Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Strains
2.2. Phage Isolates
2.3. Phage Stability in pH-Adjusted Media
2.4. Phage Stability in Simulated Gastric and Intestinal Fluids
2.5. Phage Stability in Different Thermal Conditions
2.6. Control of Salmonella by Phages in pH-Adjusted Media
2.7. Control of Salmonella by Phages in SGF and SIF
2.8. Phage Replication in SGF
2.9. Phage Persistence in Different Water Sources
2.10. Data Analysis
3. Results
3.1. Isolating and Characterizing the Biological Materials
3.2. Assessing Phage Stability in Media at Low and High pH
3.3. Assessing Phage Stability in Simulated Gastric and Intestinal Fluids
3.4. Phage Stability at Different Temperatures
3.5. Control of Salmonella by Phages in pH-Adjusted Media
3.6. Control of Salmonella by Phages in SGF and SIF
3.7. Phage Replication in SGF
3.8. Phage Persistence in Water from Different Sources
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sal 16 | Sal 73 | Sal 157 | Sal 172 | Sal 177 | Sal 181 | Sal 182 | Sal 187 | Sal 188 | Sal 192 | Sal 194 | Sal 312 | Sal 568 | Sal 569 | Sal 571 | Sal 572 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
invA | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + |
Group O (A-S) | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + |
Poly H (Phase 1 & 2) | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + |
Group D (9) | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + | + |
CRISPR 1 | E | E | C | K | E | K | K | H | H | C | C | E | E | E | K | E |
CRISPR 2 | E | E | H | K | E | K | K | H | H | H | H | E | E | E | K | E |
Phages | Original Salmonella Strain | Identity of Poultry Farm (PF)/Slaughter House (SH) | Region | Remarks |
---|---|---|---|---|
ILRI_K1 | Sal16 | PF_16 | Kiambu (Peri-Urban) | Salmonella isolated |
ILRI_K3 | Sal16 | SH_6 | Nairobi (Urban) | Salmonella absent |
ILRI_K6 | Sal16 | SH_7 | Nairobi (Urban) | Salmonella absent |
ILRI_K9 | Sal16 | PF-58 | Nairobi (Urban) | Salmonella absent |
ILRI_K11 | Sal73 | SH_1 | Kiambu (Peri-Urban) | Salmonella isolated |
ILRI_K14 | Sal73 | PF_33 | Kiambu (Peri-Urban) | Salmonella isolated |
ILRI_K22 | Sal177 | PF_16 | Kiambu (Peri-Urban) | Salmonella isolated |
ILRI_K24 | Sal177 | SH_6 | Nairobi (Urban) | Salmonella absent |
ILRI_K26 | Sal177 | SH_6 | Nairobi (Urban) | Salmonella absent |
ILRI_K47 | Sal312 | SH_6 | Nairobi (Urban) | Salmonella absent |
Most Similar Kenyan Phage Genome | Most Similar Phage Genome from the NCBI Public Database | ||||
---|---|---|---|---|---|
Phage Name | Nucleotide Similarity % (Aligned Nucleotide %) | Phage Name | NCBI Accession Number | Nucleotide Similarity % (Aligned Nucleotide %) | |
ILRI_K1 * | ILRI_K22 | 99.99 (100%) | Salmonella phage wast | MT074451.1 | 93.72% (90%) |
ILRI_K3 | ILRI_K24 | 99.79% (100%) | Salmonella phage wast | MT074451.1 | 92.18% (90%) |
ILRI_K6 | ILRI_K24 | 98.23% (97%) | Salmonella phage wast | MT074451.1 | 92.30% (86%) |
ILRI_K9 | ILRI_K26 | 99.99 (100%) | Salmonella phage wast | MT074451.1 | 92.70% (90%) |
ILRI_K11 | None | -- | Salmonella phage SP6 | AY288927.2 | 89.67% (90%) |
ILRI_K14 | ILRI_K1 & _K22 | 97.27% (96%) | Salmonella phage wast | MT074451.1 | 93.59% (92%) |
ILRI_K22 | ILRI_K1 | 99.99 (100%) | Salmonella phage wast | MT074451.1 | 93.72% (90%) |
ILRI_K24 | ILRI_K3 | 99.79% (100%) | Salmonella phage wast | MT074451.1 | 92.41% (90%) |
ILRI_K26 ** | ILRI_K9 | 99.99 (93%) | Salmonella phage wast | MT074451.1 | 92.55% (90%) |
ILRI_K47 | ILRI_K9 | 96.74% (93%) | Salmonella phage wast | MT074451.1 | 92.44% (91%) |
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Mhone, A.L.; Makumi, A.; Odaba, J.; Guantai, L.; Gunathilake, K.M.D.; Loignon, S.; Ngugi, C.W.; Akhwale, J.K.; Moineau, S.; Svitek, N. Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract. Viruses 2022, 14, 1788. https://doi.org/10.3390/v14081788
Mhone AL, Makumi A, Odaba J, Guantai L, Gunathilake KMD, Loignon S, Ngugi CW, Akhwale JK, Moineau S, Svitek N. Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract. Viruses. 2022; 14(8):1788. https://doi.org/10.3390/v14081788
Chicago/Turabian StyleMhone, Amos Lucky, Angela Makumi, Josiah Odaba, Linda Guantai, K. M. Damitha Gunathilake, Stéphanie Loignon, Caroline Wangari Ngugi, Juliah Khayeli Akhwale, Sylvain Moineau, and Nicholas Svitek. 2022. "Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract" Viruses 14, no. 8: 1788. https://doi.org/10.3390/v14081788