Evidence for naturally occurring recombination in the gene encoding the major outer membrane protein of lymphogranuloma venereum isolates of Chlamydia trachomatis.

The nucleotide sequence of the major outer membrane protein gene (omp1) was determined for three geographically distinct lymphogranuloma venereum isolates which were serologically untypeable. The three omp1 sequences were hybrids of serovars L1 and L2, containing a putative DNA recombination site in variable segment 2. Efforts to manipulate the chlamydial genome in vitro by recombination should be intensified.     

PCR detection and molecular identification of Chlamydiaceae species

Recent taxonomic developments, based on 16s and 23s rRNA gene sequences, have divided the family Chlamydiaceae into two genera and nine species, of which five have been found to infect humans. Few simple methods are available to detect and identify all species sensitively and specifically. In this study the suitability of the omp2 gene as a target for molecular identification of Chlamydiaceae is demonstrated. Phylogenetic analysis of partial omp2 gene sequences from all nine species agrees with the recently published taxonomic changes based on the ribosomal genes. The use of a family-specific PCR primer pair, which is able to amplify the 5' end of the omp2 gene from all Chlamydiaceae except some Chlamydophila pecorum strains, is described. Identification of all nine species was achieved using restriction fragment length polymorphism analysis with a single enzyme, AluI, confirmed by DNA sequencing. A PCR enzyme-linked oligonucleotide assay was developed which can detect a single chlamydial genome and may be applied to DNA extracts from any specimen or culture for the detection of single or mixed human chlamydial infection.     

Identification of the Chlamydia trachomatis RecA-encoding gene.

DNA sequencing of the major outer membrane protein (MOMP) gene (omp1) from Chlamydia trachomatis shows that some strains have a mosaic structure suggestive of homologous recombination between two distinct omp1 genes. On the basis of this conjecture, we attempted to clone by complementation and sequence the chlamydial recA homolog from C. trachomatis serovar L2. Chlamydial genomic DNA was partially restricted with XbaI, and fragments of 2 to 4 kb were ligated into pUC19. The recombinant plasmid was electroporated into Escherichia coli HB101 (RecA-), and colonies were selected in the presence of methyl methanesulfonate (MMS). A 2.1-kb fragment of C. trachomatis DNA in pUC19 conferred relative MMS resistance to E. coli HB101. When this recombinant plasmid (pX203) was electroporated into E. coli JC14604 (RecA- lacZ), lac+ recombinants were isolated. Rabbit polyclonal antibodies produced to purified E. coli RecA were immunoreactive in an immunoblot assay with a 35-kDa antigen in RecA- strains of E. coli transformed with pX203. The 2.1-kb insert was cycle sequenced by the dideoxy chain termination method. An open reading frame of 1,056 bp encoding 352 amino acids that had 44% sequence identity with E. coli RecA was identified. The finding of a recA homolog in C. trachomatis suggests that homologous recombination may occur in this organism. The cloned C. trachomatis RecA-encoding gene will be useful for the construction of a recA mutant once a gene transfer system is developed for chlamydiae.     

Vesicle-associated membrane protein 4, a positional candidate gene on 1q24-q25, is not associated with type 2 diabetes in the Old Order Amish

OBJECTIVE: The vesicle-associated membrane protein-4 (VAMP4) gene is an excellent type 2 diabetes (T2DM) positional candidate gene. It is located on chromosome 1q24-q25, a region of linkage to T2DM in the Amish and several other populations. VAMP4 is expressed in liver and skeletal muscle and participates in intracellular trafficking of secreted and membrane-associated proteins. DESIGN AND METHODS: We sequenced VAMP4 in 20 Amish subjects. Polymorphisms in and around VAMP4 were genotyped in 65 Amish subjects with T2DM, 64 subjects with impaired glucose homeostasis (IGH), and 126 normal glucose tolerant controls, as well as in an expanded set of 749 participants of the Amish Family Diabetes Study for whom glucose and insulin levels during an oral glucose tolerance test (OGTT) and other quantitative traits related to diabetes were available. Case-control and quantitative trait association analyses were performed. RESULTS: We found three common non-coding intragenic polymorphisms: a 23bp insertion/deletion (I/D) in the 5' untranslated region (UTR) in exon 1 at position 73127, and G35319T and C335296T single nucleotide polymorphisms (SNPs) in the 3' UTR (NCBI Accession No. Z98751). The two 3' UTR SNPs were in complete linkage disequilibrium (LD) and both were in strong LD with the exon 1 I/D polymorphism (|D'|=0.82). Similarly, three extragenic flanking SNPs (rs978985, rs203255, and rs1023479) showed moderate LD with the neighboring intragenic SNPs (|D'|=0.23-0.69). None of the SNPs individually nor any of the 2-, 3-, 4-, or 5-polymorphism haplotypes were associated with T2DM or IGH. The exon 1 I/D polymorphism was not associated with significant differences in mean fasting or stimulated glucose or insulin levels during an OGTT or other diabetes-related quantitative traits in the expanded set of 749 subjects. CONCLUSION: Variation in VAMP4 does not significantly influence risk of T2DM or IGH in the Amish.     

Serotyping and Genotyping of Genital Chlamydia trachomatis Isolates Reveal Variants of Serovars Ba, G, and J as Confirmed by omp1 Nucleotide Sequence Analysis

Urogenital isolates (n = 93) of Chlamydia trachomatis were differentiated into serovars and variants by serotyping with monoclonal antibodies and genotyping by restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified omp1 gene, respectively. The types of 87 of the 93 isolates (94%) were identical, as determined by both methods. Among these 87 isolates, 3 isolates were identified as the recently described new serovariant Ga/IOL-238 by omp1 nucleotide sequence analysis of the variable domains. Of the remaining six isolates, three isolates serotyped as both L2 and Ba but were identified as Ba/A-7 by genotyping by RFLP analysis of omp1. The omp1 nucleotide sequences of variable domains VD1, VD2, and VD4 of these urogenital Ba strains were identical to the sequences of the variable domains of Ba/J160, an ocular Ba type. The three remaining isolates were serotyped as J, but the patterns obtained by RFLP analysis of omp1, which were identical for the three isolates, differed from that of prototype serovar J/UW36. omp1 nucleotide sequence analysis revealed that these strains are genovariants of serovar J/UW36. Nucleotide sequence differences between serovar J/UW36 and this J genovariant, designated Jv, were found in both variable and constant domains. In conclusion, this study shows that the PCR-based genotyping of clinical C. trachomatis isolates by RFLP analysis of omp1 has a higher discriminatory power and is more convenient than serotyping. Variants of C. trachomatis serovars Ba, G, and J were identified and characterized.     

Direct detection and genotyping of Chlamydia trachomatis in cervical scrapes by using polymerase chain reaction and restriction fragment length polymorphism analysis.

Detection and genotyping of Chlamydia trachomatis were optimized by using a polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis performed directly with crude cells of cervical scrapes. Different PCR pretreatment methods were evaluated on samples which were positive for C. trachomatis by cell culture. In comparison with DNA extraction and different proteolytic digestion methods, a simple pretreatment of 10 min of boiling appeared to be optimal for PCR amplification. Crude samples (n = 209) were first screened for C. trachomatis by both cell culture and plasmid PCR. Subsequently, positive samples found by plasmid PCR were subjected to a direct omp1 PCR-based RFLP analysis to differentiate C. trachomatis serovars A to K, Ba, Da, and L1 to L3 and serovariant D-. All cervical scrapes that were found positive for C. trachomatis by cell culture (n = 30) were also positive by plasmid PCR and omp1 PCR and could be easily genotyped. In addition, of the culture-negative group, eight samples were found positive by plasmid PCR. Five of these eight samples were also positive by omp1 PCR; of these five, two were positive by a nested omp1 PCR. Genotyping by RFLP analysis of the 35 omp1 PCR-positive samples showed that serovars D, E, and F are the most prevalent types found in cervical scrapes, while serovariant D- was also detected. This study shows that direct PCR and PCR-based RFLP analysis are feasible for detection and genotyping of C. trachomatis in cervical scrapes and are more sensitive than culture-based serotyping.     

Evidence for numerous omp1 alleles of porcine Chlamydia trachomatis and novel chlamydial species obtained by PCR.

A nested PCR for genus-specific amplification of the Chlamydia omp1 locus was established. This PCR detected single template molecules in 200-microl specimen aliquots. Amplified chlamydial omp1 alleles were typed by heminested species PCRs and allele PCRs. We applied this method to 407 specimens from several host animals with various clinical conditions, and we detected prevalences of chlamydiae from 6 to 50%. Amplicons from peacock enteritis and equine infertility specimens were not typeable according to present omp1 allelic criteria for the chlamydial species. DNA sequencing revealed novel omp1 alleles which were 29.9 and 47.6% divergent in the deduced peptide sequences from the most closely related chlamydiae. Phylogenetic reconstruction indicated segregation of these alleles from the current four chlamydial species (90 and 97% bootstrap support), thus strongly suggesting the existence of additional chlamydial species. Allele typing of amplicons from swine with intestinal, urogenital, and respiratory infections demonstrated several unique omp1 allelic variants of Chlamydia trachomatis. These novel alleles had deduced peptide sequences which were 11.6 to 19% divergent from porcine C. trachomatis S45. Mutations were clustered in the C-terminal region of variable segment IV of the omp1 locus encoding subspecies and serovar determinants of the chlamydial major outer membrane protein, thus implying that there are numerous serovars of porcine C. trachomatis. These results demonstrate the need for routine application of sensitive genus-specific detection of chlamydiae in animal specimens and suggest a more prominent role than anticipated for chlamydiae in animal diseases.     

High-resolution genotyping of Chlamydia trachomatis from recurrent urogenital infections

A method for Chlamydia trachomatis restriction fragment length polymorphism (RFLP) analysis and complete sequencing of omp1 was developed for use on samples collected at home, and results were compared. Genotyping by sequencing was superior to RFLP analysis. The omp1 gene in 31 clinical strains harbored few mutations compared to the same gene in ATCC reference strains. Follow-up samples obtained during a 24-week period from 31 patients showed recurrence with the same genotype in five cases and a new genotype in one case.     

Characterization of a Brucella sp. strain as a marine-mammal type despite isolation from a patient with spinal osteomyelitis in New Zealand

Naturally acquired infection of humans with a marine mammal-associated Brucella sp. has only been reported once previously in a study describing infections of two patients from Peru. We report the isolation and characterization of a strain of Brucella from a New Zealand patient that appears most closely related to strains previously identified from marine mammals. The isolate was preliminarily identified as Brucella suis using conventional bacteriological tests in our laboratory. However, the results profile was not an exact match, and the isolate was forwarded to four international reference laboratories for further identification. The reference laboratories identified the isolate as either B. suis or B. melitensis by traditional bacteriological methods in three laboratories and by a molecular test in the fourth laboratory. Molecular characterization by PCR, PCR-restriction fragment length polymorphism, and DNA sequencing of the bp26 gene; IS711; the omp genes omp25, omp31, omp2a, and omp2b; IRS-PCR fragments I, III, and IV; and five housekeeping gene fragments was conducted to resolve the discrepant identification of the isolate. The isolate was identified to be closely related to a Brucella sp. originating from a United States bottlenose dolphin (Tursiops truncatus) and common seals (Phoca vitulina).     

Characterization of Chlamydia trachomatis omp1 gene among sexually transmitted disease patients in south China

Chlamydia trachomatisinfections are the leadingcause of bacterial sexually transmitted diseases(STD) [1] .Fifteen prototypic serovarslabelled Ato Kand L1,L2,and L3were initiallyrecognisedby polyclonal antibodies ,and additional immuno-variants (Ba ,Da ,Ia ,L2a ,etc) ,whichin somepublications are referred to as distinct serovars ,have been identified by monoclonal antibodies .Most serovars can cause urogenital infections andare associated with a spectrumof clinical diseases[2] ,including ur…     

Identification of the Brucella melitensis vaccine strain Rev.1 in animals and humans in Israel by PCR analysis of the PstI site polymorphism of its omp2 gene

Adverse effects of strain persistence and secretion in milk have been encountered with the Brucella melitensis vaccine strain Rev.1. Field isolates obtained from vaccinated animals and from a human resembled the vaccine strain Rev.1 by conventional bacteriological tests. The lack of a specific molecular marker that could specifically characterize the commercial vaccine strain prevented confirmation of the homology of the Rev.1-like field isolates to the vaccine strain. The composition of the omp2 locus from two gene copies with differences in their PstI restriction endonuclease sites was used to establish an epidemiologic fingerprint for the omp2 gene in the Rev.1 vaccine strain. Primers designed to amplify DNA sequences that overlap the PstI site revealed a single 282-bp DNA band common to all Brucella spp. Agarose gel electrophoresis of the PstI digests of the PCR products from strains 16M and the vaccine strain Rev.1 revealed a distinctive profile that included three bands: one band for the intact 282-bp fragment amplified from omp2a and two bands resulting from the digestion of the amplified omp2b gene fragment, 238- and 44-bp DNA fragments, respectively. Amplified fragments of 37 Rev.1-like isolates, including 2 human isolates, also exhibited this pattern. In contrast, DNA digests of all other Israeli field isolates, including atypical B. melitensis biotype 1 and representatives of the biotype 2 and 3 isolates, produced two bands of 238 and 44 bp, respectively, corresponding with the digestion of both omp2a and omp2b genes. This method facilitates identification of the Rev.1 vaccine strain in both animals and humans in Israel.     

Characterization of Chlamydia trachomatis omp1 Genotypes among Sexually Transmitted Disease Patients in Sweden

A method for detection and genotyping of genital Chlamydia trachomatis infections based on omp1 gene amplification and sequencing was developed. DNA was extracted from urogenital or urine samples using a Chelex-based method, and an approximately 1,100-bp-long fragment from the omp1 gene was directly amplified and sequenced. Genotyping was performed by BLAST similarity search, and phylogenetic tree analysis was used to illustrate the evolutionary relationships between clinical isolates and reference strains. The method was used to determine the genotypes of C. trachomatis in 237 positive urogenital and/or urine specimens collected at a Swedish sexually transmitted disease clinic during 1 year. The most common genotypes corresponded to serotypes E (47%) and F (17%). The omp1 gene was highly conserved for genotype E (106 of 112 samples without any mutation) and F (41 of 42 samples without any mutation) strains but appear slightly less conserved for genotypes G (n = 6) and H (n = 6), where the sequences displayed one to four nucleotide substitutions relative to the reference sequence. Genotyping of samples collected at the follow-up visit indicated that two patients had become reinfected, while three other patients suffered treatment failure or reinfection. One woman appeared to have a mixed infection with two different C. trachomatis strains. This omp1 genotyping method had a high reproducibility and could be used for epidemiological characterization of sexually transmitted Chlamydia infections.     

Transcription mapping of mouse adenovirus type 1 early region 3

Early region 3 (E3) of mouse adenovirus type 1 was analyzed using S1 nuclease protection and primer extension assays, cDNA sequencing, and genomic sequencing. We present the genomic sequence from 79 to 83 map units of the viral genome, the precise ends and splice sites of the E3 mRNAs, and the predicted protein sequence encoded by the mRNAs. Three major classes of early mRNAs were identified; all were approximately 1 kb long, consisted of three exons, and shared 5' and 3' ends. The three classes had alternative splicing at the junction between the second and third exon. The three proteins predicted by the three mRNAs were slightly similar to the E3 19K glycoprotein of human adenovirus type 3; the longest of the three was the most similar. Open reading frames corresponding to late proteins were also identified in the translated mouse adenovirus type 1 DNA sequence. In mouse adenovirus, as in the human adenoviruses, L4 overlaps E3, and L5 starts just downstream of the E3 region.     

环丙沙星耐药肠杆菌科细菌临床株qnr和aac(6')-Ⅰ b-cr基因的检测

目的 了解温州地区环丙沙星耐药肠杆菌科细菌临床株的qnr、aac(6')-Ⅰ b-cr基因的分布情况.方法 收集2005年8月-2008年4月间温州医学院附属第一医院环丙沙星耐药的肠杆菌科细菌共461株,其中大肠埃希菌370株,阴沟肠杆菌39株,克雷伯菌属细菌52株.应用PCR方法 检测qnr和aac(6')-Ⅰ b幕因,DNA测序检测qnrA、qnrB、qnrS和aac(6')-Ⅰ b-cr基因;接合传递试验方法 探讨细菌质粒介导的耐药性传递情况.结果 461株环丙沙星耐药的肠杆菌科细菌临床株中检出含qnr基因阳性菌株15株(3.25%),包括qnrA基因阳性株5株(4株阴沟肠杆菌和1株解鸟氨酸克雷伯菌)、qnrB基因阳性株4株(2株肺炎克雷伯菌和2株大肠埃希菌)、qnrS基因阳性株6株(2株肺炎克雷伯菌和4株大肠埃希菌);检出52株细菌(包括42株大肠埃希菌、4株阴沟肠杆菌和6株克雷伯菌属细菌)携带aac(6')-Ⅰ b-cr.15株qnr基因阳性的菌株同时携带aac(6')-Ⅰ b-cr,药敏结果 显示对业胺培南敏感但对多种抗生素耐药.15株qnr基因阳性的菌株中7株质粒接合传递试验成功,临床株对喹诺酮类和氨基糖苷类的耐药性部分传递给了受体株.结论 qnr基因在温州地区环丙沙星耐药的肠杆菌科细菌临床株中较少见,而aac(6')-Ⅰ b-cr基因存在较普遍.     

Identification of clinically relevant viridans group streptococci by sequence analysis of the 16S-23S ribosomal DNA spacer region

The feasibility of sequence analysis of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (ITS) for the identification of clinically relevant viridans group streptococci (VS) was evaluated. The ITS regions of 29 reference strains (11 species) of VS were amplified by PCR and sequenced. These 11 species were Streptococcus anginosus, S. constellatus, S. gordonii, S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguinis, S. salivarius, S. sanguinis, and S. uberis. The ITS lengths (246 to 391 bp) and sequences were highly conserved among strains within a species. The intraspecies similarity scores for the ITS sequences ranged from 0.98 to 1.0, except for the score for S. gordonii strains. The interspecies similarity scores for the ITS sequences varied from 0.31 to 0.93. Phylogenetic analysis of the ITS regions revealed that evolution of the regions of some species of VS is not parallel to that of the 16S rRNA genes. One hundred six clinical isolates of VS were identified by the Rapid ID 32 STREP system (bioMérieux Vitek, Marcy l'Etoile, France) and by ITS sequencing, and the level of disagreement between the two methods was 18% (19 isolates). Most isolates producing discrepant results could be unambiguously assigned to a specific species by their ITS sequences. The accuracy of using ITS sequencing for identification of VS was verified by 16S rDNA sequencing for all strains except strains of S. oralis and S. mitis, which were difficult to differentiate by their 16S rDNA sequences. In conclusion, identification of species of VS by ITS sequencing is reliable and could be used as an alternative accurate method for identification of VS.     

Antigenic and molecular analyses of different Chlamydia pneumoniae strains.

Chlamydia pneumoniae is an important human respiratory pathogen. Classification of C. pneumoniae isolates into distinguishable serovars or genotypes has not yet been reported. To determine whether antigenic or molecular variants among C. pneumoniae isolates exist, six strains were studied via immunoblot analysis and DNA sequence determination of the entire major outer membrane protein (MOMP) gene omp1. The strains included four prototype strains and two clinical isolates from our laboratory. Immunoblot analysis of sera from patients infected with C. pneumoniae revealed antigenic differences between the C. pneumoniae strains. Strong reactivity of one serum sample with a 65-kDa protein in two C. pneumoniae strains which was not observed with the other strains was the most prominent finding. All sera reacted with the 40-kDa MOMP. Comparison of the omp1 DNA sequences revealed that the omp1 genes of all strains were identical and were 100% identical to the sequence of the omp1 gene of C. pneumoniae AR-39. The results of this study demonstrate that unlike C. trachomatis, the omp1 gene is conserved in C. pneumoniae. Furthermore, it was shown that C. pneumoniae strains are antigenically different. This finding indicates that more than one serovar of C. pneumoniae exist.     

On the nomenclature and classification of chlamydiae

Results of molecular genetic research on typical specimens of the genus Chlamydophila, the family Chlamydiaceae, which were provided by the Federal Center of Toxicological and Radiation Safety of Animals from its collection of microorganisms, are presented in this paper as to their taxonomic attribution on the basis of a comparative analysis of the omp1, omp2, 16S rRNA and 23S rRNA genes with the corresponding genomic fragments of officially registered species of chlamydiae and the presence of an extrachromosomal plasmid. According to the results of the omp1-restriction-fragment-length-polymorphism (RFLP)-AluI-profile analysis, the strains Rostinovo-70, 250, PP-87 and KC-93 are distinguished by the characteristic of a novel chlamydial genotype, earlier unstudied, G, by our designation. In the course of comparative omp2-gene analysis in the strains Rostinovo-70, 250, PP-87, and KC-93, a new, previously undescribed, omp2-RFLP-AluI profile of chlamydiae was described. According to the chlamydial species identification by genetic and ecological criteria, the Rostinovo-70, 250, PP-87, and KC-93 strains can be classified as a new species of Chlamydiaceae—Chlamydophila parapsittaci sp. nov. It is also suggested to combine into a new species the following Chlamydophila psittaci strains: WC, NJ1, 92-1293, TT3, 7344/2, GD, CT1, Par1, 84/2334, R54, VS225, 777B15, and Prk/Daruma.     

hNaDC1基因5''''侧翼区转录调控序列系列载体构建与鉴定

目的构建hNaDC1基因5’侧翼区转录调控序列系列萤火虫荧光素酶报告基因表达载体。方法PCR扩增获得hNaDC1基因5’侧翼转录调控区不同长度片段:hNaDC1A(-2232/ 136,2368bp)、hNaDC1B(-1640/ 136,1776bp)、hNaDC1C(-1084/ 136,1221bp)、hNaDC1D(-253/ 136,389bp)、hNaDC1E(-2232/-12,2244bp),以pGL3-Basic为载体构建hNaDC1基因5’侧翼序列系列缺失质粒。重组体通过特异限制性内切酶酶切鉴定,并送样测序鉴定。结果成功构建hNaDC1基因5’侧翼区转录调控元件萤火虫荧光素酶报告基因表达载体5个:pGL3-hNaDC1A～E。结论为进一步研究NaDC1基因5’侧翼区转录调控元件的分布特点及转录调控元件与转录因子间的相互作用提供了基本实验条件。