ICU下呼吸道多重耐药菌医院感染的病原学临床特征及易感因素分析

摘要 目的：研究ICU下呼吸道多重耐药菌医院感染的病原学临床特征及易感因素。方法：选择2020年1月到2022年12月于我院ICU住院治疗的216例下呼吸道感染者,按照是否发生多重耐药菌感染分为研究组113例,对照组103例。分析两组患者感染相关因素的数量分布情况,通过Logistic回归分析多重耐药菌医院感染的危险因素。采用全自动细菌鉴定仪对菌种进行鉴定,采用K-B纸片法进行药敏试验,并分析多重耐药菌感染的病原学分布及对常用抗菌药物的耐药性。结果：（1）与对照组相比,研究组患者感染相关因素的分布率更高;（2）住院时间>3个月、使用糖皮质激素治疗、应用机械通气治疗、其他细菌感染、血红蛋白含量<100 g/L、抗菌药物使用时间>15 d、抗菌药物使用种类>4种、使用免疫抑制剂是ICU下呼吸道多重耐药菌感染的危险因素;（3）113例研究组共培养出细菌菌株93株,其中革兰氏阴性菌52株（55.91%）,革兰氏阳性菌25株（26.88%）,革兰氏阴性菌中较多的是铜绿假单胞菌（22株）、鲍曼不动杆菌（13株）、肺炎克雷伯菌（12株）;革兰氏阳性菌中最多的是肺炎链球菌（11株）和金黄色葡萄球菌（11株）;（4）耐药情况：铜绿假单胞菌对莫西沙星耐药率较低（15.83%）,肺炎克雷伯菌对亚胺培南耐药率较低（17.56%）,鲍曼不动杆菌对头孢哌酮/舒巴坦耐药率较低（16.37%）,金黄色葡萄球菌、肺炎链球菌对万古霉素无耐药性。结论：住院时间>3个月、使用糖皮质激素治疗、应用机械通气治疗、其他细菌感染、血红蛋白含量<100 g/L、抗菌药物使用时间>15 d、抗菌药物使用种类>4种、使用免疫抑制剂是多重耐药感染的独立危险因素。本院ICU下呼吸道感染以革兰氏阴性杆菌为主,应根据病原菌选择耐药性低的药物,并针对危险因素采取有效措施。     

综合性医院肿瘤相关感染病原菌分布及耐药性分析

摘要 目的：通过对某院住院肿瘤患者感染的病原菌分布情况及耐药性分析，为肿瘤相关感染患者的经验性抗感染治疗提供参考。方法：对2015年细菌培养结果阳性的157例肿瘤内科住院患者的感染情况进行统计分析。结果：肿瘤内科患者的感染率为22.62%，分离出病原菌436株，其中革兰阴性菌占比58.26％，检出的金黄色葡萄球菌中MRSA的检出率为50%，粪肠球菌对万古霉素的敏感率为80%，屎肠球菌对万古霉素的敏感率为97.22%。主要G-杆菌中大肠埃希菌对阿米卡星耐药率1.79%，对碳青霉烯类、哌拉西林他唑巴坦耐药率为6.25%、26.79%；肺炎克雷伯菌对碳青霉烯类的耐药率25.58%-38.10%，对头孢哌酮舒巴坦耐药率15%。白色念珠菌对唑类耐药率<10%。结论：医院必须加强对常见细菌的耐药率的动态监测，降低细菌耐药率和多重耐药菌的产生。     

2017年至2019年阜阳某三级医院常见病原菌分布和细菌耐药性分析

摘要 目的：分析本院2017年~2019年常见病原菌分布和细菌耐药性情况,以指导临床用药。方法：将送检标本中的病原菌进行鉴定,参照CLSI 2017版判读药敏结果。结果：收集2017年7月~2019年6月临床分离菌共2292株,其中革兰阴性菌1862株,占81.2%,革兰阳性菌430株,占18.8%。大肠埃希菌占比最高,占25.7%。主要分离于尿液标本（55.9%）、血液标本（12.2%）和痰液标本（10.8%）。金黄色葡葡球菌中MRSA（耐甲氧西林金黄色葡萄球菌）和凝固酶阴性葡萄球菌中耐甲氧西林凝固酶阴性葡萄球菌（MRCNS）的检出率分别为61.4%和74.4%。MRSA主要分布于普外科、神经外科和骨科。未检出替考拉宁、利奈唑胺或万古霉素耐药的葡萄球菌。肠球菌属中屎肠球菌对测试药物的耐药率均较高。16株肺炎链球菌,其中3株对青霉素耐药。肠杆菌科细菌中,肺炎克雷伯菌对碳青霉烯耐药率为14.5%。鲍曼不动杆菌对碳青霉烯的耐药率为76.9%。铜绿假单胞菌为19.3%。14株流感嗜血杆菌中,β内酰胺酶检出率为35.7%（5/14）。结论：2017年~2019年我院常见病原菌以革兰阴性杆菌为主,病原菌的耐药性较高,临床应加强科室管理,合理应用抗生素,防耐药菌株的流行,降低医院感染的发生风险。     

通辽地区犊牛腹泻大肠杆菌耐药性检测及一株多重耐药菌全基因组测序分析

【背景】大肠杆菌(Escherichia coli)是引起犊牛腹泻的最主要病原菌,其耐药性菌株的不断出现引起广泛关注。【目的】了解内蒙古自治区通辽市犊牛腹泻大肠杆菌耐药性及耐药基因流行情况。【方法】从通辽市多个旗县采集犊牛腹泻样品40份,经细菌分离纯化及16S rRNA基因测序,最终鉴定出20株大肠杆菌。采用药敏试验和PCR方法对分离菌进行耐药性及耐药基因检测分析,并对其中1株多重耐药菌株进行全基因组测序。【结果】20株分离菌均具有多重耐药性,对链霉素、环丙沙星、恩诺沙星和复方新诺明的耐药率达80%以上。所检耐药基因中,aphA1、strB、TEM-1和qnrS检出率达100%。通过对代表性菌株TL-13全基因组测序发现,其基因组大小为4897185bp,GC含量为50.68%,同时携带2个质粒,大小分别为108288bp(pTL13-1)和64018bp(pTL13-2)。质粒中共携带18个可移动耐药基因。【结论】通辽地区犊牛腹泻大肠杆菌多重耐药性普遍存在,4种常见耐药基因普遍流行。     

红树林土壤中产聚羟基脂肪酸酯细菌的分离及其评估

[背景] 细菌能通过合成聚羟基脂肪酸酯（Polyhydroxyalknoates,PHA）在细胞内储存物质和能量,提高对环境的适应能力。在红树林中,由于土壤周期性受海水浸没,形成营养物质种类丰富和含量波动大的特殊生境,为细菌进化出特殊的PHA合成途径提供了条件。[目标] 为了增加对红树林产PHA细菌资源的了解,获得产PHA细菌,使用纯培养方法分离和鉴定细菌,并评估菌株的产PHA能力。[方法] 采集红树植物海桑根系和红树滩涂土壤样品,连续5周培养、分离纯化获得细菌菌株;通过16S rRNA基因相似性及系统进化分析鉴定细菌分类地位,利用PHA合成酶基因（phaC）鉴定细菌合成PHA的能力;通过基因组草图测序,分析细菌的phaC基因种类、代谢通路及系统进化关系;通过气相色谱分析细菌产PHA的累积量及组成。[结果] 从红树林土壤样品中分离得到97株细菌,其中13株带有phaC基因,包括坚强芽孢杆菌（Cytobacillus firmus）、弯曲芽孢杆菌（Bacillus flexus）、除烃海杆菌（Marinobacter hydrocarbonoclasticus）和酯香微杆菌（Microbacterium esteraromaticum）。B. flexus MN15-19以丙酮酸盐为碳源,可累积细胞干重11%的PHA,同时具有固碳功能的还原性三羧酸循环通路,有开发成为固碳产PHA工程菌株的潜力。酯香微杆菌可产PHA,但是其phaC基因结构特殊,基因组注释未能识别出任何已知phaC基因。[结论] 研究发现红树林土壤可培养细菌中存在未知的PHA合成途径,说明红树林生态系统中的细菌具有资源挖掘的重要价值。     

一株猪源化脓隐秘杆菌的鉴定、生物学特性研究与基因组分析

[背景] 化脓隐秘杆菌作为一种条件致病菌,常与蓝耳病病毒、猪圆环病病毒、巴氏杆菌等混合感染猪,引起各种非特异性化脓性感染,部分临床症状与副猪嗜血杆菌相似。本试验从江西某猪场一起因呼吸道症状急性死亡病猪的肺脏分离到一株具有β溶血特性、疑似化脓隐秘杆菌的细菌病原。[目的] 鉴定该病原的菌属种类、生物学特性及基因组特征,为该菌疾病的基础研究与临床防控奠定理论基础。[方法] 采用透射电镜、扫描电镜结合PCR鉴定等方法对菌属种类进行鉴定;通过动物实验、药敏试验,分析菌株的生物学特性;借助全基因组测序、生物信息学等技术发掘该菌的基因组特征。[结果] 形态观察、16S rRNA基因鉴定及系统发育分析证实,该分离菌株是化脓隐秘杆菌,命名为JX18;药敏试验表明,该菌株对克林霉素和林可霉素不敏感,对其余所选药物均敏感;动物实验结果显示,对小鼠腹腔攻毒后,小鼠腹部出现明显脓肿病灶,最高剂量组的小鼠全部死亡;全基因组测序结果表明,该菌株携带plo、nanH、nanP、fimA、fimC、fimE等重要毒力基因,并且与其他化脓隐秘杆菌菌株毒力基因的相似性较高;根据同源基因数据库（Cluster of Orthologous Groups,COG）预测,菌株JX18中参与碳水化合物代谢的基因占比最高;通过毒力基因数据库（virulence factor database,VFDB）、UniProtKB/Swiss-Prot等数据库预测,JX18菌株基因组中携带有多个组氨酸激酶、反应调节因子等与细菌双组分调控系统相关基因,以及多种与粘附、侵入及分泌系统相关的毒力基因。[结论] 在江西省分离鉴定出一株猪源强致病性化脓隐秘杆菌,丰富了猪源化脓隐秘杆菌病原信息,为进一步开展猪源化脓隐秘杆菌相关研究与防控奠定了理论依据。     

多株功能菌种混合培养条件的响应面优化及其生长关系

对3种具有土壤中多种重金属污染修复和病虫害防治功能的光合细菌（Photosynthetic bacteria,PSB,包括Rhodobacter sphaeroides H菌株、Rhodopseudomonas palustris N菌株和Rhodospirillium rubrum M菌株）、枯草芽胞杆菌（Bacillus subtilis, BS）和植物乳酸杆菌（Lactobacillus plantarum, LP）进行混合培养,利用单因素和响应面试验优化培养基配方以及培养条件。确定功能菌混合培养的最佳条件：以光合细菌培养基为基础培养基,外加碳源为10 g/L蔗糖、氮源为1.25 g/L硫酸铵、培养温度为31.5 ℃、初始pH值为7.1、接种量为接种后的初始培养活菌数1.90×10⁹cfu/mL、培养时间为28.0 h。通过功能菌的加性模型法、生长动力学以及混合培养的生长关系分析表明,光合细菌、枯草芽胞杆菌和植物乳酸杆菌的生长均存在互惠互利关系。     

2017-2019年某某医院ICU患者痰液病原菌分布及耐药性分析

摘要 目的：探究医院ICU患者痰液病原菌分布,并就其耐药性进行分析,以期为临床经验性选择抗生素治疗提供必要的细菌学依据。方法：选择2017年1月至2019年12月于北京中医医院顺义医院入住ICU的84例患者为研究对象,采集其痰液标本,并实施细菌学培养和药敏学试验。结果：（1）84例患者合计提取菌株91种,其中G^-杆菌45种,占比49.45 %,G⁺菌36种,占比39.56 %,真菌10种,占比10.99 %;（2）分析显示亚胺培南对G^-杆菌的敏感性较好,万古霉素对G⁺菌的敏感性较好,尚未发现耐万古霉素的肠球菌和葡萄球菌出现。结论：ICU患者痰液病原菌类型较多,其中以G^-杆菌为主,病原菌呈现多重耐药性,亚胺培南对G^-杆菌敏感性较好,万古霉素对G⁺菌敏感性较好。     

细菌超弱光的初步研究

用高敏单光子式超弱光测量仪,测量了大肠埃希氏菌(E．Coli),枯草芽孢杆菌(Bac. Subiilis)和产氨短杆菌(Brc.ammoniagenes)的超弱光光谱分布,超弱发光动力学过程和超弱光强度：并确定超弱光强度与细菌数之间的定量关系。     

甘草内生细菌的分离及拮抗菌株鉴定

从乌拉尔甘草健康植株的根茎叶中共分离到内生细菌98株,经初步鉴定芽孢杆菌属（Bacillus sp.）为优势种群,约占30%;从不同生长年份甘草的根、茎、叶组织中分离内生细菌种群密度从5.0×10⁴ cfu/g～2.9×10⁷ cfu/g鲜重不等。采用平板对峙方法筛选出6株对植物病原菌有明显体外拮抗活性的菌株,通过菌落、菌体形态观察、生理生化反应及16S rDNA序列分析,同时结合Biolog细菌自动鉴定系统验证,鉴定这6株拮抗菌分属萎缩芽孢杆菌(Bacillus atrophaeus)、多粘类芽孢杆菌(Paenibacillus polymyxa)、枯草芽孢杆菌(Bacillus subtilis)、Paenibacillus ehimensis。     

肠球菌属血流感染耐药性特征及短期预后的危险因素分析

摘要 目的：观察肠球菌属血流感染（EBSI）耐药性特征,并分析患者短期预后的危险因素。方法：收集我院2020年2月~2021年9月期间收治的130例EBSI患者的临床资料进行回顾性分析,观察EBSI耐药性特征,并分析患者短期预后的危险因素。结果：130例EBSI患者共分离出130株非重复性肠球菌属,分别为：粪肠球菌37株,屎肠球菌84株,鹑鸡肠球菌3株,鸟肠球菌6株。屎肠球菌对利奈唑胺、万古霉素、喹奴普汀/达福普汀、替考拉宁的耐药率较低。粪肠球对青霉素G、氨苄西林、万古霉素、替考拉宁、利奈唑胺呈较低的耐药率。单因素分析结果显示,EBSI短期预后与糖皮质激素治疗、植入导管或其他人工装置、急性生理学与慢性健康状况评分Ⅱ（APACHEⅡ）评分、血液透析情况、休克情况、选用敏感药物治疗情况有关（P<0.05）。多因素Logistic回归分析结果显示,有糖皮质激素治疗、未选用敏感药物治疗、有休克、植入导管或其他人工装置是EBSI短期预后的危险因素（P<0.05）。结论：EBSI患者肠球菌属分布以屎肠球菌、粪肠球菌为主,两种肠球菌属耐药率均较高,应严格控制用药。应着重注意有糖皮质激素治疗、未选用敏感药物治疗、有休克、有导管或其他人工装置的患者,以改善EBSI患者短期预后。     

Tolerance to challenges miming gastrointestinal transit by spores and vegetative cells of Bacillus clausii

AIMS: To study Bacillus clausii from a pharmaceutical product (Enterogermina O/C, N/R, SIN, T) and reference strains (B. clausii and Bacillus subtilis) for eco-physiological aspects regarding the gut environment. METHODS AND RESULTS: Spores and vegetative cells were challenged in vitro miming the injury of gastrointestinal transit: pH variations, exposure to conjugated and free bile salts, microaerophilic and anaerobic growth. No relevant differences were found studying the growth at pH 8 and 10, whereas at pH 7 the yields obtained for O/C and SIN were higher than those obtained for N/R and T strains. The spores were able to germinate and grow in the presence of conjugated bile salts (up to 1%, w/v) or free bile salts (0.2%) and also exhibited tolerance for the combined acid-bile challenge. As evidenced by lag-time, growth rate and cell yield the tolerance of Enterogermina isolates for conjugated salts was comparable with that of B. clausii type strain (DSM 8716(T)), and resulted higher than that observed for B. subtilis (ATCC 6051(T)). All the considered B. clausii strains demonstrated microaerophilic growth, but only some grew anaerobically in a nitrate medium. CONCLUSIONS: The ability of B. clausii spores to germinate after an acid challenge and grow as vegetative cells both in the presence of bile and under limited oxygen availability is consistent with the beneficial health effects evidenced for spore-forming probiotics in recent clinical studies. SIGNIFICANCE AND IMPACT OF THE STUDY: The experimental evidence from this study emphasizes some functional properties of B. clausii strains regarding their use as probiotics.     

思他宁联合美常安治疗重症急性胰腺炎的临床研究

目的 探讨思他宁联合美常安治疗重症急性胰腺炎(SAP)的疗效.方法 将2005年至2009年SAP患者35例设为A组,按照SAP常规处理原则予监护、止痛、禁食、胃肠减压、抑酸、抗生素、纠正水电解质酸碱平衡治疗及给予静脉持续滴注思他宁(250 μg/h),连用5～10 d;另将SAP患者45例设为B组,B组在A组治疗方案...     

牦牛源产细菌素屎肠球菌的分离鉴定和益生特性

【背景】抗生素的滥用导致牦牛肠道常见病原菌耐药性增加,益生菌作为对抗耐药性细菌的新型武器,应用前景广阔。【目的】获取益生特性优良的牦牛源益生菌。【方法】将20份牦牛粪便样本在含0.5%CaCO3的MRS培养基上分离纯化,以大肠杆菌和金黄色葡萄球菌为指示菌,用牛津杯法筛选有抑菌活性的菌株;排除酸和过氧化氢后,经耐酸耐热试验和蛋白酶敏感试验筛选产细菌素菌株,用形态学和16S rRNA基因序列分析鉴定;通过对大肠杆菌、沙门氏菌等腹泻病原菌体外抑菌试验、耐模拟胃肠液、测定自聚集能力和疏水性及抗生素敏感试验分析益生特性。【结果】从20份牦牛粪便样本中共分离出11株产生溶钙圈的菌株,其中6株对大肠杆菌和金黄色葡萄球菌抑菌效果显著,经复筛得到2株产细菌素的乳酸菌SC6和SC9,经鉴定均为屎肠球菌(Enterococcus faecium)。其中SC9对腹泻病原菌抑菌效果明显,有良好的耐受性和肠道黏附能力,对5种常用抗生素均敏感。【结论】屎肠球菌SC9有一定的抗逆性和潜在的益生能力,具备作为益生菌的潜力。     

胆总管结石患者胆汁病原菌分布特点及耐药性分析

目的:探讨胆总管结石患者胆汁病原菌的分布特点以及耐药性的分析。方法:选择2016年6月-2017年6月期间我院收治的胆总管结石合并胆道感染患者160例为研究对象,所有患者均进行逆行内镜胰胆管造影(ERCP)并抽取胆汁标本,进行细菌培养和耐药性实验,评价分析胆汁病原菌的分布特点及耐药性情况。结果:160例患者中有117例(73.13%)检出病原菌,共培养出病原菌130株,其中有13例患者为两种病原菌同时感染。革兰阴性菌有95株(73.08%)、革兰阳性菌有31株(23.85%)、真菌有4株(3.08%)。比例由高到低的前六位病原菌依次为:大肠埃希菌、肺炎克雷伯菌、阴沟肠杆菌、屎肠球菌、铜绿假单胞菌、粪肠球菌。革兰阴性菌对亚胺培南、阿米卡星、美罗培南、他唑巴坦、头孢吡肟等三四代头孢菌素耐药率较低,对头孢曲松、环丙沙星、左氧氟沙星、哌拉西林、氨苄西林等耐药率较高。革兰阳性菌对替拉考宁、万古霉素、利奈唑胺等耐药率较低,对四环素、环丙沙星、左氧氟沙星、克林霉素、氨苄西林等耐药率较高。真菌对酮康唑、伊曲康唑、氟康唑等耐药率较低,对两性霉素B耐药率较高。结论:胆总管结石患者胆汁病原菌主要为革兰阴性菌、其次为革兰阳性菌,各病原菌对各种抗菌药物表现出不同的耐药性,因此在临床治疗时应参考药敏试验结果进行合理选择治疗药物。     

斑节对虾(非洲群体)肠道中哈维氏弧菌拮抗菌的筛选、鉴定及生理特性分析

基于斑节对虾(非洲群体)(Penaeus monodon)肠道菌的生理生化特性, 为解决斑节对虾急性肝胰腺坏死综合征(AHPND)提供新思路, 文章分离纯化健康斑节对虾肠道中的优势菌株; 以致病性哈维氏弧菌为指示菌, 用牛津杯法从纯化菌株中筛选拮抗菌; 通过生理生化特征、Biolog系统鉴定及16S rDNA技术综合方法对菌株进行鉴定; 通过药敏实验, 评价拮抗菌株的安全性; 绘制高敏拮抗菌株的生长曲线, 得出其生长特性; 通过测定其产酶活性, 形成对其益生机制的初步推断。从斑节对虾肠道中共分离得到14株的优势土著菌, 分别标记为P.m-1、P.m-2······P.m-14, 经过拮抗实验得到了3株拮抗菌(P.m-1、P.m-9和P.m-13)。经鉴定P.m-1、P.m-9和P.m-13分别为枯草芽孢杆菌(Bacillus subtilis)、屎肠球菌(Enterococcus faecium)和溶藻弧菌(Vibrio alginolyticus)。药敏实验结果表明, 3株拮抗菌均不属于耐药菌, P.m-1对药物高度敏感。生长特征实验表明: P.m-1在2h进入对数期, 10h达到生长高峰, 菌体密度可达1.14×109 cfu/mL, 表现出了强劲的生命力。经过蛋白酶活性测定, P.m-1具有较强的产酶能力。优势菌P.m-1具有成为益生菌的潜力, 后续将作为功能性饲料添加剂或水质调节剂进行应用, 为AHPND进行生物防治提供新思路。     

Characterization of faecal enterococci from rabbits for the selection of probiotic strains

AIMS: To characterize the facultative anaerobic intestinal microbiota of healthy rabbits, especially enterococci, for the selection of potential probiotic strains. METHODS AND RESULTS: Phenotypic and molecular methods were used to identify enterococcal isolates. Results obtained indicated that enterococcal microbiota widely varied among individuals both in size and in composition. Antibacterial and haemolytic activities, and resistance to acid and bile salts were determined. A small group of strains produced bacteriocins active against listeriae and indigenous clostridia and therefore they were selected as potential probiotics. One such strain, 8G, was assayed for colonization capacity. Results obtained suggested that the fate of the introduced strain depended on the composition of the enterococcal indigenous microbiota. CONCLUSIONS: Enterococcus faecalis and Ent. faecium are the predominant enterococcal species in the gut of rabbits. Other species of lactic acid bacteria were not recovered. SIGNIFICANCE AND IMPACT OF THE STUDY: The enterococcal intestinal microbiota of healthy rabbits has been characterized in detail. Monitoring the fate of an introduced probiotic in vivo is required in order to evaluate potential probiotic strains.     

The isolation and characterization of the aerobic endospore-forming bacteria present in the liquid phase of an anaerobic fixed-bed digester,while treating a petrochemical effluent

Sixty-nine gram-positive endospore-forming rods were isolated from the liquid phase of an anaerobic digester, while treating a fatty acid-rich petrochemical effluent. These strains, including eight reference strains, were characterized and the similarities between the different strains were calculated using Sokal and Michener's simple matching coefficient. Phenotypic characteristics, determined by the API 20E and API 50CHB galleries, other biochemical tests, and morphological characteristics, were used for the numerical analysis. The strains were grouped into 12 (five major and seven minor) clusters. Nine of the clusters were positively identified asBacillus pumilus, B. subtilis, B. sphaericus, B. laterosporus, B. brevis, B. cereus, B. coagulans, B. megaterium, andB. circulans. Three clusters could not be identified using Gordon's classical system or the API identification system. Most of the aerobic endospore-forming rods (72%) utilized both acetic and propionic acid, and 17% utilized acetic acid as carbon source, but only under aerobic conditions. A small percentage of the strains studied (11%) was unable to utilize the fatty acids present in the petrochemical substrate, and no explanation could be given as to how they obtained their carbon source. Seventy-eight percent of the strains did not show growth in anaerobic agar. It was possible that sufficient oxygen, required for growth by these members of the genusBacillus, was introduced by the substrate. Since ample time had been allowed for population selection, their presence indicates that these aerobic strains can survive, grow, and compete in the digester environment but their relative importance and role in the primary digestion reactions is not clear.     

Characterization of bacterial pectinolytic strains involved in the water retting process

Pectinolytic microorganisms involved in the water retting process were characterized. Cultivable mesophilic anaerobic and aerobic bacteria were isolated from unretted and water-retted material. A total of 104 anaerobic and 23 aerobic pectinolytic strains were identified. Polygalacturonase activity was measured in the supernatant of cell cultures; 24 anaerobic and nine aerobic isolates showed an enzymatic activity higher than the reference strains Clostridium felsineum and Bacillus subtilis respectively. We performed the first genotypic characterization of the retting microflora by a 16S amplified ribosomal DNA restriction analysis (ARDRA). Anaerobic isolates were divided into five different groups, and the aerobic isolates were clustered into three groups. 84.6% of the anaerobic and 82.6% of the aerobic isolates consisted of two main haplotypes. Partial 16S rRNA gene sequences were determined for 12 strains, representative of each haplotype. All anaerobic strains were assigned to the Clostridium genus, whereas the aerobic isolates were assigned to either the Bacillus or the Paenibacillus genus. Anaerobic isolates with high polygalacturonase (PG) activity belong to two clearly distinct phylogenetic clusters related to C. acetobutylicum-C. felsineum and C. saccharobutylicum species. Aerobic isolates with high PG activity belong to two clearly distinct phylogenetic clusters related to B. subtilisT and B. pumilusT.     

Measurements of Fitness and Competition in Commensal Escherichia coli and E. coli O157:H7 Strains

Although the main reservoirs for pathogenic Escherichia coli O157:H7 are cattle and the cattle environment, factors that affect its tenure in the bovine host and its survival outside humans and cattle have not been well studied. It is also not understood what physiological properties, if any, distinguish these pathogens from commensal counterparts that live as normal members of the human and bovine gastrointestinal tracts. To address these questions, individual and competitive fitness experiments, indirect antagonism assays, and antibiotic resistance and carbon utilization analyses were conducted using a strain set consisting of 122 commensal and pathogenic strains. The individual fitness experiments, under four different environments (rich medium, aerobic and anaerobic; rumen medium, anaerobic; and a minimal medium, aerobic) revealed no differences in growth rates between commensal E. coli and E. coli O157:H7 strains. Indirect antagonism assays revealed that E. coli O157:H7 strains more frequently produced inhibitory substances than commensal strains did, under the conditions tested, although both groups displayed moderate sensitivity. Only minor differences were noted in the antibiotic resistance patterns of the two groups. In contrast, several differences between commensal and O157:H7 groups were observed based on their carbon utilization profiles. Of 95 carbon sources tested, 27 were oxidized by commensal E. coli strains but not by the E. coli O157:H7 strains. Despite the observed physiological and biochemical differences between these two groups of E. coli strains, however, the O157:H7 strains did not appear to possess traits that would confer advantages in the bovine or extraintestinal environment.