December 2021 PhD Graduands

Name: Ndukui James Gakunga

Degree: Doctor of Philosophy Degree in Pharmacology and Toxicology

Commercial poultry production is an important farming enterprise in most parts of Kenya. However, accurate statistics on the frequency and mechanism of antimicrobial resistance development in enterobacteriaceae micro-organisms isolated from poultry and persons in Kenya is scarce. This current study determined the extent of antimicrobial use, and resistance patterns in selected Enterobacteriaceae isolated from commercial poultry production systems in Kiambu County, Kenya. A descriptive cross-sectional study was conducted on commercial poultry production systemsof Kiambu County. One hundred and fifty six commercial poultry farmers were purposively selected from the following sub counties; Ruiru (n=33), Juja (n=20), Gatundu North (n=20), Gatundu South (n=19), Thika (n=27) and Kikuyu (n=37) respectively. One hundred and fifty-six (n=156) semi-structured questionnaires imprinted in a mobile Open data kit were administered to capture the knowledge level, attitudes, and practices on antimicrobial usage in commercial poultry production systems of Kiambu County. A total of 437 fecal samples (cloacal swabs (n=365), and Human stool (n=72)) were collected, followed by bacterial isolation, identification, confirmation, antibiotics susceptibility tests, and molecular detection of ESBLs genes and Quinolones resistance (QNRs) were detected using Polymerase chain reaction (PCR) methods. In this study, females accounted for (64%) with 51% of them keeping layers as medium-scale farmers. Sixty-one percent (61%) of the farmerswere 45 years and above, and they had obtained a secondary level of education (34%). Sixty seven percent (67%) of the farmers obtained antimicrobials through self-prescription/personal experience from the drug shops. Farmers identified lack of enough veterinary officers (77%) and consultation services (72%) as key challenges in poultry production system. Sixty three percent (63%) of the respondents, indicated tetracycline and amoxicillin as the most commonly used antibiotics in their farms. Nearness to veterinary services, area of residence, type of production, number of years in poultry farming, and numbers of birds kept  significantly (P<0.05) influenced the level of knowledge, attitudes,  and practices on antimicrobial usage. Out of 437 fecal and stool samples collected, 591 (Cloacal isolates=544; human isolates= 47) isolates were recovered, with E.coli (48.9%) being the most frequently identified, followed by Shigella spp. (18.8%), Salmonella spp. (18.3%), and Klebsiella spp. (14.0%). Multiple drugs resistance among the isolateswas towards sulfamethoxazole (79%), trimethoprim (71%), and tetracyclines (59%), respectively. Out of the isolates (n=78) collected with potential ESBLs production, only 66 (84%) tested positive for the target genes with blaOXA (n=20; 26%) from Escherichia colibeing the most detected. Additionally, most of the AMR gene co-carriage was detected in both E.coli and Salmonella spps. It was concluded that fecal materials from commercial poultry systems can be a reservoir of multi-drug resistance enterics. This being a potential route of spreading out resistance genes amongst livestock and Humans, which pose a great danger to public health of Kiambu County residence. It was recommended that the results of the current study be used in formulating strategies and informed decisions in combating antibiotic resistance and irrational usage of antibiotics in commercial poultry production in Kiambu County and other areas with similar poultry production systems in Kenya.


Omwenga Isaac Mokaya

Doctor of Philosophy Degree in Pharmacology and Toxicology


Staphylococcus aureus (S. aureus) is a ubiquitous Gram-positive bacterium commonly encountered in the environment as well as mucus membranes of animals and humans. S. aureus food poisoning results from consumption of preformed S. aureus enterotoxins in food. The prevalence of antimicrobial resistant (AMR)-S. aureus including methicillin-resistant S. aureus (MRSA) in livestock raw milk consumed by pastoralists in Kenya remains unclear. This study determined the phenotypes, genetic determinants for virulence associated with S. aureus enterotoxins, the phenotypic resistance profiles, genetic determinants responsible for antimicrobial resistance phenotypes of milk borne S. aureus and the relationship between antimicrobial usage (AMU) and emergence of multidrug-resistant (MDR) S. aureus.

A cross-sectional study design involving 188 households in the Marsabit and Isiolo Counties was conducted. In total, 603 milk samples from various livestock including cattle, goats, sheep, camels and 188 pooled from all animals were collected from Isiolo and Marsabit counties of Kenya. S. aureus isolates were cultured from milk samples using a selective media and biochemical tests followed by amplification of S. aureus specific staphylococcal terminase gene (satm) and BLAST analysis.


Antimicrobial susceptibility testing was performed using the Kirby-Bauer disc diffusion method. At least one type of S. aureus enterotoxin gene (SE) was detected in 74.11% (95% CI: 63.91–82.24%) of the 85 isolates. The most frequently encountered gene was see (51; 60%) followed by sea (22; 25.88) and sec (19; 22.35%). None of the isolates tested positive for sed. Overall, 21 of the 85 (24.7%) strains harbored more than one enterotoxin gene.The S. aureus isolates were mainly resistant to tetracycline (79%), ampicillin (58%), and oxacillin (33%), respectively. A few isolates (5–18%) were resistant to clindamycin, cephalexin, erythromycin, kanamycin, and ciprofloxacin. Most of the MDR-S. aureus isolates were MRSA (94%). The genetic determinants found in the AMR isolates included tetK/tetM (96.5%/19%) for tetracycline, blaZ (79%) for penicillin, aac (6’)/aph (2”)/aph (3’)-IIIa (53%) for aminoglycosides, mecA (41%) for oxacillin, and msrA/ermA (24%/7%) for macrolides.

The antimicrobial classes used in the study site were as follows; 4,168 kg of oxytetracycline, 70 kg of sulfonamides, 49.7 kg of aminoglycosides, 46 kg of beta-lactams, 39.4 kg of macrolides, and 0.52 kg for trimethoprim. Oxytetracycline usage was correlated to tetK/tetM (r = 0.62/1) detection, penicillins to mecA/blaZ (r = 0.86/0.98), aminoglycoside to aac (6’)/aph (2”)/aph (3’)-IIIa (r = 0.76/-13), and macrolide usages for detection of ermA/msrA (r = 0.94/0.77).

In conclusion, milk consumed in Marsabit and Isiolo counties is contaminated with enterotoxigenic multidrug resistant S. aureus that harbour antimicrobial resistance genes hence its consumption could increase the risk of staphylococcal food poisoning. Judicious use of antimicrobials is recommended in the study areas to mitigate against development of AMR

Omwenga Isaac Mokaya  Doctor of Philosophy Degree in Pharmacology and Toxicology