High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.

Prevalence and molecular characterization of Giardia duodenalis in dogs in Israel

Three hundred and two stool samples were collected from municipal shelters and owned dogs in different geographical locations in Israel from December 2016 to September 2017 and examined for Giardia and assemblage type by PCR targeting the 18S rRNA and β-giardin genes. Overall Giardia prevalence was 24.5 % (74/30). Giardia prevalence was 1.9-fold higher in dogs ≤ 6 months old compared to > 6 ≤ 12 months old and older dogs [25/61 (41 %), 18/73 (24.6 %) and 31/166 (18.7 %), respectively, (p = 0.001)], 2.3-fold higher in winter [32/90 (35.5 %)] compared to its prevalence during autumn [15/60 (25 %)], spring [10/62 (16.1 %)] and summer [17/89 (19.1 %), p = 0.003)], and 2.7-fold more frequent among diarrheic dogs [23/43 (53.4 %)] compared to those with formed stools [51/253 (20.1 %)], (p = 0.001)]. The Giardia sp. assemblages detected were C and D. Higher infection rates in young, diarrheic dogs, sampled during winter, and housed in municipal shelters, indicates the need for targeted preventive measures.