Antimicrobial Resistance in Slaughterhouses, Kenya.

Slaughterhouses are hotspots for the transmission of antimicrobial-resistant pathogens. We conducted stakeholder discussions on antimicrobial-resistant pathogens within the slaughterhouse setting. Butchers were described as powerful stakeholders; challenges included limited funding and staff, inadequate infrastructure, and limited laboratory capacity. Slaughterhouse workers understood that their work increased their risk for exposure.

Electronic data collection to enhance disease surveillance at the slaughterhouse in a smallholder production system.

Globally, meat inspection provides data for animal health surveillance. However, paper-based recording of data is often not reported through to higher authorities in sufficient detail. We trialled the use of an electronic meat inspection form in Kenyan slaughterhouses, in lieu of the currently used paper-based format. Meat inspectors in two ruminant slaughterhouses completed and submitted an electronic report for each animal slaughtered at their facility. The reports, which captured information on the animal demographics and any eventual condemnations, were stored in a central database and available in real-time. A stakeholder meeting was held towards the end of the study. Over the 2.75 year study period, 16,386 reports were submitted; a downward linear trend in the monthly submissions was noted. There was a week effect, whereby more reports were submitted on the market day. Of the slaughtered animals, 23% had at least a partial condemnation. The most frequently condemned organs were the liver, lungs and intestines; the primary reasons for condemnations were parasitic conditions. Lack of feedback and difficulty capturing animal origin information were the primary challenges highlighted. The study demonstrated that electronic data capture is feasible in such challenging environments, thereby improving the timeliness and resolution of the data collected.

Who let the dogs out? Exploring the spatial ecology of free-roaming domestic dogs in western Kenya.

The spatial ecology of free-roaming dogs determines their role in the transmission of zoonoses. This study describes the geographic range of and identifies sites frequently visited by free-roaming domestic dogs in western Kenya. Eight sites in Busia county, western Kenya, were selected. At each site, ten dog-keeping households were recruited, a questionnaire was administered, and a GPS logger was fixed around the neck of one dog in each household. Loggers were programmed to capture the dog's position every minute, for five consecutive days. Individual summaries of GPS recordings were produced, and the daily distance traveled was calculated. 50% and 95% utilization distribution isopleths were produced, and the area within these isopleths was extracted to estimate the size of the core and extended Home Ranges (HRs), respectively. Linear regression analyses were performed to identify factors associated with the movement parameters. The centroid points of the 10, 50, and 90% isopleths were reproduced, and the corresponding sites identified on the ground. Seventy-three dogs were included in the final analyses. The median daily distance traveled was 13.5km, while the median core and extended HRs were 0.4 and 9.3 ha, respectively. Older dogs had a larger extended HR and traveled more daily, while the effect of sex on dog movement depended on their neutering status. Dogs spent most of their time at their household; other frequently visited sites included other household compounds, fields, and rubbish dumps. One of the centroids corresponded to a field located across the international Kenya-Uganda border, emphasizing the fluidity across the border in this ecosystem. Multiple dogs visited the same location, highlighting the heterogeneous contact networks between dogs, and between dogs and people. The field data presented are of value both in understanding domestic dog ecology and resource utilization, and in contextualizing infectious and parasitic disease transmission models.

The Genome of Caenorhabditis bovis.

The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans has also become a model for parasitic nematodes despite being only distantly related to most parasitic species. All of the ∼65 Caenorhabditis species currently in culture are free-living, with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species that has been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa, where it is associated with the disease bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism. However, as C. bovis is not in laboratory culture, it remains little studied. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolated C. bovis from the ear of adult female Zebu. We sequenced the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and used the data to generate a chromosome-scale draft genome sequence. We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identified expansions in several gene families that have been implicated in parasitism in other nematode species. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.