Universal ribotyping method using a chemically labelled oligonucleotide probe mixture

Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes

About 63 species of Dendrobium are identified in China, making the identification of the origin of a particular Dendrobium species on the consumer market very difficult. We report evaluation of multiple species-specific probes screened from genomic DNA for closely related Dendrobium species identification, based on DNA array hybridization. Fourteen species-specific probes were screened from five closely related Dendrobium species, D. aurantiacum Kerr, D. officinale Kimura et Migo, D. nobile Lindl., D. chrysotoxum Lindl. and D. fimbriatum Hook., based on the SSH-Array technology we developed. Various commercial Dendrobium samples and unrelated samples were definitely identified. The specificity and accuracy of the multiple species-specific probes for species identification was assessed by identifying various commercial Dendrobium samples (Herba Dendrobii). Hybridization patterns of these multiple probes on digested genomic DNAs of Dendrobium species indicated that there are distinct polymorphic sequence fragment in the higher eukaryotes. This is the first report on detection and utilization of multiple species-specific probes of Dendrobium in whole genomic DNA, and this could be useful tools not only for a new technical platform for the closely related species identification but also for epidemiological studies on higher eukaryotes.

Endemic, epidemic clone of Salmonella enterica serovar typhi harboring a single multidrug-resistant plasmid in Vietnam between 1995 and 2002

Salmonella enterica serovar Typhi strains resistant to ampicillin, chloramphenicol, tetracyclines, streptomycin, and cotrimoxazole, isolated from sporadic cases and minor outbreaks in Vietnam between 1995 and 2002, were typed and compared. Plasmid fingerprinting, Vi bacteriophage typing, XbaI pulsed-field gel electrophoresis, and PstI ribotyping showed that endemic, epidemic multidrug-resistant typhoid fever was due, for at least 74.1% of the isolates, to one or two clones of serovar Typhi harboring a single resistance plasmid. PstI ribotyping was used as a basic technique to ensure that a serovar Typhi expansion was clonal.

International nomenclature for Corynebacterium diphtheriae ribotypes

The nomenclature of Corynebacterium diphtheriae ribotypes is presented. A total of 86 ribotypes obtained after BstEII digestion were given a geographic name chosen to reflect the place where one of the strains was isolated or studied.

Repeatability and reproducibility of ribotyping and its computer interpretation

Many molecular typing methods are difficult to interpret because their repeatability (within-laboratory variance) and reproducibility (between-laboratory variance) have not been thoroughly studied. In the present work, ribotyping of coryneform bacteria was the basis of a study involving within-gel and between-gel repeatability and between-laboratory reproducibility (two laboratories involved). The effect of different technical protocols, different algorithms, and different software for fragment size determination was studied. Analysis of variance (ANOVA) showed, within a laboratory, that there was no significant added variance between gels. However, between-laboratory variance was significantly higher than within-laboratory variance. This may be due to the use of different protocols. An experimental function was calculated to transform the data and make them compatible (i.e., erase the between-laboratory variance). The use of different interpolation algorithms (spline, Schaffer and Sederoff) was a significant source of variation in one laboratory only. The use of either Taxotron (Institut Pasteur) or GelCompar (Applied Maths) was not a significant source of added variation when the same algorithm (spline) was used. However, the use of Bio-Gene (Vilber Lourmat) dramatically increased the error (within laboratory, within gel) in one laboratory, while decreasing the error in the other laboratory; this might be due to automatic normalization attempts. These results were taken into account for building a database and performing automatic pattern identification using Taxotron. Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained.

A novel method for screening species-specific gDNA probes for species identification

We report a method called SSH array which combines the suppression subtraction hybridization (SSH) and DNA array techniques to find species-specific DNA probes from genomic DNA (gDNA) for species identification. The method first obtains the differential gDNA fragments between two species by SSH and then hybridizes the differential gDNA fragments with arrays made of multiple whole genomes from several species to screen the unique gDNA fragments for one species. The screened unique gDNA fragments can be used as species-specific probes to differentiate the species they represent from all other species. We used five species of the genus Dendrobrium, D.aurantiacum Kerr, D.officinale Kimura et Migo, D.nobile Lindl., D.chrysotoxum Lindl. and D.fimbriatum Hook., as experimental materials to study the feasibility of the method. The results showed that the method could efficiently obtain different species-specific probes for each of the five species.

Comparative study of three different DNA fingerprint techniques for molecular typing of Shigella flexneri strains isolated in Romania

In this study, 97 epidemiologically unrelated Shigella flexneri strains isolated during 1994 (69 isolates) and 1997 (28 isolates) were characterised by ribotyping, enterobacterial repetitive intergenic consensus sequence-based PCR typing, and pulsed-field gel electrophoresis. Number of strains belonging to each of the six serotypes is selected equal to their distribution in Romania. The isolates comprise 24 ribotypes based on combination of two restriction patterns obtained with HindlII and PstI, respectively, 7 enterobacterial repetitive intergenic consensus (ERIC)-PCR types, and 92 XbaI pulsed-field gel electrophoresis (PFGE) patterns grouped in 31 pulsotypes at Dice coefficients of 85% similarity. We find no significant difference in the distribution of isolates collected during the two periods. Macrorestriction analysis by PFGE offers maximal discrimination. There seems to be little genetic variability among circulating S. flexneri strains of serotype 2a, suggesting that even a combination of several molecular techniques, including PFGE, could not easily differentiate an outbreak strain from temporally associated independent isolates.

Molecular and biochemical characterization of a novel class A beta-lactamase (HER-1) from Escherichia hermannii

Escherichia hermannii showed a low level of resistance to amoxicillin and ticarcillin, reversed by clavulanate, and a moderate susceptibility to piperacillin but was susceptible to all cephalosporins. A bla gene was cloned and encoded a typical class A beta-lactamase (HER-1, pI 7.5), which shares 45, 44, 41, and 40% amino acid identity with other beta-lactamases, AER-1 from Aeromonas hydrophila, MAL-1/Cko-1 from Citrobacter koseri, and TEM-1 and LEN-1, respectively. No ampR gene was detected. Only penicillins were efficiently hydrolyzed, and no hydrolysis was observed for cefuroxime and broad-spectrum cephalosporins. Sequencing of the bla gene in 12 other strains showed 98 to 100% identity with bla(HER-1).

Genotypic and phenotypic characteristics of Corynebacterium diphtheriae strains isolated from patients in belarus during an epidemic period

One hundred two Corynebacterium diphtheriae strains (93 of the gravis biotype and nine of the mitis biotype) isolated from clinical cases during the Belarus diphtheria epidemic were characterized by biotyping, toxigenicity testing by the Elek test and an indirect hemagglutination assay, phage typing, and ribotyping. The gravis biotype strains were characterized as high and medium toxin producers, and strains of biotype mitis were characterized as low and medium toxin producers. Most strains (82 of 102) were distributed among five phage types. Seventy-two strains (64 of the gravis biotype and 8 of the mitis biotype) belonged to phage type VI ls5,34add. Hybridization of genomic DNA digested with BstEII and PvuII revealed five ribotype patterns, namely, D1, D4, D6, D7, and D13. The majority of gravis biotype strains belonged to ribotypes D1 (49 of 93) and D4 (33 of 93) and included one clonal group of C. diphtheriae. This clone predominated in all regions in Belarus. There was a statistical association between ribotypes and phage types but not between ribotypes and levels of toxin production.

Comparison of ribotyping and repetitive extragenic palindromic-PCR for identification of fecal Escherichia coli from humans and animals

This report compares the performances of two popular genotypic methods used for tracking the sources of fecal pollution in water, ribotyping and repetitive extragenic palindromic-PCR (rep-PCR). The rep-PCR was more accurate, reproducible, and efficient in associating DNA fingerprints of fecal Escherichia coli with human and animal hosts of origin.

Identification of Legionella species by ribotyping and other molecular methods

There are currently more than 40 species of Legionella and the identification of most of them by standard methods is often technically difficult. The aim of this study was to use a ribotyping method with endonuclease HindIII and a probe consisting of a set of five oligonucleotides (referred to as OligoMix5). A total of 123 strains, including 78 type or reference strains corresponding to 44 species, eight clinical and 37 environmental isolates were tested. The usefulness of the method was demonstrated for the identification at the species level of all of the 123 Legionella isolates tested, with each species showing a specific profile. Among the 15 serogroups of Legionella pneumophila, eight patterns were obtained. For the 45 field strains, the randomly amplified polymorphic DNA (RAPD) technique and intergenic 16S-23S ribosomal spacer PCR analysis (ITS 16-23S) were also used. Altogether, these three methods allowed the identification of all of strains tested. However, ribotyping has proven to be more effective than the other methods.

[Bacteriological risks: detection and tracing]

Advances in molecular taxonomy of bacteria have generated many tools allowing identification of any bacteria, whether culturable or not. In addition to taxonomic identification, growing knowledge on pathogenicity mechanisms allows the detection of bacteria with given virulence genes. The problem is in asking the proper questions so that the most appropriate tools can be chosen. Some rapid identification tools (gene amplification, in situ hybridisation) require a starting hypothesis. Other tools (rrs gene amplification and sequencing) can be used without prior hypothesis, but take longer. To face the bioterrorist threat, particular attention should be given to laboratory and strain dispatch (within- and between-laboratory) organisation.

A rapid and easy PCR-RFLP method for genotyping Serratia marcescens strains isolated in different hospital outbreaks and patient environments in the Lyon area, France

A new genotyping method for Serratia marcescens is described. This method uses the flagellin gene as target for polymerase chain reaction amplification and Alu I restriction fragment length polymorphism. The strains tested belonged to 13 different hospital clusters of S. marcescens isolated between 1983 and 1988, concerning outbreaks and/or patient environments in different hospital units in Lyon and the Rhone-Alpes region of France. Initially, the classification had been performed by marcescinotyping. These strains were then tested by ribotyping and genotyping of the flagellin gene. Genotyping showed similar classification to ribotyping. The genotyping method is the easiest technique, as reproducible as ribotyping, and with almost the same ability to discriminate different strains. It does not need expensive equipment, is more rapid, and is less labor intensive than ribotyping. With this method, all strains of S. marcescens including sporadic isolates could be amplified and typed. Antibiotic sensitivity determination was found to be a useful complementary and confirmation test for all these typing methods.

Molecular characterization of Corynebacterium diphtheriae isolates, Russia, 1957-1987

In the 1990s, the Newly Independent and Baltic States of the former Soviet Union experienced the largest diphtheria outbreak since the 1960s; it was caused by Corynebacterium diphtheriae strains of a unique clonal group. To address its origin, we studied 47 clinical isolates from Russia and demonstrated that this clonal group was an integral part of the endemic reservoir that existed in Russia at least 5 years before the epidemic began.

Study of Corynebacterium diphtheriae strains isolated in Romania, northwestern Russia and the Republic of Moldova

A selection of 167 Corynebacterium diphtheriae strains isolated in Romania, the Russian Federation and the Republic of Moldova were analysed by biotyping, phage typing, the toxin production test and by molecular techniques such as ribotyping, pulsed field gel electrophoresis and random amplified polymorphic DNA, in order to establish the epidemiological relatedness, genetic divergence and strain circulation within and between the bordering countries. Using a set of five digoxigenin-labeled oligonucleotides and BstEII digestion, 34 ribotypes were identified. The strains isolated in the epidemic areas (Russia and Moldova) were very closely related but different from those isolated in Romania. C1 and C5 were the main ribotypes identified in these areas. Neither ribotype was found in Romania, where the main circulating types were C3 and C7. Field inversion gel electrophoresis was more discriminative than ribotyping and revealed 54 macrorestriction profiles after SfiI restriction. Both methods showed a significant homogeneity of the strains from epidemic areas and a large diversity among the Romanian strains. Random amplification was useful as an identification method for the epidemic strains, but not for the Romanian ones which displayed a large number of amplification profiles. The phenotypic methods associated with molecular typing techniques enabled distinguishing between strains, detecting the epidemic clone, and sustaining the absence of transmission across borders.

Identification of fecal Escherichia coli from humans and animals by ribotyping

Fecal pollution of water resources is an environmental problem of increasing importance. Identification of individual host sources of fecal Escherichia coli, such as humans, pets, production animals, and wild animals, is prerequisite to formulation of remediation plans. Ribotyping has been used to distinguish fecal E. coli of human origin from pooled fecal E. coli isolates of nonhuman origin. We have extended application of this technique to distinguishing fecal E. coli ribotype patterns from human and seven individual nonhuman hosts. Classification accuracy was best when the analysis was limited to three host sources. Application of this technique to identification of host sources of fecal coliforms in water could assist in formulation of pollution reduction plans.

Molecular and phenotypic characterization of potentially new Shigella dysenteriae serotype

From September 1997 to November 1998, the French National Center for Salmonella and Shigella received 22 Shigella isolates recovered from 22 different patients suffering from dysentery. None of these isolates reacted with any of the antisera used to identify established Shigella serotypes, but all of them agglutinated in the presence of antisera to a previously described potentially new Shigella dysenteriae serotype (represented by strain 96-204) primarily isolated from stool cultures of imported diarrheal cases in Japan. All French isolates, as well as strain 96-204, showed biochemical reactions typical of S. dysenteriae and gave positive results in a PCR assay for detection of the plasmid ipaH gene coding for invasiveness. No Shiga toxin gene was detected by PCR. These isolates were indistinguishable by molecular analysis of ribosomal DNA (ribotyping) and seemed to be related to S. dysenteriae serotypes 3 and 12. However, further characterization by restriction of the amplified O-antigen gene cluster clearly distinguished this new serotype from all other Shigella or Escherichia coli serotypes.

Computer identification of Shigella species by rRNA gene restriction patterns

We describe a MluI ribotyping scheme for Shigella which approaches correlation with serotyping. One hundred and seventeen reference strains and previously serotyped clinical isolates representing the 57 Shigella serotypes and biotypes were included in this study. A total of 51 distinct ribotypes were obtained and a database was built with them. The number of bands composing each ribotype varied from 9 to 15. The fragments ranged in size from 1.6 to 18.8 kbp. One hundred and eleven clinical isolates were successfully identified in a double blind study with standard biochemical/serologic methods, by automatic comparison of their ribotypes with our database using the software Taxotron.

Rapid identification of Corynebacterium diphtheriae clonal group associated with diphtheria epidemic, Russian Federation

We used 199 Corynebacterium diphtheriae isolated from 1995 to 1997 in Russia to evaluate the ability of random amplified polymorphic DNA (RAPD) to identify the unique clonal group that emerged there in 1990. Our data show that RAPD can reliably, reproducibly, and rapidly screen a large number of strains to identify the epidemic clonal group.

Evaluation of pulsed-field gel electrophoresis in epidemiological investigations of meningococcal disease outbreaks caused by Neisseria meningitidis serogroup C

Since 1990, the frequency of Neisseria meningitidis serogroup C (NMSC) outbreaks in the United States has increased. Based on multilocus enzyme electrophoresis (MEE), the current molecular subtyping standard, most of the NMSC outbreaks have been caused by isolates of several closely related electrophoretic types (ETs) within the ET-37 complex. We chose 66 isolates from four well-described NMSC outbreaks that occurred in the United States from 1993 to 1995 to evaluate the potential of pulsed-field gel electrophoresis (PFGE) to identify outbreak-related isolates specific for each of the four outbreaks and to differentiate between them and 50 sporadic isolates collected during the outbreak investigations or through active laboratory-based surveillance from 1989 to 1996. We tested all isolates collected during the outbreak investigations by four other molecular subtyping methods: MEE, ribotyping (ClaI), random amplified polymorphic DNA assay (two primers), and serotyping and serosubtyping. Among the 116 isolates, we observed 11 clusters of 39 NheI PFGE patterns. Excellent correlation between the PFGE and the epidemiological data was observed, with an overall sensitivity of 85% and specificity of 71% at the 95% pattern relatedness breakpoint using either 1.5 or 1.0% tolerance. For all four analyzed outbreaks, PFGE would have given public health officials additional support in declaring an outbreak and making appropriate public health decisions.

Molecular techniques open up new vistas for typing of coagulase-negative staphylococci

Several methods were used to type 64 clinical isolates of coagulase-negative staphylococci (CNS) derived from hospitals in Morocco. The clinical isolates originated principally from blood cultures and wound sources. These isolates provided the opportunity to substantially compare the proficiency of developing molecular techniques with conventional phenotypic tests for use in the identification of clinical staphylococci. The following molecular methods were examined: Utility ribotyping analysis (Ribotyping); PCR analysis performed with 16S-23S ribosomal-DNA intergenic spacer (ITS-PCR); PCR-based random amplified polymorphic DNA (RAPD). The results obtained by the molecular techniques were contrasted to those of conventional phenotypic tests. Conventional phenotypic tests allowed the outright recognition of the majority of isolates (50/64). These 50 isolates were subdivided into 33 novobiocin-susceptible and 17 novobiocin-resistant strains of CNS. However, 2 other novobiocin-susceptible and 12 other novobiocin-resistant isolates remained unclassified by these tests. There was a good agreement between the conventional phenotypic tests and RAPD for the 33 novobiocin-susceptible isolates. But, the RAPD technique permitted the assignment of the two unidentified novobiocin-susceptible isolates to the Staphylococcus hominis species. A complete correlation was obtained between the three molecular tools for recognition of the 12 novobiocin-resistant isolates that were not identified by phenotypic typing; these were in fact identified as 5 Staphylococcus cohnii and 4 Staphylococcus equorum. Three isolates remained unidentified by all three systems of molecular techniques.

Improvement of the identification of staphylococci isolated from bovine mammary infections using molecular methods

Fifty-six Staphylococcus strains isolated from cases of bovine mammary infections were identified by using phenotypic and genotypic methods. Twenty-eight strains (50%) were identified at the species level according to their phenotypic characteristics, whereas the remaining 28 strains presented atypical or unreliable profiles. A combination of phenotypic and genotypic methods allowed the 56 strains studied to be classified. Internal transcribed spacer-polymerase chain reaction (ITS-PCR) based on the polymorphism of the 16S-23S rDNA spacer region appeared as a rapid and reliable method for the classification of bovine staphylococcal isolates at the species and subspecies levels.

Epidemiologic typing of Escherichia coli using RAPD analysis, ribotyping and serotyping

OBJECTIVE

To compare random amplified polymorphic DNA (RAPD) analysis and ribotyping with serotyping for epidemiologic typing of Escherichia coli.

METHODS

Thirty-two epidemiologically unrelated strains, nine cerebrospinal fluid isolates with the O7K1 serotype from nine patients, and nine sets of epidemiologically related E. coli isolates from nine patients were typed by RAPD analysis, ribotyping and serotyping.

RESULTS

Among the 32 epidemiologically unrelated E. coli isolates, 29 types were distinguished by RAPD analysis, 25 by ribotyping and 27 by serotyping. Indistinguishable patterns were obtained by RAPD analysis and ribotyping within the collection of nine cerebrospinal fluid isolates. For the epidemiologically related isolates, intrapatient variation was only found by RAPD analysis among the isolates of one set and by ribotyping among the isolates of two sets. No interpatient variation was observed between three sets of isolates. With serotyping, the epidemiologically related isolates yielded similar typing relationships to those obtained by RAPD analysis and ribotyping.

CONCLUSIONS

RAPD analysis had the highest discriminatory capacity for typing E. coli isolates. RAPD analysis, ribotyping and serotyping can all be used for assessment of strain relationships.

Distribution of Staphylococcus sciuri subspecies among human clinical specimens, and profile of antibiotic resistance

The distribution of three subspecies comprising Staphylococcus sciuri was determined for a collection of 30 clinical isolates originating from Morocco, the United Kingdom, and France. The sources of these isolates were principally wounds, skin, and soft tissue infections. At the species level, the isolates were identified according to biochemical characteristics and at the subspecies level by the ribotyping technique. PCR analysis performed with the 16S-23S ribosomal DNA intergenic spacer was less powerful for subspecies differentiation. S. sciuri subsp. sciuri was the most frequent subspecies (21 isolates) found in the collection, whereas S. sciuri subsp. rodentium (seven isolates) and S. sciuri subsp. carnaticus (two isolates) were less common. mecA or a mecA-related gene was detected by PCR and Southern blot in all 30 S. sciuri isolates, supporting the suggestion that S. sciuri species are the natural reservoir of the mecA gene. While the linA/linA' gene coding for lincomycin resistance was present in five isolates, an uncharacterized gene for this resistance was suspected in seventeen other isolates.

Molecular characterization of the genera Proteus, Morganella, and Providencia by ribotyping

The so-called Proteus-Providencia group is constituted at present by three genera and 10 species. Several of the recognized species are common opportunistic pathogens for humans and animals. Different methods based on the study of phenotypic characters have been used in the past with variable levels of efficiency for typing some species for epidemiological purposes. We have determined the rRNA gene restriction patterns (ribotypes) for the type strains of the 10 different species of the genera Proteus, Morganella, and Providencia. Visual inspection of EcoRV- and HincII-digested DNA from the type strains showed remarkably different patterns for both enzymes, but EcoRV provided better differentiation. Both endonucleases were retained to study a large number of wild and collection strains belonging to the different species. Clinical isolates of Proteus mirabilis, Proteus penneri, Morganella morganii, and Providencia heimbachae showed patterns identical or very similar to those of the respective type strains, so that groups of related patterns (ribogroups) were found to correspond to the diverse species. On the contrary, distinct ribogroups were detected within Providencia alcalifaciens (two ribogroups with both enzymes), Providencia rettgeri (four ribogroups with EcoRV and five with HincII), Providencia stuartii (two ribogroups with EcoRV), Providencia rustigianii (two ribogroups with HincII), and Proteus vulgaris (two ribogroups with both enzymes). The pattern shown by the ancient P. vulgaris type strain NCTC 4175 differed considerably from both P. vulgaris ribogroups as well as from the newly proposed type strain ATCC 29905 and from any other strain in this study, thus confirming its atypical nature. Minor differences were frequently observed among patterns of strains belonging to the same ribogroup. These differences were assumed to define ribotypes within each ribogroup. No correlation was observed between ribogroups or ribotypes and biogroups of P. vulgaris, P. alcalifaciens, P. stuartii, and P. rettgeri. Since, not only different species showed different rRNA gene restriction patterns, but also different ribogroups and ribotypes have been found in the majority of the species, ribotyping would be a sensitive method for molecular characterization of clinical isolates belonging to the genera Proteus, Morganella, and Providencia.

Use of molecular subtyping to document long-term persistence of Corynebacterium diphtheriae in South Dakota

Enhanced surveillance of patients with upper respiratory symptoms in a Northern Plains community revealed that approximately 4% of them were infected by toxigenic Corynebacterium diphtheriae of both mitis and gravis biotypes, showing that the organism is still circulating in the United States. Toxigenic C. diphtheriae was isolated from five members of four households. Four molecular subtyping methods-ribotyping, multilocus enzyme electrophoresis (MEE), random amplified polymorphic DNA (RAPD), and single-strand conformation polymorphism-were used to molecularly characterize these strains and compare them to 17 archival South Dakota strains dating back to 1973 through 1983 and to 5 isolates collected from residents of diverse regions of the United States. Ribotyping and RAPD clearly demonstrated the household transmission of isolates and provided precise information on the circulation of several distinct strains within three households. By MEE, most recent and archival South Dakota strains were identified as closely related and clustered within the newly identified ET (electrophoretic type) 215 complex. Furthermore, three recent South Dakota isolates and eight archival South Dakota isolates were indistinguishable by both ribotyping and RAPD. All of these molecular methods showed that recent South Dakota isolates and archival South Dakota isolates were more closely related to each other than to the C. diphtheriae strains isolated in other parts of the United States or worldwide. The data also supported the improbability of importation of C. diphtheriae into this area and rather strongly suggest the long-term persistence of the organism in this region.