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genomic epidemiology of Carbapenemaseproducing Klebsiella pneumoniae in China

genomics, Proteomics & Bioinformatics 2022年第6期20卷 1154-1167页

作者： Cuidan Li Xiaoyuan Jiang Tingting Yang Yingjiao Ju Zhe Yin Liya Yue Guannan Ma Xuebing Wang Ying Jing Xinhua Luo Shuangshuang Li Xue Yang Fei Chen Dongsheng Zhou CAS Key Laboratory of Genome Sciences&Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Pathogenesis Prevention and Treatment of High Incidence Diseases in Central AsiaUrumqi 830011China Beijing Key Laboratory of Genome and Precision Medicine Technologies Beijing 100101China

The rapid spread of carbapenemase-producing Klebsiella pneumoniae(cpKP)poses serious threats to public health;however,the underlying genetic basis for its dissemination is still *** conducted a comprehensive genomic epidemiology analysis on 420 cpKP isolates collected from 70 hospitals in 24 provinces/autonomous regions/municipalities of China during 2009–2017 by short-/long-read *** results showed that most cpKP isolates were categorized into clonal group 258(CG258),in which ST11 was the dominant *** analysis revealed three major clades including the top one of Clade 3 for CG258 cpKP ***,carbapenemase gene analysis indicated that blaKPC was dominant in the cpKP isolates,and most blaKPC genes were located in five major incompatibility(Inc)groups of blaKPC-harboring ***,three advantageous combinations of host–blaKPC-carrying plasmid(Clade 3.1+3.2–IncFIIpHN7A8,Clade 3.1+3.2–IncFIIpHN7A8:IncR,and Clade 3.3–IncFIIpHN7A8:IncpA1763-KPC)were identified to confer cpKP isolates the advantages in both genotypes(strong correlation/coevolution)and phenotypes(resistance/growth/competition)to facilitate the nationwide spread of ST11/CG258 ***,Bayesian skyline analysis illustrated that the three advantageous combinations might be directly associated with the strong population expansion during 2007–2008 and subsequent maintenance of the population of ST11/CG258 cpKP after *** then examined drug resistance profiles of these cpKP isolates and proposed combination treatment regimens for CG258/non-CG258 cpKP ***,the findings of our systematical analysis shed light on the molecular epidemiology and genetic basis for the dissemination of ST11/CG258 cpKP in China,and much emphasis should be given to the close monitoring of advantageous cpKP–plasmid combinations.

关键词： Klebsiella pneumoniae Drug resistance Carbapenemase Plasmid genomic epidemiology

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Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco

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Biosafety and Health 2021年第2期3卷 124-127页

作者： Bouabid Badaoui Khalid Sadki Chouhra Talbi Driss Salah Lina Tazi Faculty of Sciences Mohamed V University in RabatMorocco

Coronavirus disease 2019(COVID-19)is an infectious disease caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),declared as a pandemic due to its rapid *** this study,we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2,using 22 virus genome sequences reported by three different laboratories in Morocco till June 7,2020,as well as 40,366 virus genomes from all around the *** SARSCoV-2 genomes from Moroccan patients revealed 62 mutations,of which 30weremis-sense *** Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences,followed by N_G204R and N_R203K,which occurred in 9 among the 22 *** mutations NSP10_R134S,NSP15_D335N,NSP16_I169L,NSP3_L431H,NSP3_P1292L and Spike_V6F occurred once in Moroccan sequences,with no record in other sequences *** analyses revealed that Moroccan SARS-CoV-2 genomes included 9 viruses belonging to Clade 20A,9 to Clade 20B and 2 to Clade 20C,suggesting that the epidemic spread inMorocco did not display a predominant SARS-CoV-2 ***,multiple and unrelated introductions of SARS-CoV-2 into Morocco through different routes have occurred,giving rise to the diversity of virus genomes in the ***,in all probability,the SARS-CoV-2 circulated in a cryptic way inMorocco,starting fromJanuary 15,2020 before the first case was officially discovered on March 2,2020.

关键词： SARS-CoV-2 Genetic diversity genomic epidemiology Morocco

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Primary assessment of the diversity of Omicron sublineages and the epidemiologic features of autumn/winter 2022 COVID-19 wave in Chinese mainland

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Frontiers of Medicine 2023年第4期17卷 758-767页

作者： Gang Lu Yun Ling Minghao Jiang Yun Tan Dong Wei Lu Jiang Shuting Yu Fangying Jiang Shuai Wang Yao Dai Jinzeng Wang Geng Wu Xinxin Zhang Guoyu Meng Shengyue Wang Feng Liu Xiaohong Fan Saijuan Chen Shanghai Institute of Hematology National Research Center for Translational MedicineState Key Laboratory of Medical GenomicsRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China Shanghai Public Health Clinical Center Fudan UniversityShanghai 200083China Department of Infectious Diseases Research Laboratory of Clinical VirologyNational Research Center for Translational MedicineRuijin Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200025China State Key Laboratory of Microbial Metabolism School of Life Sciences and BiotechnologyThe Joint International Research Laboratory of Metabolic and Developmental SciencesShanghai Jiao Tong UniversityShanghai 200240China

With the recent ongoing autumn/winter 2022 COVID-19 wave and the adjustment of public health control measures,there have been widespread SARS-CoV-2 infections in Chinese *** we have analyzed 369 viral genomes from recently diagnosed COVID-19 patients in Shanghai,identifying a large number of sublineages of the SARS-CoV-2 Omicron *** analysis,coupled with contact history tracing,revealed simultaneous community transmission of two Omicron sublineages dominating the infections in some areas of China(BA.5.2 mainly in Guangzhou and Shanghai,and BF.7 mainly in Beijing)and two highly infectious sublineages recently imported from abroad(XBB and BQ.1).Publicly available data from August 31 to November 29,2022 indicated an overall severe/critical case rate of 0.035%nationwide,while analysis of 5706 symptomatic patients treated at the Shanghai Public Health Center between September 1 and December 26,2022 showed that 20 cases(0.35%)without comorbidities progressed into severe/critical conditions and 153 cases(2.68%)with COVID-19-exacerbated comorbidities progressed into severe/critical *** observations shall alert healthcare providers to place more resources for the treatment of severe/critical ***,mathematical modeling predicts this autumn/winter wave might pass through major cities in China by the end of the year,whereas some middle and western provinces and rural areas would be hit by the upcoming infection wave in mid-to-late January 2023,and the duration and magnitude of upcoming outbreak could be dramatically enhanced by the extensive travels during the Spring Festival(January 21,2023).Altogether,these preliminary data highlight the needs to allocate resources to early diagnosis and effective treatment of severe cases and the protection of vulnerable population,especially in the rural areas,to ensure the country’s smooth exit from the ongoing pandemic and accelerate socio-economic recovery.

关键词： SARS-CoV-2 COVID-19 Omicron genomic epidemiology

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Origin and Evolution of the Kiwi fruit Canker Pandemic

Origin and Evolution of the Kiwi fruit Canker Pandemic

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中国植物病理学会2017年学术年会

作者： Honour C.McCann Li Li Liu Yifei Li Dawei Pan Hui Zhong Caihong Erik H.A.Rikkerink MatthewD.Templeton Christina Straub Elena Colombi Paul B.Rainey Huang Hongwen New Zealand Institute for Advanced Study Massey University Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenChinese Academy of Sciences Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenChinese Academy of Sciences The New Zealand Institute for Plant and Food Research Limited School of Biological Sciences University of Auckland Department of Microbial Population Biology Max Planck Institute for Evolutionary Biology EcoleSupérieure de Physique et de Chimielndustrielles de la Ville de Paris(ESPCI ParisTech) CNRS UMR8231 PSL Research University

Recurring epidemics of kiwifruit（Actinidia spp.） bleeding canker disease are caused by Pseudomonas syringae ***（Psa）.In order to strengthen understanding of population structure,phylogeography,and evolutionary dynamics,we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in *** on the analysis of 80 sequenced Psa genomes,we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single *** contrast,Korea and Japan harbor strains from multiple *** independent transmission events marked introduction of the pandemic lineage into New Zealand,Chile,Europe,Korea,and *** high similarity within the core genome and minimal impact of within-clade recombination,we observed extensive variation even within the single clade from which the global pandemic arose.

关键词： Pathogen evolution genomic epidemiology Bacterial plant pathogen Plant-microbe interactions Disease emergence

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genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020

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Biosafety and Health 2020年第4期2卷 202-205页

作者： Yong Zhang Yang Pan Xiang Zhao Weifeng Shi Zhixiao Chen Sheng Zhang Peipei Liu Jinbo Xiao Wenjie Tan Dayan Wang William J.Liu Wenbo Xu Quanyi Wang Guizhen Wu NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Beijing Center for Disease Control and Prevention Beijing 100013China Key Laboratory of Etiology and epidemiology of Emerging Infectious Diseases in Universities of Shandong Shandong First Medical University and Shandong Academy of Medical SciencesTai'an 271000China The First Affiliated Hospital of Shandong First Medical University(Shandong Provincial Qianfoshan Hospital) Jinan 271099China

After 56 days without coronavirus disease 2019(COVID-19)cases,reemergent cases were reported in Beijing,China on June 11,***,we report the genetic characteristics of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)sequenced from the clinical specimens of 4 human cases and 2 environmental *** nucleotide similarity among six SARS-CoV-2 genomes ranged from 99.98%to 99.99%.Compared with the reference strain of SARS-CoV-2(GenBank ***_045512),all six genome sequences shared the same substitutions at nt241(C→T),nt3037(C→T),nt14408(C→T),nt23403(A→G),nt28881(G→A),nt28882(G→A),and nt28883(G→C),which are the characteristic nucleotide substitutions of L-lineage European branch *** was also proved by themaximum likelihood phylogenetic tree based on the full-length genome of *** also have a unique shared nucleotide substitution,nt6026(C→T),which is the characteristic nucleotide substitution of SARS-CoV-2 in Beijing's Xinfadi *** is noteworthy that there is an amino acid D614Gmutation caused by nt23403 substitution in all six genomes,which may enhance the virus's infectivity in humans and help it become the leading strain of the virus to spread around the world *** is necessary to continuously monitor the genetic variation of SARS-CoV-2,focusing on the influence of key mutation sites of SARS-CoV-2 on viral transmission,clinical manifestations,severity,and course of disease.

关键词： COVID-19 SARS-CoV-2 genomic epidemiology L-lineage European branch I D614G mutation

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