Metagenomic Characterization of Poultry Enteric Viral and Bacterial Pathogens and Gut Microbiota in Selected Regions in Kenya and Associated Antimicrobial Resistance Genes

Abstract

Indigenous backyard poultry, which is the most commonly reared poultry in Africa, is often raised fsdain a free-range production system that exposes them to a wide array of microorganisms due to their diverse diet. These microorganisms, including viruses, bacteria, archaea, and protozoa, colonize the host’s gastrointestinal tract. Some of these gut microorganisms can be pathogenic or beneficial to the host. Additionally, the continued use/misuse of antimicrobial agents in animal production has led to the development of antimicrobial resistance against these antimicrobial agents. Metagenomics reveals novel and highly divergent pathogens and microbiota in the gut of poultry. Unfortunately, most metagenomic studies on poultry microbiomes have been carried out on poultry reared under controlled and regulated feeding regimes. This study characterized and detected enteric viral and bacterial pathogens in Kenyan poultry, evaluated poultry gut microbial community profiles, and detected the antimicrobial resistance genes in poultry in Kenya. A stratified, cross-sectional, purposive approach was used during sample collection. Cloacal swabs were collected from 599 birds (based on the Fisher equation) in Bungoma, Busia, Kilifi, Kwale, Nairobi, and Trans Nzoia for detecting enteric viral and bacterial pathogens in poultry and also investigating the presence of antimicrobial resistance genes. Faecal and caecal contents were also collected from 24 male and 24 female birds in Bungoma, Kilifi, Kwale, Siaya, and Turkana and used to profile the entire microbiota in the poultry samples and also determine antimicrobial resistance genes. DNA and RNA were extracted from cloacal samples and sequenced using the Illumina Miseq platform. The whole genome shotgun sequences were then analyzed using bioinformatics and statistical tools. DNA was also extracted from the faecal and caecal samples and sequenced using the Illumina Miseq platform. Thereafter, the whole genome shotgun sequ-ences were analyzed using statistical and bioinformatics analyses. The most abundant viral families were Coronaviridae (43.4%), Reoviridae (36.6%), and Retroviridae (11.4%). The study also demonstrated the presence of several viral pathogens, with the most abundant being Infectious bronchitis virus (42.6%), Rotavirus (35.0%), Reticuloendotheliosis virus (6.0%) and Lymphoproliferative disease virus (2.7%), thus providing important insights into the prevalence and diversity of pathogenic enteric viruses in poultry in Kenya. Additionally, the results indicate the presence of several potentially pathogenic bacteria, including Chlamydiae (11.38-98.43%) and Proteobacteria (1.57-85.46%) which were the most frequently detected phyla in the chicken cloacal samples, and Proteobacteria (28.51-100%) and Firmicutes (3.13-100%) which were the most frequently detected in other poultry. Furthermore, the study elucidates the presence of many commensals and potentially pathogenic microorganisms in the faecal and caecal contents of poultry. Bacteroidetes (1.60-93.48%), Firmicutes (3.22-48.40%), Proteobacteria (2.57-34.64%), and Euryarchaeota (0.32-22.72%) were the most frequently detected phyla in faecal samples, while Bacteroidetes (3.31-90.85%), Firmicutes (12.90-67.28%) and Proteobacteria (1.18-85.93%) were the most frequently detected phyla in caecal samples. Finally, the abundance of tetracycline, aminoglycoside, β-lactamase, and sulfonamide-resistance genes in most of the poultry analyzed raises concern about the dangers associated with continuous and inappropriate use of these antimicrobials in poultry production. These results provide useful information for managing viral and bacterial diseases while broadening our understanding of the poultry gut microbiome in indigenous backyard poultry. Additionally, the antimicrobial resistance genes data provides a valuable indicator of the use of antimicrobials in poultry by smallholder backyard farmers in Kenya.