Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacteria
2.2. Resources
2.3. Phages
2.4. Model Settings
2.4.1. Primary Adsorption: Standard Model
2.4.2. Secondary Adsorption: Poisson
2.4.3. Resistance Mutation
2.4.4. Refuge Cells
2.4.5. Time Step Size
3. Results
4. Technical Information
Supplementary Materials
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Start Values | ||||
---|---|---|---|---|
Symbol | Description | Default | Allowed Range | Unit |
Bacteria | ||||
S | Uninfected, susceptible bacteria | 1 × 105 | 10−1 × 1012 | CFU/mL |
IA | Bacteria infected by phage A | - | - | | |
IB | Bacteria infected by phage B | - | - | | |
IAB | Bacteria infected by phages A and B | - | - | | |
RA | Bacteria resistant to phage A | 1 × 10−7 | 0–1 × 10−2 | | |
RB | Bacteria resistant to phage B | 1 × 10−7 | 0–1 × 10−2 | | |
RAB | Bacteria resistant to phages A and B | 1 × 10−14 | 0–1 × 10−6 | | |
RAIB | Bacteria resistant to A infected with B | - | - | | |
RBIA | Bacteria resistant to B infected with A | - | - | | |
Sr | Susceptible bacteria in a refuge | 0 | - | | |
RrA | Bacteria resistant to A in a refuge | - | - | | |
RrB | Bacteria resistant to B in a refuge | - | - | | |
RrAB | Bacteria resistant to AB in a refuge | - | - | CFU/mL |
Parameters | ||||
ψ | Growth rate of S | 0.7 | 0–1.5 | /h |
K | Monod constant | 5.0 | 0.01–100 | µg/mL * |
ε | Resource for division of one bacterium | 2 × 10−6 | 1 × 10−8–1 × 10−4 | µg/cell * |
γ | Bacterial decay rate | 0 | 0–1 | /h |
µA | Mutation rate for resistance against A | 1 × 10−7 | 0–1 × 10−2 | /cell div. |
µB | Mutation rate for resistance against B | 1 × 10−7 | 0–1 × 10−2 | /cell div. |
Growth rate of RA | 0.7 | 0–1.5 | /h | |
Growth rate of RB | 0.7 | 0–1.5 | /h | |
Growth rate of RAB | 0.7 | 0–1.5 | /h | |
σ | Rate of bacteria into refuge | 0 | 0–0.01 | /min |
ρ | Rate of bacteria out from refuge | 0 | 0–0.01 | /min |
C0 | Available resources from start | 100 | 0–1000 | µg/mL * |
C | Resources flowing in from a reservoir | 100 | 0–1000 | µg/mL * |
ω | Flow rate | 0.2 | 0–100 | /h |
Phages | ||||
Parameters | ||||
A | Titre of phage A | 1 × 108 | 0–1 × 1013 | PFU/mL |
B | Titre of phage B | 1 × 108 | 0–1 × 1013 | PFU/mL |
δA | Adsorption rate of A | 1 × 10−10 | 1 × 10−14–1 × 10−7 | mL/min |
δB | Adsorption rate of B | 1 × 10−10 | 1 × 10−14–1 × 10−7 | mL/min |
lA | Latent period of A | 30 | 1–60 | min |
lB | Latent period of B | 20 | 1–60 | min |
βA | Burst size of A | 100 | 0–1000 | PFU/cell |
βB | Burst size of B | 100 | 0–1000 | PFU/cell |
φA | Decay rate of phage A | 0 | 0–1 | /h |
φB | Decay rate of phage B | 0 | 0–1 | /h |
Primary Adsorption Setting | Standard | Poisson | ||
---|---|---|---|---|
Secondary Adsorption Setting | Uninfected | Susceptible | Uninfected | Susceptible |
Phages adsorb one at a time to uninfected non-resistant cells | Phages adsorb one at a time to non-resistant cells | A number of phages adsorb according to a Poisson probability with lambda = MOI to uninfected non-resistant cells | A number of phages adsorb according to a Poisson probability with lambda = MOI to non-resistant cells | |
Bacteria | Conceivably adsorbing phages | |||
S = Susceptible | A or B | A or B | A and B | A and B |
IA = Infected by A | B | A or B | B | A and B |
IB = Infected by B | A | A or B | A | A and B |
IAB = Infected by A and B | - | A or B | - | A and B |
RA = Resistant to infections by A | B | B | B | B |
RB = Resistant to infections by B | A | A | A | A |
RAB = Resistant to infections by A and B | - | - | - | - |
RAIB = Resistant to infections by A infected with B | - | B | - | B |
RBIA = Resistant to infections by B infected with A | - | A | - | A |
Sr = Susceptible planktonic bacteria in a refuge | - | A or B No infection | A and B No infection | A and B No infection |
RrA = Planktonic bacteria resistant to A in a refuge | - | B No infection | B No infection | B No infection |
RrB = Planktonic bacteria resistant to B in a refuge | - | A No infection | A No infection | A No infection |
RrAB = Planktonic bacteria resistant to AB in a refuge | - | - | - | - |
Sr = Susceptible bacteria in a LIFO refuge | - | - | - | - |
RrA = Bacteria resistant to A in a LIFO refuge | - | - | - | - |
RrB = Bacteria resistant to B in a LIFO refuge | - | - | - | - |
RrAB = Bacteria resistant to AB in a LIFO refuge | - | - | - | - |
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Nilsson, A.S. Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses 2022, 14, 2483. https://doi.org/10.3390/v14112483
Nilsson AS. Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses. 2022; 14(11):2483. https://doi.org/10.3390/v14112483
Chicago/Turabian StyleNilsson, Anders S. 2022. "Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics" Viruses 14, no. 11: 2483. https://doi.org/10.3390/v14112483
APA StyleNilsson, A. S. (2022). Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses, 14(11), 2483. https://doi.org/10.3390/v14112483