Objective A core genome multilocus sequence typing(cgMLST)scheme to genotype and identify potential risk clonal groups(CGs)in Proteus mirabilis.Methods In this work,we propose a publicly available cgMLST scheme for P....Objective A core genome multilocus sequence typing(cgMLST)scheme to genotype and identify potential risk clonal groups(CGs)in Proteus mirabilis.Methods In this work,we propose a publicly available cgMLST scheme for P.mirabilis using chew BBACA.In total 72 complete P.mirabilis genomes,representing the diversity of this species,were used to set up a cgMLST scheme targeting 1,842 genes,635 unfinished(contig,chromosome,and scaffold)genomes were used for its validation.Results We identified a total of 205 CGs from 695 P.mirabilis strains with regional distribution characteristics.Of these,159 unique CGs were distributed in 16 countries.CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes.Nine virulence genes(papC,papD,papE,papF,papG,papH,papI,papJ,and papK)related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20.These CGs require attention due to potential risks.Conclusion This research innovatively performs high-resolution molecular typing of P.mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline(chewBBACA).We found that the CGs of P.mirabilis showed regional distribution differences.We expect that our research will contribute to the establishment of cgMLST for P.mirabilis.展开更多
目的了解咸阳市食品中单增李斯特菌的污染状况及分子流行病学特征。方法2010—2019年采集咸阳市12类1699份食品及酱制品加工环节样本,依据《国家食品安全风险监测工作手册》进行单增李斯特菌分离鉴定,用脉冲场凝胶电泳(pulsed field gel...目的了解咸阳市食品中单增李斯特菌的污染状况及分子流行病学特征。方法2010—2019年采集咸阳市12类1699份食品及酱制品加工环节样本,依据《国家食品安全风险监测工作手册》进行单增李斯特菌分离鉴定,用脉冲场凝胶电泳(pulsed field gel electrophoresis,PFGE)进行分子分型,检测菌株血清表型,对菌株进行全基因组测序,分析其谱系、克隆群、序列型和血清群,采用核心基因组多位点序列分型方法(cgMLST)进行分子分型。结果1699份样本中检出单增李斯特菌72株,总检出率为4.24%,检出率最高的是生肉制品18.49%(22/119);1/2a、1/2b和1/2c为优势血清型(87.50%,63/72);分离株共分为40个PFGE带型,其中有3个优势带型(GX6A16.XY0009、GX6A16.XY0004、GX6A16.XY0003),初步建立了咸阳市单增李斯特菌的PFGE指纹图谱库;全基因组测序菌株分属3个谱系,以谱系II为主56.94%(41/72);血清群以Ⅱa为主,共31株(43.06%,31/71);分为15个CC型,其中CC224、CC8、CC9和CC87为优势CC型(56.94%,41/72)。cgMLST能将不同谱系、血清群和CC型的菌株明显分开,分为18个亚群,与CC型基本保持一致。结论咸阳市流通食品中单增李斯特菌污染状况持续存在,并有交叉污染的可能。建立的PFGE指纹图谱库可为单增李斯特菌引起的食源性疾病的预警和暴发溯源提供支持,基于全基因组的cgMLST分型可用于食源性疾病暴发调查中菌株的溯源。展开更多
The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and...The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and to explore potential resistance mechanisms,56 MRAB strains were collected from the clinical departments of seven hospitals in Liaocheng between 2020 and 2022.Molecular typing,antimicrobial resistance patterns,and epidemiological characteristics were determined by genome sequencing and comparative genome analysis.Sequence type(ST)540 was the most prevalent ST of the 56 MRAB in Liaocheng,and most strains(92.86%)were grouped into CC92.Core genome multilocus sequence typing subdivided the strains according to the number of allelic differences and could distinguish different outbreaks caused by ST540 isolates in the hospitals.All the isolates harbored blaOXA-23 and blaADC-25,and at least 92.86%of the isolates were resistant to 10 antibiotics.The major MRAB epidemic clone detected in Liaocheng was ST540,which was different from the results reported in other regions in China.Furthermore,several inter-hospital transmissions of ST540 isolates were observed.The findings highlight the urgent need for effective nosocomial infection control measures and the continuous surveillance of ST540 MRAB in Liaocheng.展开更多
目的对珠海市2013—2021年不同来源分离的创伤弧菌病原学特征与种群进化进行研究,初步建立该菌在本地的病原学特征数据库。方法采用国家标准方法分离鉴定不同来源的创伤弧菌,采用PCR技术对119株分离菌株进行毒力相关基因(vcgC/E)、生物...目的对珠海市2013—2021年不同来源分离的创伤弧菌病原学特征与种群进化进行研究,初步建立该菌在本地的病原学特征数据库。方法采用国家标准方法分离鉴定不同来源的创伤弧菌,采用PCR技术对119株分离菌株进行毒力相关基因(vcgC/E)、生物型(BT)和血清分型(SerE)的鉴定;脉冲场凝胶电泳(PFGE)技术对分离菌株分子分型,全基因组测序技术对分离菌株二代测序,构建核心基因组多位点序列分型(cgMLST)进化树,分析菌株的种群进化特征。结果119株创伤弧菌毒力相关基因vcg C/E和16S r RNA A/B分型结果显示共有5种型别,分别为CB型(104株,87.40%)、CA型(4株,3.36%)、EA型(4株,3.36%)、EB型(1株,0.84%)和CAB型(6株,5.04%);生物分型分为BT1型(109株,91.60%)和BT2型(10株,8.40%)。PFGE聚类呈现多样性,显示119株创伤弧菌可分为108种PFGE分子带型,相似度61.1%~100.0%。119株创伤弧菌通过cgMLST分析,共分为5个分支。结论珠海市2013—2021年不同来源创伤弧菌毒力相关基因型以CB型为优势型别,生物型以BT1为主。不同来源的创伤弧菌菌株遗传进化弥散性高,临床病人中分离出来的菌株有聚集成簇的现象,提示可能来源于同一克隆,遗传高度相关。展开更多
基金supported by grants from the National Natural Science Foundation of China[82073624]Military Biosafety Research Special Project[20SWAQX04]Independent Project[Grant No.2017ZZKTB03]。
文摘Objective A core genome multilocus sequence typing(cgMLST)scheme to genotype and identify potential risk clonal groups(CGs)in Proteus mirabilis.Methods In this work,we propose a publicly available cgMLST scheme for P.mirabilis using chew BBACA.In total 72 complete P.mirabilis genomes,representing the diversity of this species,were used to set up a cgMLST scheme targeting 1,842 genes,635 unfinished(contig,chromosome,and scaffold)genomes were used for its validation.Results We identified a total of 205 CGs from 695 P.mirabilis strains with regional distribution characteristics.Of these,159 unique CGs were distributed in 16 countries.CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes.Nine virulence genes(papC,papD,papE,papF,papG,papH,papI,papJ,and papK)related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20.These CGs require attention due to potential risks.Conclusion This research innovatively performs high-resolution molecular typing of P.mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline(chewBBACA).We found that the CGs of P.mirabilis showed regional distribution differences.We expect that our research will contribute to the establishment of cgMLST for P.mirabilis.
文摘目的了解咸阳市食品中单增李斯特菌的污染状况及分子流行病学特征。方法2010—2019年采集咸阳市12类1699份食品及酱制品加工环节样本,依据《国家食品安全风险监测工作手册》进行单增李斯特菌分离鉴定,用脉冲场凝胶电泳(pulsed field gel electrophoresis,PFGE)进行分子分型,检测菌株血清表型,对菌株进行全基因组测序,分析其谱系、克隆群、序列型和血清群,采用核心基因组多位点序列分型方法(cgMLST)进行分子分型。结果1699份样本中检出单增李斯特菌72株,总检出率为4.24%,检出率最高的是生肉制品18.49%(22/119);1/2a、1/2b和1/2c为优势血清型(87.50%,63/72);分离株共分为40个PFGE带型,其中有3个优势带型(GX6A16.XY0009、GX6A16.XY0004、GX6A16.XY0003),初步建立了咸阳市单增李斯特菌的PFGE指纹图谱库;全基因组测序菌株分属3个谱系,以谱系II为主56.94%(41/72);血清群以Ⅱa为主,共31株(43.06%,31/71);分为15个CC型,其中CC224、CC8、CC9和CC87为优势CC型(56.94%,41/72)。cgMLST能将不同谱系、血清群和CC型的菌株明显分开,分为18个亚群,与CC型基本保持一致。结论咸阳市流通食品中单增李斯特菌污染状况持续存在,并有交叉污染的可能。建立的PFGE指纹图谱库可为单增李斯特菌引起的食源性疾病的预警和暴发溯源提供支持,基于全基因组的cgMLST分型可用于食源性疾病暴发调查中菌株的溯源。
基金funded by the Shandong Medical and Health Science and Technology Development Program,grant number 202212061076.
文摘The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and to explore potential resistance mechanisms,56 MRAB strains were collected from the clinical departments of seven hospitals in Liaocheng between 2020 and 2022.Molecular typing,antimicrobial resistance patterns,and epidemiological characteristics were determined by genome sequencing and comparative genome analysis.Sequence type(ST)540 was the most prevalent ST of the 56 MRAB in Liaocheng,and most strains(92.86%)were grouped into CC92.Core genome multilocus sequence typing subdivided the strains according to the number of allelic differences and could distinguish different outbreaks caused by ST540 isolates in the hospitals.All the isolates harbored blaOXA-23 and blaADC-25,and at least 92.86%of the isolates were resistant to 10 antibiotics.The major MRAB epidemic clone detected in Liaocheng was ST540,which was different from the results reported in other regions in China.Furthermore,several inter-hospital transmissions of ST540 isolates were observed.The findings highlight the urgent need for effective nosocomial infection control measures and the continuous surveillance of ST540 MRAB in Liaocheng.
文摘目的对珠海市2013—2021年不同来源分离的创伤弧菌病原学特征与种群进化进行研究,初步建立该菌在本地的病原学特征数据库。方法采用国家标准方法分离鉴定不同来源的创伤弧菌,采用PCR技术对119株分离菌株进行毒力相关基因(vcgC/E)、生物型(BT)和血清分型(SerE)的鉴定;脉冲场凝胶电泳(PFGE)技术对分离菌株分子分型,全基因组测序技术对分离菌株二代测序,构建核心基因组多位点序列分型(cgMLST)进化树,分析菌株的种群进化特征。结果119株创伤弧菌毒力相关基因vcg C/E和16S r RNA A/B分型结果显示共有5种型别,分别为CB型(104株,87.40%)、CA型(4株,3.36%)、EA型(4株,3.36%)、EB型(1株,0.84%)和CAB型(6株,5.04%);生物分型分为BT1型(109株,91.60%)和BT2型(10株,8.40%)。PFGE聚类呈现多样性,显示119株创伤弧菌可分为108种PFGE分子带型,相似度61.1%~100.0%。119株创伤弧菌通过cgMLST分析,共分为5个分支。结论珠海市2013—2021年不同来源创伤弧菌毒力相关基因型以CB型为优势型别,生物型以BT1为主。不同来源的创伤弧菌菌株遗传进化弥散性高,临床病人中分离出来的菌株有聚集成簇的现象,提示可能来源于同一克隆,遗传高度相关。
