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Saida NB, Thabet L, Messadi A, Bouselmi K, Turki A, Boukadida J. Clonality of Providencia stuartii isolates involved in outbreak that occurred in a burn unit. Burns 2008; 34:829-34. [PMID: 18241997 DOI: 10.1016/j.burns.2007.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 09/30/2007] [Indexed: 10/22/2022]
Abstract
In order to investigate an outbreak of multidrug-resistant Providencia stuartii that occurred in a burn unit, we analyzed by pulsed-field gel electrophoresis (PFGE) all isolates of P. stuartii collected during 4 months of 2005 from patients and from a tracheal aspirator. Seventeen clinical isolates of P. stuartii, extended-spectrum beta-lactamase (ESBL) producing, were collected from 17 patients. All these isolates were nosocomially acquired. Three other isolates were collected from the aspirator probe, the aspirator reservoir and from the aspirator tube. Three different antibiotypes were identified without correlation with the genotype. Two PFGE types were obtained (types A and B) with predominance of one (type A) that was observed for 15 isolates. P. stuartii isolates collected from different components of the aspirator (probe, reservoir and tube) yielded PFGE type A. This study suggests the bi-clonality of the outbreak and that transmission of epidemic P. stuartii isolates was through a common source. The aspirator probe, contaminated from aspirator that functioned as a reservoir of bacteria, seems to be the route of transmission of P. stuartii. Furthermore, this study shows the utility of PFGE in typing for the purpose of understanding the epidemiological behaviour of P. stuartii and as a basis for the development of rational control strategies.
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Affiliation(s)
- N Ben Saida
- Microbiology and Immunology Laboratory UR 16/02, CHU Farhat-Hached, avenue Ibn-Jazzar, Sousse, Tunisia
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2
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SETO Y, KIMURA A, AKAI Y, FUJIWARA S. Distribution of theLactobacillus acidophilusComplex in Human Fecal Specimens Examined by Restriction Fragment Length Polymorphism of the 16S rRNA Genes. Biosci Microflora 2003. [DOI: 10.12938/bifidus1996.22.75] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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3
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Pignato S, Giammanco GM, Grimont F, Grimont PA, Giammanco G. Molecular characterization of the genera Proteus, Morganella, and Providencia by ribotyping. J Clin Microbiol 1999; 37:2840-7. [PMID: 10449462 PMCID: PMC85391 DOI: 10.1128/jcm.37.9.2840-2847.1999] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Affiliation(s)
- S Pignato
- Istituto di Igiene e Medicina Preventiva, Università di Catania, I-95124 Catania, Italy
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4
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Abstract
The past two decades have brought significant changes to the clinical laboratory. Microbiologists now have highly sensitive, rapid and specific molecular methods of identifying infectious agents by the direct detection of DNA or RNA sequences unique to a particular organism. Advanced DNA technology such as nucleic-acid hybridization, PCR and DNA fingerprinting have been used in the direct detection of causative organisms in clinical specimens, with resultant benefits such as increased sensitivity and specificity of the diagnostic approach and reduction of turnaround time. This review outlines a brief description of the various DNA diagnostic tools used in the detection of pulmonary infections with emphasis on their applications in the diagnosis of Mycobacterium tuberculosis.
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Affiliation(s)
- W C Tan
- Department of Medicine, National University of Singapore, Republic of Singapore
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5
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Wilson MJ, Wade WG, Weightman AJ. Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of human Capnocytophaga. THE JOURNAL OF APPLIED BACTERIOLOGY 1995; 78:394-401. [PMID: 7538106 DOI: 10.1111/j.1365-2672.1995.tb03424.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The confusion in the taxonomic status of the genus Capnocytophaga has made identification of strains and studies on the role of this genus in infectious diseases equivocal. In this study 33 strains of Capnocytophaga including reference strains and various clinical isolates, were studied using RFLP analysis of 16S ribosomal RNA genes. The 16S ribosomal RNA (rRNA) gene sequences from whole cell suspensions and isolated genomic DNA samples were amplified by the polymerase chain reaction (PCR) using eubacterial specific primers. PCR products were purified and characterized by single digestions with 12 restriction endonucleases. Five of these, BanI, CfoI, HaeIII, HphI and RsaII were found to discriminate reproducibly between strains, and restriction patterns (ribotypes) produced by these were analysed to clarify the classification of Capnocytophaga strains. Dendrograms inferring similarities were derived from these data by the UPGMA method. This analysis produced three major clusters of strains, each of which was associated with a previously proposed species type strain: C. gingivalis, C. sputigena and C. ochracea. The results support the division of Capnocytophaga into three species and demonstrate that, despite the heterogeneity of this genus, the modified ribotyping method provides a simple, rapid and reproducible way to identify Capnocytophaga strains.
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Affiliation(s)
- M J Wilson
- Department of Periodontology, University of Wales College of Medicine, Cardiff, UK
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6
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Fontana C, Jezzi T, Testore GP, Dainelli B. Differentiation of Clostridium difficile, Clostridium bifermentans, Clostridium sordellii, and Clostridium perfringens from diarrheal stool by API ZYM and API LRA oxidase test. Microbiol Immunol 1995; 39:231-5. [PMID: 7651236 DOI: 10.1111/j.1348-0421.1995.tb02194.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A simple, rapid and reliable outline for identification of clostridia isolates from human infections was developed. It consists of a combination of API ZYM and API LRA Oxidase tests. The enzymatic activities were performed with strains sub-cultured onto carbohydrate-free medium (Columbia blood agar). Fifty-five strains of Clostridium difficile, C. bifermentans, C. sordellii, and C. perfringens from clinical specimens and eight reference standard strains representing different species of the same genus were analyzed. The accuracy of the new method was evaluated by comparison with the results obtained by DNA/DNA analysis.
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Affiliation(s)
- C Fontana
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università degli Studi di Roma Tor Vergata, Italy
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7
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Salzano G, Moschetti G, Villani F, Pepe O, Mauriello G, Coppola S. Genotyping of Streptococcus thermophilus evidenced by restriction analysis of ribosomal DNA. Res Microbiol 1994; 145:651-8. [PMID: 7746954 DOI: 10.1016/0923-2508(94)90036-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Twenty strains of Streptococcus thermophilus were classified into five different types characterized by ribotyping after DNA digestion with HindIII and hybridization with cDNA from 16S-23S rDNA of Escherichia coli. Ribotyping after digestion with HaeIII and XhoI enabled the same strains to be gathered into three groups as a consequence of the reduced influence of the flanking sequences within the analysis of rRNA operons. Amplified rDNA restriction analysis clearly confirmed the discrimination of these three different ribotypes, producing evidence to suggest that subtaxa are to be recognized within this species.
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Affiliation(s)
- G Salzano
- Istituto di Microbiologia agraria e Stazione di Microbiologia industriale, Università degli Studi di Napoli Federico II, Portici, Italy
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8
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Bingen EH, Denamur E, Elion J. Use of ribotyping in epidemiological surveillance of nosocomial outbreaks. Clin Microbiol Rev 1994; 7:311-27. [PMID: 7923052 PMCID: PMC358328 DOI: 10.1128/cmr.7.3.311] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Over the past few years, genotypic methods based on the study of bacterial DNA polymorphism have shown high discriminatory power for strain differentiation and superiority over most phenotypic methods commonly available in the clinical microbiology laboratory. Some of the methods used, however, required either a high level of technology and sophisticated equipment (e.g., pulsed-field gel electrophoresis) or species-specific reagents of restricted availability (randomly cloned DNA probes or gene-specific probes). Because ribotyping uses a universal probe (rRNA) and is a rather simple technology, particularly since the advent of nonradioactive labelling systems, it has been widely used for strain differentiation of most bacterial species involved in nosocomial outbreaks. In vitro and in vivo stability of the markers studied has been demonstrated. Although there may be limitation to this approach, ribotyping was found to be highly discriminative, particularly for typing members of the family Enterobacteriaceae, Pseudomonas cepacia, and Xanthomonas maltophilia. In many cases, it has improved the understanding of the mechanism of nosocomial acquisition of organisms by allowing a distinction between endogenous and exogenous infections. Among exogenous infections, it has distinguished between individual and epidemic strains, thus differentiating cross-infection from independent acquisition.
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Affiliation(s)
- E H Bingen
- Laboratoire de Microbiologie, Hôpital Robert Debré, Paris, France
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9
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Rahav G, Pinco E, Silbaq F, Bercovier H. Molecular epidemiology of catheter-associated bacteriuria in nursing home patients. J Clin Microbiol 1994; 32:1031-4. [PMID: 7913094 PMCID: PMC267175 DOI: 10.1128/jcm.32.4.1031-1034.1994] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Urine samples from 19 nursing home patients with long-term urinary catheters were cultured every 3 months for 18 months. Providencia stuartii, present in 74% of the elderly and in 59% of urine specimens, was the most frequently isolated bacteria. The persistence of P. stuartii was significantly higher among females than among males. In order to study the epidemiology of bacteriuria in this nursing home, bacteria were characterized by biochemical tests, antibiotic susceptibility pattern, and restriction fragment length polymorphism (RFLP) analysis. The antibiotic susceptibility pattern indicated that each patient had two to three different strains of P. stuartii during the 18 months of follow-up. In contrast, the RFLP analysis revealed that a specific strain had persisted in the urinary tract of the patient during the entire follow-up period. According to the biochemical profile, 74% of the patients had the same bacteria in urine cultures, pointing to a common source of transmission. RFLP analysis, however, demonstrated different patterns of RFLP, suggesting concomitant multiple sources of infection.
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Affiliation(s)
- G Rahav
- Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
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10
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Restriction Fragment Length Polymorphism of Lactobacillus reuteri and Lactobacillus fermentum, Originating from Intestinal Mucosa, Based on 16S rRNA Genes. Syst Appl Microbiol 1994. [DOI: 10.1016/s0723-2020(11)80038-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Rudner R, Studamire B, Jarvis ED. Determinations of restriction fragment length polymorphism in bacteria using ribosomal RNA genes. Methods Enzymol 1994; 235:184-96. [PMID: 7520118 DOI: 10.1016/0076-6879(94)35140-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- R Rudner
- Department of Biological Sciences, Hunter College of the City University of New York, New York 10021
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12
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Fontana C, Cellini L, Dainelli B. Twelve aberrant strains of Staphylococcus aureus subsp. aureus from clinical specimens. J Clin Microbiol 1993; 31:2105-9. [PMID: 8370737 PMCID: PMC265705 DOI: 10.1128/jcm.31.8.2105-2109.1993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A new biovar of Staphylococcus aureus subsp. aureus was isolated from human clinical specimens and described on the basis of studies of 12 isolates that were compared with 11 standard reference strains. Both DNA hybridization experiments and numerical taxonomy analysis demonstrated that these strains were strictly related to S. aureus subsp. aureus; however, they were significantly different from the latter. The atypical strains belonging to the new biovar can be distinguished from typical S. aureus subsp. aureus strains by their alpha-chymotrypsin, alpha-glucosidase, beta-N-acetylglucosaminidase, lipase (C-14), and leucine arylamidase enzymatic activities and novobiocin resistance. Thus, the combination of alpha-glucosidase and beta-N-acetyl-glucosaminidase is more useful for distinguishing these S. aureus strains from the other, typical ones.
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Affiliation(s)
- C Fontana
- Dipartimento di Medicina Sperimentale e Scienze Biochimiche, Università Tor Vergata di Roma, Italy
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13
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Bowden G, Johnson J, Schachtele C. Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes. J Dent Res 1993; 72:1171-79. [PMID: 8360358 DOI: 10.1177/00220345930720080201] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.
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Affiliation(s)
- G Bowden
- Department of Oral Sciences and Clinical Research Center for Periodontal Diseases, School of Dentistry, University of Minnesota, Minneapolis 55455
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14
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Woods CR, Versalovic J, Koeuth T, Lupski JR. Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of bacterial isolates. J Clin Microbiol 1993; 31:1927-31. [PMID: 8349778 PMCID: PMC265663 DOI: 10.1128/jcm.31.7.1927-1931.1993] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Repetitive element sequence-based polymerase chain reaction (rep-PCR) enables the generation of DNA fingerprints which discriminate bacterial species and strains. We describe the application of whole-cell methods which allow specimens from broth cultures or colonies from agar plates to be utilized directly in the PCR mixture. The rep-PCR-generated DNA fingerprints obtained with whole-cell samples match results obtained with genomic DNA templates. Examples with different gram-negative bacteria (e.g., Citrobacter diversus, Escherichia coli, and Pseudomonas aeruginosa) and gram-positive bacteria (e.g., Staphylococcus aureus and Streptococcus pneumoniae) are demonstrated. Rapid specimen preparation methods enable rep-PCR-based fingerprinting to be completed in several hours and, therefore, allows the timely analysis of epidemiological relationships.
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Affiliation(s)
- C R Woods
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030
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15
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Nastasi A, Pignato S, Mammina C, Giammanco G. rRNA gene restriction patterns and biotypes of Shigella sonnei. Epidemiol Infect 1993; 110:23-30. [PMID: 7679353 PMCID: PMC2271974 DOI: 10.1017/s0950268800050640] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Shigella sonnei is a major agent of diarrhoeal disease in developed as well as in developing countries. Several phenotypic methods to define strain differences have been applied to this species of Shigella including, more recently, analysis of extrachromosomal and chromosomal DNA. In this study, 432 endemic and epidemic strains isolated between 1975 and 1991 in Italy, France and Switzerland were submitted to rRNA gene restriction pattern analysis, after digestion of whole-cell DNA by Hinc II, and to concomitant biotyping. Thirteen ribotypes, H1 to H13, and five biotypes, a, d, e, f, g, were detected. Ninety-five percent of the sporadic strains were assigned to ribotypes H1 to H4, which could be subtyped, except for H4, in different biotypes. Strains from each of seven different outbreaks had indistinguishable ribotype-biotype patterns. In contrast, 65 strains, isolated in Sicily in 1980 over an extended period of apparently epidemic increase of isolations and which had previously been considered to be a single bacterial clone on the basis of resistance pattern and phage type, were found to belong to two different and scarcely related ribotypes. Ribotyping and biochemical subtyping appear to be a useful epidemiological tool in studies on the circulation and distribution of strains of S. sonnei.
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Affiliation(s)
- A Nastasi
- Dipartimento di Igiene e Microbiologia G. D'Alessandro, Università di Palermo, Italy
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16
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Woods CR, Versalovic J, Koeuth T, Lupski JR. Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence-based primers in the polymerase chain reaction. J Clin Microbiol 1992; 30:2921-9. [PMID: 1452663 PMCID: PMC270553 DOI: 10.1128/jcm.30.11.2921-2929.1992] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Oligonucleotide probes which match consensus sequences of the repetitive extragenic palindromic (REP) element hybridize to genomic DNA of diverse bacterial species. Primers based on the REP sequence generate complex band patterns with genomic DNA in the polymerase chain reaction (PCR), a technique named REP-PCR. We used REP-PCR with genomic DNA to fingerprint 47 isolates of Citrobacter diversus. Previously, 37 were assigned electrophoretic types (ETs) by multilocus enzyme electrophoresis and 35 were evaluated by using outer membrane protein profiles. Fingerprints were compared by visual inspection and by similarity coefficients (SimCs) based on the number of common bands versus total bands between two given isolates. DNA fingerprints were highly similar visually for patient pairs and outbreak-related sets. SimCs for these were > or = 0.952. Fingerprints of isolates with different ETs generally were distinctive. Among 21 unrelated isolates representing 15 ETs, only 6 of 210 comparisons had SimCs of > or = 0.952. REP-PCR rapidly generated DNA fingerprints which were highly similar for epidemiologically linked isolates of C. diversus and distinct for previously characterized strains within this species. The ability of this method to discriminate between C. diversus isolates with the same biotype was similar to that of multilocus enzyme electrophoresis and outer membrane protein profiles. REP-PCR may be useful in evaluation of apparent outbreaks of this or other bacterial species which possess these extragenic, repetitive elements.
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Affiliation(s)
- C R Woods
- C. T. Parker Laboratory, Texas Children's Hospital, Baylor College of Medicine, Houston 77030
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17
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Owen RJ, Hunton C, Bickley J, Moreno M, Linton D. Ribosomal RNA gene restriction patterns of Helicobacter pylori: analysis and appraisal of Hae III digests as a molecular typing system. Epidemiol Infect 1992; 109:35-47. [PMID: 1379934 PMCID: PMC2272230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ribosomal RNA gene restriction patterns (ribopatterns) of 162 strains of Helicobacter pylori from 93 patients were studied to assess their suitability for use as the basis of a molecular typing system. Computer-assisted numerical analysis of Hae III ribopatterns of 122 strains from 9 countries in 4 continents showed that almost every strain had a distinct and unique ribopattern and only strains from the same individual were genomically matched in all bands or with minor (1-2 band) differences. Hae III ribopatterns offered high typability and reproducibility but were too discriminatory for large-scale epidemiological typing purposes because no rational basis for grouping strains was evident. In contrast, composite band profiles based on 21 band loci within the Hae III ribopatterns, which were used to compare strain sets selected on toxigenicity and geographical origin, were more conserved. Minor differences between some strain sets in several band loci were detected but generally the composite profiles were a reproducible feature of H. pylori. We conclude that Hae III ribopatterns provide an excellent fingerprint for small-scale studies of genomic variation in defined populations, such as sequential patient isolates, but are too specific for general typing of H. pylori.
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Affiliation(s)
- R J Owen
- National Collection of Type Cultures, Central Public Health Laboratory, London, UK
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18
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Blumberg HM, Rimland D, Kiehlbauch JA, Terry PM, Wachsmuth IK. Epidemiologic typing of Staphylococcus aureus by DNA restriction fragment length polymorphisms of rRNA genes: elucidation of the clonal nature of a group of bacteriophage-nontypeable, ciprofloxacin-resistant, methicillin-susceptible S. aureus isolates. J Clin Microbiol 1992; 30:362-9. [PMID: 1371517 PMCID: PMC265061 DOI: 10.1128/jcm.30.2.362-369.1992] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of DNA restriction fragment length polymorphisms of rRNA genes (ribotyping) was employed to assist in the epidemiologic investigation of the emergence and spread of ciprofloxacin-resistant Staphylococcus aureus at the Atlanta VA Medical Center because many isolates of interest were nontypeable by phages and harbored few plasmids useful as strain markers. Chromosomal DNAs of selected S. aureus isolates were digested initially with 20 different restriction enzymes. EcoRI appeared to give the best discrimination of hybridization banding patterns (ribotypes) and was used with all study isolates. Overall, 15 different ribotypes were seen among the 50 S. aureus isolates studied (7 ribotypes among 13 methicillin-susceptible S. aureus [MSSA] isolates and 9 ribotypes among 37 methicillin-resistant S. aureus [MRSA] isolates). Seven of eight ciprofloxacin-resistant MSSA (CR-MSSA) patient isolates had identical antibiograms, were nontypeable by phages, and had a single 22-MDa plasmid. Six of these seven CR-MSSA isolates had an identical ribotype pattern. Ribotyping distinguished this CR-MSSA strain or clone from MRSA and other MSSA isolates, including nontypeable isolates that contained a 22-MDa plasmid. Five ciprofloxacin-susceptible MSSA isolates studied had five ribotypes; one pattern was identical to the CR-MSSA clone. Twenty-three CR-MRSA isolates recovered from the Atlanta VA Medical Center had four different ribotypes. Ribotyping proved to be a useful molecular epidemiologic tool in the study of S. aureus because it differentiated isolates which were indistinguishable by more traditional methods. In addition, this technique demonstrated that at our institution, ciprofloxacin resistance emerged in multiple strains of MRSA, as opposed to primarily a single strain or clone of MSSA.
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Affiliation(s)
- H M Blumberg
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
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19
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Wasteson Y, Lund A, Olsvik O. Characterization of Escherichia coli strains isolated from pigs with edema disease. Vet Microbiol 1992; 30:179-90. [PMID: 1557896 DOI: 10.1016/0378-1135(92)90112-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Escherichia coli strains belonging to serogroups O 138 and O 139 isolated from pigs with edema disease, were characterized with respect to the presence of genes encoding Shiga-like toxin I, Shiga-like toxin II and Shiga-like toxin IIv (SLT I, SLT II and SLT IIv). Genes coding for the heat-stable and heat-labile enterotoxins (ST I and LT I) were also detected. Plasmid profiling, restriction enzyme digestion of total DNA, and ribotyping were performed for further characterization of the strains. The oligonucleotide probes applied in this study appeared to be useful tools for detecting genes coding cytotoxins and enterotoxins. DNA from 12 of 16 strains hybridized with two SLT II probes, and DNA from two SLT IIv encoding strains also hybridized with the ST I probe. DNA from one SLT IIv negative strain hybridized with the LT I probe. The results from plasmid profiling, restriction enzyme digestion, and ribotyping were compared with serogrouping in attempts to distinguish between the different E. coli edema disease isolates. Fourteen different plasmid profiles were identified, and as restriction patterns barely did, and ribotyping patterns did not, reveal any information useful for differentiation of the strains beyond serogroup level, plasmid profiling seemed to be the most suitable method for discrimination between the edema disease strains investigated here.
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Affiliation(s)
- Y Wasteson
- Department of Microbiology and Immunology, Norwegian College of Veterinary Medicine, Oslo
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20
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Woods TC, Helsel LO, Swaminathan B, Bibb WF, Pinner RW, Gellin BG, Collin SF, Waterman SH, Reeves MW, Brenner DJ. Characterization of Neisseria meningitidis serogroup C by multilocus enzyme electrophoresis and ribosomal DNA restriction profiles (ribotyping). J Clin Microbiol 1992; 30:132-7. [PMID: 1734044 PMCID: PMC265008 DOI: 10.1128/jcm.30.1.132-137.1992] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We compared multilocus enzyme electrophoresis (MEE) and ribosomal DNA fingerprinting (ribotyping) for subtyping 44 strains of Neisseria meningitidis serogroup C that were isolated in Los Angeles County, California, between December 1985 and July 1986. The isolates were divided into six enzyme types (ETs) by MEE, but 36 of the isolates were clustered in one ET, 3. The same isolates were divided into 17 ribotypes by use of restriction endonucleases ClaI, EcoRI, and XhoI. Twenty of the 36 ET 3 isolates were divided into 17 ribotypes by use of restriction endonucleases ClaI, EcoRI, and XhoI. Twenty of the 36 ET 3 isolates were grouped in a single ribotype, J. The rate of infection with ribotype J strains was higher in the southern part of the study area than in the northern part. Isolates from each of eight pairs (each isolate pair was cultured from the same patient from the same or different sites) were found identical by MEE, but ribotyping revealed a difference in one pair. In this study, ribotyping showed a greater discriminating capacity than MEE for subtyping N. meningitidis serogroup C, but the epidemiologic relevance of this increased sensitivity needs further assessment.
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Affiliation(s)
- T C Woods
- Meningitis and Special Pathogens Branch, Centers for Disease Control, Atlanta, Georgia 30333
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21
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Rodrigues UM, Aguirre M, Facklam RR, Collins MD. Specific and intraspecific molecular typing of lactococci based on polymorphism of DNA encoding rRNA. THE JOURNAL OF APPLIED BACTERIOLOGY 1991; 71:509-16. [PMID: 1685731 DOI: 10.1111/j.1365-2672.1991.tb03825.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The rRNA gene restriction patterns or species of the genus Lactococcus were determined. Chromosomal DNA was digested with endonucleases and probed with radiolabelled DNA complementary to rRNA synthesized by random oligonucleotide priming using reverse transcriptase. Highly discriminatory restriction patterns were obtained which served to distinguish the five currently recognized lactococcal species. In addition the observed variations in the patterns at intra-specific level indicate that rRNA gene restriction fingerprinting may be of value in distinguishing the individual strains for epidemiological studies, and monitoring and checking authenticity of starter strains.
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Affiliation(s)
- U M Rodrigues
- Department of Microbiology, AFRC Institute of Food Research, Shinfield, Reading, UK
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22
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Picard B, Picard-Pasquier N, Krishnamoorthy R, Goullet P. Correlation between DNA polymorphism and enzyme polymorphism argues in favour of the delineation of two species within Providencia alcalifaciens. Res Microbiol 1991; 142:965-9. [PMID: 1805310 DOI: 10.1016/0923-2508(91)90006-v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ribosomal DNA (rDNA) polymorphism was compared to enzyme polymorphism and DNA/DNA hybridization data for the intraspecies differentiation of Providencia alcalifaciens. DNA from 27 strains previously classified into two zymotypes A1 and A2 and discriminated by two levels of DNA/DNA hybridization (delta Tm values of 0 to 1 degree C and 6 to 10 degrees C, respectively) were analysed by Southern blotting for rDNA polymorphism. The ribotypes fell into two ribogroups A1 and A2, which correlated with the corresponding zymotypes. This correlation argues for the proposed creation of two species within P. alcalifaciens.
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Affiliation(s)
- B Picard
- Laboratoire de Microbiologie, Faculté de Médecine Xavier Bichat, Université Paris VII
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23
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Hinojosa-Ahumada M, Swaminathan B, Hunter SB, Cameron DN, Kiehlbauch JA, Wachsmuth IK, Strockbine NA. Restriction fragment length polymorphisms in rRNA operons for subtyping Shigella sonnei. J Clin Microbiol 1991; 29:2380-4. [PMID: 1723069 PMCID: PMC270342 DOI: 10.1128/jcm.29.11.2380-2384.1991] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Shigella sonnei is the most frequent cause of shigellosis in the United States. Epidemiologic studies of this organism have been hampered by the lack of adequate typing procedures. Ribosomal DNA analysis (ribotyping), a method which analyzes restriction fragment length polymorphisms in the chromosomal genes that encode rRNA, has recently been shown to be useful for microbial species identification and subtyping. To determine whether ribotyping could be used to distinguish between S. sonnei isolates, we conducted Southern hybridization studies on isolates from 16 different geographic locations and from four recent outbreaks. S. sonnei genomic DNA fragments generated following digestion with SalI hybridized with Escherichia coli 16S and 23S rRNAs to produce six distinct patterns; strains with patterns 1, 2, and 3 were each further subdivided into two additional patterns by using PvuII, SmaI, and SstI, respectively. Epidemiologically related strains had identical patterns. Ribotyping appears to be a useful tool for epidemiologic studies of shigellosis caused by S. sonnei.
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Affiliation(s)
- M Hinojosa-Ahumada
- Instituto Nacional de Diagnostico y Referencia Epidemiologicos, Mexico City, Mexico
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24
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Blumberg HM, Kiehlbauch JA, Wachsmuth IK. Molecular epidemiology of Yersinia enterocolitica O:3 infections: use of chromosomal DNA restriction fragment length polymorphisms of rRNA genes. J Clin Microbiol 1991; 29:2368-74. [PMID: 1723068 PMCID: PMC270340 DOI: 10.1128/jcm.29.11.2368-2374.1991] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Yersinia enterocolitica is a major enteric pathogen associated with a wide variety of clinical and immunologic manifestations, including transfusion-associated disease, from which there is a high mortality. Although previously rare in the United States, in the late 1980s Y. enterocolitica O:3 emerged as the predominant serotype in the United States, as it has been in Canada, Europe, and Japan. Epidemiologic investigation of this serogroup has been hampered by the limited availability of a phage typing system and the fact that Y. enterocolitica harbors few plasmids that are useful as strain markers. We therefore analyzed whole-cell DNA restriction fragment length polymorphisms of rRNA genes (ribotyping) to study a group of 61 (50 human, 11 porcine) Y. enterocolitica isolates. Initially, 20 different restriction enzymes were used: NciI appeared to give the best discrimination of hybridization banding patterns (ribotypes) within Y. enterocolitica O:3. Ribotyping distinguished seven clones among all the study isolates and four clones within Y. enterocolitica O:3 (53 isolates studied) and clearly differentiated Y. enterocolitica O:3 from Y. enterocolitica O:9; O:1,2,3; O:20; and O:5,27. Most serogroup O:3 isolates belonged to two clones, ribotypes I and II, including 23 of 24 Y. enterocolitica O:3 (13 human, 11 porcine chitterling) isolates recovered from a recent outbreak of Y. enterocolitica in children in Atlanta associated with chitterling preparation and 3 transfusion-associated O:3 isolates from the United States. Y. enterocolitica O:3 ribotypes I and II were also isolated in Japan, ribotypes II and IV were isolated in Belgium, and ribotype I was isolated in Canada. Ribotype patterns I and II corresponded to phage types 9b and 8, respectively. Ribotyping was able to distinguish individual strains of Y. enterocolitica O:3, but suggests that a limited number of clones have disseminated within the United States and globally. The finding of identical ribotype patterns in chitterling and human specimens from the Atlanta outbreak supports epidemiologic evidence that swine were the source of infection and major reservoir for Y. enterocolitica O:3.
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Affiliation(s)
- H M Blumberg
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30303
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25
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Sarafian SK, Woods TC, Knapp JS, Swaminathan B, Morse SA. Molecular characterization of Haemophilus ducreyi by ribosomal DNA fingerprinting. J Clin Microbiol 1991; 29:1949-54. [PMID: 1663518 PMCID: PMC270240 DOI: 10.1128/jcm.29.9.1949-1954.1991] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Intraspecies genotypic heterogeneity among Haemophilus ducreyi isolates was examined by using genomic fingerprints with rRNA from Escherichia coli as a probe. DNA from 44 isolates of H. ducreyi was digested by restriction endonuclease HincII or HindIII, separated by agarose gel electrophoresis, transferred to nylon membranes, and hybridized with 32P-labeled 16S and 23S rRNA. HincII digests yielded four hybridization patterns (ribotypes), whereas HindIII digests yielded eight ribotypes. Four HincII and five HindIII ribotypes were observed among 14 H. ducreyi isolates collected within a period of 1 month in Kenya, where chancroid is endemic. In contrast, one HincII and two HindIII ribotypes were observed among 28 isolates collected during the Orange County, Calif., chancroid epidemic that occurred in 1981 and 1982. The plasmid content, in conjunction with ribotyping, provided additional differentiation among some isolates of H. ducreyi. This study demonstrates that ribotyping of H. ducreyi may be used to study the epidemiology of chancroid.
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Affiliation(s)
- S K Sarafian
- Division of Sexually Transmitted Diseases Laboratory Research, Center for Infectious Diseases, Centers for Disease Control, Atlanta, Georgia 30333
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26
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Kiehlbauch JA, Plikaytis BD, Swaminathan B, Cameron DN, Wachsmuth IK. Restriction fragment length polymorphisms in the ribosomal genes for species identification and subtyping of aerotolerant Campylobacter species. J Clin Microbiol 1991; 29:1670-6. [PMID: 1684797 PMCID: PMC270182 DOI: 10.1128/jcm.29.8.1670-1676.1991] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Whole-cell chromosomal digests of 84 strains of aerotolerant Campylobacter (AC) were examined by using PvuII restriction fragment length polymorphisms of rRNA genes followed by hybridization with Escherichia coli 16S and 23S rRNA (ribotyping). The AC strains belonged to Campylobacter cryaerophila (n = 13) and a newly defined species, "C. butzleri" (n = 64). Strains of C. cryaerophila belonged to two hybridization groups: DNA group 1A (including the type strain of C. cryaerophila) and DNA group 1B (J. A. Kiehlbauch, D. J. Brenner, M. A. Nicholson, C. N. Baker, C. M. Patton, A. G. Steigerwalt, and I. K. Wachsmuth, J. Clin. Microbiol. 29:376-385, 1991). Six AC strains not classified as C. cryaerophila or "C. butzleri" were also included. All 35 sporadic human and animal isolates of "C. butzleri" sent to the Centers for Disease Control for identification showed different ribotype patterns. However, most "C. butzleri" strains contained common bands at approximately 3.0, 6.2, 12.0, and 15.0 kb; the 3.0-kb band was present in all but four strains. An additional 23 strains of "C. butzleri," isolated as part of special studies, contained the 3.0-kb band. Thus, on the basis of visual identification of the 3.0-kb band, 94% of available strains were correctly identified as "C. butzleri." Ribotyping demonstrated that C. cryaerophila strains (DNA groups 1A and 1B) were different from C. butzleri strains. All C. cryaerophila strains demonstrated a common ribosomal DNA restriction fragment of 3.2 kb; DNA group 1B strains contained an additional common band at 2.6 kb. Ribotyping patterns of AC species were easily distinguished from patterns of other Campylobacter, Helicobacter, and Wolinella species.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J A Kiehlbauch
- Enteric Diseases Branch, Center for Infectious Diseases, Centers for Disease Control, Atlanta, Georgia 30333
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27
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Baloga AO, Harlander SK. Comparison of methods for discrimination between strains of Listeria monocytogenes from epidemiological surveys. Appl Environ Microbiol 1991; 57:2324-31. [PMID: 1662932 PMCID: PMC183571 DOI: 10.1128/aem.57.8.2324-2331.1991] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Total cellular DNA from 28 strains of Listeria monocytogenes isolated from food implicated in food-borne illness and from patients with listeriosis was digested with the restriction endonucleases HindIII, HaeIII, and EcoRI. Following agarose gel electrophoresis, the fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for classifying L. monocytogenes strains, and the resulting subtypes were compared with serotyping and multilocus enzyme electrophoresis classification schemes. A total of 15 distinct and identical groups were obtained when genomic DNA was digested with either HindIII or HaeIII. The most discriminating enzyme for ribotyping of strains was EcoRI, which divided the 28 strains of L. monocytogenes into 6 ribotype groups. DNA fingerprinting and ribotyping differentiated L. monocytogenes from other Listeria spp., including L. ivanovii, L. welshimeri, and L. innocua as well as the lactic acid bacteria Lactococcus lactis subsp. lactis and subsp. cremoris. L. monocytogenes strains isolated from four independent food-borne illness incidents were analyzed by all typing methods. Patient and product isolates were not distinguishable by serotyping, ribotyping, or multilocus enzyme electrophoresis. DNA fingerprinting was the only method capable of differentiating these strains, or conversely, of proving relatedness of patient-product pairs of isolates. This method was a relatively simple, sensitive, reproducible, and highly discriminating method for epidemiological tracking of L. monocytogenes implicated in food-borne illness.
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Affiliation(s)
- A O Baloga
- Department of Food Science and Nutrition, University of Minnesota, St. Paul 55108
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28
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Garaizar J, Kaufmann ME, Pitt TL. Comparison of ribotyping with conventional methods for the type identification of Enterobacter cloacae. J Clin Microbiol 1991; 29:1303-7. [PMID: 1715880 PMCID: PMC270105 DOI: 10.1128/jcm.29.7.1303-1307.1991] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
An Escherichia coli rRNA probe was compared with a combination of O serotyping, phage susceptibility, and biotype pattern for the type identification of strains of Enterobacter cloacae. Forty-five isolates of E. cloacae from 36 patients in nine hospitals were examined. By conventional typing, only 26 (57.7%) could be assigned to a specific serotype and 6 (13.3%) were autoagglutinating owing to rough lipopolysaccharide antigens. All isolates could be assigned to one of three biotypes, but many phage sensitivity patterns were evident. Twenty-nine distinct strains were identified by combined typing. Probing of EcoRI and BamHI digests of chromosomal DNA with a cDNA copy of E. coli rRNA proved to be highly discriminating between strains. Thirty different ribotypes based on 28 bands were recorded. Overall, agreement between the ribotyping and combined typing methods was good (84.4%), and discrepancies were generally confined to serologically unclassifiable strains and variability in biotype codes. Ribotyping was reproducible, and five of six pairs of isolates from the same and different patients gave identical hybridization profiles on separate occasions. We conclude that ribotyping is a highly discriminatory and reproducible method for the typing of E. cloacae, but in most outbreaks it offers little increase in discrimination over traditional methods.
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Affiliation(s)
- J Garaizar
- Division of Hospital Infection, Central Public Health Laboratory, London, United Kingdom
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29
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Williams AM, Collins MD. DNA fingerprinting of Streptococcus uberis based on polymorphism of DNA encoding rRNA. Lett Appl Microbiol 1991; 12:23-8. [PMID: 1370023 DOI: 10.1111/j.1472-765x.1991.tb00493.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rRNA gene restriction patterns of strains of Streptococcus uberis and Strep. parauberis were determined. Chromosomal DNA was digested with endonucleases and probed with radiolabelled DNA complementary to rRNA synthesized by random oligonucleotide priming using reverse transcriptase. Reproducible restriction patterns were obtained which readily distinguished Strep. uberis and Strep. parauberis. In addition, considerable variations in the patterns at the intra-specific level were observed indicating that rRNA gene restriction profiles are of epidemiological, as well as taxonomic value.
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Affiliation(s)
- A M Williams
- Department of Microbiology, AFRC Institute of Food Research, Reading Laboratory, Shinfield, UK
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30
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Picard B, Denis JB, Decoux G, Goullet P. Computer-assisted statistical analyses of enzyme and ribosomal DNA electrophoretic polymorphism in Yersinia. Electrophoresis 1991; 12:264-9. [PMID: 1676966 DOI: 10.1002/elps.1150120406] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The intra- and inter-species differentiation of 90 strains of Yersinia belonging to six species were studied independently by computer-assisted statistical analysis of data from enzyme electrophoretic polymorphism and ribosomal DNA (rDNA) restriction fragment length polymorphism. Two correspondence analyses (CA) demonstrated the concordance between the bacterial classification obtained from enzymatic and genomic data. This concordance was reinforced by an algorithm of the correspondence established between the two dendrograms drawn from previous computations. Comparison of CA with similarity analysis (also called "numerical taxonomy") indicated that the intra- and inter-species differentiation obtained by the two methods are similar. The advantage of CA is that it gives a synthetic geometrical representation of the results (factorial planes), displaying both the main features of the clusters of strains (location and dispersion) and their essential character (i.e.: enzyme electrophoretic variant, rDNA fragment size).
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Affiliation(s)
- B Picard
- Laboratoire de Microbiologie, Faculté de Médecine Xavier Bichat, Université Paris VII, France
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31
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Graves LM, Swaminathan B, Reeves MW, Wenger J. Ribosomal DNA fingerprinting of Listeria monocytogenes using a digoxigenin-labeled DNA probe. Eur J Epidemiol 1991; 7:77-82. [PMID: 1902798 DOI: 10.1007/bf00221345] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A nonisotopic ribosomal DNA fingerprinting technique was developed for the characterization of Listeria monocytogenes. Plasmid pKK3535 (a pBR322-derived plasmid containing rrnB ribosomal RNA operon of Escherichia coli) was labeled with digoxigenin-11-dUTP by random priming and used to probe EcoRI fragments of L. monocytogenes chromosomal DNA on nylon filters. The method was successfully applied to the characterization of two sets of patient and food isolates of L. monocytogenes.
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Affiliation(s)
- L M Graves
- Meningitis and Special Pathogens Branch, Centers for Disease Control, Atlanta, Georgia 30333
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32
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Holmes B, Costas M, Wood AC, Owen RJ, Morgan DD. Differentiation of Achromobacter-like strains from human blood by DNA restriction endonuclease digest and ribosomal RNA gene probe patterns. Epidemiol Infect 1990; 105:541-51. [PMID: 2249718 PMCID: PMC2271814 DOI: 10.1017/s0950268800048160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Variation amongst Achromobacter-like strains was examined by DNA restriction endonuclease digestion and rDNA gene patterns generated using a non-radioactive probe. Chromosomal DNA was extracted from 12 cultures representing Achromobacter groups B, E and F, all from human blood cultures. DNA fingerprinting using EcoRI, Hae III or HindIII sub-divided the strains in a similar manner to that obtained by their protein patterns. The HaeIII patterns, with their small number of bands, were the easiest to interpret. The EcoRI patterns included a species-species triplet of bands but minor band patterns allowed further differentiation. The Achromobacter group F strains comprised a separate taxon and were distinct from the group B and E strains by all techniques examined. The study demonstrates that, in addition to total DNA digest analysis, rDNA gene restriction patterns provide a simple but discriminatory electrophoretic method for distinguishing within Achromobacter groups B and E.
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Affiliation(s)
- B Holmes
- National Collection of Type Cultures, Central Public Health Laboratory, London, England
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33
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Nastasi A, Mammina C, Villafrate MR, Pontello M, Corbellini M. rRNA probing of chromosomal DNA of epidemic and sporadic isolates of Salmonella enterica subsp. enterica serovar Kottbus from northern and southern Italy. Eur J Epidemiol 1990; 6:407-11. [PMID: 2091942 DOI: 10.1007/bf00151716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fifty-two strains of Salmonella enterica subsp. enterica serovar Kottbus, identified at the Centres of Enterobacteriaceae of Northern and Southern Italy, were investigated by molecular genetic methods. Thirteen isolates were recovered during two food-poisoning outbreaks that occurred in May 1987 in Lombardy. The rDNA gene restriction patterns, obtained by probing endonuclease cleaved chromosomal DNA with photobiotin labeled Escherichia coli rRNA, revealed some heterogeneity among strains isolated from Southern Italy, whereas Northern Italy isolates exhibited virtually identical banding patterns.
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Affiliation(s)
- A Nastasi
- Istituto di Igiene, Università di Palermo, Italy
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34
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Nastasi A, Villafrate MR, Mammina C, Pontello M, Ricci M. Molecular analysis of strains of Shigella boydii isolated in northern and southern Italy. Res Microbiol 1990; 141:1163-72. [PMID: 2092367 DOI: 10.1016/0923-2508(90)90089-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the years 1981-1988, Shigella boydii played a very limited role in the aetiology of diarrhoeal disease in Italy. However, between September and November, 1985, 19 isolates of serotype 2 were recovered in northern Italy from a dysentery outbreak which occurred in a geriatrics hospital in Abbiategrasso (Milan, Lombardy) and seven were identified in southern Italy during the period January-July, 1986 from apparently unrelated infection cases occurring in Brindisi (Apulia). These isolates were compared by molecular methods to seven strains of S. boydii of serotype 2 isolated since 1981 from the same geographic areas. Plasmid DNA analysis showed a large variety of patterns, whereas hybridization of chromosomal DNA with E. coli rRNA identified only two different profiles, one of which was exclusively found in all isolates from the hospital outbreak. No differences were detected among rDNA patterns of the remaining strains of S. boydii, irrespective of their geographic origin. These findings are consistent with the hypothesis that the infrequent cases of infection from S. boydii of serotype 2 which occurred during the years under study could probably be attributed to two different bacterial clones. Hybridization procedure and detection of hybrids were simplified by replacement of radioactive labelling of rRNA by the use of photobiotin.
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Affiliation(s)
- A Nastasi
- Istituto di Igiene G. D'Alessandro, Università degli Studi di Palermo, Italy
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35
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Costas M, Holmes B, Wood AC. Numerical analysis of electrophoretic protein patterns of Providencia stuartii strains from urine, wound and other clinical sources. THE JOURNAL OF APPLIED BACTERIOLOGY 1990; 68:505-18. [PMID: 2370236 DOI: 10.1111/j.1365-2672.1990.tb02903.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Eighty-six strains of Providencia stuartii (mainly of human origin) were characterized by one-dimensional SDS-PAGE of cellular proteins. The strains came from various countries; 52 were from urine, 11 from wounds, five from blood (one of these also from urine), four from ear infections, two each from faeces and sputum, one from 'alimentation' and nine from unknown sources. The protein patterns, which contained 45 to 50 discrete bands, were highly reproducible. The patterns of 46 Prov. stuartii strains (selected to represent the full range of protein pattern diversity) plus those of the type strains of the four other Providencia species were used as the basis for two numerical analyses. In the first, which included all the protein bands, the Prov. stuartii strains formed 13 clusters at the 88% S level. In the second analysis, in which the principal protein bands (in the 33.8-40.7 kDa range) were excluded, 45 of the 46 Prov. stuartii strains formed a single cluster at the 82% S level, whilst the four Providencia reference strains remained unclustered. The 40 strains of Prov. stuartii not included in the cluster analysis were assigned to a protein type by calculating their similarity with the strains in the database used for the cluster analysis. We conclude that high resolution PAGE combined with computerized analysis of protein patterns provides the basis for typing clinical strains of Prov. stuartii. Reference strains of each of the 13 PAGE types identified are available from NCTC for inclusion in future studies.
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Affiliation(s)
- M Costas
- National Collection of Type Cultures, Central Public Health Laboratory, London, UK
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36
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Pitcher D, Saunders N, Owen R. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 1989. [DOI: 10.1111/j.1472-765x.1989.tb00262.x] [Citation(s) in RCA: 1532] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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