 | NC_008617 | 44,061 | 32.99 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_008617.1 | |
phiNM4 | NC_028864 | 43,189 | 34.74 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_028864.1 | |
80 | 42,140 | ||||||
80alpha | NC_009526 | 43,864 | 34.10 | linear | 10/11/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_009526.1 | |
phiMR11 | NC_010147 | 43,011 | 35.63 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_010147.1 | |
phiMR25 | NC_010808 | 44,342 | 34.33 | linear | lysogenic | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_010808.1 |
phiSauS-IPLA88 | NC_011614 | 42,526 | 34.91 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_011614.1 | |
phiSauS-IPLA35 | NC_011612 | 45,344 | 33.25 | linear | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_011612.1 | |
TEM126 | NC_054978 | 41,882 | 33.68 | linear | temperate | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_054978.1 |
SA11 | NC_019511 | 136,326 | 30.04 | linear | lytic | 10/12/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019511.1 |
SAP2 | 17,938 | ||||||
vB_SauH_SAP1 | MT786458 | 143,375 | 30.16 | linear | 08/24/2020 | https://www.ncbi.nlm.nih.gov/nuccore/MT786458.1 | |
SAP3 | MT724048 | 41,949 | 35.35 | linear | 08/03/2020 | https://www.ncbi.nlm.nih.gov/nuccore/MT724048.1 | |
SK311 | 141,100 | ||||||
SA039 | AP018375 | 141,038 | 30.38 | linear | 02/28/2018 | https://www.ncbi.nlm.nih.gov/nuccore/AP018375.1 |
Phage Name | Locus | Genome (bp) | GC% | Linear/Circular DNA | Lytic/Lysogenic | Date | Genome |
---|---|---|---|---|---|---|---|
SOCP | KJ617393 | 19,347 | 38.82 | linear | Lytic | 2/25/2015 | https://www.ncbi.nlm.nih.gov/nuccore/KJ617393 |
Dp-1 | HQ268735 | 56,506 | 40.34 | linear | Lytic | 7/25/2016 | https://www.ncbi.nlm.nih.gov/nuccore/HQ268735.1/ |
Cp-1 | NC_001825 | 19,343 | 38.83 | linear | Lytic | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_001825 |
HB-3 | linear | Temperate | https://www.ncbi.nlm.nih.gov/nuccore/215055 | ||||
EJ-1 | NC_005294 | 42,935 | 39.64 | linear | Temperate | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_005294.1 |
Dp-4 | |||||||
Cp-7 | NC_042114 | 19,741 | 39.19 | linear | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_042114.1 | |
Cp-9 | linear | ||||||
MM1-1998 | DQ113772 | 38,893 | 38.16 | circular | Temperate | 7/24/2006 | https://www.ncbi.nlm.nih.gov/nuccore/DQ113772.1 |
MM1 | NC_003050 | 40,248 | 38.46 | linear | Temperate | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_003050.2 |
MS1 | KY629621 | 56,075 | 42.26 | linear | Lytic | 5/11/2017 | https://www.ncbi.nlm.nih.gov/nuccore/KY629621 |
MS2 | NC_001417 | 3,569 | Linear RNA | 6/4/2019 | https://www.ncbi.nlm.nih.gov/nuccore/NC_001417.2 | ||
ϕX174 |
Phage Name | Locus | Genome (bp) | GC% | Linear/Circular DNA | Lytic/Lysogenic | Date | Genome |
---|---|---|---|---|---|---|---|
T4 | NC_000866 | 168,903 | 35.30 | linear | lytic | 01/23/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_000866.4 |
lambda | NC_001416 | 48,502 | 49.86 | linear | temperate | 12/20/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_001416.1 |
HK620 | AF335538 | 38,297 | 46.69 | circular | 4/23/2002 | https://www.ncbi.nlm.nih.gov/nuccore/AF335538.1 | |
T5 | AY543070 | 121,750 | 39.27 | linear | lytic | 4/19/2004 | https://www.ncbi.nlm.nih.gov/nuccore/AY543070.1 |
Goslar | |||||||
PTXU04 | |||||||
vB_EcoM_KWBSE43-6 | NC_048186 | 158,607 | 46.09 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_048186.1 | |
JLK-2012 | NC_049942 | 57,198 | 50.72 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_049942.1 | |
Rac-SA53 | |||||||
vB_EcoM_G17 | MK327931 | 370,817 | 34.33 | linear | 3/25/2019 | https://www.ncbi.nlm.nih.gov/nuccore/MK327931.1 | |
vB_EcoM_Schickermooser | NC_048196 | 151,194 | 39.01 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_048196.1 | |
EdH4 | MK327930 | 136,031 | 43.65 | linear | 3/25/2019 | https://www.ncbi.nlm.nih.gov/nuccore/MK327930.1 | |
teqsoen | MN895436 | 166,468 | 35.47 | linear | 02/01/2021 | https://www.ncbi.nlm.nih.gov/nuccore/MN895436.1 | |
teqdroes | NC_054932 | 166,833 | 35.44 | linear | 6/8/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_054932.1 | |
teqhal | MN895435 | 168,070 | 35.45 | linear | 02/01/2021 | https://www.ncbi.nlm.nih.gov/nuccore/MN895435.1 | |
teqskov | NC_054934 | 165,017 | 35.36 | linear | 6/8/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_054934.1 | |
vB_EcoM_WFC | NC_048195 | 72472 | 46.01 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_048195.1 | |
vB_EcoM_AYO145A | NC_028825 | 87,372 | 39.00 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_028825.1 | |
teqhad | NC_054933 | 167,892 | 35.33 | linear | 6/8/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_054933.1 | |
moskry | MN850651 | 169,410 | 37.64 | linaer | 2/1/2021 | https://www.ncbi.nlm.nih.gov/nuccore/MN850651.1 | |
vB_EcoS_HdH2 | NC_048748 | 120,120 | 39.32 | linear | 12/21/2020 | https://www.ncbi.nlm.nih.gov/nuccore/NC_048748.1 | |
mogra | MN850579 | 168,724 | 37.69 | linear | 2/1/2021 | https://www.ncbi.nlm.nih.gov/nuccore/MN850579.1 | |
mobilu | MN850622 | 163,063 | 37.68 | linear | 2/1/2021 | https://www.ncbi.nlm.nih.gov/nuccore/MN850622.1 |
Phage Name | Locus | Genome (bp) | GC% | Linear/Circular DNA | Lytic/Lysogenic | Date | Genome |
---|---|---|---|---|---|---|---|
StB12 | NC_020490 | 44,714 | 34.17 | linear | 10/21/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_020490.2 | |
StB27 | NC_019914 | 40,071 | 33.22 | linear | 10/21/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019914.1 | |
StB20 | NC_019915 | 40,917 | 34.07 | linear | 10/21/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_019915.1 | |
118II | |||||||
phi29 | NC_011048 | 19,282 | 39.99 | linear | 10/11/2021 | https://www.ncbi.nlm.nih.gov/nuccore/NC_011048.1 | |
phi68 | |||||||
95 | |||||||
127 | |||||||
171A | |||||||
207 | |||||||
113 | |||||||
113A | |||||||
188 | |||||||
112 | |||||||
108 | |||||||
phi187 |
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