Daniel Wambua Wanja

Background and Aim: Foodborne diseases caused by bacterial contamination of meat remain a major global public health concern, particularly in low- and middle-income countries. Escherichia coli and Salmonella are among the most important zoonotic pathogens associated with raw meat, and their increasing antimicrobial resistance (AMR) further complicates treatment and control. In Kenya, limited data exist on bacterial contamination and resistance patterns along the meat value chain, especially in peri-urban and rural settings. This study aimed to quantify bacterial contamination levels and determine the prevalence and AMR profiles of E. coli and Salmonella species isolated from raw chicken meat and pork collected from slaughterhouses and retail outlets in Murang’a County, Kenya. Materials and Methods: A cross-sectional study was conducted between November 2024 and June 2025. A total of 320 meat samples (105 chicken and 215 pork) were collected from slaughterhouses, butcher shops, supermarkets, and public wet markets. Total viable counts (TVC) were determined using standard plate count methods. Isolation and identification of E. coli and Salmonella species were performed using conventional culture techniques and confirmed by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry. Antimicrobial susceptibility testing was conducted using the Kirby–Bauer disk diffusion method following Clinical and Laboratory Standards Institute guidelines. Multiple antibiotic resistance (MAR) indices and resistance phenotypes were also determined. Results: High levels of bacterial contamination were observed, with mean TVC exceeding recommended limits (6.45 log₁₀ CFU/cm² for chicken and 6.39 log₁₀ CFU/cm² for pork). Overall prevalence of E. coli was 61.6%, while Salmonella species were detected in 7.2% of samples. AMR was widespread, particularly in E. coli, with high resistance to ampicillin (95.3%), amoxicillin–clavulanate (78.7%), gentamicin (72.7%), and tetracycline (72.0%). Multidrug resistance was detected in 87.3% of E. coli isolates, with 16.0% classified as extensively drug-resistant and one isolate identified as possible pandrug-resistant. All isolates exhibited MAR indices ≥0.1, indicating exposure to high-risk antimicrobial environments. Salmonella isolates showed the highest resistance to ciprofloxacin (86.4%) and lower multidrug resistance (13.6%). Conclusion: The study demonstrates substantial bacterial contamination and high prevalence of antimicrobial-resistant pathogens in raw meat along the Kenyan meat value chain. These findings highlight the urgent need for strengthened hygiene practices, improved food safety regulation, and enhanced AMR surveillance within a One Health framework to mitigate public health risks. Keywords: antimicrobial resistance, Escherichia coli, food safety, Kenya, meat contamination, multidrug resistance, pork and chicken, Salmonella.

Background and Aim: The growing burden of infectious diseases and antimicrobial resistance (AMR) in aquaculture demands safe, host-adapted alternatives to antibiotics. Probiotics derived from the gastrointestinal tract (GIT) of the target host are considered more ecologically compatible and effective than non-host strains. This study aimed to isolate and characterize indigenous gut bacteria from wild Nile tilapia (Oreochromis niloticus) collected from Lake Naivasha, Kenya, to evaluate their probiotic attributes, assess pathogenicity, and identify promising candidates using conventional phenotypic methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Materials and Methods: Thirty-eight apparently healthy O. niloticus were sampled, and bacteria were isolated from the entire GIT using standard bacteriological techniques. Fifty autochthonous isolates were obtained and subjected to stepwise screening, including hemolytic activity, antibiotic susceptibility, enzymatic activity (protease and amylase), tolerance to low pH and bile salts, adhesion to stainless steel surfaces, growth kinetics, and in vivo pathogenicity in O. niloticus. Species-level identification was performed using biochemical tests and MALDI-TOF MS. Results: Of the 50 isolates, 10 (20%) were nonhemolytic and sensitive to at least eight antibiotics. Functional screening reduced these to four candidates exhibiting enzymatic activity, acid and bile tolerance, and adhesion. Three isolates, identified as Rossellomorea marisflavi, Micrococcus luteus, and Paucilactobacillus vaccinostercus, were nonpathogenic to O. niloticus. In contrast, Aeromonas ichthiosmia, despite exhibiting several probiotic-like traits in vitro, caused 80% cumulative mortality and was excluded. Among the nonpathogenic isolates, P. vaccinostercus demonstrated the strongest overall probiotic profile, including superior acid and bile tolerance, high enzymatic indices, robust adhesion (~4.7 × 10⁴ CFU/mL), and favorable growth kinetics. Conclusion: The gut microbiota of wild O. niloticus from Lake Naivasha harbors a limited but valuable pool of indigenous bacteria with probiotic potential. This study provides the first evidence that P. vaccinostercus is a promising, nonpathogenic probiotic candidate for tilapia aquaculture. These findings support the development of locally adapted, antibiotic-free probiotic strategies to enhance fish health and sustainable aquaculture in Kenya. Further in vivo feeding trials and genomic safety assessments are warranted. Keywords: aquaculture, aquaculture probiotics, fish gut microbiota, Kenya aquaculture, Lake Naivasha, MALDI-TOF MS, Nile tilapia, Paucilactobacillus vaccinostercus, sustainable aquaculture.

Poultry production is a key source of income and animal protein in Kenya, especially for smallholders. Chickens are important reservoirs of zoonotic bacteria such as Campylobacter spp., which can infect humans via direct contact or contaminated products. Identifying farm‐level factors linked to Campylobacter colonization in chickens is crucial for improving biosecurity and reducing public health risks. This cross‐sectional study was conducted in four selected subcounties of Murang′a County between August and December 2024 and aimed to identify farm‐level risk factors associated with Campylobacter colonization in the chicken gut in Murang′a County, Kenya. We collected 340 cloacal swabs from chickens reared on smallholder farms. Swabs were processed using standard bacteriological isolation and preliminary phenotypic identification, followed by genus‐level confirmation using matrix‐assisted laser desorption/ionization–time of flight mass spectrometry (MALDI‐TOF MS). Epidemiological data on potential risk factors were collected using a pretested semistructured questionnaire administered to poultry farmers. Logistic regression analysis was used to evaluate associations between farm‐level factors and isolation of Campylobacter spp. in chickens. Among the 340 farms, 215 were positive for Campylobacter spp., resulting in a farm‐level prevalence of 63.2% (95% CI: 58.1%–68.3%). Campylobacter colonization was significantly associated with poor poultry house hygiene (OR = 2.880, p = 0.018), larger flock size (OR = 2.678, p = 0.017) and higher farmer education level ( OR = 1.984, p = 0.044). The education association likely suggests a proxy for production intensity rather than an independent biological risk factor. Campylobacter occurrence is influenced by farm hygiene, farmer education and flock size in smallholder poultry systems. Improving farm biosecurity practices, farmer awareness and hygiene could reduce zoonotic bacterial risk along the poultry value chain in Murang′a County and similar smallholder production systems.

Fish parasitic infections present a growing threat to freshwater aquaculture in Kenya, affecting fish health, reducing productivity, and limiting the economic potential of small‐scale and commercial farms. This review provides the first consolidated national checklist of freshwater fish parasites in Kenya, synthesizing evidence from lakes, rivers, and aquaculture systems across multiple counties. By integrating data from diverse host species and production environments, it establishes a comprehensive baseline on parasite diversity, host range, and geographic distribution that has previously been fragmented across isolated studies. Studies were identified through a structured search of scientific databases. The review highlights the widespread occurrence of parasitic infections in economically important species, such as Oreochromis , Clarias , Lates , Haplochromis , Barbus , and Cyprinus . Parasites identified included ectoparasites, a haemoparasite, helminths, and an acanthocephalan. Helminths, especially digenean trematodes, were the most commonly reported. Infection prevalence varied across production systems, with higher diversity and burden in earthen ponds and natural lakes compared with lined or concrete ponds. The most frequently encountered genera were Gyrodactylus , Diplostomum , Contracaecum , and Proteocephalus , affecting both wild and cultured fish populations. Risk factors influencing parasite prevalence were linked to environmental conditions and farm management practices. Poor water quality, overstocking, reuse of contaminated nets, retention of pond bottom sediments after harvest, and use of untreated livestock manure were frequently associated with increased infections. Ecological factors such as the presence of wild birds and aquatic snails were also implicated in sustaining transmission cycles. Seasonal flooding further contributed to parasite dispersal in some regions. The review underscores the need for integrated parasite management strategies. This includes routine monitoring using advanced diagnostics, improved biosecurity practices at farm level, targeted training of farmers and extension workers, and reduced dependence on high‐risk inputs such as raw manure. Public awareness on zoonotic risks of fish‐borne parasites should also be strengthened. Investing in research to explore vaccine development and the role of environmental drivers in parasite ecology will be essential in safeguarding the sustainability of Kenya′s freshwater aquaculture sector.

Aeromonas veronii biotype sobria is a potential aquatic zoonotic pathogen and a major cause of freshwater bacterial infections in cultured fish globally, leading to substantial economic losses. This study aimed to establish the median lethal dose (LD _50-96 h ) for Aeromonas veronii biovar sobria A4 strain and to demonstrate induction of clinical signs, gross and microscopic lesions in experimentally infected juvenile Nile tilapia ( Oreochromis niloticus ). Aeromonas veronii biotype sobria A4 strain used in this study were obtained from water samples from ponds with high fish mortality at Cavarino farm in Narok County, Kenya. Six groups each comprising 10 fish were intraperitoneally injected with 0.1 mL of A. veronii biovar sobria A4 strain suspension at: 1.5 × 10 ⁴ , 1.5 × 10 ⁵ , 1.5 × 10 ⁶ , 1.5 × 10 ⁷ , 1.5 × 10 ⁸ , and 1.5 × 10 ⁹ colony forming units per mL (CFU/mL) respectively and the bacteria was afterward recovered from kidney and hepatopancreas of freshly dead fish. Duplicate control groups (each n = 10) were injected with sterile physiological saline before the lethal dose group were injected with varying concentration of the A. veronii biovar sobria A4 strain. The LD _50-96 h of A. veronii biovar sobria A4 strain was found to be 1.5 × 10 ⁸ CFU/mL. Clinical signs and gross lesions observed in the lethal dose group were: skin hemorrhages (20%), erosion of the fins including caudal fin with scale loss exposing underlying skin (13.7%), congested and hemorrhagic gills (15%), hepatic hemorrhages and enlargement (21.3%), distension of gall bladder (18.8%), splenomegaly and congestion (22.5%), and ascites (16.3%). The main histopathological lesions observed in the gills were focal hemorrhages, atrophy of the filaments and loss of lamellae in some filaments with mononuclear cellular infiltration; on the liver there were; hemorrhages, infiltration with lymphocytes and melanomacrophages, degenerative hepatocytes and focal necrosis. There was extensive hemosiderosis with increased melanomacrophages in the spleen. The kidney showed extensive hemorrhages, localized coagulative necrosis, atrophied glomeruli and multifocal mononuclear cellular infiltration in the interstitium. The findings will lay a foundational basis for subsequent investigations into the host‐pathogen interaction, therapeutic approaches, and epidemiology of Aeromonas veronii biovar sobria .

Globally, parasitic infections hinder aquaculture productivity and sustainability. Improper water quality parameters reduce fish immunity, make them susceptible to parasites, and enhance parasitic proliferation in culture systems. Subsequently, this study aimed to determine the prevalence and intensity of ecto‐ and endo‐parasite infesting Oreochromis niloticus in varying water quality in aquaculture systems in Kericho, Bomet, and Nakuru counties. A total of 220 Oreochromis niloticus samples were captured from 11 liner ponds, eight earthen ponds, two concrete ponds, and one plastic tank from 22 farms in the three counties. External and internal organs were examined for parasite infestation. Skin scrapings and squash preparation of fish eyes were also examined to reveal the organisms through microscopic examination. A Pearson’s correlation analysis between physicochemical parameters and parasitic prevalence was used to determine the strength and direction of correlation coefficients with significance at 95%. Overall parasitic prevalence infestation was 39.6% (87/220). Ten parasite genera were recovered, with Dactylogyrus species dominating overall at 15.9% (35/220), followed by Trichodina spp. (7.7%; 17/220). Epistylis species had the highest mean intensity of 12.8 ± 35.7 (total number of Epistylis parasites (141)/total of infested fish (11)). Earthen ponds had a significantly higher (36.2%, 29/80) prevalence of Dactylogyrus sp. than liner ponds (3.6%, 4/110) (p < 0.001). Dissolved oxygen levels were 16.9 ± 0.7 mgL⁻¹ in Bomet, 14.9 ± 0.3 mgL⁻¹ in Kericho, and 12.5 ± 0.5 mgL⁻¹ in Nakuru which were above desirable range for fish culture. The electrical conductivity in Bomet was 76 ± 5 µS/cm and Kericho 52 ± 4 µS/cm below the desirable range. Temperature, pH, phosphate, nitrates, and nitrites were within the desirable limit for fish farming. Electrical conductivity and pH had positive correlation of 1 and 0.97, respectively, with the prevalence of Acanthocephalus, Euclinostomum, and Trichodina species. Temperature and nitrate positively correlated between 0.80–0.89 and 0.90–0.99, respectively, with the prevalence of Dactylogyrus, Riboscyphidia, Epistylis, Camallanus, and Paracamallanus species. The study demonstrates that water quality significantly influences parasitic prevalence in aquaculture systems. Therefore, it is crucial for farmers to monitor water quality parameters to mitigate parasitic infestations.

Campylobacter is a zoonotic foodborne pathogen that is often linked with gastroenteritis and other extraintestinal infections in humans. This study is aimed at determining the genetic determinants of virulence‐encoding genes responsible for flagellin motility protein A (flaA), Campylobacter adhesion to fibronectin F (cadF), Campylobacter invasion antigen B (ciaB) and cytolethal distending toxin (cdt) A (cdtA) in Campylobacter species. A total of 29 Campylobacter coli isolates (16 from cattle, 9 from chicken, and 4 from water samples) and 74 Campylobacter jejuni isolates (38 from cattle, 30 from chicken, and 6 from water samples) described in an earlier study in Kajiado County, Kenya, were examined for the occurrence of virulence‐associated genes using polymerase chain reaction (PCR) and amplicon sequencing. The correlations among virulence genes were analyzed using Pearson’s correlation coefficient (R) method. Among the 103 Campylobacter strains screened, 89 were found to harbour a single or multiple virulence gene(s), giving an overall prevalence of 86.4%. C. jejuni strains had the highest prevalence of multivirulence at 64.9% (48/74), compared to C. coli (58.6%, 17/29). The ciaB and flaA genes were the most common virulence genes detected in C. jejuni (81.1% [60/74] and 62.2% [46/74], respectively) and in C. coli (each at 62.1%; 18/29). Campylobacter isolates from chicken harboured the most virulence‐encoding genes. C. jejuni strains from chicken and cattle harboured the highest proportions of the cdtA and ciaB genes, respectively. All the C. coli strains from water samples harboured the cadF and flaA genes. The results obtained further revealed a significant positive correlation between cadF and flaA (R = 0.733). C. jejuni and C. coli strains from cattle, chicken, and water harbour virulence markers responsible for motility/colonization, invasion, adherence, and toxin production, evoking their important role in campylobacteriosis development among humans and livestock. The identification of cattle, chicken, and water samples as reservoirs of virulent Campylobacter spp. highlights the possible risk to human health. These data on some virulence genes of Campylobacter will assist food safety and public health officials in formulating policy statements.

Campylobacter organisms are the major cause of bacterial gastroenteritis and diarrhoeal illness in man and livestock. Campylobacter is growingly becoming resistant to critically crucial antibiotics; thereby presenting public health challenge. This study aimed at establishing antimicrobial use, susceptibility profiles, and resistance genes in Campylobacter isolates recovered from chicken, cattle, and cattle-trough water samples. The study was conducted between October 2020 and May 2022 and involved the revival of cryopreserved Campylobacter isolates confirmed by PCR from a previous prevalence study in Kajiado County, Kenya. Data on antimicrobial use and animal health-seeking behaviour among livestock owners (from the same farms where sampling was done for the prevalence study) were collected through interview using a pretested semistructured questionnaire. One hundred and three isolates (29 C. coli (16 cattle isolates, 9 chicken isolates, and 4 water isolates) and 74 C. jejuni (38 cattle isolates, 30 chicken isolates, and 6 water isolates)) were assayed for phenotypic antibiotic susceptibility profile using the KirbyBauer disk diffusion method for ampicillin (AX), tetracycline (TE), gentamicin (GEN), erythromycin (E), ciprofloxacin (CIP), and nalidixic acid (NA). Furthermore, detection of genes conferring resistance to tetracyclines (tet (O), β-lactams (bla_OXA-61), aminoglycosides (aph-3-1), (fluoro)quinolones (gyrA), and multidrug efflux pump (cmeB) encoding resistance to multiple antibiotics was detected by mPCR and confirmed by DNA sequencing. The correlation between antibiotic use and resistance phenotypes was determined using the Pearsons correlation coefficient (r) method. Tetracyclines, aminoglycosides, and β-lactam-based antibiotics were the most commonly used antimicrobials; with most farms generally reported using antimicrobials in chicken production systems than in cattle. The highest resistance amongst isolates was recorded in ampicillin (100), followed by tetracycline (97.1), erythromycin (75.7), and ciprofloxacin (63.1). Multidrug resistance (MDR) profile was observed in 99 of 103 (96.1) isolates; with all the Campylobacter coli isolates displaying MDR. All chicken isolates (39/39, 100) exhibited multidrug resistance. The AX-TE-E-CIP was the most common MDR pattern at 29.1. The antibiotic resistance genes were detected as follows: tet (O), gyrA, cmeB, bla_OXA-61, and aph-3-1 genes were detected at 93.2, 61.2, 54.4, 36.9, and 22.3 of all Campylobacter isolates, respectively. The highest correlations were found between tet (O) and tetracycline-resistant phenotypes for C. coli (96.4) and C. jejuni (95.8). A moderate level of concordance was observed between the KirbyBauer disk diffusion method (phenotypic assay) and PCR (genotypic assay) for tetracycline in both C. coli (kappa coefficient=0.65) and C. jejuni (kappa coefficient=0.55). The study discloses relatively high resistance profiles and multidrug resistance to antibiotics of critical importance in humans. The evolution of the multidrug-resistantCampylobacter isolates has been linked to the use and misuse of antimicrobials. This poses a potential hazard to public and animal health, necessitating need to reduce the use of antibiotics in livestock husbandry practice coupled with stringent biosecurity measures to mitigate antimicrobial resistance.

Thermophilic Campylobacter species are a leading cause of human gastroenteritis throughout the world and have been implicated in reproductive disorders (abortion), mastitis, enteritis, and/or diarrhoea in livestock. A cross-sectional survey was conducted in Kajiado County to determine prevalence, seasonality, and molecular detection of thermophilic Campylobacter species (with emphasis on C. jejuni, C. coli, and other thermophilic Campylobacter species) in chicken, cattle, and respective pooled drinking water. A total of 457 samples comprising 265 cattle rectal swabs, 142 chicken cloacal swabs, and 50 trough water samples were collected from 55 randomly selected smallholder farms. Individual samples were subjected to standard techniques for isolation and biochemical tests, followed by singleplex polymerase chain reaction (sPCR) assays for identification and confirmation of genus and species. Overall, thermophilic Campylobacter prevalence was 35.4% (95% confidence interval (95% CI) = 31.0–39.8), with C. jejuni dominating at 55.6% (95% CI = 47.9–63.3%) over C. coli in all sample types. The highest thermophilic Campylobacter prevalence was observed in cloacal swabs of live chicken at 44.4% (95% CI = 36.2–52.6%), followed by rectal swabs from live cattle at 30.9% (95% CI = 25.3–36.5%). Water samples from cattle drinkers/trough were found to be contaminated at 34% (95% CI = 20.9–47.1%). The isolation rate was higher in cattle under the confinement system (44.3%) (95% CI = 36.1–52.5%) than in those under the free-roaming grazing system. Thermophilic Campylobacter species were isolated in both seasons, with higher prevalence (39.8% (95% CI = 33.6–45.9)) recorded during rainy and cold season in all sample types except for water. There was significant ( ) association between season and thermophilic Campylobacter occurrence, even though there were no statistical differences in the prevalence values across the two seasons. Results of this study demonstrate that cattle, chicken, and respective drinking water harbour potentially pathogenic thermophilic campylobacters, with C. jejuni being widely distributed among farms. It is possible that seasonal variations and cattle confinement result in differences in thermophilic Campylobacter carriage. Further epidemiological and phylogenetic studies comparing distribution of thermophilic Campylobacter spp. isolates in livestock, environmental, and human samples are recommended to establish source attribution to reduce the impact of resultant diseases for the wellbeing of public and livestock.

Fish bacterial pathogens cause diseases which result in a considerable economic impact on the aquaculture industry, necessitating the use of antimicrobials for their control. However, intensive and indiscriminate use of antimicrobials has led to increased occurrence of drug resistance in pathogenic bacteria, as well as normal flora. The aim of the current study was to determine the susceptibility patterns of bacteria isolated from fish, with respect to some commonly used antibiotics and disinfectants. Bacteria were isolated between December 2017 and April 2018 from farmed Nile tilapia, African catfish, goldfish, and koi carp in Kirinyaga County, Kenya. Antibiotic and disinfectant susceptibility patterns of 48 isolates belonging to the genera Aeromonas, Proteus, Klebsiella, Citrobacter, Salmonella, Streptococcus, Pseudomonas, Escherichia, Serratia, and Micrococcus were established using the Kirby–Bauer disc diffusion method and agar well diffusion technique, respectively. The antibiotics evaluated included ampicillin, tetracycline, co-trimoxazole, streptomycin, kanamycin, gentamicin, co-trimoxazole, and chloramphenicol, while the disinfectants tested were quaternary ammonium compound, formalin, hydrogen peroxide, sodium hypochlorite, and iodine. All the bacteria except Micrococcus, Escherichia, and Salmonella species showed multiple drug resistance patterns. Streptococcus showed resistance to six antibiotics, while Proteus, Pseudomonas, and Serratia were resistant to five antibiotics. The multiple antibiotic resistance index ranged from 0.1 to 0.8, with Streptococcus spp. having the highest score value. All the organisms were sensitive to gentamicin, while co-trimoxazole and ampicillin showed the highest resistance at 73% (n = 34) and 62% (n = 31), respectively. Most of the disinfectants showed antibacterial activity with varying magnitudes. The isolates were 100% sensitive to hydrogen peroxide and formalin, but were resistant to sodium hypochlorite at recommended user-dilution. The study has shown that some of the bacterial isolates were resistant to common antibiotics and disinfectants; thus, it is recommended to include an antibiogram whenever making any therapeutic decision. The resistant bacteria may transmit resistance genes to other fish bacteria and also to human bacteria, thus making it difficult to treat the resultant disease(s); thus, there is a possibility that these resistant bacteria may be transmitted to humans who consume or handle the carrier fish. It is, therefore, advisable that fish are cooked properly before consumption, so as to kill bacteria that may be present.