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Antibiotic resistome mostly relates to bacterial taxonomy along a suburban Transmission chain

Frontiers of Environmental Science & Engineering 2022年第3期16卷 63-72页

作者： Ziyan Qin Qun Gao Qiang Dong Joy D.Van Nostrand Qi Qi Yifan Su Suo Liu Tianjiao Dai Jingmin Cheng Jizhong Zhou Yunfeng Yang State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China Institute of Chemical Defense Beijing 102205China Institute for Environmental Genomics and Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOK 73019USA School of Civil Engineering and Environmental Sciences University of OklahomaNormanOK 73019USA Earth and Environmental Sciences Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA

Antibiotic resistance genes comprising antibiotic resistome are of great concern due to their increase in the environment.Recent evidence of shared resistomes between soils and animal husbandry has imposed potential risks to human health.However,the correlation between a given community’s resistome and bacterial taxonomic composition is controversial.Here,a Transmission chain of resistomes from swine manure to compost and compost-amended soil were analyzed in five suburban areas of Beijing,China,with unamended agricultural soils as control soils.Antibiotic resistomes and bacterial taxonomic compositions were distinct between(I)manure and compost;and(II)compost-amended and control soils.In manure,compost,and compost-amended soils,theβ-diversity of the resistome and bacterial taxonomic composition was significantly correlated,while no correlation was detected in control soils.Bacterial taxonomic composition explained 36.0%of total variations of the resistome composition,much higher than environmental factors.Together,those results demonstrated that antibiotic resistome was closely related to bacterial taxonomic composition along the suburban Transmission chain.

关键词： Antibiotic resistance genes Resistome Bacterial taxonomy Transmission chain

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Exploration of Transmission chain and prevention of the recurrence of coronavirus disease 2019 in Heilongjiang Province due to inhospital transmission

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World Journal of Clinical Cases 2021年第20期9卷 5420-5426页

作者： Qi Chen Yang Gao Chang-Song Wang Kai Kang Hong Yu Ming-Yan Zhao Kai-Jiang Yu Department of Critical Care Medicine Harbin Medical University Cancer HospitalHarbin Medical UniversityHarbin 150081Heilongjiang ProvinceChina Department of Critical Care Medicine The sixth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbin 150028Heilongjiang ProvinceChina Department of Critical Care Medicine The First Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbin 150001Heilongjiang ProvinceChina Department of Critical Care Medicine The Second Hospital of HarbinHarbin 150056Heilongjiang ProvinceChina Institute of Critical Care Medicine The Sino Russian Medical Research Center of Harbin Medical UniversityHarbin 150081Heilongjiang ProvinceChina Key Laboratory of Hepatosplenic Surgery Ministry of EducationHarbin 150001Heilongjiang ProvinceChina The Cell Transplantation Key Laboratory of National Health Commission Harbin 150001Heilongjiang ProvinceChina

The coronavirus disease 2019(COVID-19)epidemic is a major public health emergency characterized by fast spread,a wide range of infections,and enormous control difficulty.Since the end of December 2019,Wuhan has become the first core infection area of China's COVID-19 outbreak.Since March 2020,the domestic worst-hit areas have moved to the Heilongjiang Province due to the increased number of imported COVID-19 cases.Herein,we reported the major COVID-19 outbreak,which caused a rebound of the epidemic in Harbin,China.After the rebound,different levels of causes for the recurrence of COVID-19,including citylevel,hospital-level,and medical staff-level cause,were investigated.Meanwhile,corresponding countermeasures to prevent the recurrence of the epidemic were also carried out on the city level,hospital level,and medical staff level,which eventually showed the effect of infection control function in a pandemic.In this study,we described the complete Transmission chain,analyzed the causes of the outbreak,and proposed corresponding countermeasures from our practical clinical experience,which can be used as a valuable reference for COVID-19 control.

关键词： Transmission chain Prevention of the recurrence COVID-19 Heilongjiang Province In-hospital transmission

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Study on the genotyping of Mycobacterium leprae and Transmission chain in Xingyi County, Guizhou Province

Study on the genotyping of Mycobacterium leprae and transmis...

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2013年全国麻风皮肤性病学术年会

作者： Li Jinlan Wang Yonghong Wang Zhenghua Xing Yan Liu Jian Wong Xiaoman Guizhou Provincial Center for Disease Control and Prevention

Objective To explore the genotypes of Mycobacterium leprae and characters of Transmission chain in Xingyi County as a high endemic area. Methods The skin biopsies from 49 new or relapse patients during 2006 to 2009 were genotyped on 17 VNTR（ various number of tandem repeat） loci and analyze the epidemic character of the clusters based on epidemiologic information. Results M leprae in Xingyi were grouped into the 6 clusters according to the alleles of AC8 b、AC9、AC8 a and phylogenetic analysis. Each cluster was included relapse patient except for 6 th cluster. 1 st cluster and 4 th cluster were major one which distributed on south-east of Xingyi City. Besides patient distribution relating with environment or higher prevalence, most patients of 4 th cluster derived from Buyi minority group and lived in same village. 2 nd and 5 th clusters with special loci were unique genotypes in China. Meanwhile, the different genotypes were detected respectively from patients within two families. Conclusion Long coexisting diversity and unique clusters rustled in high endemic situation of leprosy in Xingyi. Most patients within each cluster showed leprosy contact history obliviously. Family members, who were same susceptible to leprosy, would become patients due to being infected by different genotypes of M leprae which existed in surrounding. To strengthen early patient detection and implement chemoprevention was necessary in order to stop transmission among leprosy family contactors and in high prevalence village.

关键词： Mycobacterium leprae genotyping Transmission chain

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Reconstructing early transmission networks of SARS-CoV-2 using a genomic mutation model

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Zoological Research 2023年第3期44卷 494-504页

作者： Chao-Yuan Cheng Zhi-Bin Zhang State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China

The coronavirus disease 2019(COVID-19)pandemic has greatly damaged human society,but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pathogen remain unclear.Here,we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations.We explored the position(i.e.,root,middle,or tip)of early detected samples in the evolutionary tree of SARS-CoV-2.In total,6799 Transmission chains and 1766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1766 transmission networks were from 58 countries or regions and showed no common ancestor,indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected(i.e.,all samples were located at the tip position of the evolutionary tree).No root node sample was found in any sample(n=31,all from the Chinese mainland)collected in the first 15 days from 24 December 2019.Results using six-month data or RaTG13-referenced mutation data were similar.The reconstruction method was verified using a simulation approach.Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan,China.Thus,a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.

关键词： SARS-CoV-2 Transmission chain transmission network Ancestor-offspring relationship De novo mutation Back mutation Secondary mutation

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