Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya
Abstract Background Non-typhoidal Salmonella (NTS) typically cause self-limiting enterocolitis, but can lead to life-threatening invasive diseases, particularly in sub-Saharan Africa. In Kenya, multidrug-resistant (MDR) NTS strains with increasing non-susceptibility to third-generation cephalosporin...
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2025-07-01
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| Series: | BMC Infectious Diseases |
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| Online Access: | https://doi.org/10.1186/s12879-025-11325-3 |
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| author | Michael Mugo Abednego Musyoki Angela Makumi Ivy Mutai Kelvin Kering Peter Muturi Collins Kebenei Kristin Weber Michael Pietsch Tanja Pilz Oliver Drechsel Tobias Hoffmann Lothar Wieler Cecilia Mbae Antje Flieger Samuel Kariuki |
| author_facet | Michael Mugo Abednego Musyoki Angela Makumi Ivy Mutai Kelvin Kering Peter Muturi Collins Kebenei Kristin Weber Michael Pietsch Tanja Pilz Oliver Drechsel Tobias Hoffmann Lothar Wieler Cecilia Mbae Antje Flieger Samuel Kariuki |
| author_sort | Michael Mugo |
| collection | DOAJ |
| description | Abstract Background Non-typhoidal Salmonella (NTS) typically cause self-limiting enterocolitis, but can lead to life-threatening invasive diseases, particularly in sub-Saharan Africa. In Kenya, multidrug-resistant (MDR) NTS strains with increasing non-susceptibility to third-generation cephalosporins pose a growing public health threat. As traditional antimicrobial treatments become less effective, bacteriophages are emerging as a potential alternative. This study aimed to isolate and characterize bacteriophages targeting MDR and extended spectrum-β-lactamase (ESBL)-producing non-typhoidal Salmonella (NTS). Methods Environmental samples were collected from seven sites in Nairobi City County, Kenya. Four NTS bacterial strains were used for phage enrichment, screening, and purification via spot tests and plaque assays. Phage efficacy was assessed in vitro by testing host range and efficiency of plating (EOP) against 12 Salmonella strains isolated in Kenya over different years. Ten selected broad-host-range phages were evaluated for thermal and pH stability and their ability to disrupt pre-formed NTS biofilms. Phage genomes were sequenced using the Illumina sequencing platform, and analyzed with bioinformatics tools to screen for antimicrobial resistance (AMR), lysogeny, virulence, and allergenic genes. The morphological characteristics of four representative phages were examined using Transmission Electron Microscopy. Results Thirty-one phages were isolated, with host ranges varying from lysing one strains to all 12 strains. Ten phages lysed more than 80% of the Salmonella strains and were selected for further characterization. Most phages exhibited high production EOP on at least one bacterial strain, except KE26 and KE28. All phages were stable from − 80 °C to 40 °C and pH 5 to 11, with noticeable but statistically insignificant biofilm disruption. Genome sizes ranged from 23,215 bp to 159,981 bp, and were free of known AMR, lysogeny, or virulence genes. Allergenicity screening identified no allergenic hits across most phages, with exception of KE23, which showed potential allergenic regions in its tail fiber and endolysin proteins. All phages belonged to class Caudoviricetes, with KE23, KE26, and KE28 exhibiting a myovirus-like morphotype, and KE15 displaying a siphovirus morphotype. Conclusion This study identified phages with desirable safety and stability profiles for potential usage against MDR and ESBL-producing NTS infections. Further in vivo studies are recommended to evaluate their therapeutic potential. Importance Non-typhoidal Salmonella (NTS) typically cause self-limiting enterocolitis but can lead to life-threatening invasive diseases. In Kenya, multidrug-resistant (MDR) NTS strains with increasing nonsusceptibility to third-generation cephalosporins have been reported, posing a significant public health concern that requires urgent attention. Bacteriophages are increasingly being considered as an alternative treatment for MDR bacterial infections because of the growing ineffectiveness of conventional antibiotics. Our study reports the isolation and characterization of lytic Salmonella phages devoid of detectable antimicrobial resistance (AMR) genes, lysogeny potential, allergens or virulence factors. These attributes position them as promising candidates for therapeutic interventions against MDR NTS infections. These findings highlight the potential of our study phages as a therapy for drug-resistant NTS and underscore the need for further investigation into their clinical application against MDR strains. |
| format | Article |
| id | doaj-art-fd6dc4f97a114b7d94001bc2a678f905 |
| institution | Kabale University |
| issn | 1471-2334 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj-art-fd6dc4f97a114b7d94001bc2a678f9052025-08-20T04:01:47ZengBMCBMC Infectious Diseases1471-23342025-07-0125112010.1186/s12879-025-11325-3Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, KenyaMichael Mugo0Abednego Musyoki1Angela Makumi2Ivy Mutai3Kelvin Kering4Peter Muturi5Collins Kebenei6Kristin Weber7Michael Pietsch8Tanja Pilz9Oliver Drechsel10Tobias Hoffmann11Lothar Wieler12Cecilia Mbae13Antje Flieger14Samuel Kariuki15Centre for Microbiology Research, Kenya Medical Research InstituteDepartment of Medical Laboratory Science, Kenyatta UniversityInternational Livestock Research Institute (ILRI)School of Veterinary Medicine & Sciences, University of NottinghamCentre for Microbiology Research, Kenya Medical Research InstituteCentre for Microbiology Research, Kenya Medical Research InstituteCentre for Microbiology Research, Kenya Medical Research InstituteDivision of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch InstituteDivision of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch InstituteGenome Competence Centre (MF1), Robert Koch InstituteGenome Competence Centre (MF1), Robert Koch InstituteAdvanced Light and Electron Microscopy (ZBS 4), Robert Koch InstituteHasso-Plattner-Institute, Digital Global Public HealthCentre for Microbiology Research, Kenya Medical Research InstituteDivision of Enteropathogenic Bacteria and Legionella (FG11), Robert Koch InstituteCentre for Microbiology Research, Kenya Medical Research InstituteAbstract Background Non-typhoidal Salmonella (NTS) typically cause self-limiting enterocolitis, but can lead to life-threatening invasive diseases, particularly in sub-Saharan Africa. In Kenya, multidrug-resistant (MDR) NTS strains with increasing non-susceptibility to third-generation cephalosporins pose a growing public health threat. As traditional antimicrobial treatments become less effective, bacteriophages are emerging as a potential alternative. This study aimed to isolate and characterize bacteriophages targeting MDR and extended spectrum-β-lactamase (ESBL)-producing non-typhoidal Salmonella (NTS). Methods Environmental samples were collected from seven sites in Nairobi City County, Kenya. Four NTS bacterial strains were used for phage enrichment, screening, and purification via spot tests and plaque assays. Phage efficacy was assessed in vitro by testing host range and efficiency of plating (EOP) against 12 Salmonella strains isolated in Kenya over different years. Ten selected broad-host-range phages were evaluated for thermal and pH stability and their ability to disrupt pre-formed NTS biofilms. Phage genomes were sequenced using the Illumina sequencing platform, and analyzed with bioinformatics tools to screen for antimicrobial resistance (AMR), lysogeny, virulence, and allergenic genes. The morphological characteristics of four representative phages were examined using Transmission Electron Microscopy. Results Thirty-one phages were isolated, with host ranges varying from lysing one strains to all 12 strains. Ten phages lysed more than 80% of the Salmonella strains and were selected for further characterization. Most phages exhibited high production EOP on at least one bacterial strain, except KE26 and KE28. All phages were stable from − 80 °C to 40 °C and pH 5 to 11, with noticeable but statistically insignificant biofilm disruption. Genome sizes ranged from 23,215 bp to 159,981 bp, and were free of known AMR, lysogeny, or virulence genes. Allergenicity screening identified no allergenic hits across most phages, with exception of KE23, which showed potential allergenic regions in its tail fiber and endolysin proteins. All phages belonged to class Caudoviricetes, with KE23, KE26, and KE28 exhibiting a myovirus-like morphotype, and KE15 displaying a siphovirus morphotype. Conclusion This study identified phages with desirable safety and stability profiles for potential usage against MDR and ESBL-producing NTS infections. Further in vivo studies are recommended to evaluate their therapeutic potential. Importance Non-typhoidal Salmonella (NTS) typically cause self-limiting enterocolitis but can lead to life-threatening invasive diseases. In Kenya, multidrug-resistant (MDR) NTS strains with increasing nonsusceptibility to third-generation cephalosporins have been reported, posing a significant public health concern that requires urgent attention. Bacteriophages are increasingly being considered as an alternative treatment for MDR bacterial infections because of the growing ineffectiveness of conventional antibiotics. Our study reports the isolation and characterization of lytic Salmonella phages devoid of detectable antimicrobial resistance (AMR) genes, lysogeny potential, allergens or virulence factors. These attributes position them as promising candidates for therapeutic interventions against MDR NTS infections. These findings highlight the potential of our study phages as a therapy for drug-resistant NTS and underscore the need for further investigation into their clinical application against MDR strains.https://doi.org/10.1186/s12879-025-11325-3Non-typhoidal SalmonellaMultidrug-resistantAnd phage |
| spellingShingle | Michael Mugo Abednego Musyoki Angela Makumi Ivy Mutai Kelvin Kering Peter Muturi Collins Kebenei Kristin Weber Michael Pietsch Tanja Pilz Oliver Drechsel Tobias Hoffmann Lothar Wieler Cecilia Mbae Antje Flieger Samuel Kariuki Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya BMC Infectious Diseases Non-typhoidal Salmonella Multidrug-resistant And phage |
| title | Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya |
| title_full | Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya |
| title_fullStr | Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya |
| title_full_unstemmed | Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya |
| title_short | Isolation and characterization of bacteriophages with lytic activity against multidrug-resistant non-typhoidal Salmonella from Nairobi City county, Kenya |
| title_sort | isolation and characterization of bacteriophages with lytic activity against multidrug resistant non typhoidal salmonella from nairobi city county kenya |
| topic | Non-typhoidal Salmonella Multidrug-resistant And phage |
| url | https://doi.org/10.1186/s12879-025-11325-3 |
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