磁共振成像三维纹理特征结合临床参数放射组学模型评估肝细胞癌术后早期复发的初步研究

目的:初步探索磁共振成像(magnetic resonance imaging,MRI)三维纹理(three-dimensional texture,3D-texture)特征结合临床参数构建预测模型,术前评估肝细胞癌(hepatocellularcarcinoma,HCC)患者术后早期复发的可行性。方法:回顾性纳入98例术后早期复发HCC患者,记录实验室检查结果、MRI影像征象、3D-texture,经数据去冗余、Lasso回归行主要特征提取,使用监督学习算法进行建模,并将模型用于预测83例前瞻性患者术后早期复发。结果:动脉期(arterial phase,AP)和门静脉期(portal venous phase,PVP)分别提取出6和2个纹理特征进行建模,AP-3D-texture模型在训练集、验证集及测试集中的预测效能如下:预测准确性(accuracy,ACC)分别为0.735、0.735和0.651;受试者工作特征(receiver operating characteristic,ROC)曲线的曲线下面积(area under curve,AUC)分别为0.759、0.769和0.669。PVP-3D-texture模型在3个数据集中预测效能如下:训练集中ACC为0.721,AUC为0.591;验证集中ACC为0.367,AUC为0.498;测试集中ACC为0.402,AUC为0.560。AP-3D-texture结合临床参数后在3个数据集中的预测效能如下:训练集中ACC为0.838,AUC为0.876;验证集中ACC为0.833,AUC为0.864;测试集中ACC为0.663,AUC为0.656。结论:AP-3D-texture可以作为预测HCC术后早期复发的标记,与临床参数结合后预测效能进一步提高,但是在测试集中效能偏低,可能与训练集样本量偏少有关。     

临床、CT特征及影像组学联合模型评估最大径≤2cm原发性肺腺癌侵袭性

目的 观察临床、CT特征及影像组学联合模型评估最大径≤2 cm原发性肺腺癌侵袭性的价值。方法 回顾性纳入116例最大径≤2 cm肺腺癌患者，依据病理结果将其分为高侵袭组(n=51)及低侵袭组(n=65),并按7∶3比例随机分为训练集(n=81)和测试集(n=35)。比较组间临床及CT特征差异；提取并筛选CT影像组学特征，计算影像组学评分(Rad-score)。采用logistic回归分析建立临床、CT特征及Rad-score联合模型，评估其预测效能及临床获益。结果 组间患者恶性肿瘤家族史，病灶分叶征、毛刺征、存在提示预后不良病理表现占比差异均有统计学意义(P均<0.05);基于训练集数据筛选出8个影像组学特征并构建的联合模型评估训练集和验证集最大径≤2 cm肺腺癌侵袭性的曲线下面积分别为0.96和0.87,其预测值与真实值的误差较小，准确度较高，可使临床获益。结论 临床、CT特征及影像组学联合模型可用于评估最大径≤2 cm原发性肺腺癌的侵袭性。     

基于TCGA和ICGC数据库构建肾透明细胞癌的免疫相关预后模型

摘要:目的构建和验证肾透明细胞癌(kidneyclearcellcarcinoma,KIRC)的免疫相关预后模型在临床风险分层和预后预测的应用价值，探索肿瘤免疫微环境的特征。方法从癌症基因组图谱(TheCancerGenomeAtlas,TCGA)和国际癌症基因组联盟 ( International Cancer Genome Consortium,ICGC)下载KIRC队列mRNA表达数据集,分别作为目标数据集和验证数据集,从免疫学数据库和分析平台( Immunology Database and Analysis Portal, ,ImmPort)中 下载免疫相关基因列表。基于以上数据集,筛选出差异表达的免疫相关基因并以此构建和验证预后模型。基于预后模型得出的风险评分对肿瘤样本进行分组,探究不同风险评分等级下的免疫细胞浸润水平、免疫检查位点及其配体表达水平的差异。结果共筛选出 11 个差异表达且关联预后的免疫相关基因,以此构建的预后模型预测3年、4年、5年生存率的ROC曲线下面积分别为0.669. 0.707和0.750。基于该模型得到的高风险评分与较高的肿瘤分期(P<0.05)、较差的预后(P<0.0001)均显著相关,并在验证数据集中得到进一步验证。在对总生存时间的风险率上,风险评分比差异表达的任一单个免疫相关基因高(风险率:1.93 vs 1.37), 但与肿瘤分期I期相当(风险率:1.93 vs 1.97)。基于风险评分分组,在高风险组和低风险组间的浸润程度存在显著差异的免疫细胞类型达12 种(P<0.05),其中,调节T细胞、M0型巨噬细胞、活化的记忆CD4*T细胞和休眠树突状细胞的浸润程度高低与预后均显著相关.(P<0.05)。此外,免疫治疗相关靶点的表达水平在不同风险评分等级中存在显著差异(P<0.05)。结论构建的 KIRC免疫相关预后模型在评估肿瘤分期和预后具有潜在的临床应用价值,有望为临床风险分层和免疫治疗提供证据。     

基于长链非编码RNA的表达谱特征构建乳腺癌患者预后的风险模型

目的构建长链非编码RNA(long non-coding RNA,LncRNA)表达特征的乳腺癌患者预后的预测模型。方法分析癌症基因组图谱(the cancer genome atlas,TCGA)数据库1081例乳腺癌患者的转录组测序数据中LncRNA表达图谱及临床特征,对TCGA数据库中112对配对的乳腺癌及正常乳腺组织的转录组测序数据进行差异表达分析和单因素分析筛选得到差异表达且与乳腺癌患者预后显著相关的LncRNA(DELncRNA),利用DEseq2包进行差异表达分析(为减弱批次效应,测序数据已用DESeq函数标准化)。1081例乳腺癌患者被分成两组:训练集(541例)和验证集(540例)。将DELncRNA纳入Cox比例风险回归模型,在训练集中筛选和建立多LncRNA预后模型并对模型进行比例风险假定检验(proportional hazards assumption,PH假定检验),计算多基因风险评分,并基于此将患者分为高风险组和低风险组,采用Kaplan-Meier方法进行生存分析,并用验证集540例患者的数据进行验证。评价该模型在TCGA数据库肺鳞癌和肝细胞肝癌等患者中的预后评估价值。基因集富集分析(gene set enrichment analysis,GSEA)分析LncRNA影响患者生存的具体机制。结果转录组测序分析筛选得到2815个差异表达基因,其中与乳腺癌患者预后显著相关的LncRNA共91个(P<0.05)。利用541例训练集乳腺癌患者的91个DELncRNA表达数据进行Cox回归分析,构建了基于5个LncRNA的Cox比例风险回归模型(训练集AUC=0.746,验证集AUC=0.650):AC004551.1、MTOR-AS1、KCNAB1-AS2、FAM230G和LINC01283,并进行PH假定检验(P=0.388)。K-M生存分析发现,训练集中高风险组的生存明显差于低风险组(中位生存时间:7.049年与12.21年,HR 0.367,95%CI 0.228~0.597,P<0.001),在验证集中高风险组患者生存时间也明显短于低风险组(中位生存时间:7.57年与10.85年,HR 0.412,95%CI 0.214~0.793,P<0.001)。在TCGA其他癌种中也得到相似的预测结果:肺鳞癌(HR 0.604,95%CI 0.383~0.951,P=0.007)及肝细胞肝癌(HR 0.551,95%CI 0.307~0.987,P=0.011)。GSEA结果提示,上述5个LncRNA的表达模式与肿瘤细胞的细胞周期调控有关。结论基于AC004551.1、MTOR-AS1、KCNAB1-AS2、FAM230G和LINC01283表达谱构建的预后模型可用于预测乳腺癌患者的预后,有利于进一步指导临床治疗。     

基于术前超声及炎症指标的列线图预测早期乳腺癌腋窝高淋巴结负荷的价值

目的探讨超声、病理联合炎症指标对早期乳腺癌患者腋窝高淋巴结负荷(HNB)的预测价值并构建列线图, 为个体化诊疗提供参考。方法回顾性分析2014年1月至2022年7月于上海交通大学附属第六人民医院南院经病理证实的378例早期乳腺癌女性患者的超声、病理特征及术前炎症指标, 以8∶2比例将其随机分为训练集(n=302)和测试集(n=76), 比较两者基线资料的差异。采用ROC曲线确定中性粒细胞/淋巴细胞比值(NLR)、血小板/淋巴细胞比值(PLR)和淋巴细胞/单核细胞比值(LMR)的最佳截断值。训练集中, 以腋窝HNB(≥3个转移淋巴结)为因变量, 通过单因素、多因素Logistic回归分析筛选HNB的独立影响因素并构建列线图, 基于测试集数据验证模型, 利用ROC曲线下面积(AUC)和C-index评价模型区分度, Brier score和校准曲线评价模型校准度, 临床决策曲线评价模型临床适用性。结果训练集与测试集之间所有变量差异无统计学意义(均P>0.05)。ROC曲线分析显示, 术前NLR、PLR和LMR预测早期乳腺癌HNB的AUC分别为0.578、0.547和0.516, 最佳...     

基于SEER数据库老年肺鳞癌患者的预后分析

目的 基于SEER数据库分析影响老年肺鳞癌患者预后的危险因素,并构建预测模型。方法 基于SEER数据库,选取2004—2015年确诊为肺鳞癌的25 602例患者作为研究对象,按照7∶3随机分为训练集(17 921例)与验证集(7 681例);通过Kaplan-Meier生存曲线分析肺鳞癌患者基本资料与预后的相关性;利用Cox回归和LASSO回归分析确定影响老年肺鳞癌患者预后的独立危险因素并构建列线图模型;以C-index、受试者工作特征(ROC)曲线、决策曲线评估列线图模型的预测性能。结果 25 602例患者中死亡17 717例(69.2%);多因素Cox回归分析结果显示,年龄越大、高T分期、高N分期、高M分期、未接受手术是影响老年肺鳞癌患者预后不良的危险因素(P<0.05);训练集和验证集中用于评估列线图模型的C-index分别为0.732(95%CI:0.727～0.736)和0.733(95%CI:0.725～0.739),训练集列线图模型预测半年、1年、3年肺鳞癌患者预后的曲线的曲线下面积(AUC)分别为0.772(95%CI:0.764～0.779)、0.795(95%...     

肺腺癌中关键RNA结合蛋白预后评估模型的构建

目的基于生物信息学方法,评估肺腺癌中关键RNA结合蛋白的表达及预后作用。方法从癌症基因组图谱(TCGA)数据库中下载526例肺腺癌组织、59例正常组织,以及从基因型-组织表达(GTEx)数据库中下载288例正常组织的RNA测序数据,筛选差异表达RNA结合蛋白;单因素和多因素Cox回归分析筛选关键RNA结合蛋白并构建预后评估模型。结果共发现375个差异表达RNA结合蛋白,筛选出8个预后相关的关键RNA结合蛋白(WDR3、SMG9、DARS2、CARHSP1、LARP6、GAR1、INTS7和EXO1)。构建基于8个关键RNA结合蛋白的预后评估模型发现,试验组和验证组模型的高风险患者较低风险患者总体生存时间更短(P<0.05),两组受试者工作特征曲线下面积分别为0.761和0.666,该预后模型具有有效性和准确性。结论该研究成功构建肺腺癌中关键RNA结合蛋白预后评估模型,上述8个关键RNA结合蛋白可作为预测肺腺癌预后的分子标志物。     

基于生物信息学筛选影响胃癌患者预后的糖酵解相关基因

目的 通过利用生物信息学开发糖酵解相关基因以预测胃癌(gastric cancer,GC)患者预后。方法 使用癌症基因组图谱数据库中GC患者信使核糖核酸表达谱数据,通过进行基因集富集分析以鉴定GC组织和正常组织间显著差异的基因集。通过最小绝对收缩和选择算子回归分析构建糖酵解相关基因预测GC患者预后的模型,并使用Kaplan-Meier分析、受试者工作特征曲线、单因素及多因素Cox回归分析验证模型预测性能。采用基因集变异分析分析高低风险组间生物途径状态的差异。结果 获得15个糖酵解相关基因(PFKFB2、UHRF1、ACYP1、CLDN9、STC1、EFNA3、NUP50、ADH4、ANGPTL4、PKP2、VCAN、HIF1A、LHX9、ANKZF1、ALDH3A2)与GC患者预后相关。根据15个基因特征风险评分,通过Cox回归分析将患者分为高风险组和低风险组。这15个基因标记是GC患者预后的独立生物标志物,低风险评分的GC患者预后更好。结合基因标记和临床预后因素的列线图可有效预测总生存期及无疾病生存期。结论 建立的15个糖酵解相关基因标记可作为预测GC患者预后的可靠工具,可能为GC提...     

基于梯度提升机算法的弥漫大B细胞淋巴瘤患者并发间质性肺炎预测模型构建与验证

目的 基于梯度提升机(GBM)算法构建弥漫大B细胞淋巴瘤(DLBCL)患者并发间质性肺炎(IP)的预测模型并验证模型效能。方法 回顾性分析220例DLBCL患者的临床数据,将患者按7∶3比例分为训练集154例和测试集66例,其中51例患者发生IP(占23.18%), 169例患者未发生IP。基于GBM算法构建预测模型,采用受试者工作特征(ROC)曲线评估模型的区分度,采用校准曲线评估模型的拟合情况。结果 经过筛选,年龄、疾病分期、国际预后指数(IPI)评分、吸烟史、乳酸脱氢酶(LDH)这5个最优特征被纳入GBM模型,其相对重要性从高到低依次为年龄、疾病分期、LDH、IPI评分、吸烟史。ROC曲线显示,GBM模型在训练集和测试集中的曲线下面积(AUC)分别为0.872(95%CI:0.800～0.945)、0.891(95%CI:0.755～1.000)。校准曲线显示,GBM模型在训练集和测试集中的预测概率均与实际IP发生率具有较好的一致性。结论 DLBCL患者治疗后的IP发生率为23.18%,主要与年龄、疾病分期、IPI评分、吸烟史、LDH水平有关,基于这些因素构建的GBM模型具有较高...     

基于危险因素和常规实验室指标的子痫前期风险预测模型研究

目的通过对妊娠妇女6～10周的一般资料、危险因素和常规实验室指标水平进行数据分析,构建妊娠早期子痫前期(PE)预测模型,比较Logistic回归模型和极端梯度提升(XGBoost)模型的预测能力。方法回顾性分析2015年1月至2020年8月北京大学第三医院925例PE患者和7 613例正常对照组的一般资料、PE发病危险因素和27项常规实验室指标(妊娠6～10周),包括血脂、肝肾功能、凝血、血细胞计数等指标,采用Mann-Whitney U检验、Logistic回归、XGBoost等统计学方法进行数据分析,分别建立预测模型,绘制ROC曲线抗磷脂综合征,计算曲线下面积(AUC~(ROC))、敏感性、特异性;并用XGBoost绘制特征重要性条形图。结果两组孕妇是否有糖尿病、SLE、抗磷脂综合征、肾病、子痫或PE史以及是否为初产妇的比例差异均有统计学意义(P均0.05)。27个常规实验室指标中,两组除Plt/Lym的水平差异无统计学意义(P均0.05)外,其他所有指标差异均有统计学意义(P均0.05)。仅纳入危险因素(7项)建立Logistic回归模型,AUC~(ROC)为0.621(95%CI:0.601～0.640),敏感性为34.8%,特异性为81.5%;纳入危险因素和实验室指标(6项危险因素+14项实验室指标)建立Logistic模型,AUC~(ROC)为0.752(95%CI:0.735～0.769),敏感性为64.2%,特异性为76.0%;建立XGBoost模型,AUC~(ROC)为0.867(95%CI:0.839～0.896),敏感性为73.0%,特异性为82.3%。采用XGBoost模型进行PE发病早期预测的能力最优。XGBoost筛选出重要性排在前三的指标依次为TG、Lp(a)、C1q。结论单独使用临床危险因素预测PE的效能不高,PE发病危险因素结合常规实验室指标进行妊娠早期预测PE发病风险的效果更优,而XGBoost模型早期预测PE发病的性能优于Logistic回归模型。TG、Lp(a)、C1q是早期预测PE发病的重要变量。     

3株临床分离产OXA-232碳青霉烯耐药肺炎克雷伯菌的流行病学分析

目的描述临床OXA-232肺炎克雷伯菌(OXA-232-producing Klebsiella pneumoniae,OXA-232Kp)的流行病学特征。方法收集2018年9月—2019年9月江苏5家医院临床分离的碳青霉烯耐药肺炎克雷伯菌(carbapenem-resistant Klebsiella pneumoniae, CRKP),采用微量肉汤稀释法和Phoenix-M50自动微生物系统进行药敏分析;PCR结合测序检测bla_(OXA-232)基因;脉冲场凝胶电泳(PFGE)分析菌株同源性;质粒测序分析携带bla_(OXA-232)基因的质粒周围环境。结果筛选出3株OXA-232Kp ST15型, PFGE分析呈克隆性传播,携带6 141 bp ColKP3型质粒,与中国东部研究发现携带bla_(OXA-232)基因的质粒高度同源。结论本文首次调查OXA-232Kp ST15在江苏地区的流行病学特征。携带bla_(OXA-232)的质粒具有高度的同源性,表明该6 141 bp ColE型质粒对OXA-232在江苏地区的流行具有重要作用。     

Outbreak of OXA-48-positive carbapenem-resistant Klebsiella pneumoniae isolates in France

Seventeen Klebsiella pneumoniae isolates producing the OXA-48 carbapenemase, obtained from 10 patients hospitalized from April to June 2010, mostly in the medical intensive care unit of the Villeneuve-Saint-Georges Hospital in a suburb of Paris, France, were analyzed. Seven patients were infected, of whom five were treated at least with a carbapenem, and five patients died. Molecular analysis showed that the isolates belonged to a single clone that harbored a 70-kb plasmid carrying the blaOXA-48 gene and coproduced CTX-M-15 and TEM-1 β-lactamases. This is the first reported outbreak of OXA-48-producing K. pneumoniae isolates in France.     

First outbreak of a plasmid-mediated carbapenem-hydrolyzing OXA-48 beta-lactamase in Klebsiella pneumoniae in Spain

Twenty Klebsiella pneumoniae isolates producing OXA-48 were collected from April 2009 to September 2010. Strains were clonally related and coproduced a CTX-M-15 β-lactamase. A conjugative plasmid of circa 70 kb carrying bla(OXA-48) was identified. Eleven isolates showed low-level resistance to carbapenems, whereas nine showed high-level resistance. Decreased expression of OmpK36 was related to high-level resistance to carbapenems. The isolates belonged to sequence type 101 (ST101). This is the first outbreak caused by an OXA-48-producing K. pneumoniae strain in Spain.     

Genetic features of the widespread plasmid coding for the carbapenemase OXA-48

Complete sequencing of plasmid pOXA-48a carrying the bla(OXA-48) gene from a Klebsiella pneumoniae isolate was performed. Its backbone corresponded to that of an IncL/M-type plasmid, in which the bla(OXA-48) gene had been integrated through the acquisition of the Tn1999 composite transposon without any other antibiotic resistance gene. Molecular epidemiology using a collection of international OXA-48 producers revealed the wide diffusion of pOXA-48a or closely related plasmids.     

某院ST11型耐碳青霉烯酶高毒力肺炎克雷伯菌分子流行病学研究

目的对连云港市某院ST11型耐碳青霉烯酶高毒力肺炎克雷伯菌(CR-HVKP)进行分子流行病学调查。方法收集连云港市中医院2017年1月至2019年6月临床分离的26株耐碳青霉烯酶肺炎克雷伯菌(CRKP),采用改良碳青霉烯酶灭活试验(mCIM)、EDTA-改良碳青霉烯酶灭活试验(eCIM)及PCR法分别检测菌株碳青霉烯酶耐药表型和碳青霉烯酶耐药基因。采用拉丝实验检测实验菌株的黏液表型。采用3种多重PCR进行检测,第1体系对实验菌株进行ST分型,第2体系检测最强毒力的荚膜血清型wzyK1、wzyK2,以及K位点wzyKL47、wzyKL64,第3体系检测rmpA、rmpA2、iroN、intA毒力相关基因,并采用大蜡螟感染模型检测毒力表型,采用脉冲场凝胶电泳(PFGE)进行同源性分析。结果26株CRKP菌株,携带以肺炎克雷伯菌碳青霉烯酶(KPC)为主的耐药基因菌株有22株,结果与相对应的22株菌株的mCIM结果一致。ST分型以ST11型为主,占73.1%(19/26),wzyKL47、wzyKL64阳性率分别为15.8%(3/19)、84.2%(16/19)。检出8株携带毒力相关基因且具有毒力表型的ST11型CR-HVKP以KL64为主,康复科检出率最高。采用PFGE可分为3群,带型相似度高于85%的有2株。结论连云港市中医院检出ST11型CR-HVKP 8株,可能存在克隆株的散在传播,需加强对康复科院内感染的防控。     

Nosocomial outbreak of VIM-1-producing Klebsiella pneumoniae isolates of multilocus sequence type 15: molecular basis, clinical risk factors, and outcome

We study the epidemiology, molecular basis, clinical risk factors, and outcome involved in the clonal dissemination of VIM-1-producing Klebsiella pneumoniae isolates in the hospital setting. All patients infected/colonized by carbapenem-nonsusceptible K. pneumoniae (CNSKP) in 2009 were included. Molecular epidemiology was studied by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Antibiotic resistance genes were analyzed by PCR and sequencing. Plasmids were studied by PFGE with S1 nuclease digestion and for incompatibility group by a PCR-based replicon typing scheme. Risk factors associated with CNSKP colonization/infection were assessed by an observational case-control study. All 55 patients studied were infected (n = 28) or colonized (n = 27) by VIM-1-producing K. pneumoniae. All but one acquired isolates of a single clone (PFGE cluster 1 [C1], sequence type 15 [ST15]), while another clone (PFGE C2, ST340) was detected in four patients. C1 isolates also produced the new extended-spectrum β-lactamase SHV-134. bla(VIM-1) was carried in a class 1 integron and an untypeable plasmid of ～50 bp. The number of days that the patient received mechanical ventilation, the use of parenteral nutrition, previous treatment with linezolid, and treatment with extended-spectrum cephalosporins for more than 7 days were detected to be independent risk factors for CNSKP acquisition. The VIM-1-producing K. pneumoniae ST15 clone has a high capacity to spread among intensive care unit patients with severe underlying conditions. A high rate of associated mortality and great difficulty in controlling the spread of this clone, without permanent behavioral changes in the personnel, were observed.     

Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in a neonatal intensive care unit

OBJECTIVES: To investigate the molecular epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae in the neonatal intensive care unit of a university hospital in Italy. METHODS: Antibiotic susceptibility was evaluated by disc diffusion and Etest. ESBLs were identified by isoelectric focusing, PCR and DNA sequencing analysis. Genotyping was performed by PFGE analysis. Conjugation was performed by broth mating. RESULTS: Molecular typing of K. pneumoniae isolates identified three distinct PFGE patterns. Isolates of PFGE profile A were isolated during an epidemic in 1996, while isolates of PFGE profiles B and C were sequentially isolated from September 2002 to December 2004, when 233 colonizations and 19 infections by K. pneumoniae occurred. All K. pneumoniae strains of different PFGE types were identified as ESBL producers. DNA sequencing of amplified beta-lactamase genes identified a novel bla(TEM) ESBL (bla(TEM-136)) along with bla(SHV-1) in chromosomal and plasmid DNA from K. pneumoniae of PFGE type A, respectively, and bla(TEM-1) and bla(SHV-12) in plasmid DNA from K. pneumoniae of PFGE types B and C. Conjugation experiments demonstrated that resistance to third-generation cephalosporins, along with an approximately 80 kb plasmid containing bla(SHV-12) and bla(TEM-1), was transferred from K. pneumoniae epidemic strains of PFGE types B and C to a susceptible Escherichia coli host at a frequency of 4 x 10(-6) and 1 x 10(-6) cfu/recipient cell, respectively. CONCLUSIONS: The selection of ESBL-producing clones and the transfer of the bla(SHV-12) ESBL gene between different clones were responsible for the spread of K. pneumoniae in the neonatal intensive care unit.     

Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule,Real-Time Sequencing

The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of the K. pneumoniae reference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries the bla_NDM-1, armA, and qnrB1 genes, along with tellurium and mercury resistance operons. bla_NDM-1 is carried on a unique structure in which Tn125 is further bracketed by IS26 downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, including bla_CTX-M-15 and a mercury resistance operon. The ColE-type plasmid pPKPN4 carrying bla_OXA-232 is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in the de novo assemblies.     

NDM-1-producing Klebsiella pneumoniae resistant to colistin in a French community patient without history of foreign travel

A carbapenem-resistant Klebsiella pneumoniae strain, Kp5196, was responsible for an uncomplicated cystitis in a patient living at home and without history of foreign travel. This isolate produced the metallocarbapenemase NDM-1 and was resistant to all antibiotics except tetracyclines and colistin. The K. pneumoniae strain belonged to sequence type ST15, and bla(NDM-1) was carried by a nontypeable conjugative plasmid. Two months later, a similar ST15 isolate, Kp5241, was present in the patient but was additionally colistin resistant.     

Long-term dissemination of an OXA-40 carbapenemase-producing Acinetobacter baumannii clone in the Iberian Peninsula

OBJECTIVE: The main objectives of this study were to assess the clonal relatedness of Acinetobacter baumannii carbapenem-resistant isolates recovered from the Iberian Peninsula and to investigate the production of carbapenemases. METHODS: One hundred and sixty-two imipenem-resistant A. baumannii isolates were collected from 1998 to 2003 in three Portuguese university hospitals. An imipenem-resistant isolate (988FFP strain) recovered in 1995 from a smaller hospital unit, was also included, as well as an OXA-40-producing A. baumannii Spanish strain (SM28). Susceptibility tests were carried out by disc diffusion and Etest methods. DNA fingerprints were obtained by PFGE of ApaI-digested chromosomal DNA. Carbapenemase activity was determined by a bioassay and spectrophotometry. The detection of the blaOXA-40 gene was conducted through PCR analysis, cloning and nucleotide sequencing. RESULTS: All the isolates presented a similar multi-resistance pattern, including imipenem (MIC >32 mg/L). The Iberian isolates showed an identical PFGE pattern with minor band variations, including isolate 988FFP collected in 1995. PCR results revealed a blaOXA-type gene in 65 isolates and nucleotide sequence analysis revealed the presence of the blaOXA-40 gene in seven representative Portuguese isolates from the various geographically dispersed hospitals. CONCLUSIONS: Our results indicate that a multi-resistant epidemic clone of A. baumannii, carrying blaOXA-40, is disseminated in the Iberian Peninsula, persisting in Portugal since 1995.