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Dissemination of resistance Integrons and genes Coding for Blse and Cabapenemases in the Urban Drainage Network in Cote d’Ivoire

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Advances in Microbiology 2024年第5期14卷 268-286页

作者： Coulibaly Kalpy Julien Diaby Aboubakar Sidik Vakou N’dri Sabine M’bengue Gbonon Valérie Carole Claon Jean Stephane Yao Kouamé Eric Gnali Gbohounou Fabrice Yéo Yéfougnini Bagré Issa Djaman Allico Joseph Dosso Mireille Pasteur Institute of Ivory Coast Abidjan C&#244te d&#8217Ivoire Fé lix Houphou&#235t-Boigny University Abidjan C&#244te d&#8217Ivoire

Antibiotic resistance has become a major threat to human health worldwide. Environment, particularly the water environment, has long been overlooked as a player in the antibiotic resistance cycle, although its role remains unclear. These can provide an ideal setting for the acquisition and dissemination of antibiotic resistance, as they are frequently affected by anthropogenic activities. The objective of this study was to establish a diffusion map of resistance integrons used as genetic markers of resistance associated with antibiotic resistance conferring genes (ARGs). Total DNA extracts from non-cultivable bacterial communities were used for the analyses. These communities were obtained from wastewater samples from 14 sites upstream and downstream of drainage channels or effluents in the cities of Abidjan, Bouaké, and Yamoussoukro. The results obtained correspond to the number of positives among the treated samples (n = 39). Among the genetic markers of dissemination, class 1 integrons were the most evident in 94.8% of samples in Abidjan (93.3%), Bouaké (100%) and Yamoussoukro (91.6%). Class 2 integrons and class 3 integrons were found respectively in 41% and 51% of all samples. genes coding for β-lactamases and blaTEM was identified in almost all samples at a rate of 97.4%. A co-presence of the three genes blaTEM, blaSHV and blaCTX-M is also remarkable in the sites of the city of Yamoussoukro. Among the genes coding for carbapenemases, only blaKPC 17.94%, blaNDM 30.76% and blaOXA48 38.46% were detected in the samples.

关键词： Antibiotic resistance Wastewater resistance Integrons (RIs) resistance genes

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Screening and identification of candidate Fusarium wilt-resistance genes from pumpkin

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Horticultural Plant Journal 2022年第5期8卷 583-592页

作者： Jun Xu Qianqian Xian Ke Wang Jingping Dong Chaoyang Zhang Shengli Du Xuewen Xu Xuehao Chen School of Horticulture and Plant Protection Yangzhou UniversityYangzhouJiangsu 225009China Huai’an Key Laboratory for Agricultural Biotechnology Huaiyin Institute of Agricultural Sciences in Xuhuai Region of Jiangsu ProvinceHuai’anJiangsu 223001China State Key Laboratory of Vegetable Germplasm Innovation Tianjin 300192China

Pumpkin(Cucurbita moschata)has been widely used as cucumber(Cucumis sativus L.)rootstock to defend against Fusarium wilt(FW)and increase cucumber yields and profits.However,the resistance genes and mechanisms underlying the FW tolerance in pumpkin are poorly understood.Here we analyzed the transcriptome of pumpkin inoculated with the cucumber FW causal agent Fusarium oxysporum f.***.cucumerinum(Foc),and obtained 3152 and 4735 upregulated genes induced by Foc at 24h after Foc inoculation compared with at 0h and 24h non-inoculated control,respectively.Next,404 common differentially expressed genes(DEGs)were screened using the criterion log_(2) FPKM(fold change)≥2.In total,206 of 404 DEGs were predominantly expressed in roots,which is the first tissue that Foc contacts and invades.140 DEGs were selected and classified into four groups(pathogenesis resistance,secondary metabolism-related,transcription factor and signal binding)based on their functional descriptions.Then,29 genes having high expression levels were selected to investigate the expression patterns induced by a Foc inoculation.Among them,16 genes were significantly induced by Foc and showed high expression levels at various treatment time points.These candidate genes may act as positive regulators of FW resistance in pumpkin and provide effective resources for improving cucumber FW resistance through breeding programs.

关键词： Pumpkin Rootstock Transcriptome Fusarium wilt resistance genes

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Characterization of wheat monogenic lines with known Sr genes and wheat cultivars for resistance to three new races of Puccinia graminis f. sp. tritici in China

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Journal of Integrative Agriculture 2023年第6期22卷 1740-1749页

作者： WU Xian-xin ZANG Chao-qun ZHANG Ya-zhao XU Yi-wei WANG Shu LI Tian-ya GAO Li State Key Laboratory for Biology of Plant Disease and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193P.R.China College of Plant Protection Shenyang Agricultural UniversityShenyang 110866P.R.China Institute of Plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161P.R.China Agronomy College Shenyang Agricultural UniversityShenyang 110866P.R.China

Wheat stem rust, caused by Puccinia graminis f. sp. tritici(Pgt), is a potentially devastating fungal disease of wheat worldwide. The present study was to evaluate the resistance of 42 wheat monogenic lines with known stem rust resistance(Sr) genes and 69 wheat cultivars to three new Pgt races(34C0MRGQM, 34C3MKGQM, and 34C6MTGSM)identified from aeciospores at the seedling and adult-plant stages. The phenotyping results revealed that monogenic lines harboring resistance genes Sr9e, Sr17, Sr21, Sr22, Sr26, Sr30, Sr31, Sr33, Sr35, Sr36, Sr37, Sr38, Sr47, SrTmp,and SrTt3 were effectively resistant to all three Pgt races at the seedling and adult-plant stages. In contrast, monogenic lines containing Sr5, Sr6, Sr7b, Sr9a, Sr9d, Sr9f, Sr9g, Sr9b, Sr16, Sr24, Sr28, and Sr39 were highly susceptible to these races at both seedling and adult-plant stages. The other lines with Sr8a, Sr10, Sr11, Sr13, Sr14, Sr15, Sr18, Sr20,Sr19, Sr23, Sr25, Sr27, Sr29, Sr32, and Sr34, displayed variable levels of resistance to one or two of the tested races.Seedling infection types(ITs) and adult-plant infection responses(IRs) indicated that 41(59.4%) of the wheat cultivars showed high resistance to all the three races. Molecular marker analysis showed that four wheat culitvars likely carried Sr2, 20 wheat culitvars likely carried Sr31, 9 wheat culitvars likely carried Sr38, and none of the cultivars carried Sr24,Sr25, and Sr26. Our results provide a scientific basis for rational utilization of the tested Sr genes and wheat cultivars against these novel Pgt races.

关键词： wheat stem rust Puccinia graminis f.sp.tritici wheat cultivars resistance genes

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Marker-assisted pyramiding of soybean resistance genes R_(SC4),R_(SC8),and R_(SC14Q) to soybean mosaic virus

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Journal of Integrative Agriculture 2017年第11期16卷 2413-2420页

作者： WANG Da-gang ZHAO Lin LI Kai MA Ying WANG Li-qun YANG Yong-qing YANG Yun-hua ZHI Hai-jian College of Agriculture Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory for Crop Genetics and Germplasm Enhancement Crop Institute Anhui Academy of Agricultural Sciences/Anhui Key Laboratory of Crops Quality Improving

Soybean mosaic virus （SMV） is one of the major viral pathogens affecting soybean crops worldwide. Three SMV resistance genes, Rsc4, Rsc8, and Rsc14Q, have been identified and mapped on soybean chromosomes 14, 2, and 13 from Dabaima, Kefeng 1, and Qihuang 1 cultivars, respectively. Soybean cultivar Nannong 1138-2 is widely grown in the Yangtze River Valley of China. In this study, crosses were made between Qihuang l^Kefeng 1 and DabaimaxNannong 1138-2. Ten simple sequence repeat （SSR） markers linked to three resistance loci （Rsc4, Rsc8, and Rsc^4Q） were used to assist pyramided breeding. Pyramided families containing three resistance loci （Rsc4, Rsc8, and Rsc14Q） were evaluated by inoculating them with 21 SMV strains from China. Results indicated that the 10 markers can be used effectively to assist the selection of resistant individuals containing Rsc4, Rsc8, and Rsc14Q. A total of 53 F6 plants were confirmed to contain three homozygous alleles conferring resistance to SMV. Five F7 homozygous pyramided families exhibited resistance to 21 strains of SMV and showed desirable agronomic traits using dual selection. The strategy of pyramiding resistance gene derived from different varieties has practical breeding value in providing broad-spectrum resistance against the existing strains of SMV in China.

关键词： soybean soybean mosaic virus resistance genes pyramiding marker-assisted breeding

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Molecular Screening of Rice Cultivated in Benin for the Identification of Xanthomonas oryzae Pv. oryzae and Bacterial Leaf Blight resistance genes

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Advances in Bioscience and Biotechnology 2023年第12期14卷 514-533页

作者： Chimène Nadège Mahoussi Nanoukon Koffi David Montcho Hambada Antoine Abel Missihoun Kéllya Laurinzo Déguénon Bignon Meyrix Pamela Franzel Loumédjinon Bana Wêtè Déré Félicité Bio Emilienne Zinsou Réel Gael Fael Houngbélagnon Amed Sèmèvo Havivi Lamine Baba-Moussa Lambert Gustave Djédatin Laboratory of Molecular Biology and Bioinformatics Applied to Genomics National School of Applied Biosciences and Biotechnolo-gies National University of Science Technology Engineering and Mathematics Dassa-Zoumè Benin Laboratory of Molecular Biology and Bioinformatics Applied to Genomics National School of Applied Biosciences and Biotechnologies National University of Science Technology Engineering and Mathematics Dassa-Zoumè Benin Laboratory of Plant Horticultural and Forestry Sciences National University of Agriculture Kétou Benin Laboratory of Molécular Genetics and Genome Analysis Department of Genetics and Biotechnology Faculty of Science and Technology (FAST) University of Abomey-Calavi Cotonou Benin Laboratory of Biology and Molecular Typing in Microbiology Department of Biochemistry and Cell Biology University of Abomey-Calavi Abomey-Calavi Benin

One of the most devastating diseases of rice worldwide is bacterial blight (BLB) caused by Xanthomonas oryzae pv. Oryzae (Xoo). In Benin, Xoo was first described in 2013 on wild rice Oryzae longistaminata. So far, no study has been done on Beninese Xoo strains. We do not know whether the pathogen has already passed into the rice varieties grown, or if they are exposed to other bacteria. Whereas the use of resistant varieties, carrying resistance genes, is the only highly effective and environmentally friendly way to control this disease, no information is available on these Xoo resistance genes in rice varieties grown in Benin apart from the one we recently. This study aims to identify Beninese Xoo strains, causing BLB and screen rice varieties grown in Benin for the main resistance genes. Diseased rice leaves showing typical symptoms of fire blight collected from different rice fields in the three phytogeographic areas of Benin were analyzed by PCR for Xoo-specific sequence identification. Furthermore, seventy-five collected rice accessions were screened to identify xa5, Xa7, xa13, and Xa21 resistance genes to Xoo. The results reveal that Xanthomonas oryzae was identified in two fields in Banikouara and one in Malanville. On the other hand, Sphingomonas sp. has been identified in several other rice fields in Benin. Forty-seven of seventy-five rice accessions examined (62.66%) carried Xoo resistance genes with 3 (4%) and 40 (53.33%) of xa5 and Xa21 respectively. None of the accessions had either Xa7 or xa13 resistance genes. Three accessions possess both xa5 and Xa21 genes. Isogenic lines IRBB60 and IRBB21, supposed to be a positive control, presented a Xoo sensitivity allele. These results indicate that Xoo has moved from the wild rice variety to the cultivated variety in northern Benin and varietal improvement programs must be implemented with varieties having several resistance genes for the efficient response against a possible BLB pandemic in Benin.

关键词： Bacterial Blight Xanthomonas oryzae Pv. oryzae Molecular Characterization resistance genes

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Postulation of Seedlings resistance genes to Yellow Rust in Commercial Wheat Cultivars from Yunnan Province in China

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Agricultural Sciences in China 2011年第11期10卷 1723-1731页

作者： LI Ming-ju FENG Jing CAo Shi-qin LIN Rui-ming CHENG Geng CHEN Wan-quan XU Shi-chang State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of AgriculturalSciences Beijing 100193 P.R.China Institute of Environment and Resources Yunnan Academy of Agricultural Sciences Kunming 650205 P.R.China Institute of Plant Protection Gansu Academy of Agricultural Sciences Lanzhou 730070 P.R.China Institute of Food Crops Yunnan Academy of Agricultural Sciences Kunming 650205 P.R.China

The objective of this study was to characterize yellow （stripe） rust resistance gene（s） in 52 commercial wheat cultivars from Yunnan Province in China, and to provide information for their rational deployment in field. Seedlings of wheat cultivars were inoculated with 25 differential isolates ofPuccinia striiformis from foreign and home to postulate resistance genes to yellow rust, and then validated by pedigree. There were 10 probable resistance genes characterized in these cultivars, in which, Yr9 was most commonly postulated to be present in thirteen cultivars. Yr21, the second, was present in four cultivars. Yr8, the third, were present in three cultivars. Yr6, Yrl 7 and Yr26, the fourth, was present in two cultivars respectively. The other gene（s） such as, Yr2＋YrA, Yr7 and Yr27, were only present in single cultivar（s）; unknown gene（s） or gene（s） combination（s） were present in 22 cultivars. One cultivar （Yunmai 42） had no resistance gene tested in this study. Cultivars such as Yunmai 52, Mian 1971-98, Kunmai 4, and Yunmai 56 carried effective genes and can be popularized mainly; Yr9 should be planted with other Yr genes. In the meantime other effective genes should be introduced to realize gene diversity for controlling wheat yellow rust. Yunmai 42 should be reduced to avoid rust breakout. Unknown gene cultivars should be utilized and be researched deeply.

关键词： wheat cultivars yellow （stripe） rust resistance genes gene postulation

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Effects of Microplastics on Expression of resistance genes and Virulence genes of Vibrio alginolyticus

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Asian Agricultural Research 2023年第2期15卷 42-45页

作者： Liangchuan CHEN Zehui SU Haiyun FENG Weijie ZHANG Huanying PANG Na WANG Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing 100176China

[Objectives]To study the effects of microplastics on antibiotic resistance genes and virulence genes of Vibrio alginolyticus,so as to provide a certain reference for controlling marine pollution,curbing the spread of environmental antibiotic resistance genes and virulence genes,formulating environmental policies,and maintaining food safety.[Methods]After adding V.alginolyticus into the artificial seawater,they were divided into three groups,namely blank control group(BLK),polyvinyl chloride microplastic group(PVC group)and polyvinyl alcohol microplastic group(PVA group).Aerated culture experiments were carried out,and the effects of microplastics on the expression of resistance genes and virulence genes of V.alginolyticus were studied by PCR and qPCR methods.[Results]The presence of microplastics significantly changed the resistance gene structure of V.alginolyticus.Compared with the control group,the cfxA and cfr resistance genes were detected in the microplastic group.However,only PVC group detected blaZ resistance gene,and only PVA group did not detect aaC resistance gene.In addition,compared with the control group,the expressions of virulence genes in the microplastic group were all down-regulated(Presistance genes and virulence genes,formulating environmental policies,and maintaining food safety,but the specific mechanisms of drug resistance and virulence need further research.

关键词： Vibrio alginolyticus Microplastics resistance genes Virulence genes

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From plant immunity to crop disease resistance

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Journal of Genetics and Genomics 2022年第8期49卷 693-703页

作者： Yan Zhao Xiaobo Zhu Xuewei Chen Jian-Min Zhou State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural University at WenjiangChengduSichuan 611130China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China Hainan Yazhou Bay Seed Laboratory SanyaHainan 572025China

Plant diseases caused by diverse pathogens lead to a serious reduction in crop yield and threaten food security worldwide.Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases.In the last decade,our understanding of plant immunity at both molecular and genomic levels has improved greatly.Combined with advances in biotechnologies,particularly clustered regularly interspaced short palindromic repeat(CRISPR)/Cas9-based genome editing,we can now rapidly identify new resistance genes and engineer disease-resistance crop plants like never before.In this review,we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants.We also discuss existing challenges in this field and suggest directions for future studies.

关键词： Plant immunity Disease resistance resistance genes Molecular breeding Genetic engineering Crops

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Mesophilic and thermophilic anaerobic digestion of swine manure with sulfamethoxazole and norfloxacin:Dynamics of microbial communities and evolution of resistance genes

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Frontiers of Environmental Science & Engineering 2021年第5期15卷 201-212页

作者： Qinxue Wen Shuo Yang Zhiqiang Chen State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology(SKLUWREHIT)Harbin150090China School of Environment Harbin Institute of TechnologyHarbin150090China

The role of norfloxacin(NOR)and sulfamethoxazole(SMX)in mesophilic and thermophilic anaerobic digestion(AD)of pig manure,with respect to methane production and variations in the microbial community and resistance genes,including antibiotic resistance genes(ARGs),class I integrase(intIl),and heavy metal resistance genes(MRGs),was investigated.The results indicated that NOR exerted little influence on the microbial community,whereas SMX negatively affected the acetoclastic methanogens.The abundance of two sulfonamide resistance genes(sul1 and sul2),three quinolone resistance genes(qnrS,parC,and aac(6′)-Ib-cr),and intI1 decreased by 2–3 orders of magnitude at the end of thermophilic AD.In contrast,mesophilic AD was generally ineffective in reducing the abundance of resistance genes.According to the results of redundancy analysis,the abundance of ARGs was affected primarily by microbial community dynamics(68.5%),rather than the selective pressure due to antibiotic addition(13.3%).Horizontal gene transfer(HGT)through intI1 contributed to 26.4%of the ARG variation.The archaeal community also influenced the changes in the resistance genes,and ARG reduction was significantly correlated with enhanced methane production.Thermophilic AD presented a higher methane production potential and greater reduction in resistance gene abundance.

关键词： Pig manure Antibiotics Anaerobic digestion resistance genes Microbial community

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Tomato mottle mosaic virus: Characterization, resistance gene effectiveness, and quintuplex RT-PCR detection system

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Journal of Integrative Agriculture 2022年第9期21卷 2641-2651页

作者： Carlos Kwesi TETTEY YAN Zhi-yong MA Hua-yu ZHAO Mei-sheng GENG Chao TIAN Yan-ping LI Xiang-dong Shandong Provincial Key Laboratory of Agricultural Microbiology College of Plant ProtectionShandong Agricultural University Tai'an 271018P.R.China

Tomato mottle mosaic virus(ToMMV), an economically important species of the genus Tobamovirus, causes significant loss in yield and quality of tomato fruits. Here, we identified the Shandong isolate of ToMMV(ToMMV-SD) collected from symptomatic tomato fruits in Weifang, Shandong Province of China. ToMMV-SD caused symptoms such as severe mosaic, mottling, and necrosis of tomato leaves, yellow spot and necrotic lesions on tomato fruits. The obtained full genome of ToMMV-SD was 6 399 nucleotides(accession number MW373515) and had the highest identity of 99.5% with that of isolate SC13-051 from the United States of America at the genomic level. The infectious clone of ToMMV-SD was constructed and induced clear mosaic and necrotic symptoms onto Nicotiana benthamiana leaves. Several commercial tomato cultivars, harboring Tm-2~2 resistance gene, and pepper cultivars, containing L resistance gene, were susceptible to ToMMV-SD. Plants of Solanum melongena(eggplant) and Brassica pekinensis(napa cabbage) showed mottling symptoms, while N. tabacum cv. Zhongyan 100 displayed latent infection. ToMMV-SD did not infect plants of N. tabacum cv. Xanthi NN, Brassica rapa ssp. chinensis(bok choy), Raphanus sativus(radish), Vigna unguiculata cv. Yuanzhong 28-2(cowpea), or Tm-2~2 transgenic N. benthamiana. A quintuplex RT-PCR system differentiated ToMMV from tomato mosaic virus, tomato brown rugose fruit virus, tobacco mosaic virus, and tomato spotted wilt virus, with the threshold amount of 0.02 pg. These results highlight the threat posed by ToMMV to tomato and pepper cultivation and offer an efficient detection system for the simultaneous detection of four tobamoviruses and tomato spotted wilt virus infecting tomato plants in the field.

关键词： host range multiplex RT-PCR resistance genes symptom Tobamovirus tomato mottle mosaic virus

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