The human population is growing and urbanising. These factors are driving the demand for animal-sourced proteins. The rising demand is favouring livestock intensification, a process that frequently relies on antibiotics for growth promotion, treatment and prevention of diseases. Antibiotic use in livestock production requires strict adherence to the recommended withdrawal periods. In Kenya, the risk of residues in meat is particularly high due to lack of legislation requiring testing for antibiotic residues in meat destined for the local market. We examined pig carcasses for gross pathological lesions and collected pork samples for antibiotic residue testing. Our aim was to determine if a risk-based approach to residue surveillance may be adopted by looking for an association between lesions and presence of residues. In total, 387 pork samples were tested for antibiotic residues using the Premi^®Test micro-inhibition kit. The prevalence of antibiotic residues was 41.26% (95% CI, 34.53–48.45%). A logistic regression model found no significant associations between gross pathological lesions and the presence of antibiotic residues. We recommend that the regulating authorities strongly consider routine testing of carcasses for antibiotic residues to protect meat consumers. Future studies should research on farming practices contributing to the high prevalence of residues.

Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.

Brucellosis is a zoonosis caused by bacteria of the genus Brucella, which results in economic losses relating to livestock and threatens public health. A cross-sectional study was conducted to determine the molecular prevalence of Brucella species in smallholder dairy cattle in six regions of Tanzania from July 2019 to October 2020. Dairy cattle (n = 2048) were sampled from 1371 farms. DNA extracted from blood and vaginal swabs was tested for Brucella using qPCR targeting the IS711 gene and positives were tested for the alkB marker for B. abortus and BMEI1172 marker for B. melitensis. The molecular prevalence was 3.5% (95% CI: 2.8–4.4) with the highest prevalence 8.1% (95% CI: 4.6–13.0) in Njombe region. B. melitensis was the predominant species detected (66.2%). Further studies are recommended to understand the source of B. melitensis and its implications for veterinary public health. Livestock keepers should be informed of the risks and biosecurity practices to reduce the introduction and control of Brucella. Cattle and small ruminant vaccination programs could be implemented to control brucellosis in high-risk populations in the country.

Toxoplasma gondii is a ubiquitous protozoan parasite of public health concern, with severe health consequences among immunocompromised individuals and pregnant mothers. Pigs are intermediate hosts of this zoonotic parasite and consumption of undercooked pork is a risk factor for T. gondii infection. We investigated the seroprevalence and risk factors for T. gondii in pigs in Kenya. A cross-sectional study was conducted at a non-integrated abattoir in Kiambu, Kenya, where 446 blood samples were collected from slaughtered pigs between 5 January and 5 March 2021. For each pig sampled, additional data were collected on the county of origin, farm size, sex and live weight. Serum was harvested from each pig blood sample, and these were subjected to indirect enzyme-linked immunosorbent assay tests to detect the presence of immunoglobin G (IgG) for T. gondii infection. The overall seroprevalence for T. gondii was 34.53% (95% C.I. 30.16–39.17). Risk factors for T. gondii seropositivity in pigs included farm size (p < 0.001) and the live weight of pigs (p = 0.044). The high seroprevalence of T. gondii indicates that consumers of raw and undercooked pork may be at a high risk of infection. It is therefore recommended that strategies for the mitigation of risk of exposure in populations should prioritize public health education for pig farmers, pork handlers and consumers on risk reduction measures along the pork value chains.

The control of contagious bovine pleuropneumonia (CBPP) remains constrained by institutional, financial and technical barriers in many livestock-keeping regions of sub-Saharan Africa, despite its detrimental impact on trade, pastoral livelihoods and food security. Therefore, livestock keepers are relying on suboptimal use of antimicrobials to manage CBPP outbreaks. We conducted an outbreak investigation to understand epidemiological and management practices in 95 herds with ongoing or recent cases of CBPP in five counties of Kenya. A wide range of antimicrobials including tetracycline, penicillin-streptomycin (pen & strep), tylosin, and diminazen were used in majority of herds (90/95; 94.7%), with half of these herds receiving sequential administration of two or more types of drugs to address failure of the first use. Only 33/95 (34.7%) of farmers reported to have vaccinated their animals and most of them vaccinated in response to outbreaks in their herds rather than the expected routine preventive program (28/33, 84.8%). The average case fatality rate (CFR) for CBPP was estimated at 36%, with only treatment with tylosin resulting in a significant reduction in mortalities due to CBPP ( p = 0.035). Majority of livestock keepers (83.3%) continued to consume milk from their animals during and after the treatment period, without observing the stipulated withdrawal periods. Policy emphasis should shift toward prudent use of antimicrobials and preventive vaccination as the cornerstone of CBPP control, while using multifaceted One Health strategy that bridges veterinary, public health, and environmental sectors.

Brucellosis is a zoonoses caused by bacteria of the genus Brucella, which causes economic losses in livestock and threatens public health. A cross-sectional study was conducted to determine the prevalence of Brucella species and risk factors in smallholder dairy cattle in six regions of Tanzania from July 2019 to October 2020. Dairy cattle (n=2048) were sampled from 1371 farms. DNA ex-tracted from blood and vaginal swabs was tested for Brucella using qPCR targeting the IS711 gene and positives were tested for the alkB marker for B. abortus and BMEI1172 marker for B. melitensis. The molecular prevalence was 3.5% (95% CI: 2.8-4.4) with the highest prevalence 8.1% (95%CI: 4.6-13.0) in Njombe region. B. melitensis was the predominant species detected (66.2%). Logistic regression revealed PCR positivity in dairy cattle was higher in the animals with a history of abortion (OR: 3.17, 95%CI: 1.05-9.62) and farms without dogs around (OR: 2.68, 95%CI: 1.12-5.90). Further studies are recommended to understand the source of B. melitensis and the implications to veterinary public health. Livestock keepers should be informed of the risks and biosecurity practices to reduce introduction and control Brucella. Cattle and small ruminant vaccination pro-grams could be implemented to control brucellosis in high-risk populations in the country.