Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established ...Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established for the phylogenetic and epidemiology analysis. Methods To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods. Results After comparison of the genome, seven high discrimination gene loci （recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR） were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types （STs） were identified. Based on the Hunter-Gaston Index （HGI）, MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types （ST） came into a main cluster, showing the major clonal complexes in those 44 strains. Conclusion MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.展开更多
Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule ba...Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17 bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three house-keeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.展开更多
目的以肠道定植碳青霉烯类耐药肠杆菌科细菌(carbapenem resistance Enterobacteriaceae,CRE)与同一患者后期感染细菌的关系为出发点,同源性检测和耐药基因筛查为中心,从重症医学科(intensive care unit,ICU)患者肠道CRE的定植情况、CR...目的以肠道定植碳青霉烯类耐药肠杆菌科细菌(carbapenem resistance Enterobacteriaceae,CRE)与同一患者后期感染细菌的关系为出发点,同源性检测和耐药基因筛查为中心,从重症医学科(intensive care unit,ICU)患者肠道CRE的定植情况、CRE肠道定植与后期感染的关系层次上,进行CRE防治的应用基础研究,从而为临床及时有效的抗感染治疗提供一定指导。方法收集2018—2019年来自ICU病房及由其他科室转入ICU的共11位患者的临床资料,分别分离同一患者肠道定植CRE菌株和后期其他感染部位的菌株,对所有菌株进行药物敏感性试验和耐药基因携带情况检测,采用多位点序列分析(MLST)、脉冲场凝胶电泳(PAGE)试验的方法对定植CRE菌株和后期其他感染部位的菌株进行同源性分析。结果95位ICU患者中有19位患者肠道CRE筛查阳性,定植率为20.00%。其中发生后期其他部位感染的患者11位,目标菌株耐碳青霉烯酶基因检测结果显示22株菌株中有21株检出耐药基因,占95.45%(21/22)。其中19株检出KPC-2耐药基因,阳性率为86.36%(19/22);2株检出NDM-1耐药基因,阳性率为9.09%(2/22)。其他碳青霉烯酶基因检测均为阴性。22株目标菌的MLST分型共分为3个型,主要为ST11型,11位患者中除了1位患者的后期感染菌株与定植菌株差异明显外,其余患者的肠道定植菌株与后期感染菌株均为相同的ST型;PAGE检出22株菌的分型可分为A群和B群,共7个型别,其中7位患者的肠道定植菌株与后期感染菌株之间条带位置与数目相同,视为同一克隆型,3位患者的肠道定植菌株与后期感染菌株条带有2~3个差异,同源性极高,视为高度相关菌株;1位患者的肠道定植菌株与后期感染菌株的条带异超过7条,视为不相关菌株。结论ICU患者定植率高,应加强入院CRE定植筛查;ICU患者部位检出的定植及感染CRE菌株MIC值高,为高耐药性菌株;ICU患者发生CRE感染的菌株与自身定植的菌株有极高的同源性。展开更多
基金supported by the fund of State Key Laboratory for Infectious Diseases Prevention and Control (2011SKLID208)the project "Transmission Mode of Tuberculosis"of National Key Program of Mega Infectious Diseases (2008ZX100/03-010)
文摘Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established for the phylogenetic and epidemiology analysis. Methods To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods. Results After comparison of the genome, seven high discrimination gene loci （recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR） were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types （STs） were identified. Based on the Hunter-Gaston Index （HGI）, MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types （ST） came into a main cluster, showing the major clonal complexes in those 44 strains. Conclusion MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.
文摘Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17 bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three house-keeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.
基金The National High Technology Research and Development Program of China(2012AA101501)National Infrastructure of Microbial Resources of China(NIMR2014-7)
文摘目的掌握江苏省2018年人感染布鲁氏菌主要流行株的种型和基因型。方法运用普通PCR及AMOS多重PCR确认分离株的生物种型;采用多位点序列分型(Multilocus sequence analysis,MLSA)和多位点串联重复序列分析(Multiple-locus variable number tandem repeat analysis,MLVA)鉴定基因型,并与国内外流行株进行聚类分析。结果2018年共分离到56株布鲁氏菌,MLSA分型显示一株菌为猪种布鲁氏菌ST(Sequence type)17型,其他均为羊种布鲁氏菌ST8型。MLVA将56株菌分为47个基因亚型(46个羊种,1个猪种),聚类显示羊种布鲁氏菌全部为“东地中海簇”。结论2018年江苏省人感染布病主要为“东地中海簇”的ST8型羊种布鲁氏菌,并首次发现一例人感染ST17型猪种布鲁氏菌。
文摘目的以肠道定植碳青霉烯类耐药肠杆菌科细菌(carbapenem resistance Enterobacteriaceae,CRE)与同一患者后期感染细菌的关系为出发点,同源性检测和耐药基因筛查为中心,从重症医学科(intensive care unit,ICU)患者肠道CRE的定植情况、CRE肠道定植与后期感染的关系层次上,进行CRE防治的应用基础研究,从而为临床及时有效的抗感染治疗提供一定指导。方法收集2018—2019年来自ICU病房及由其他科室转入ICU的共11位患者的临床资料,分别分离同一患者肠道定植CRE菌株和后期其他感染部位的菌株,对所有菌株进行药物敏感性试验和耐药基因携带情况检测,采用多位点序列分析(MLST)、脉冲场凝胶电泳(PAGE)试验的方法对定植CRE菌株和后期其他感染部位的菌株进行同源性分析。结果95位ICU患者中有19位患者肠道CRE筛查阳性,定植率为20.00%。其中发生后期其他部位感染的患者11位,目标菌株耐碳青霉烯酶基因检测结果显示22株菌株中有21株检出耐药基因,占95.45%(21/22)。其中19株检出KPC-2耐药基因,阳性率为86.36%(19/22);2株检出NDM-1耐药基因,阳性率为9.09%(2/22)。其他碳青霉烯酶基因检测均为阴性。22株目标菌的MLST分型共分为3个型,主要为ST11型,11位患者中除了1位患者的后期感染菌株与定植菌株差异明显外,其余患者的肠道定植菌株与后期感染菌株均为相同的ST型;PAGE检出22株菌的分型可分为A群和B群,共7个型别,其中7位患者的肠道定植菌株与后期感染菌株之间条带位置与数目相同,视为同一克隆型,3位患者的肠道定植菌株与后期感染菌株条带有2~3个差异,同源性极高,视为高度相关菌株;1位患者的肠道定植菌株与后期感染菌株的条带异超过7条,视为不相关菌株。结论ICU患者定植率高,应加强入院CRE定植筛查;ICU患者部位检出的定植及感染CRE菌株MIC值高,为高耐药性菌株;ICU患者发生CRE感染的菌株与自身定植的菌株有极高的同源性。
