Pathogens and drug resistance or virulence genes from animals and surrounding environment in Shenzhen, 2023 using targeted next-generation sequencing

Identifying the pathogen spectrum of animals and surrounding environment is essential for the prevention and control of zoonotic diseases. From February 1 to June 30, 2023, we randomly collected respiratory and intestinal samples from animals and swab samples from surrounding environment in 33 units in Shenzhen, and carried out pathogen/gene screening using pathogen targeted next-generation sequencing technology. A total of 2000 samples were collected and mixed to obtain 415 samples for detection. The detection rate of respiratory pathogens (76.9 %, χ2 = 15.892, P < 0.001), drug resistance genes (59.0 %, χ2 = 52.888, P < 0.001), the co-detection proportion of intestinal pathogens (87.0 %, χ2 = 9.605, P = 0.002) in livestock and poultry, and drug resistance genes in surrounding environment (30.5 %, χ2 = 14.932, P < 0.001) were higher than dogs and cats, and wild animals. Escherichia coli (37.3 %, 30.5 %) and β-lactamase-resistance NDM genes (31.3 %, 27.1 %) were the main respiratory pathogens in livestock and poultry, and surrounding environment. The detection rate of Pasteurella multocide was 25.0 % in dogs and cats. The detection rates of intestinal pathogens Campylobacter coli and Clostridium perfringens in livestock and pourtry were 23.9 % and 17.9 %, and Clostridium perfringens in dogs and cats and wild animal was 18.2 % and 15.7 %. The total detection rate of intestinal pathogens of wild animals in wildlife parks (44.0 %) and indoor pet parks (38.9 %) was higher than that in animal nature reserves (χ2 = 15.686, P = 0.001). The respiratory/intestinal pathogens in animals and surrounding environment was common in Shenzhen. The drug resistance genes in livestock and poultry, and intestinal pathogens of wild animals in indoor pet parks needed more attention.