ABSTRACT
Smallholder goat production plays a major role in rural livelihoods and food security in Malawi, but suffers from drastic and unpredictable production losses. While goat production is closely linked to small-scale local markets for slaughter and butchering, the perspectives of butchers and their potential as a source of animal health information are largely untapped. Butchers can provide insights into goat health status at slaughter as well as issues that go unseen before slaughter, such as the presence of indigestible foreign bodies (IFBs). IFBs include solid materials such as plastics and hardware (metals, stones, and other hard objects) that cause foreign body syndrome and can lead to impaction, oedema, malnutrition, and death. To estimate the presence of IFBs, 150 market stand butchers were surveyed across five districts in Malawi, focusing on a distinction between hardware and single-use plastics, which are still widely present in Malawi despite bans on production. Most butchers found plastic IFBs (80.7%), with over half (56.7%) reporting plastic IFBs recently among the past five slaughters. Hardware IFBs were less common, reported by 45.3% of butchers. While some butchers commented on the impact of IFBs on meat quality metrics ex-post, the majority observed no differences. While butchers unanimously considered health to be an important characteristic when sourcing goats, 70.7% consider injury status to be less important or not important. Overall, this study highlights the issue of anthropogenic waste pollution on goat production in Malawi and demonstrates the potential for the surveillance of goat health at market.
ABSTRACT
BACKGROUND: Veterinary diagnostics aid intervention strategies, track zoonoses, and direct selective breeding programs in livestock. In ruminants, gastrointestinal nematode (GIN) parasites are a major cause of production losses, but morphologically similar species limit our understanding of how specific GIN co-infections impact health in resource-limited settings. To estimate the presence and relative abundance of GINs and other helminths at the species level, we sought to develop a low-cost and low-resource molecular toolkit applied to goats from rural Malawi smallholdings. METHODS: Goats were subjected to health scoring and faecal sampling on smallholdings in Lilongwe district, Malawi. Infection intensities were estimated by faecal nematode egg counts with a faecal subsample desiccated for DNA analysis. Two DNA extraction methods were tested (low-resource magbead kit vs high-resource spin-column kit), with resulting DNA screened by endpoint polymerase chain reaction (PCR), semi-quantitative PCR, quantitative PCR (qPCR), high-resolution melt curve analysis (HRMC), and 'nemabiome' internal transcribed spacer 2 (ITS-2) amplicon sequencing. RESULTS: Both DNA isolation methods yielded comparable results despite poorer DNA purity and faecal contaminant carryover from the low-resource magbead method. GINs were detected in 100% of samples regardless of infection intensity. Co-infections with GINs and coccidia (Eimeria spp.) were present in most goats, with GIN populations dominated by Haemonchus contortus, Trichostrongylus colubriformis, Trichostrongylus axei, and Oesophagostomum columbianum. Both multiplex PCR and qPCR were highly predictive of GIN species proportions obtained using nemabiome amplicon sequencing; however, HRMC was less reliable than PCR in predicting the presence of particular species. CONCLUSIONS: These data represent the first 'nemabiome' sequencing of GINs from naturally infected smallholder goats in Africa and show the variable nature of GIN co-infections between individual animals. A similar level of granularity was detected by semi-quantitative PCR methods, which provided an accurate summary of species composition. Assessing GIN co-infections is therefore possible using cost-efficient low-resource DNA extraction and PCR approaches that can increase the capacity of molecular resources in areas where sequencing platforms are not available; and also open the door to affordable molecular GIN diagnostics. Given the diverse nature of infections in livestock and wildlife, these approaches have potential for disease surveillance in other areas.
