Isolation and Characterization of Bacteriophages with Lytic Activity against Multidrug-Resistant Non-Typhoidal Salmonella from Nairobi City County, Kenya
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Date
2025-12
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Kenyatta University
Abstract
Non-typhoidal Salmonella (NTS) commonly cause self-limiting gastroenteritis; however,
severe invasive infections occur in vulnerable populations and high-burden regions. In
Kenya, multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing
NTS with reduced susceptibility to third-generation cephalosporins present a growing
public health challenge. Rising antimicrobial resistance (AMR), coupled with slow
development of new antibiotics, highlights the urgent need for alternative treatment
strategies. Bacteriophages offer a promising option, yet phage data targeting MDR and
ESBL-producing NTS in Kenya remain limited. This study aimed to isolate and
characterize lytic bacteriophages against MDR NTS. Sampling was conducted in Nairobi
City County between April and October 2022, targeting informal settlements and Ruai
Sewage Treatment Plant using a purposive approach to maximize phage recovery. Water
samples from open drains, rivers, and a dam across seven sampling points were collected
in sterile Whirl-Pak bags and transported under chilled conditions to the Kenya Medical
Research Institute for same-day processing. Four NTS strains were used in phage
enrichment, spot tests, and plaque purification, while a panel of 12 Salmonella isolates was
used to assess host range and efficiency of plating (EOP). Ten broad-host-range phages
were further evaluated for thermal and pH stability, ability to disrupt pre-formed biofilms,
genomic features (Illumina sequencing), potential allergenicity and morphology
(Transmission Electron Microscopy). Data analysis combined descriptive summaries with
Mann–Whitney tests for biofilm assays and standard genomic and TEM evaluations.
Thirty-one phages with host ranges varying from 8% to 100% were isolated. Ten phages
demonstrating the ability to lyse more than 10 Salmonella strains tested were selected for
physicochemical and genome characterization. Except for KE26 and KE28, the study
phages exhibited high production efficiency EOP in at least one bacterial strain. Phages
were stable at temperature from -80°C to 40°C and pH 5 to 11, and showed noticeable but
statistically insignificant biofilm disruption. Genomic analysis revealed linear doublestranded DNA genomes size ranging from 23,215 bp to 159,981 bp, with no virulence
genes, AMR genes or lysogeny genes detected. 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. This study identifies safe and promising lytic
phages with strong potential for development as therapeutic candidates against MDR and
ESBL-producing NTS infections in Kenya, and recommends further preclinical evaluation
using appropriate animal models
Description
A Research Thesis Submitted in Partial Fulfilment of the Requirements for the Award of the Degree of Master of Science in Medical Laboratory Sciences (Medical Bacteriology) in the School of Health Sciences of Kenyatta University, December, 2025
Supervisor:
1.Abednego Musyoki
2.Angela Makumi