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

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution Pub Date : 2025-04-29 DOI:10.1016/j.meegid.2025.105755

Dandan Niu , Yankun Ke , Qiuying Lv , Zhen Zhang , Tengyingzi Liu , Zhongyao Xu , Tong Li , Yingluan Zhang , Renli Zhang , Xiaomin Zhang , Shunping Cai , Xiaonan You , Yuqing Chen , Hanguang Wu , Yingxin Li , Chan Yin , Danzhu Wang , Xinhua Duan , Yongchao Guo , Rongqi Liu , Tiejian Feng

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Abstract

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.

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2023年深圳市动物及周边环境病原菌及耐药或毒力基因测序

确定动物和周围环境的病原谱是预防和控制人畜共患疾病的必要条件。2023年2月1日至6月30日，我们在深圳市33个单位随机采集动物呼吸道和肠道样本以及周围环境拭子样本，采用病原体靶向新一代测序技术进行病原体/基因筛选。共采集样品2000份，混合后得到检测样品415份。呼吸道病原菌检出率(76.9%,χ2 = 15.892；0.001),耐药性基因(59.0%,χ2 = 52.888,P & lt;畜禽肠道病原菌共检率（87.0%,χ2 = 9.605, P = 0.002）与周围环境耐药基因共检率(30.5%,χ2 = 14.932, P <；0.001)高于狗、猫和野生动物。畜禽及其周围环境呼吸道病原菌主要为大肠杆菌（37.3%,30.5%）和耐β-内酰胺酶NDM基因（31.3%,27.1%）。犬、猫多杀巴氏杆菌检出率为25.0%。畜禽肠道病原菌大肠弯曲杆菌和产气荚膜梭菌检出率分别为23.9%和17.9%，狗猫和野生动物肠道病原菌产气荚膜梭菌检出率分别为18.2%和15.7%。野生动物园和室内宠物公园野生动物肠道病原菌总检出率（44.0%）高于动物自然保护区（38.9%）（χ2 = 15.686, P = 0.001）。深圳市动物及周围环境呼吸道/肠道病原菌普遍存在。畜禽耐药基因、室内宠物公园野生动物肠道病原菌等情况需要进一步关注。

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来源期刊

Infection Genetics and Evolution 医学-传染病学

CiteScore

8.40

自引率

0.00%

发文量

215

审稿时长

82 days

期刊介绍： (aka Journal of Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases -- MEEGID) Infectious diseases constitute one of the main challenges to medical science in the coming century. The impressive development of molecular megatechnologies and of bioinformatics have greatly increased our knowledge of the evolution, transmission and pathogenicity of infectious diseases. Research has shown that host susceptibility to many infectious diseases has a genetic basis. Furthermore, much is now known on the molecular epidemiology, evolution and virulence of pathogenic agents, as well as their resistance to drugs, vaccines, and antibiotics. Equally, research on the genetics of disease vectors has greatly improved our understanding of their systematics, has increased our capacity to identify target populations for control or intervention, and has provided detailed information on the mechanisms of insecticide resistance. However, the genetics and evolutionary biology of hosts, pathogens and vectors have tended to develop as three separate fields of research. This artificial compartmentalisation is of concern due to our growing appreciation of the strong co-evolutionary interactions among hosts, pathogens and vectors. Infection, Genetics and Evolution and its companion congress [MEEGID](http://www.meegidconference.com/) (for Molecular Epidemiology and Evolutionary Genetics of Infectious Diseases) are the main forum acting for the cross-fertilization between evolutionary science and biomedical research on infectious diseases. Infection, Genetics and Evolution is the only journal that welcomes articles dealing with the genetics and evolutionary biology of hosts, pathogens and vectors, and coevolution processes among them in relation to infection and disease manifestation. All infectious models enter the scope of the journal, including pathogens of humans, animals and plants, either parasites, fungi, bacteria, viruses or prions. The journal welcomes articles dealing with genetics, population genetics, genomics, postgenomics, gene expression, evolutionary biology, population dynamics, mathematical modeling and bioinformatics. We also provide many author benefits, such as free PDFs, a liberal copyright policy, special discounts on Elsevier publications and much more. Please click here for more information on our author services .