Comparison between two PCR-based bacterial identification methods through artificial neural network data analysis

The 16S ribosomal ribonucleic acid (rRNA) and 16S-23S rRNA spacer region genes are commonly used as taxonomic and phylogenetic tools. In this study, two pairs of fluorescent-labeled primers for 16S rRNA genes and one pair of primers for 16S-23S rRNA spacer region genes were selected to amplify target sequences of 317 isolates from positive blood cultures. The polymerase chain reaction (PCR) products of both were then subjected to restriction fragment length polymorphism (RFLP) analysis by capillary electrophoresis after incomplete digestion by Hae III. For products of 16S rRNA genes, single-strand conformation polymorphism (SSCP) analysis was also performed directly. When the data were processed by artificial neural network (ANN), the accuracy of prediction based on 16S-23S rRNA spacer region gene RFLP data was much higher than that of prediction based on 16S rRNA gene SSCP analysis data (98.0% vs. 79.6%). This study proved that the utilization of ANN as a pattern recognition method was a valuable strategy to simplify bacterial identification when relatively complex data were encountered.     

细菌rDNA分类鉴定的方法学研究

目的 研究细菌rDNA快速鉴定方法.方法 以细菌16S rDNA、16S-23S rDNA基因间隔区（ISR）和常见细菌耐药基因为对象,通过改进标本中细菌DNA提取方法,指纹分析、直接测序与多重聚合酶链反应（PCR）技术,建立快速细菌分子鉴定方法.结果 细菌属种不同表现出独特的16S-23S rDNA ISR指纹,在分析软件指导下进行初步细菌鉴定和亲缘关系研究;16S rDNA和16S-23SrDNA ISR序列可确定细菌种与型;序列分析与生化鉴定一致.多重PCR可解决葡萄球菌16S rDNA与mecA基因、产超广谱β内酰胺酶菌16S rDNA与TEM和SHV基因同步检测.结论 细菌rDNA分类方法,提高了非培养细菌的鉴定能力.     

54株分枝杆菌国际标准株16S-23S rRNA转录间隔区序列分析

目的分析54株分枝杆菌国际标准株16S-23SrRNA转录间隔区(ITS)序列,为临床分离株的鉴定提供参考。方法用16S-23SrRNA ITS序列分析法对54株分枝杆菌国际标准株进行分析,构建系统发育树,计算相似性百分比。结果除灰尘与微黄分枝杆菌;田野与千田分枝杆菌;抗热与副偶然分枝杆菌,奥布与母牛结核分枝杆菌;杜氏与猪分枝杆菌;金色与东海分枝杆菌,海与溃疡分枝杆菌、科莫斯分枝杆菌;2株结核分枝杆菌与田鼠分枝杆菌、非洲分枝杆菌的16S-23SrRNA ITS序列完全相同无法鉴别外,其他各分枝杆菌菌种间16S-23SrRNAITS序列均不相同,可以得到很好的鉴别。结论 16S-23SrRNA ITS序列分析是一种很好的鉴定分枝杆菌的方法,国际标准株16S-23SrRNA ITS序列的研究弥补了基因数据库的不足。     

Identification of Flavobacterium columnare by a species-specific polymerase chain reaction and renaming of ATCC43622 strain to Flavobacterium johnsoniae

Species-specific polymerase chain reaction (PCR) primers have been designed to identify the causative agent of columnaris disease, Flavobacterium columnare. The 16S rRNA gene sequences of F. columnare (eight sequences representing the different genotypes of the species) and related species (18 sequences) were aligned and compared to choose specific regions that are unique to F. columnare and do not have significant intraspecies variability. The species-specific regions in the 16S rRNA gene were used to design a pair of species-specific PCR primers, ColF and ColR. The PCR technique produced a specific amplicon of about 675 base pairs (bp) in 27 isolates of F. columnare and there was no amplification in the closely related species. The specificity of the amplified product was confirmed by digesting with HhaI. The PCR primers did not produce a 675 bp product with F. columnare ATCC43622 strain. This ATCC43622 strain was characterized by biochemical and ribotyping methods and renamed Flavobacterium johnsoniae. The American Type Culture Collection has confirmed these findings and made the change.     

54株分枝杆菌国际参考株16S rRNA序列分析

目的分析54株分枝杆菌国际参考株16S rRNA序列,为临床分离株的鉴定提供参考。方法用16S rRNA序列分析法对54株分枝杆菌国际参考株进行分析,构建系统发育树,计算相似性百分比。结果除11株（共9种4组）分枝杆菌,即产鼻疽分枝杆菌与塞内加尔分枝杆菌;溃疡分枝杆菌与海分枝杆菌;堪萨斯与胃分枝杆菌;3株结核分枝杆菌与田鼠分枝杆菌、非洲分枝杆菌16S rRNA基因序列完全相同无法相互鉴别,其它41株（共41种）分枝杆菌菌种间16S rRNA均不相同可以得到很好的鉴别。结论 16S rRNA基因序列分析是一种很好的鉴定分枝杆菌的方法,国际参考株16S rRNA基因序列的研究弥补了基因数据库的不足。     

多重耐药不动杆菌16S rRNA甲基化酶和同源性研究

目的 调查2007年7月-2008年5月山西医科大学第二附属医院临床分离的61株多重耐药不动杆菌中介导氨基糖苷类抗生素高水平耐药的16S rRNA甲基化酶基因和Ⅰ类整合子携带耐药基因的分布.方法 利用blaOXA-51基因及16S rRNA-23S rRNA序列进行菌株鉴定,琼脂稀释法测定12种抗菌药物对61株不动杆菌的MIC,PCR筛选6种16S rRNA甲基化酶基因以及整合子基因盒,脉冲场凝胶电泳(PFGE)分析菌株同源性.结果 61株临床分离不动杆菌中55株为鲍曼不动杆菌、3株为3TU不动杆菌、l株13TU不动杆菌、1株醋酸钙不动杆菌、l株溶血不动杆菌.48株不动杆菌对阿米卡星、庆大霉素、妥布霉素均耐药,其中有47株检出armA基因;未检出rmtA、rmtB、rmtC、mad和npmA基因.armA基因阳性的菌株中Ⅰ类整合子阳性27株,分别携带arr-3、accA4、aacCl、catB8、aadA1和dfrA12基因.PFGE条带分析发现47株armA阳性菌株分为5个克隆,其中A、B为主要克隆,分布在我院多个科室中.结论 16S rRNA甲基化酶基因armA在多重耐药不动杆菌中广泛存在,armA基因不位于Ⅰ类整合子中,不动杆菌Ⅰ类整合子携带耐药基因主要介导对氨基糖苷类及氯霉素的耐药性.PFGE结果显示armA基因阳性菌株在我院呈克隆播散,必须采取有效的措施来控制耐药菌的传播.     

16SrRNA、16S-23SrRNA基因测序分析检测主要血流感染病原菌比较

目的比较细菌16SrRNA、16S-23SrRNA基因测序分析在血流感染病原菌检测中的作用。方法提取临床上血流感染常见的金黄色葡萄菌、表皮葡萄球菌、大肠埃希菌、粪肠球菌、肺炎链球菌、铜绿假单胞菌、阴沟肠杆菌、鲍曼不动杆菌、洛菲不动杆菌、肺炎克雷伯杆菌、化脓性链球菌、奇异变形杆菌、潘尼变形杆菌、屎肠球菌、粘质沙雷菌、宋内志贺菌、产气肠杆菌、小肠结肠炎耶尔森菌、腐生葡萄球菌基因组DNA,运用16SrRNA、16S-23SrRNA基因进行PCR扩增。扩增产物经测序后在美国国家生物技术中心（NCBI）上进行比对分析,确定菌种。结果在所分析的19种临床血流感染常见细菌中,16SrRNA基因测序分析可将除粘质沙雷菌外的细菌鉴定到种的水平,但无法完全区分近缘种属;16S-23SrRNA成功鉴定17种细菌,除大肠埃希菌、宋内志贺菌外所有细菌均成功鉴定到单一种的水平。结论16S-23SrRNA基因可作为血流感染细菌检测较好的分子靶标。     

嗜麦芽寡氧单胞菌临床株与环境株的16S rRNA基因序列及系统发育分析

目的:比较嗜麦芽寡氧单胞菌临床株与环境株16S rRNA基因序列,构建系统发育树,分析其进化关系.方法:对选取的3株嗜麦芽寡养单胞菌临床株和1株环境株的16S rRNA基因进行PCR扩增并测序.将上述及从GenBank中挑选出的其他32株不同来源的嗜麦芽寡养单胞菌的16S rRNA基因序列进行对比分析.并绘制系统发育树.结果:系统发育分析表明大部分菌株可根据来源分为3个簇,序列分析显示某些高度可变区可能存在可区分临床株与环境株的关键序列.结论:嗜麦芽寡养单胞菌基因型及表现型具有多样性:大部分嗜麦芽寡氧单胞菌临床株与环境株可根据16S rRNA基因序列进行鉴别.     

小儿常见感染菌16S—23S rRNA基因区间的分子生物学研究

目的：探讨聚合酶链反应（PCR）加限制性内切酶片段长度多态性（RFLP）分析在细菌rDNA区间检测中的应用。方法：以16S－23S RNA基因区间为靶序列,设计引物,选择合适的内切酶,采用PCR法加RFLP法检测标准菌株及临床菌株的rDNA区间。结果：26株不同的标准菌株经PCR扩增后,分别出现一条带,两条带,三条带及多条带的不同DNA图谱,敏感性试验可检出2．5CFU的细菌,与人类基因组DNA,真菌及病毒无交叉反应,其中14种菌经一步PCR扩增即可区分,另12种菌除肺炎克雷伯氏菌与坚韧肠球菌经Hinf I或Alu I酶切后仍不能区分外,其余经其中一内切酶酶切后均能区分,32例血培养阳性标本均扩增出与相应标准菌株相一致的图谱。结论：16S－22S rRNA区间基因PCR．扩增加RFLP技术检测细菌rDNA区间,具有特异,敏感,快速,准确的特点,为细菌感染的病原诊断提供新的科学依据。     

大肠埃希菌16S rRNA甲基化酶基因的接合传递及其与整合子的相关性

目的 对临床分离的多重耐药（MDR）大肠埃希菌株的16S rRNA甲基化酶基因特征与接合传递效率进行研究,探讨其与整合子的相关性。 方法 136株MDR大肠埃希菌经PCR筛检16S rRNA甲基化酶基因armA、rmtA、rmtB、rmtC、rmtD;对阳性菌株作整合酶基因intI1、intI2和intI3检测,并扩增Ⅰ类整合子可变区插入片段,对扩增产物进行测序与鉴定所含耐药基因盒;以阳性菌株为供体菌,耐叠氮化钠大肠埃希菌J53为受体菌进行接合试验,并结合质粒图谱对16S rRNA甲基化酶基因进行初步定位。 结果 在136株多重耐药大肠埃希菌中,共检出16S rRNA甲基化酶阳性菌12株（8.8%）,其中,armA阳性3株（2.2%）,rmtB阳性10株（7.4%）,未检出rmtA、rmtC、rmtD基因。阳性菌株均只含Ⅰ类整合子,对其可变区扩增片段（1 000～2 300 bp）的测序结果显示,该区域含有多种耐药基因盒,但不含16S rRNA甲基化酶基因。接合试验与质粒图谱结果初步表明armA和rmtB编码基因位于约23 000 bp的质粒上,接合试验的耐药质粒传递率高达83.3%(10/12)。 结论 在MDR大肠埃希菌中,armA和rmtB编码基因位于约23 000 bp质粒上,其中,rmtB为优势基因,接合试验和质粒图谱证明该类耐药质粒很容易在同种菌间传播。Ⅰ类整合子与16S rRNA甲基化酶基因虽然存在于同一菌体内和/或同处于一个质粒上,但整合子基因盒对该类基因的捕获率很低或根本不捕获。     

Subtyping of uncultured bartonellae using sequence comparison of 16 S/23 S rRNA intergenic spacer regions amplified directly from infected blood

This study aimed to assess the usefulness of a PCR-based approach to the detection and differentiation of Bartonella strains in infected blood. The conservation of potential genus-specific PCR primer hybridisation sites within the 16 S/23 S rRNA gene intragenic spacer regions of Bartonella species was confirmed following sequence analysis of the intragenic spacer regions of four previously untested species. The extent of intra-species variation within the specific amplicons was assessed by comparison of sequences obtained from 17 strains of four Bartonella species. Eight sequence variants were obtained. Each species for which multiple strains were tested possessed at least two intragenic spacer regions variants, but the differences between these strains were markedly less than those observed inter-species. Sequence analysis was performed on 60 amplicons obtained from blood pellets collected from woodland rodent communities in which bartonella infections were known to be highly prevalent. Twelve variants were encountered, only five of which had been found among the studied isolates. Partial intragenic spacer region amplification followed by product sequence analysis offers a potentially sensitive and totally transferable means of inter- and intra-species differentiation of Bartonella strains, and its use in this study has broadened our knowledge of the genotypic spectrum of bartonellae associated with natural infections among UK woodland rodents.     

基于16S rRNA和gyrB基因的施万菌种水平鉴定分析

  目的   构建基于16S rRNA和gyrB基因对施万菌(Shewanella)进行种水平鉴定的方法,比较2个基因的鉴定能力差异。   方法   利用DnaSP 6.0软件对施万菌16S rRNA 和gyrB 基因的信息位点数及其百分比、核苷酸多态性值、平均G＋C含量、非同义突变率与同义突变率的比值（Ka/Ks）、Tajima检验进行基因多态性分析。 用MEGA 6.06软件的邻接距离矩阵法对90株测试菌株和54株模式菌株构建16S rRNA 和gyrB 基因的进化树。 用MEGA 6.06软件的Kimura’s 2-parameter模型,确定90株测试菌株的菌种后,计算16S rRNA 和gyrB 基因的遗传距离和序列相似性。 比较两者对施万菌种水平鉴定能力差异。   结果   16S rRNA和gyrB基因序列相似性平均值分别为95.0%、80.8%。 在16S rRNA基因进化树中,S. marinintestina和S. sairae、S. livingstonensis和S. vesiculosa的进化分支几乎完全相同,gyrB基因则能在种水平将所有菌株区分开。 16S rRNA基因的种内和种间相似性范围小。   结论   与16S rRNA基因相比,gyrB基因能够更准确的用于施万菌的种水平鉴定。     

DNA probes for Bordetella species and a colorimetric reverse hybridization assay for the detection of Bordetella pertussis.

Three oligonucleotide probe sequences were inferred from the 16S ribosomal ribonucleic acid (rRNA) and the 16S-23S rRNA spacer sequences of Bordetella pertussis ATCC 10380. These probes were used in hybridization tests with deoxyribonucleic acid from Bordetella species and other relevant bacterial taxa. A probe from the spacer region hybridized exclusively to the B. pertussis strains tested and not to strains from other species. Using a combination of three probes, B. pertussis, B. parapertussis/B. bronchiseptica and B. avium could be specifically identified and differentiated from other taxa. Differentiation between B. parapertussis and B. bronchiseptica was not possible with the probes used. Using the spacer probe, a colorimetric hybridization assay specific for B. pertussis was developed based on enzymatic amplification of the 16S-23S rRNA spacer and reverse hybridization in microtitre wells. As compared with results using agarose gel electrophoresis, and Southern and dot-spot hybridization with a 32P-labelled probe, this assay proved to be faster and easier to perform and was found to be at least as sensitive and specific.     

鲍曼不动杆菌临床分离株分子生物学鉴定分析

目的了解目前鲍曼不动杆菌临床鉴定分析的准确性及可能存在的问题。方法本研究随机抽取100株临床鉴定为鲍曼不动杆菌的临床分离鉴定株开展了扩增核糖体DNA限制酶切分析,16S rRNA编码基因及16S~23S rRNA间区测序鉴定分析。结果鉴定出5个不动杆菌种,分别为鲍曼不动杆菌(77%),菌种3(9%),菌种10(6%),菌种13TU(3%),琼氏不动杆菌(2%),还有3%为非不动杆菌。结论目前临床实验室对鲍曼不动杆菌的鉴定准确性较低,可能影响对不动杆菌不同种的流行病学特征和临床状况的认知,临床不动杆菌的鉴定能力有待加强。     

Emergence of ArmA and RmtB aminoglycoside resistance 16S rRNA methylases in Belgium

OBJECTIVES: 16S rRNA methylase-mediated high-level resistance to aminoglycosides has been reported recently in clinical isolates of Gram-negative bacilli only from a limited number of countries. This study was conducted to investigate the occurrence of this type of resistance in clinical isolates of Enterobacteriaceae from two Belgian hospitals and the characteristics of the strains. METHODS: We screened for high-level gentamicin, tobramycin and amikacin resistance in clinical isolates of Enterobacteriaceae consecutively collected between 2000 and 2005 at two laboratories by PCR for the armA, rmtA and rmtB 16S rRNA methylase genes. The beta-lactamase presence in the strains was also determined by phenotypic and genotypic methods. RESULTS: Overall armA genes were detected in 18 Klebsiella pneumoniae, Escherichia coli, Enterobacter aerogenes, Enterobacter cloacae and Citrobacter amalonaticus whereas rmtB was detected in a single E. coli isolate. The rmtA gene was not found. All 16S rRNA methylase-bearing strains produced extended-spectrum beta-lactamases (ESBLs), predominantly type CTX-M-3, as well as various types of beta-lactamases. In the majority of the strains, the armA gene was carried by conjugative plasmids of the IncL/M incompatibility group whereas rmtB was borne by an IncFI plasmid. CONCLUSIONS: This is the first report of the emergence of 16S rRNA methylases in Enterobacteriaceae in Belgium. The rapid spread of multidrug-resistant isolates producing both ESBLs and 16S rRNA methylases raises clinical concern and may become a major therapeutic threat in the future.     

Sequestering from host and characterization of sequence of a ribosomal RNA operon (rrn) from "Candidatus Liberibacter asiaticus"

A 5005bp rrn DNA sequence of "Candidatus Liberibacter asiaticus" was obtained by PCR using primers conserved to Rhizobiaceae of alpha-proteobacteria. The rrn locus consisted of a 16S rRNA gene (rrs), an intergenic transcribed spacer (ITS) containing two genes of tRNA(Ile) and tRNA(Ala), a 23S rRNA gene (rrl), an ITS without tRNA gene and a 5S rRNA gene (rrf). Like rrs, rrl and rrf were also related (89-90%) to those of the members of Rhizobiaceae. Interestingly, the genes of tRNA(Ile) and tRNA(Ala) were more related to those of non-Rhizobiaceae alpha-proteobacteria. The non-tRNA gene regions of the 16S-23S ITS and 23S-5S rRNA ITS did not share significant similarity to any known non-Liberibacter DNA sequences, and could be used for specific and efficient detection of "Ca. L. asiaticus".     

Characterization and molecular differentiation of 16SrI-E and 16SrIX-E phytoplasmas associated with blueberry stunt disease in New Jersey

A nested PCR assay was employed to detect the presence of phytoplasmas in 127 blueberry plants exhibiting typical or a portion of blueberry stunt (BBS) syndrome collected in 2010 and 2011, from 11 commercial farms predominantly located in two counties in New Jersey, USA. Ninety plants exhibiting typical stunt syndrome tested positive for phytoplasma infection. Restriction fragment length polymorphism (RFLP) analysis indicated that two distinct phytoplasmas were associated with BBS-diseased plants. About 95% of phytoplasmas detected were very closely related to BBS phytoplasma strains BBS3-AR (subgroup 16SrI-E) and BBS1-MI (unidentified) identified previously, and 4.4% of phytoplasmas detected belonged to the pigeon pea witches'-broom phytoplasma group (16SrIX). Sequence and phylogenetic analysis of cloned 16S rDNA further indicated the subgroup 16SrI-E related phytoplasmas represented a variant of 16SrI-E reference strain BBS3-AR, while the 16SrIX related phytoplasmas were closely related to juniper witches'-broom (JunWB) phytoplasma (16SrIX-E), representing a 16SrIX-E variant. Ribosomal protein (rp) and secY gene-based phylogenies revealed that BBS3-AR and BBS-NJ 16SrI-E strains belonged to a closely related lineage, while BBS-NJ 16SrIX-E strains and JunWB strains represented two distinct lineages. Single nucleotide polymorphisms (SNPs) analyses of rp and secY gene sequences further revealed that no specific rp gene SNPs and only two specific secY gene SNPS were present between BBS-NJ 16SrI-E strains and BBS3-AR. In contrast, BBS-NJ 16SrIX-E strains/clones had 15 consensus rp SNPs and 28 consensus secY SNPs that separated them from JunWB strains/clones. For the first time, two distinct phytoplasmas that cause BBS-disease in the U.S. was revealed.     

Investigation of an anaerobic microbial community associated with a corneal ulcer by denaturing gradient gel electrophoresis and 16S rDNA sequence analysis

The bacterial community manifested in a corneal ulcer was investigated with culture-independent techniques. DNA was extracted from the eye swab, 200-bp fragments spanning the hypervariable V3 region of the 16S rRNA gene (16S rDNA) were amplified by broad-range PCR and genetic fingerprinting of the total bacterial community was performed by denaturing gradient gel electrophoresis (DGGE). Additionally, 16S rDNA clone libraries containing 1500-bp fragments were constructed, clones were screened by DGGE and sequenced. Microorganisms were phylogenetically most closely related to the Cytophaga/Flavobacterium/Bacteroides phylum (eight clones), Fusobacteria (four clones), spirochetes (three clones) and to the low G+C Gram-positive bacteria (two clones). Low sequence similarity values less than 93% to sequences of known bacteria indicated that some bacteria belonged to hitherto unknown genera. Bacteria which were detected in the healthy eye of the same patient, were phylogenetically related to the low G+C and high G+C Gram-positive bacteria (two clones) and to the Proteobacteria (one clone). To our knowledge, this is the first time that such a complex and anaerobic bacterial community normally found in subgingival crevices is reported to play a role in corneal ulceration. Previous treatment of the ulcer with several topical antibiotics had shown no effect for six months. The followed culture-independent identification of spirochetes and Gram-negative, anaerobic bacilli facilitated the appropriate treatment with topical penicillin G, which stopped further destruction of the eye. Results demonstrated that 16S rDNA genotyping in combination with DGGE fingerprinting are appropriate molecular methods for the investigation of severe bacterial infections which might not be detected by conventional cultivation.     

High-resolution melt analysis for species identification of coagulase-negative staphylococci derived from bovine milk

Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens isolated from bovine milk. In this study, we report a rapid assay for species identification of CNS using high-resolution melt analysis (HRMA) of 16S rDNA sequences. Real-time polymerase chain reaction amplification of 16S rRNA gene fragment, spanning the variable region V1 and V2, was performed with a resulting amplicon of 215 bp. A library of distinct melt curves of reference strains of 13 common CNS species was created using HRMA. Sequencing of 16S rRNA and rpoB genes, and, when needed, tuf gene, of 100 CNS isolates obtained from Canadian Bovine Mastitis Research Network was done to determine their species identity, allowing for subsequent evaluation of the performance of HRMA for field isolates of bovine CNS. A combination of HRMA and sequencing revealed that Staphylococcus chromogenes, S. xylosus, S. simulans, and S. sciuri had multiple genotypes, complicating their resolution by HRMA. As the 3 genotypes of S. chromogenes had distinct melt curves, the 3 distinct genotypes were employed as reference strains in a blinded trial of 156 CNS isolates to identify S. chromogenes. HRMA correctly identified all S. chromogenes isolates which were later confirmed by sequencing. Staphylococcus chromogenes (68%) was most frequently found among the CNS isolates, followed by S. haemolyticus (10%) and S. xylosus (6%). The present study revealed that HRMA of 16S rRNA gene (V1–V2) could be used as a rapid, efficient, low-cost, and minimally cumbersome technique for S. chromogenes identification, the most common CNS derived from bovine milk.