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Journal articles on the topic 'PFGE typing'

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Published: 4 June 2021
Last updated: 3 February 2022

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1

Chen, Kuo-Wei, Hsiu-Jung Lo, Yu-Hui Lin, and Shu-Ying Li. "Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan." Journal of Medical Microbiology 54, no. 3 (March 1, 2005): 249–58. http://dx.doi.org/10.1099/jmm.0.45829-0.

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This report describes the investigation of the genetic profiles of 53 Candida albicans isolates collected from 18 hospitals in Taiwan using three PFGE-based typing methods (PFGE karyotyping, and PFGE of SfiI and BssHII restriction fragments) and one repetitive-sequence-PCR (rep-PCR) method. All four methods were able to identify clonal related isolates from the same patients. PFGE-BssHII exhibited the highest discriminatory power by discriminating 40 genotypes, followed by PFGE-SfiI (35 genotypes) and then by rep-PCR (31 genotypes), while PFGE karyotyping exhibited the lowest discriminatory power (19 genotypes). High discriminatory power can also be achieved by combining typing methods with different typing mechanisms, such as rep-PCR and PFGE-based typing methods. The results also showed that the genotype of each isolate was patient-specific and not associated with the source of the isolation, geographic origin or antifungal resistance.
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2

Doran, Geraldine, Dearbhaile Morris, Colette O'Hare, Niall DeLappe, Bernard Bradshaw, Geraldine Corbett-Feeney, and Martin Cormican. "Cost-Effective Application of Pulsed-Field Gel Electrophoresis to Typing of Salmonella enterica Serovar Typhimurium." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8236–40. http://dx.doi.org/10.1128/aem.71.12.8236-8240.2005.

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ABSTRACT Salmonella enterica serovar Typhimurium is frequently isolated from humans and animals. Phage typing is historically the first-line reference typing technique in Europe. It is rapid and convenient for laboratories with appropriate training and experience, and costs of consumables are low. Phage typing and pulsed-field gel electrophoresis (PFGE) were performed on 503 isolates of serovar Typhimurium. Twenty-nine phage types and 53 PFGE patterns were observed. Most isolates of phage types DT104, DT104b, and U310 are not distinguishable from other members of their phage type by PFGE. By contrast, PFGE of isolates of phage types DT193 and U302 shows great heterogeneity. Analysis of experience with PFGE and phage typing can facilitate the selective application of PFGE to maximize the yield of epidemiologically relevant additional information while controlling costs.
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3

LOUIE, M., S. READ, L. LOUIE, K. ZIEBELL, K. RAHN, A. BORCZYK, and H. LIOR. "Molecular typing methods to investigate transmission of Escherichia coli O157[ratio ]H7 from cattle to humans." Epidemiology and Infection 123, no. 1 (August 1999): 17–24. http://dx.doi.org/10.1017/s0950268899002551.

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The utility of phage typing, pulsed-field gel electrophoresis (PFGE), and plasmid profile analysis was compared, to differentiate between Canadian Escherichia coli O157[ratio ]H7 strains of human (n = 27) and cattle (n = 24) origin. The diversity indices for phage typing, plasmid analysis and PFGE were 0·85, 0·69 and 0·93, respectively. PFGE and phage typing were also applied to study the role of direct transmission of E. coli O157[ratio ]H7 from cattle to humans on isolates collected from two separate farm outbreaks. PFGE showed that more than one E. coli O157[ratio ]H7 strain with varying PFGE DNA subtype profiles, may be responsible for an outbreak, and that more than one E. coli O157[ratio ]H7 subtype may be circulating on a particular farm at any one time. To our knowledge, this is one of the first reports where PFGE typing was used to verify the direct transmission of E. coli O157[ratio ]H7 from cattle to humans.
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4

D'Agata, Erika M. C., Monique M. Gerrits, Yi-Wei Tang, M. Samore, and Johannes G. Kusters. "Comparison of Pulsed-Field Gel Electrophoresis and Amplified Fragment-Length Polymorphism for Epidemiological Investigations of Common Nosocomial Pathogens." Infection Control & Hospital Epidemiology 22, no. 9 (September 2001): 550–54. http://dx.doi.org/10.1086/501950.

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AbstractObjective:To compare molecular typing by amplified fragment-length polymorphism (AFLP) analysis with pulsed-field gel electrophoresis (PFGE) with respect to the ability to differentiate between epidemiologically related and unrelated isolates of common nosocomial pathogens recovered during a period of endemicity.Design:Retrospective laboratory analysis.Setting:Tertiary-care institution.Methods:17 isolates ofAcinetobacter baumannii,22 isolates ofPseudomonas aeruginosa,and 22 vancomycin-resistantEnterococcus faecium(VRE) were typed by both methods.Results:AFLP generated comparable results to PFGE forA baumanniiandP aeruginosaisolates; both methods identified epidemiologically related and unrelated isolates. However, strain typing of VRE isolates produced discordant results between the two methods. PFGE identified 10 different strain types and differentiated between all epidemiologically related and unrelated isolates. In contrast, AFLP generated only five different strain types, three of which contained both epidemiologically related and unrelated isolates.Conclusion:Molecular typing by AFLP is comparable to PFGE forA baumanniiandP aeruginosaisolates. For VRE isolates, however, PFGE remains the method of choice.
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Tang, Yi-Wei, Michael G. Waddington, Douglas H. Smith, Janice M. Manahan, Peggy C. Kohner, Leanne M. Highsmith, Haijing Li, et al. "Comparison of Protein A Gene Sequencing with Pulsed-Field Gel Electrophoresis and Epidemiologic Data for Molecular Typing of Methicillin-Resistant Staphylococcus aureus." Journal of Clinical Microbiology 38, no. 4 (2000): 1347–51. http://dx.doi.org/10.1128/jcm.38.4.1347-1351.2000.

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The epidemiologic relatedness of methicillin-resistantStaphylococcus aureus (MRSA) isolates is currently determined by analysis of chromosomal DNA restriction patterns by pulsed-field gel electrophoresis (PFGE). We have evaluated an alternative typing system (MicroSeq StaphTrack Kit; Perkin-Elmer Biosystems) based on the sequence analysis of the chromosomally encoded polymorphic repeat X region of the S. aureus protein A (spa) gene. A total of 69 clinical MRSA isolates were divided into 18 groups according to the number and nucleotide sequences of the spa repeats. Molecular typing results obtained both by spa sequencing and from the PFGE patterns were concordant except for one group, which contained 20 isolates recovered over a 2-year period from hospitalized patients at the Mayo Clinic. Although the spa typing patterns were indistinguishable for those isolates, PFGE analysis yielded seven related but distinguishable patterns. Further coagulase gene sequence analysis subtyped those 20 strains into four groups which followed distinct temporal and geographic distributions. During a 2-year epidemic period there were up to 7 fragment changes in PFGE patterns among epidemiologically related isolates, suggesting that PFGE may be unsuitable for long-term typing of strains involved in epidemics. Although more limited than PFGE in discriminatory power, spa sequencing analysis could be used as a screening method for typing of MRSA strains because of the shorter turnaround time, ease of use, and the inherent advantages of sequence analysis, storage, and sharing of information.
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6

Shaaly, Aishath, Marit Gjerde Tellevik, Nina Langeland, E. Arne Høiby, and Roland Jureen. "Comparison of serotyping, pulsed field gel electrophoresis and amplified fragment length polymorphism for typing of Streptococcus pneumoniae." Journal of Medical Microbiology 54, no. 5 (May 1, 2005): 467–72. http://dx.doi.org/10.1099/jmm.0.45912-0.

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The aim of the present study was to compare serotyping, PFGE and AFLP for typing of Streptococcus pneumoniae with regard to discriminatory power, typeability and typing system concordance. Thirty-four isolates from cerobrospinal fluid and 34 time-matched blood culture isolates collected from in-patients at two hospitals in western Norway during the period from January 1994 to May 2002 were included in the study. The discriminatory powers of serotyping, PFGE and AFLP were 0.93, 0.99 and 0.95, respectively. The typeabilities for serotyping, PFGE and AFLP were 1, 1 and 0.99, respectively. A good concordance was shown between all the typing methods. Serotyping would most probably have a higher discriminatory power if further subtyping had been performed. PFGE was more discriminatory than AFLP, and AFLP grouped more-distantly related isolates together. The two typing methods thus provided different information, and therefore both could be useful adjuncts to serotyping for the characterization of S. pneumoniae.
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7

Boekhout, Teun, Marga Kamp, and Eveline Guého. "Molecular typing ofMalasseziaspecies with PFGE and RAPD." Medical Mycology 36, no. 6 (January 1998): 365–72. http://dx.doi.org/10.1080/02681219880000581.

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8

de Boer, Paulo, Birgitta Duim, Alan Rigter, Jan van der Plas, Wilma F. Jacobs-Reitsma, and Jaap A. Wagenaar. "Computer-Assisted Analysis and Epidemiological Value of Genotyping Methods for Campylobacter jejuni andCampylobacter coli." Journal of Clinical Microbiology 38, no. 5 (2000): 1940–46. http://dx.doi.org/10.1128/jcm.38.5.1940-1946.2000.

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For epidemiological tracing of the thermotolerantCampylobacter species C. jejuni and C. coli, reliable and highly discriminatory typing techniques are necessary. In this study the genotyping techniques of flagellin typing (flaA typing), pulsed-field gel electrophoresis (PFGE), automated ribotyping, and amplified fragment length polymorphism (AFLP) fingerprinting were compared. The following aspects were compared: computer-assisted analysis, discriminatory power, and use for epidemiological typing of campylobacters. A set of 50 campylobacter poultry isolates from The Netherlands and neighboring countries was analyzed. Computer-assisted analysis made cluster analysis possible and eased the designation of different genotypes. AFLP fingerprinting was the most discriminatory technique, identifying 41 distinct genotypes, while PFGE identified 38 different types, flaA typing discriminated 31 different types, and ribotyping discriminated 26 different types. Furthermore, AFLP analysis was the most suitable method for computer-assisted data analysis. In some cases combining the results of AFLP fingerprinting, PFGE, and flaA typing increased our ability to differentiate strains that appeared genetically related. We conclude that AFLP is a highly discriminatory typing method and well suited for computer-assisted data analysis; however, for optimal typing of campylobacters, a combination of multiple typing methods is needed.
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9

Torpdahl, M., G. Sørensen, S. Ethelberg, G. Sandø, K. Gammelgard, and L. Jannok Porsbo. "A regional outbreak of S. Typhimurium in Denmark and identification of the source using MLVA typing." Eurosurveillance 11, no. 5 (May 1, 2006): 5–6. http://dx.doi.org/10.2807/esm.11.05.00621-en.

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In Denmark, as part of the national laboratory-based surveillance system of human enteric infections, all S. Typhimurium isolates are currently sub-typed using phage typing, antibiogram typing, and pulsed-field gel electrophoresis (PFGE). However, the discriminatory ability of PFGE is not always high enough to discriminate within certain phage types, and it is not always possible to separate unrelated and related isolates. We have therefore applied multiple locus variable number of tandem repeats analysis (MLVA) for surveillance typing of S. Typhimurium since 2004. In May and June 2005, an outbreak with 26 cases of S. Typhimurium infection was identified by MLVA. The isolates were fully sensitive and had one of the most frequently occurring Danish phage types (DT12) and PFGE types. S. Typhimurium DT12 isolates from routine surveillance of animals and food were typed using MLVA and PFGE for comparison with the human isolates. The typing results revealed that an isolate from a pig herd and its corresponding slaughterhouse located in the same geographic region as the outbreak had the same PFGE and MLVA type as the human isolates. In contrast, all other DT12 isolates investigated, which had the same PFGE profile, had different MLVA types. The conclusion that the pig herd was the source of the human infections was supported by patient information, and pork from the herd stopped entering the market on 29 June. MLVA may contribute significantly to both surveillance and outbreak investigations of S. Typhimurium, as without MLVA typing this outbreak would not have been found nor its origin traced.
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10

Garaizar, Javier, Nuria L�pez-Molina, Idoia Laconcha, Dorte Lau Baggesen, Aitor Rementeria, Ana Vivanco, Ana Audicana, and Ildefonso Perales. "Suitability of PCR Fingerprinting, Infrequent-Restriction-Site PCR, and Pulsed-Field Gel Electrophoresis, Combined with Computerized Gel Analysis, in Library Typing of Salmonella enterica Serovar Enteritidis." Applied and Environmental Microbiology 66, no. 12 (December 1, 2000): 5273–81. http://dx.doi.org/10.1128/aem.66.12.5273-5281.2000.

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ABSTRACT Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate of PCR fingerprinting interassay and intercenter reproducibility was low and was only increased when DNA samples were extracted at the same time and amplified with the same reaction mixtures. Reproducibility of IRS-PCR technique reached 100%, but discrimination was low (D= 0.52). The PFGE procedure showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI,BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.0 software. Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance ofSalmonella serovar Enteritidis, specially if the prevalence of genetic events that could be responsible for changes in PFGE profiles in this serovar was low.
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11

Sloos, J. H., L. Dijkshoorn, L. Vogel, and C. P. A. van Boven. "Performance of Phenotypic and Genotypic Methods To Determine the Clinical Relevance of Serial Blood Isolates ofStaphylococcus epidermidis in Patients with Septicemia." Journal of Clinical Microbiology 38, no. 7 (2000): 2488–93. http://dx.doi.org/10.1128/jcm.38.7.2488-2493.2000.

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Five typing methods, including biotyping (API ID32; BioMérieux, Marcy l'Etoile, France), quantitative antibiogram typing based on actual zone sizes, plasmid typing, randomly amplified polymorphic DNA (RAPD) analysis (with primer M13 and primer set ERIC-2–1026), and pulsed-field gel electrophoresis (PFGE), were compared with a previously performed method of DNA fingerprinting by AFLP (amplified fragment length polymorphism analysis) for their performance in the typing of blood isolates of Staphylococcus epidermidis. Sixteen epidemiologically unrelated strains and 11 sets of four blood culture isolates from 11 patients with septicemia were used. The stabilities and reproducibilities of the patterns, the discriminatory capacities of the methods, and the ability to apply the methods to blood culture isolates were used as performance criteria. All strains tested were typeable by each method, and the patterns were stable and reproducible. The numbers of different types within the collection of 16 epidemiologically different isolates were 5 by biotyping, 14 by antibiogram typing, 4 by plasmid typing, 9 by the RAPD assay (combination of results with primer M13 and primer set ERIC-2–1026), and 16 by PFGE. Within the 11 sets of four blood culture isolates the types found by quantitative antibiogram typing, plasmid typing, and PFGE were unique for each set, whereas by biotyping and RAPD analysis some types were observed in more than one set. The results of biotyping did not correspond with the results of the other methods or the results of AFLP. For 6 of the 11 sets, the results of all methods except those of biotyping corresponded completely. Quantitative antibiogram typing, PFGE, and AFLP proved to be the most accurate of the six typing methods tested.
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Park, Eun-Hee, Mi-Hee Kim, Joung-A. Kim, Nan-Sook Han, Ju Hyeoun Lee, Sang Gi Min, Yon Koung Park, Seong Hyun Jin, Gu Young Jeong, and Jae Hun Bin. "Molecular Typing of Legionella pneumophila Isolated in Busan, Using PFGE." Journal of Life Science 15, no. 2 (April 1, 2005): 161–68. http://dx.doi.org/10.5352/jls.2005.15.2.161.

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13

Golding, George R., Jennifer L. Campbell, Dave J. Spreitzer, Joe Veyhl, Kathy Surynicz, Andrew Simor, and Michael R. Mulvey. "A Preliminary Guideline for the Assignment of Methicillin-ResistantStaphylococcus aureusto a Canadian Pulsed-Field Gel Electrophoresis Epidemic Type UsingspaTyping." Canadian Journal of Infectious Diseases and Medical Microbiology 19, no. 4 (2008): 273–81. http://dx.doi.org/10.1155/2008/754249.

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BACKGROUND: Increasing rates of methicillin-resistantStaphylococcus aureus(MRSA) infections on a global scale is a major health concern. In Canada, there are 10 known epidemic types of MRSA as determined by pulsed-field gel electrophoresis (PFGE). Despite the excellent discriminatory power of PFGE, there are several disadvantages of using this technique, such as high degree of labour intensity and the inability to easily develop an MRSA typing database due to the subjective interpretation of results.OBJECTIVES: The purpose of the present study was to determine whetherspatyping, an established DNA sequence-based typing method, could be used as an alternative to PFGE for the typing of Canadian MRSA (CMRSA) epidemic isolates.RESULTS:spatypes were determined for 1488 CMRSA isolates, and the method was analyzed for its ability to identify and cluster CMRSA1-10 strains. Minimal spanning tree analysis of 1452spatypes revealed individual clonal clusters for PFGE epidemic types CMRSA1, 2, 7 and 8, butspatyping could not distinguish CMRSA5 from CMRSA9 and CMRSA10, and CMRSA3 from CMRSA4 and CMRSA6. However, specificspatypes were generally associated with only one PFGE epidemic type. Based on these results, aspatyping guideline for CMRSA isolates was developed and tested using the first 300 MRSA isolates received in 2007 through the Canadian Nosocomial Infection Surveillance Program.CONCLUSIONS: The high concordance ofspatypes with PFGE epidemic types using this guideline demonstrated the feasibility ofspatyping as a more rapid and less technically demanding alternative typing method for MRSA in Canada.
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ATYEO, R. F., S. L. OXBERRY, and D. J. HAMPSON. "Analysis of Serpulina hyodysenteriae strain variation and its molecular epidemiology using pulsed-field gel electrophoresis." Epidemiology and Infection 123, no. 1 (August 1999): 133–38. http://dx.doi.org/10.1017/s0950268899002691.

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Pulsed-field gel electrophoresis (PFGE) was applied as a molecular typing tool for the spirochaete Serpulina hyodysenteriae, the agent of swine dysentery. Analysis of a collection of 40 mainly Australian isolates, previously characterized by other methods, divided these into 23 PFGE types. This confirmed that there are many strains of the spirochaete in Australia. PFGE was more discriminatory for strain typing than both multilocus enzyme electrophoresis and serotyping. It had similar discriminatory power to restriction endonuclease analysis, but the results of PFGE were easier to interpret. When applied to 29 isolates collected from 4 farms over periods of up to 8 years, 2 PFGE patterns were found on 3 farms, and a single pattern on the other. In each case a new strain had apparently emerged as a variant of an original parent strain. PFGE was found to be a powerful technique for investigating the molecular epidemiology of swine dysentery outbreaks.
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Vautor, Eric, Corinne Jay, Nicolas Chevalier, Nathalie Visomblin, Guy Vernet, and Michel Pépin. "Characterization of 26 Isolates of Staphylococcus Aureus, Predominantly from Dairy Sheep, Using Four Different Techniques of Molecular Epidemiology." Journal of Veterinary Diagnostic Investigation 17, no. 4 (July 2005): 363–68. http://dx.doi.org/10.1177/104063870501700411.

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Little information is available regarding the molecular epidemiology of Staphylococcus aureus–induced mastitis in dairy sheep. In this study, 4 different typing techniques were compared in typing 26 S. aureus isolates, predominantly from cases of subclinical mastitis in dairy ewes. The 4 techniques were pulsed-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP) on 2 genes (coagulase and clumping factor B), randomly amplified polymorphic DNA–polymerase chain reaction (PCR) (RAPD-PCR), and multilocus sequence typing (MLST). On the basis of discriminatory power as the key parameter of typing systems, MLST and PFGE were found to be the most powerful techniques. The MLST and PFGE could contribute to epidemiological surveillance and evaluation of mastitis control programs, by documenting prevalence and dissemination of endemic clones in infected populations. The results of this study show that a single clone of S. aureus is widely distributed in infected ewe mammary glands.
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Wain, John, Tran T. Hien, Phillippa Connerton, Tahir Ali, Christopher M. Parry, Nguyen T. T. Chinh, Ha Vinh, et al. "Molecular Typing of Multiple-Antibiotic-ResistantSalmonella enterica Serovar Typhi from Vietnam: Application to Acute and Relapse Cases of Typhoid Fever." Journal of Clinical Microbiology 37, no. 8 (1999): 2466–72. http://dx.doi.org/10.1128/jcm.37.8.2466-2472.1999.

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The rate of multiple-antibiotic resistance is increasing amongSalmonella enterica serovar Typhi strains in Southeast Asia. Pulsed-field gel electrophoresis (PFGE) and other typing methods were used to analyze drug-resistant and -susceptible organisms isolated from patients with typhoid fever in several districts in southern Vietnam. Multiple PFGE and phage typing patterns were detected, although individual patients were infected with strains of a single type. The PFGE patterns were stable when the S. entericaserovar Typhi strains were passaged many times in vitro on laboratory medium. Paired S. enterica serovar Typhi isolates recovered from the blood and bone marrow of individual patients exhibited similar PFGE patterns. Typing of S. enterica serovar Typhi isolates from patients with relapses of typhoid indicated that the majority of relapses were caused by the same S. enterica serovar Typhi strain that was isolated during the initial infection. However, some individuals were infected with distinct and presumably newly acquiredS. enterica serovar Typhi isolates.
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Sulakvelidze, Alexander, Merab Kekelidze, Tsaro Gomelauri, Yingkang Deng, Nino Khetsuriani, Ketino Kobaidze, Aruni De Zoysa, Androulla Efstratiou, J. Glenn Morris, and Paata Imnadze. "Diphtheria in the Republic of Georgia: Use of Molecular Typing Techniques for Characterization of Corynebacterium diphtheriae Strains." Journal of Clinical Microbiology 37, no. 10 (1999): 3265–70. http://dx.doi.org/10.1128/jcm.37.10.3265-3270.1999.

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Sixty-six Corynebacterium diphtheriae strains (62 of the gravis biotype and 4 of the mitis biotype) isolated during the Georgian diphtheria epidemic of 1993 to 1998 and 13 non-GeorgianC. diphtheriae strains (10 Russian and 3 reference isolates) were characterized by (i) biotyping, (ii) toxigenicity testing with the Elek assay and PCR, (iii) the randomly amplified polymorphic DNA (RAPD) technique, and (iv) pulsed-field gel electrophoresis (PFGE). Fifteen selected strains were ribotyped. Six RAPD types and 15 PFGE patterns were identified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribotyped. The Georgian epidemic apparently was caused by one major clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epidemic strain(s) isolated during the concurrent diphtheria epidemic in Russia. A dendrogram based on the PFGE patterns revealed profound differences between the minor (nonpredominant) epidemic strains found in Georgia and Russia. The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains were improved to enable rapid and convenient molecular typing of the strains. The RAPD technique was adequate for biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at discriminating between epidemiologically related and unrelated isolates.
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Hänninen, Marja-Liisa, Sini Pajarre, Marja-Liisa Klossner, and Hilpi Rautelin. "Typing of Human Campylobacter jejuniIsolates in Finland by Pulsed-Field Gel Electrophoresis." Journal of Clinical Microbiology 36, no. 6 (1998): 1787–89. http://dx.doi.org/10.1128/jcm.36.6.1787-1789.1998.

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A total of 69 pulsed-field gel electrophoresis (PFGE) types were identified among 176 Campylobacter jejuni isolates from Finnish patients. In two geographic areas studied, five predominant PFGE types comprised over 40% of the isolates. One-third of the isolates had unique PFGE types. In small outbreaks, identical PFGE patterns were demonstrated, indicating a common source of infection.
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Deplano, Ariane, Annette Schuermans, Johan Van Eldere, Wolfgang Witte, Hèléne Meugnier, Jerome Etienne, Hajo Grundmann, et al. "Multicenter Evaluation of Epidemiological Typing of Methicillin-Resistant Staphylococcus aureus Strains by Repetitive-Element PCR Analysis." Journal of Clinical Microbiology 38, no. 10 (2000): 3527–33. http://dx.doi.org/10.1128/jcm.38.10.3527-3533.2000.

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Rapid and efficient epidemiologic typing systems would be useful to monitor transmission of methicillin-resistant Staphylococcus aureus (MRSA) at both local and interregional levels. To evaluate the intralaboratory performance and interlaboratory reproducibility of three recently developed repeat-element PCR (rep-PCR) methods for the typing of MRSA, 50 MRSA strains characterized by pulsed-field gel electrophoresis (PFGE) (SmaI) analysis and epidemiological data were blindly typed by inter-IS256, 16S-23S ribosomal DNA (rDNA), and MP3 PCR in 12 laboratories in eight countries using standard reagents and protocols. Performance of typing was defined by reproducibility (R), discriminatory power (D), and agreement with PFGE analysis. Interlaboratory reproducibility of pattern and type classification was assessed visually and using gel analysis software. Each typing method showed a different performance level in each center. In the center performing best with each method, inter-IS256 PCR typing achieved R = 100% and D = 100%; 16S-23S rDNA PCR, R = 100% and D = 82%; and MP3 PCR, R = 80% and D = 83%. Concordance between rep-PCR type and PFGE type ranged by center: 70 to 90% for inter-IS256PCR, 44 to 57% for 16S-23S rDNA PCR, and 53 to 54% for MP3 PCR analysis. In conclusion, the performance of inter-IS256 PCR typing was similar to that of PFGE analysis in some but not all centers, whereas other rep-PCR protocols showed lower discrimination and intralaboratory reproducibility. None of these assays, however, was sufficiently reproducible for interlaboratory exchange of data.
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Feng, Jia-Li, Jin-Yan Lin, Xiao-Bing Jiang, Ou Zhang, Jiang-Feng Zhu, Jing Hu, Lei Shi, and Qing Chen. "Development of an ERIC sequence typing scheme for Laribacter hongkongensis, an emerging pathogen associated with community-acquired gastroenteritis and travellers’ diarrhoea." Journal of Medical Microbiology 62, no. 5 (May 1, 2013): 701–7. http://dx.doi.org/10.1099/jmm.0.049858-0.

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Laribacter hongkongensis is a potential emerging pathogen, associated with community-acquired diarrhoea. For epidemiological purposes, different molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing, have been developed for this pathogen. However, these methods require specialized equipment and costly reagents. More importantly, they are labour-intensive and time-consuming, which is not really suitable for foodborne disease outbreak investigations. In this study, we developed a rapid and reliable method using 22-mer primers specific for the enterobacterial repetitive intergenic consensus sequence (ERIC). PFGE was used for comparison, to evaluate this method. A total of 81 isolates of L. hongkongensis were examined: 79 isolates recovered from food of diverse origins and two strains derived from patients with L. hongkongensis-associated infection. Typing patterns and clustering analysis indicated that the 81 L. hongkongensis isolates were grouped into 21 and 13 genotypes by ERIC-PCR and PFGE, respectively. ERIC-PCR was found as reproducible as PFGE. A high percentage (70.4 %) of isolates yielded distinguishable ERIC-PCR patterns, which were concordant with the results from PFGE. These results suggest that ERIC-PCR is valuable for use in the epidemiological investigation of L. hongkongensis.
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Staley, Christopher, and Valerie J. Harwood. "The Use of Genetic Typing Methods to Discriminate Among Strains of Vibrio cholerae, V. parahaemolyticus, and V. vulnificus." Journal of AOAC INTERNATIONAL 93, no. 5 (September 1, 2010): 1553–69. http://dx.doi.org/10.1093/jaoac/93.5.1553.

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Abstract This review article summarizes the findings of recent typing studies conducted on Vibrio cholerae, V. parahaemolyticus, and V. vulnificus. The DNA-based methods used to type the Vibrio spp. include whole genome approaches, such as pulsed field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic (REP)-PCR, single gene targets, and multiple gene targets (multilocus approaches). The goals of these studies include establishing the relatedness of isolates from disease epidemics, discriminating among strains with more or less potential to cause disease or epidemics, and exploring the population biology of these waterborne pathogens. PFGE was consistently among the more discriminatory of the typing methods for all three Vibrio spp., and was useful for tracing the temporal and geographic relatedness of epidemic strains of V. cholerae and V. parahaemolyticus. However, PFGE did not group V. vulnificus strains according to the genotypes that have been proposed as markers of virulence potential. Typing methods that target repetitive elements distributed throughout the genome, such as BOX-PCR and REP-PCR, and DNA sequence-based methods, such as multilocus sequence typing, were also highly discriminatory and, in some cases, superior to PFGE for phylogenetic analysis and identification of strains with high epidemic or virulence potential. As typing methods and strategies are refined and used, the epidemiology, virulence potential, and ecology of these pathogenic Vibrio spp. will become better understood.
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Akinyemi, Kabiru Olusegun, Werner Philipp, Wolfgang Beyer, and Reinhard Böhm. "Application of phage typing and pulsed-field gel electrophoresis to analyse Salmonella enterica isolates from a suspected outbreak in Lagos, Nigeria." Journal of Infection in Developing Countries 4, no. 12 (September 10, 2010): 828–33. http://dx.doi.org/10.3855/jidc.744.

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Introduction: Inadequate potable water supply and poor sanitation predispose to food- and water-borne diseases associated with Salmonella enterica serovars in developing countries. In this study the possible source of an unprecedented upsurge of Salmonella-associated community gastroenteritis was traced using both phage-typing and pulsed-field gel electrophoresis (PFGE). Methodology: Nineteen Salmonella Typhimurium (three sporadic isolates included) and 13 Salmonella Enteritidis isolates from clinical, animal, and environmental samples were subjected to antimicrobial susceptibility testing, phage-typing, and PFGE analysis using standard procedures. Results: Eleven (68.8%) of the 16 outbreak-related multidrug resistant S. Typhimurium belonged to DT 71 phage type with cluster PFGE type X3, representing the most prevalent strain identified among human, animal, and environmental isolates. The remaining five (31.2%) outbreak-related strains reacted but did not conform with clear phage types (RDNC) with cluster PFGE types X1 and X2 (96.8% similarity). Sporadic strains were untypable and belonged to X4 PFGE type. However, the evaluated S. Enteritidis strains that were multidrug resistant without a definite phage type belonged to PFGE cluster type X1e and were identified among the water and human strains. None of the Typhimurium and Enteritdis isolates was resistant to the fluoroquinolone antibiotics that were evaluated. Conclusion: This study emphasizes the epidemiological usefulness of PFGE typing in the detection of emerging strains of multipledrug resistant Salmonella, particularly S. Typhimurium DT71, that pose serious health implications in our environment. The study provides epidemiological links between environmental reservoirs and human infection in this community.
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FOLEY, STEVEN L., SHABBIR SIMJEE, JIANGHONG MENG, DAVID G. WHITE, PATRICK F. McDERMOTT, and SHAOHUA ZHAO. "Evaluation of Molecular Typing Methods for Escherichia coli O157:H7 Isolates from Cattle, Food, and Humans." Journal of Food Protection 67, no. 4 (April 1, 2004): 651–57. http://dx.doi.org/10.4315/0362-028x-67.4.651.

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Escherichia coli O157:H7, a Shiga toxin–producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for β-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.
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24

Ostojić, Maja. "Epidemiologic Genotyping of Methicillin-Resistant Staphylococcus aureus (MRSA) by Pulsed-Field Gel Electrophoresis (PFGE)." Bosnian Journal of Basic Medical Sciences 8, no. 3 (August 20, 2008): 259–65. http://dx.doi.org/10.17305/bjbms.2008.2930.

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čćStaphylococcus aureus has long been recognized as one of the leading cause of hospital infections all over the world. Increased frequency of methicillin-resistant Staphylococcus aureus (MRSA) in hospitalized patients and possibility of vancomycin resistance requires rapid and reliable characterization of isolates and control of MRSA spread in hospitals. Typing of isolates helps to understand pathogenesis and route of the hospital pathogen spread. In this study in the analysis of an outbreak of MRSA infections in one surgical ward, we used pulsed-field gel electrophoresis (PFGE) as a method of typing. PFGE revealed one epidemic strain type A in 13 out of 16 patients, and another two types (type B in two patients and type C in one patient). Discussing the typing results in the ward has changed the admission policy of patients with infected vascular ulcers who were then cured as outpatients, and admitted for surgery after that. This policy resulted with the stopping of the outbreak; during next 2,5 year there was no further MRSA outbreak in the ward. PFGE also showed subtypes which enabled the insight into dynamics of MRSA strain changes during the outbreak. PFGE could be recommended as a screening method in the MRSA outbreak analysis. Because of it’s high discriminatory power still remains the gold standard for MRSA typing
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25

Silbert, Suzane, Michael A. Pfaller, Richard J. Hollis, Afonso L. Barth, and Hélio S. Sader. "Evaluation of Three Molecular Typing Techniques for Nonfermentative Gram-Negative Bacilli." Infection Control & Hospital Epidemiology 25, no. 10 (October 2004): 847–51. http://dx.doi.org/10.1086/502307.

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AbstractObjective:To evaluate three different DNA techniques for typing nonfermentative gram-negative bacilli isolated from Latin American hospitals.Design:One hundred twenty-six nonfermentative gram-negative bacilli were typed.Participants:Pseudomonas aeruginosa(n = 64) andAcinetobacter baumannii(n = 42) samples were obtained from blood cultures of patients admitted to 10 medical centers in Latin America during 1998 andStenotrophomonas maltophilia(n = 20) samples were obtained from patients admitted to the Hospital São Paulo between 1999 and 2001.Methods:All samples were typed using automated ribotyping, PFGE, and ERIC-PCR. The discriminatory power for each technique was calculated using Hunter's generalized formula.Results:All strains could be typed by automated ribotyping and ERIC-PCR, but two strains (1.6%) were not typeable by PFGE. All three techniques showed 100% reproducibility. The time to obtain the results was shorter for automated ribotyping and ERIC-PCR compared with PFGE. Likewise, the costs for ERIC-PCR and PFGE were lower than those for automated ribotyping. The interpretation of results was more complicated and more difficult with ERIC-PCR than with both PFGE and automated ribotyping. All techniques presented excellent discriminatory power forP. aeruginosa(0.98). PFGE presented the highest discriminatory power (0.94) forA. baumannii,and both PFGE and ERIC-PCR showed higher discriminatory power (0.90 for both) than automated ribotyping (0.82) for S.maltophilia.Conclusions:PFGE showed the highest discriminatory power for typing these nonfermentative gram-negative bacilli. However, automated ribotyping and ERIC-PCR can provide results in a shorter time period with similar discriminatory power.
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Singh, Samir P., Hugh Salamon, Carol J. Lahti, Mehran Farid-Moyer, and Peter M. Small. "Use of Pulsed-Field Gel Electrophoresis for Molecular Epidemiologic and Population Genetic Studies ofMycobacterium tuberculosis †." Journal of Clinical Microbiology 37, no. 6 (1999): 1927–31. http://dx.doi.org/10.1128/jcm.37.6.1927-1931.1999.

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Pulsed-field gel electrophoresis (PFGE) is a powerful molecular biology technique which has provided important insights into the epidemiology and population biology of many pathogens. However, few studies have used PFGE for the molecular epidemiology ofMycobacterium tuberculosis. A laboratory protocol was developed to determine the typeability, stability, and reproducibility of PFGE typing of M. tuberculosis. Formal data-analytical techniques were used to assess the genetic diversity elucidated by PFGE analyses using four separate restriction enzymes and by IS6110 RFLP analyses, as well as to assess the concordance among these typing methods. One hundred epidemiologically characterized clinical isolates of M. tuberculosis were genotyped with four different PFGE enzymes (AseI, DraI,SpeI, and XbaI), as well as by RFLP analysis with IS6110. Identical patterns were found among 34 isolates known to be genetically related, suggesting that the PFGE protocol is robust and reproducible. Among 66 isolates representing population-sampled cases, heterozygosity and information content dependency estimates indicate that all five genotyping systems capture quantitatively similar levels of genetic diversity. Nevertheless, comparisons between PFGE analyses and IS6110 typing reveals that PFGE provided more discrimination among isolates with fewer than five copies of IS6110 and less clustering in isolates with five or more copies. The comparisons confirm the hypothesis that the resolution of IS6110 RFLP genotyping is dependent upon the number of IS6110 elements in the genome of isolates. The general concordance among the results obtained with four independent enzymes suggests that M. tuberculosis is a clonal organism. The availability of a robust genotyping technique largely independent of repetitive elements has implications for the molecular epidemiology of M. tuberculosis.
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Bidet, Philippe, Valérie Lalande, Béatrice Salauze, Béatrice Burghoffer, Véronique Avesani, Michel Delmée, Anne Rossier, Frédéric Barbut, and Jean-Claude Petit. "Comparison of PCR-Ribotyping, Arbitrarily Primed PCR, and Pulsed-Field Gel Electrophoresis for Typing Clostridium difficile." Journal of Clinical Microbiology 38, no. 7 (2000): 2484–87. http://dx.doi.org/10.1128/jcm.38.7.2484-2487.2000.

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Clostridium difficile is now recognized as the major agent responsible for nosocomial diarrhea in adults. Among the genotyping methods available, arbitrarily primed PCR (AP-PCR), PCR-ribotyping, and pulsed-field gel electrophoresis (PFGE) have been widely used for investigating outbreaks of C. difficileinfections. However, the comparative typing ability, reproducibility, discriminatory power, and efficiency of these methods have not been fully investigated. We compared the results of three methods—AP-PCR with three different primers (AP3, AP4, and AP5), PCR-ribotyping, and PFGE (with SmaI endonuclease)—to differentiate 99 strains of C. difficile that had been previously serogrouped. Typing abilities were 100% for PCR-ribotyping and AP-PCR with AP3 and 90% for PFGE, due to early DNA degradation in strains from serogroup G. Reproducibilities were 100% for PCR-ribotyping and PFGE but only 88% for AP-PCR with AP3, 67% for AP-PCR with AP4, and 33% for AP-PCR with AP5. Discriminatory power for unrelated strains was >0.95 for all the methods but was lower for PCR-ribotyping among serogroups D and C. PCR-based methods were easier and quicker to perform, but their fingerprints were more difficult to interpret than those of PFGE. We conclude that PCR-ribotyping offers the best combination of advantages as an initial typing tool for C. difficile.
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28

CHUNG, YUN-HEE, YOUNG-IL KWON, SOO-YOUNG KIM, SHUK-HO KIM, BOK-KWON LEE, and YUN-HEE CHANG. "Antimicrobial Susceptibilities and Epidemiological Analysis of Salmonella Enteritidis Isolates in Korea by Phage Typing and Pulsed-Field Gel Electrophoresis." Journal of Food Protection 67, no. 2 (February 1, 2004): 264–70. http://dx.doi.org/10.4315/0362-028x-67.2.264.

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A total of 81 isolates of Salmonella Enteritidis were analyzed by antibiotic susceptibility, phage typing, and pulsed-field gel electrophoresis (PFGE). Thirty-two isolates came from broiler carcasses and pig feces, and 49 isolates were from humans in Seoul and suburbs of Seoul, Korea. Antibiotic resistance was most prevalent among human isolates. Of human isolates, 89.8% were resistant to more than two antibiotics, while 64.7% of poultry isolates and 13.3% of pig isolates showed multiple resistance to more than two antibiotics. The most common phage type (PT) was PT1, followed by PT30 or 33, PT21 and PT20a. The isolates showed six PFGE patterns with XbaI or SpeI digestion, and five PFGE patterns with NotI digestion. But a single pattern, PFGE X1, S1, or N1, was predominant and the rest of the PFGE patterns differed by only one or two bands. Results indicated the spread of a genetically related clone of Salmonella Enteritidis in foods and humans in Korea and that phage typing as well as PFGE may offer an improved level of discrimination for the epidemiological investigation of Salmonella Enteritidis.
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29

Saito, Mitsumasa, Akiko Umeda, and Shin-ichi Yoshida. "Subtyping of Haemophilus influenzaeStrains by Pulsed-Field Gel Electrophoresis." Journal of Clinical Microbiology 37, no. 7 (1999): 2142–47. http://dx.doi.org/10.1128/jcm.37.7.2142-2147.1999.

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A total of 200 isolates of Haemophilus influenzae were analyzed by serotyping, biotyping, and pulsed-field gel electrophoresis (PFGE). A total of 178 epidemiologically unrelated strains of H. influenzae demonstrated a variety of genome patterns by PFGE, and 165 genotypes were thus obtained in this study. PFGE typing proved to have a much stronger discriminatory power than either serotyping or biotyping. Six serotype b strains were all classified into discrete genotypes. A PFGE analysis of 18 strains obtained from the nasopharynx, blood, and cerebrospinal fluid of patients with meningitis also supported the hypothesis that invasive H. influenzaedisseminates from the nasopharynx to the bloodstream and then subsequently to other body sites. PFGE typing of 10 other strains isolated from household contacts of patients with H. influenzae infection revealed that the strain that caused theH. influenzae infection often colonized the nasopharynges of household contacts. Our findings suggest that PFGE analysis is useful for the epidemiological study of H. influenzaeinfection, even when the invasive disease is caused by serotype b strains.
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30

Dmowska, Katarzyna, Kinga Wieczorek, Orla Lynch, and Jacek Osek. "Typing of Listeria Monocytogenes Isolated from Slaughtered Cattle and Beef Meat." Bulletin of the Veterinary Institute in Pulawy 57, no. 2 (June 1, 2013): 179–83. http://dx.doi.org/10.2478/bvip-2013-0033.

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Abstract A total of 135 L. monocytogenes strains isolated from slaughtered cattle and beef meat were tested by the pulsed field gel electrophoresis (PFGE). The AscI restriction analysis revealed a genetic heterogeneity among investigated isolates since 31, 9, and 35 profiles were distinguished among hide, carcass, and meat strains, respectively. The PFGE profiles of the isolates were also analysed in relation to serotypes, virulence genes, and antimicrobial resistance. It was shown that strains displaying the same PFGE type were of the same serotype while correlation between pulsotype and antimicrobial resistance was poor. The obtained results suggest that a cross-contamination between bovine hides and carcasses may occur during the slaughter process. Moreover, identification of identical PFGE types among L. monocytogenes found during a study period may suggest a common source of contamination or presence of persistent strains able to survive for a long time. These results emphasise the importance of molecular subtyping methods, including PFGE, in monitoring and tracking pathogen contamination along food chain.
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31

Zhou, Haijian, Hongyu Ren, Bingqing Zhu, Biao Kan, Jianguo Xu, and Zhujun Shao. "Optimization of Pulsed-Field Gel Electrophoresis for Legionella pneumophila Subtyping." Applied and Environmental Microbiology 76, no. 5 (January 8, 2010): 1334–40. http://dx.doi.org/10.1128/aem.01455-09.

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ABSTRACT A total of 32 strains of Legionella pneumophila were used to optimize pulsed-field gel electrophoresis (PFGE) for subtyping of L. pneumophila. Twenty-six isolates of L. pneumophila with various origins and 11 isolates from five different water systems were used as the panels. For optimization of electrophoretic parameters (EPs) of SfiI PFGE, 26 isolates were analyzed with SfiI digestion, using four EPs yielding the same D value. The EP of a switch time of 5 to 50 s for 21 h had the smallest similarity coefficients and was declared the optimal EP for SfiI PFGE of L. pneumophila. By software analysis and pilot study, AscI was chosen as another PFGE enzyme. AscI PFGE could cluster the isolates from each water system into the same or very similar patterns and had a high degree of typing concordance with other molecular methods. In evaluating the discriminatory power of AscI with the panel of 26 isolates, AscI PFGE gave one single pattern and a D value of 100%. AscI PFGE had a high discriminatory power and a high degree of consistency with epidemiological data and other molecular typing methods for L. pneumophila subtyping, and hence, AscI could be used as a restriction enzyme in PFGE subtyping of L. pneumophila.
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32

Salipante, Stephen J., Dhruba J. SenGupta, Lisa A. Cummings, Tyler A. Land, Daniel R. Hoogestraat, and Brad T. Cookson. "Application of Whole-Genome Sequencing for Bacterial Strain Typing in Molecular Epidemiology." Journal of Clinical Microbiology 53, no. 4 (January 28, 2015): 1072–79. http://dx.doi.org/10.1128/jcm.03385-14.

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Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistantEnterococcus faecium(n= 19), methicillin-resistantStaphylococcus aureus(n= 17), andAcinetobacter baumannii(n= 15). WGS was highly reproducible (average ≤ 0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P= 5.6 × 10−8to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. ForA. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.
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33

Burucoa, Christophe, Vincent Lhomme, and Jean Louis Fauchere. "Performance Criteria of DNA Fingerprinting Methods for Typing of Helicobacter pylori Isolates: Experimental Results and Meta-Analysis." Journal of Clinical Microbiology 37, no. 12 (1999): 4071–80. http://dx.doi.org/10.1128/jcm.37.12.4071-4080.1999.

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Typing systems are used to discriminate between isolates ofHelicobacter pylori for epidemiological and clinical purposes. Discriminatory power and typeability are important performance criteria of typing systems. Discriminatory power refers to the ability to differentiate among unrelated isolates; it is quantitatively expressed by the discriminatory index (DI). Typeability refers to the ability of the method to provide an unambiguous result for each isolate analyzed; it is quantitatively expressed by the percentage of typeable isolates. We evaluated the discriminatory power and the typeability of the most currently used DNA fingerprinting methods for the typing of H. pyloriisolates: ribotyping, PCR-based restriction fragment length polymorphism (PCR-RFLP) analysis, and random amplified polymorphism DNA (RAPD) analysis. Forty epidemiologically unrelated clinical isolates were selected to constitute a test population adapted to the evaluation of these performance criteria. A meta-analysis of typeability and discriminatory power was conducted retrospectively with raw data from published studies in which ribotyping, PCR-RFLP, RAPD, repetitive extragenic palindromic DNA sequence-based PCR (REP-PCR), or pulsed-field gel electrophoresis (PFGE) was used. Experimental results and the meta-analysis demonstrated the optimal typeability (100%) and the excellent discriminatory powers of PCR-based typing methods: RAPD analysis, DIs, 0.99 to 1; REP-PCR, DI, 0.99; and PCR-RFLP analysis, DIs, 0.70 to 0.97). Chromosome restriction-based typing methods (ribotyping and PFGE) are limited by a low typeability (12.5 to 75%) that strongly decreases their discriminatory powers: ribotyping, DI, 0.92; PFGE, DIs, 0.24 to 0.88. We do not recommend the use of ribotyping and PFGE for the typing of H. pylori isolates. We recommend the use of PCR-based methods.
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34

MILLER, T., P. G. BRAUN, K. FEHLHABER, R. PRAGER, Y. PFEIFER, and W. RABSCH. "Typing ofSalmonella entericaserovar Infantis isolates from 51 outbreaks in Germany between 1974 and 2009 by a novel phage-typing scheme." Epidemiology and Infection 142, no. 1 (March 21, 2013): 75–83. http://dx.doi.org/10.1017/s095026881300037x.

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SUMMARYWe developed a new phage-typing method and evaluated its application in combination withXbaI macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) as a useful tool for the long-term epidemiology ofSalmonella entericaserovar Infantis. In this study, we investigated 1008S.Infantis isolates recovered from humans, various animal species and food products from 1973 to 2009. The typing scheme is based on 17 typing phages, defining 61 different patterns within the strain collection. The experiments showed that phage typing is a reliable method for differentiation of outbreaks and sporadic clinical cases as well as for elucidation of chains of transmission. The combined analysis of phage typing and PFGE revealed the existence of epidemic clones with a high stability over time like PT29/XB27 which was identified in nosocomial salmonellosis, community outbreaks as well as in broiler chickens from 2002 to 2009.
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35

YOKOYAMA, EIJI, and MASAKO UCHIMURA. "Variable Number of Tandem Repeats and Pulsed-Field Gel Electrophoresis Cluster Analysis of Enterohemorrhagic Escherichia coli Serovar O157 Strains." Journal of Food Protection 70, no. 11 (November 1, 2007): 2583–88. http://dx.doi.org/10.4315/0362-028x-70.11.2583.

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Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.
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36

Shimizu, Akira, Manabu Fujita, Hideo Igarashi, Michihiro Takagi, Naoko Nagase, Asako Sasaki, and Junichi Kawano. "Characterization of Staphylococcus aureus Coagulase Type VII Isolates from Staphylococcal Food Poisoning Outbreaks (1980–1995) in Tokyo, Japan, by Pulsed-Field Gel Electrophoresis." Journal of Clinical Microbiology 38, no. 10 (2000): 3746–49. http://dx.doi.org/10.1128/jcm.38.10.3746-3749.2000.

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Staphylococcus aureus coagulase type VII strains have been the strains most frequently isolated from staphylococcal food poisoning outbreaks in Tokyo, Japan. We applied pulsed-field gel electrophoresis (PFGE) of chromosomal DNA digested withSmaI to characterize 129 coagulase type VII strains. These were isolated from 129 cases occurring in outbreaks in 35 districts during a 16-year period (1980–1995). The 129 outbreak strains were classified into three types, designated A (n = 115), B (n = 10), and C (n = 4). Types A and C were further divided into 33 (A1 to A33) and 4 (C1 to C4) subtypes, respectively. Strains of the same subtypes were isolated from food poisoning cases in the same districts at time intervals of 1 or 2 to 5 years. PFGE typing appears to be a useful method for subdividing strains of S. aureus coagulase type VII. A combination of coagulase typing and PFGE typing would provide more detailed information than the former method alone in epidemiologic investigations of staphylococcal food poisoning.
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37

Zafar, A., M. Stone, S. Ibrahim, Z. Parveen, Z. Hasan, E. Khan, R. Hasan, J. Wain, and K. Bamford. "Prevalent genotypes of meticillin-resistant Staphylococcus aureus: report from Pakistan." Journal of Medical Microbiology 60, no. 1 (January 1, 2011): 56–62. http://dx.doi.org/10.1099/jmm.0.022707-0.

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Meticillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen in Pakistan and is emerging in the community. This is one of the first reports of the prevalent genotypes of MRSA in both hospital and community settings in Pakistan. Isolates collected in 2006–2007 were characterized by PFGE, staphylococcal cassette chromosome mec (SCCmec) typing and multilocus sequence typing (MLST). PFGE identified nine pulsotypes, the majority of isolates belonging to pulsotypes A (n=70) and B (n=38), which were predominant among hospital-onset MRSA (HO-MRSA) and community-onset MRSA (CO-MRSA) isolates, respectively. Among the HO-MRSA isolates, variants of SCCmec type III were prevalent, whilst SCCmec type IV or variants were predominant in the CO-MRSA isolates. MLST identified two principal sequence types, ST8 and ST239. An association was observed between ST8, PFGE pulsotype B and SCCmec type IV in the CO-MRSA (ST8-MRSA-IV). Similarly, ST239, PFGE pulsotype A and SCCmec type III were associated with HO-MRSA (ST239-MRSA-III). Therefore, the prevalent genotypes circulating in Pakistan at the time of study were ST8-MRSA-IV and ST239-MRSA-III in the community and hospital settings, respectively. A set of HO-MRSA isolates collected in 1997 were characterized by PFGE and SCCmec typing for comparison. The isolates belonged to two PFGE pulsotypes (A, n=28; B, n=11) and contained just two SCCmec types. These results suggest that an increase in genetic diversity occurred over the period 1997–2007 as a result of either microevolution or the importation of strains from surrounding areas.
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38

Shabir, Sahida, Katherine J. Hardy, Waseem S. Abbasi, Claire L. McMurray, Salman A. Malik, Chand Wattal, and Peter M. Hawkey. "Epidemiological typing of meticillin-resistant Staphylococcus aureus isolates from Pakistan and India." Journal of Medical Microbiology 59, no. 3 (March 1, 2010): 330–37. http://dx.doi.org/10.1099/jmm.0.014910-0.

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The levels of meticillin-resistant Staphylococcus aureus (MRSA) in Pakistan and India are known to be high, but few studies have described the epidemiology of the different MRSA clones present. In order to gain an understanding of the epidemiology of MRSA within this region, 60 MRSA isolates from Pakistan (49) and India (11) were genotyped. All isolates were typed using PFGE, staphylococcal interspersed repeat units (SIRUs), a restriction–modification method and staphylococcal cassette chromosome mec (SCCmec) typing. A subset of isolates that were distinct by PFGE and SIRUs were typed using multilocus sequence typing (MLST). Clonal complex (CC) 8 was the dominant clonal complex (57/60) and was present in both Pakistan and India. Within CC8, there were 10 SIRU profiles and 24 PFGE profiles. Two SIRU profiles were present in isolates from both India and Pakistan, whilst seven were distinct for Pakistan and one for India. All PFGE profiles were distinct for each of the two countries. Thirty-four of the 57 isolates carried SCCmec type III/IIIa and the remainder carried type IV SCCmec. MLST analysis of 14 CC8 isolates with diverse SIRU and PFGE profiles showed that all were single-locus variants, with nine belonging to sequence type (ST) 239, three to ST8 and two to ST113. From a single hospital in Pakistan, three isolates belonged to CC30 and all were indistinguishable by PFGE and SIRUs and carried the Panton–Valentine leukocidin gene. Thus, epidemiological typing of strains from three distinct locations in India and Pakistan revealed the predominance of one clonal complex and highly related STs. The ability of SIRUs and PFGE to differentiate within ST239 demonstrates their utility in defining local epidemiology in these countries.
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39

Cheng, Tingting, Xiaochao Shi, Wei Yong, Jianping Wang, Guoxiang Xie, and Jie Ding. "Molecular typing of Shigella sonnei isolates circulating in Nanjing, China, 2007–2011." Journal of Infection in Developing Countries 8, no. 12 (December 15, 2014): 1525–32. http://dx.doi.org/10.3855/jidc.4933.

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Introduction: Shigellosis is a major public health concern worldwide. This study intended to assess the baseline genotyping data among local Shigella sonnei strains spanning over five years. Methodology: Fifty non-repeat clinical strains of S. sonnei isolated from stools of patients in different hospitals in Nanjing, China, were studied. Three subtyping tools, pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable-number tandem-repeat (VNTR) analysis (MLVA), were used for routinely subtyping local S. sonnei. Results: DNA sequencing only identified two sequence types (STs) among the 50 isolates in the MLST profiles, whereas PFGE and MLVA both showed suitable discriminatory power and yielded 19 and 30 different patterns, respectively. The major PFGE pattern comprised 21 strains isolated from different years. A total of four complexes were identified by MLVA, with the isolates differing by a single locus (single-locus variants). Conclusions: The S. sonnei strains circulating in Nanjing, China, in 2007–2011 originated from different clones with a degree of diversity. Most of the clones were closely related to each other. Overall, the strains were distinguishable by PFGE and MLVA. MLVA based on eight selected VNTR loci represented a more favorable degree of discrimination than did PFGE and may be a reliable complement for PFGE for routine subtyping of S. sonnei. The problems of MLST in subtyping regarding S. sonnei were also demonstrated.
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40

Nair, S., C. L. Poh, Y. S. Lim, L. Tay, and K. T. Goh. "Genome fingerprinting of Salmonella typhi by pulsed-field gel electrophoresis for subtyping common phage types." Epidemiology and Infection 113, no. 3 (December 1994): 391–402. http://dx.doi.org/10.1017/s0950268800068400.

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SUMMARYThe genomic DNA of 39 strains of Salmonella typhi isolated from local residents and patients who had visited countries in the Asian region was analysed for restriction fragment length polymorphisms (RFLP). Pulsed-field gel electrophoretic (PFGE) analysis of Xba I- and Spe I-generated genomic restriction fragments established 22 PFGE types whereas phage typing differentiated the 39 isolates into 9 distinct phage types. This study showed that PFGE is more discriminatory than phage typing as it is capable of subtyping S. typhi strains of the same phage types. Genetic relatedness among the isolates was determined. Seven major clusters were identified at SABSof > 0–80 and the remaining 13 isolates were distributed into minor clusters which were related at SABS of less than O.80. In conclusion, PFGE analysis in conjunction with distance matrix analysis served as a useful tool for delineating common S. typhi phage types of diverse origins from different geographical localesand separated in time.
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Liu, Yudong, Hui Wang, Na Du, Enhua Shen, Hongbin Chen, Junqi Niu, Huifen Ye, and Minjun Chen. "Molecular Evidence for Spread of Two Major Methicillin-Resistant Staphylococcus aureus Clones with a Unique Geographic Distribution in Chinese Hospitals." Antimicrobial Agents and Chemotherapy 53, no. 2 (November 24, 2008): 512–18. http://dx.doi.org/10.1128/aac.00804-08.

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ABSTRACT Methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) is a serious problem worldwide. To investigate the molecular epidemiology of MRSA isolates in China, a total of 702 MRSA isolates collected from 18 teaching hospitals in 14 cities between 2005 and 2006 were characterized by antibiogram analysis, pulsed-field gel electrophoresis (PFGE), staphylococcal cassette chromosome mec (SCCmec) typing, and spa typing; and 102 isolates were selected for multilocus sequence typing (MLST). Overall, SCCmec type III was the most popular type and was found in 541 isolates (77.1%), followed by SCCmec type II (109/702; 15.5%). Twenty-four PFGE types were obtained among 395 isolates collected in 2005, and 18 spa types were obtained among 702 isolates. spa type t030, which corresponded to PFEG types A to E, constituted 52.0% (365/702) of all isolates, and isolates of this type were present in all 14 cities; spa type t037, which corresponded to PFGE types F and G, accounted for 25.5% (179/702) of all isolates, and isolates of this type were identified in 12 cities. The two spa genotypes belonged to sequence type 239 (ST239) and carried SCCmec type III. spa type t002, which included isolates of PFGE types L to T, made up 16.0% (112/702) of the isolates that belonged to ST5 and SCCmec type II, and isolates of this type were distributed in 12 cities. The distribution of spa types varied among the regions. spa type t002 was the most common in Dalian (53.4%) and Shenyang (44.4%); spa type t037 was predominant in Shanghai (74.8%), whereas spa type t030 was the most common in the other cities. Two isolates from Guangzhou that harbored SCCmec type IVa with ST59 and ST88 were identified as community-associated MRSA. The prevalence of the Panton-Valentine leukocidin gene was 2.3%. The data documented two major epidemic MRSA clones, ST239-MRSA-SCCmec type III and ST5-MRSA-SCCmec type II, with unique geographic distributions across China.
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Aires-de-Sousa, Marta, Carlos E. S. R. Parente, Olney Vieira-da-Motta, Isabel C. F. Bonna, Denise A. Silva, and Herm�nia de Lencastre. "Characterization of Staphylococcus aureus Isolates from Buffalo, Bovine, Ovine, and Caprine Milk Samples Collected in Rio de Janeiro State, Brazil." Applied and Environmental Microbiology 73, no. 12 (April 20, 2007): 3845–49. http://dx.doi.org/10.1128/aem.00019-07.

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ABSTRACT Eighty-four staphylococcal isolates were obtained from milk samples from cows, sheep, goats, and buffalo with subclinical mastitis and from colonization samples from ostriches. The animals were hosted in 18 small dairy herds and an ostrich breeding located in 10 municipalities of the state of Rio de Janeiro, Brazil. Thirty isolates were identified as Staphylococcus aureus by biochemical and molecular techniques and were comparatively characterized by phenotypic and genotypic methods. The molecular characterization by pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing (MLST) revealed five clonal types (PFGE A, spa type t359, sequence type 747 [ST747]; PFGE B, spa type t1180, ST750; PFGE C, spa type t605, ST126; PFGE D, spa type t127, ST751; and PFGE F, spa type t002, ST5). None of the isolates harbored the Panton-Valentine leukocidin or exfoliative toxin D gene. The detection of major clone A (in 63% of the isolates) in different herds, among all animal species studied, and in infection and colonization samples evidenced its geographical spread among Rio de Janeiro State and no host preference among the animal species. Comparison with S. aureus from a human origin suggested that all but one clone found in the present study might be animal specific.
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43

VOGEL, BIRTE FONNESBECH, VIVIAN FUSSING, BENTE OJENIYI, LONE GRAM, and PETER AHRENS. "High-Resolution Genotyping of Listeria monocytogenes by Fluorescent Amplified Fragment Length Polymorphism Analysis Compared to Pulsed-Field Gel Electrophoresis, Random Amplified Polymorphic DNA Analysis, Ribotyping, and PCR–Restriction Fragment Length Polymorphism Analysis." Journal of Food Protection 67, no. 8 (August 1, 2004): 1656–65. http://dx.doi.org/10.4315/0362-028x-67.8.1656.

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The purpose of this study was to evaluate fluorescent amplified fragment length polymorphism (AFLP) analysis for the inter- and intraspecies differentiation of a collection of 96 strains of Listeria monocytogenes and 10 non–L. monocytogenes strains representing six other Listeria species of different origin. The AFLP technique was compared with three other molecular typing methods—ribotyping, random amplified polymorphic DNA analysis (RAPD), and pulsed-field gel electrophoresis (PFGE)—in terms of discriminatory ability. PCR–restriction fragment length polymorphism was included for virulence gene allele characterization. The 96 L. monocytogenes strains were divided into two major clusters by AFLP fingerprinting at a similarity level of 82% in concordance with the results of PFGE, RAPD, and ribotyping. One main cluster consisted of all of the 24 L. monocytogenes hly allele 1 strains, while another main cluster consisted of all of the 72 L. monocytogenes hly allele 2 strains. This indicates the existence of two distinct phylogenetic divisions. Isolates of the remaining Listeria species were not included in the clusters. AFLP, PFGE, and RAPD typing were highly discriminatory methods, with discrimination (D) indices of 0.974, 0.969, and 0.954, respectively, whereas ribotyping had a lower D index of 0.874. AFLP, PFGE, and RAPD typing showed some level of agreement in terms of strain grouping and differentiation. However, all three methods subdivided types of strains grouped by the other methods. Isolates with identical DNA profiles were distributed across the spectrum of origin. It was not possible to associate certain types with specific food sectors or clinical cases, which is indicative of the spread of L. monocytogenes clones across species. Overall, AFLP fingerprinting was suitable for the high-resolution genotyping of L. monocytogenes and had an equally high or higher differentiation power compared to PFGE or RAPD typing.
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Alkharsah, Khaled R., Suriya Rehman, Amani Alnimr, Asim Diab, Abbas Hawwari, and Sima Tokajian. "Molecular typing of MRSA isolates by spa and PFGE." Journal of King Saud University - Science 31, no. 4 (October 2019): 999–1004. http://dx.doi.org/10.1016/j.jksus.2018.07.018.

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45

Bahnan, Wael, Fuad Hashwa, George Araj, and Sima Tokajian. "emm typing, antibiotic resistance and PFGE analysis of Streptococcus pyogenes in Lebanon." Journal of Medical Microbiology 60, no. 1 (January 1, 2011): 98–101. http://dx.doi.org/10.1099/jmm.0.023317-0.

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One hundred and three Streptococcus pyogenes isolates recovered mainly from streptococcal throat infections in Lebanon were characterized by emm and PFGE typing. Thirty-three emm types and subtypes were detected among the isolates. PFGE was more discriminatory as a typing method. The prevalent emm types were emm1 (12.6 %), emm22 (8.7 %), emm28 (7.7 %), emm88 (7.7 %) and emm4 (6.8 %) and all isolates were susceptible to vancomycin and penicillin G. Ten per cent of the isolates were resistant to erythromycin and 3 % were resistant to erythromycin and clindamycin, showing the macrolide–lincosamide–streptogramin B phenotype. The emm sequences and PFGE pattern database that were generated in this study will serve as a basis for information for long-term evolutionary and epidemiological studies of local S. pyogenes recovered not only in Lebanon, but also in neighbouring countries.
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46

Gibson, J. R., C. Fitzgerald, and R. J. Owen. "Comparison of PFGE, ribotyping and phage-typing in the epidemiological analysis ofCampylobacter jejuniserotype HS2 infections." Epidemiology and Infection 115, no. 2 (October 1995): 215–25. http://dx.doi.org/10.1017/s0950268800058349.

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SummaryIn this study we have evaluated the ability of three typing methods, pulsed field gel electrophoresis (PFGE), phage-typing and ribotyping, to discriminate not only between strains of differing serotypes but also between strains within a single serotype, heat stable serotype 2 (HS2). Forty-five isolates derived from cases of campylobacter enteritis occurring in the Cardiff area were examined. These included 18, mostly HS2, strains associated with an outbreak. The typing results for these and a further 39 epidemiologically unrelated strains of serotype HS2 were compared. This is the first report documenting the use of PFGE in an epidemiological investigation ofCampylobacter jejuniin the UK. The results presented suggest that this technique is the most discriminatory of the three subtvping methods examined.
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47

Casini, B., P. Valentini, A. Baggiani, F. Torracca, C. Lorenzini, S. Frateschi, B. Matteoli, and G. Privitera. "Comparison of two molecular methods used for subtyping of Legionella pneumophila 1 strains isolated from a hospital water supply." Water Science and Technology 58, no. 3 (August 1, 2008): 683–88. http://dx.doi.org/10.2166/wst.2008.434.

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The results of the pulsed-field gel electrophoresis and the sequence-based typing (using the loci flaA, pilE, asd, mip, mompS and proA) were compared for subtyping of Legionella pneumophila 1 strains isolated from a hospital water supply. Molecular typing was carried out on 61 isolates (38% of the positive samples) selected on space and temporal criteria in order to follow the evolution of the water-system colonization. For all the 61 isolates, the sequence of the amplified mip gene fragment identified Legionella pneumophila strain Wadsworth. Genotype testing by PFGE analysis showed three different patterns, correspondent to three SBT types according to the allelic profiles. Both PFGE and SBT indicated the circulation and the persistence in the hospital potable water-system of three types randomly distributed in space and time. The two molecular methods adopted showed a 100% concordance, although a low degree of genetic heterogeneity characterized the isolates. The electrophoretic patterns were sufficiently unambiguous to consider PFGE a highly discriminatory typing method, but the SBT technique besides accurately characterizing isolates, was able to identify Legionella strains through analysis of the mip gene. A typing method with this level of discriminatory power has great potential for assisting in epidemiological studies.
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48

Cornelius, Angela J., Brent Gilpin, Philip Carter, Carolyn Nicol, and Stephen L. W. On. "Comparison of PCR Binary Typing (P-BIT), a New Approach to Epidemiological Subtyping of Campylobacter jejuni, with Serotyping, Pulsed-Field Gel Electrophoresis, and Multilocus Sequence Typing Methods." Applied and Environmental Microbiology 76, no. 5 (December 18, 2009): 1533–44. http://dx.doi.org/10.1128/aem.02215-09.

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ABSTRACT To overcome some of the deficiencies with current molecular typing schema for Campylobacter spp., we developed a prototype PCR binary typing (P-BIT) approach. We investigated the distribution of 68 gene targets in 58 Campylobacter jejuni strains, one Campylobacter lari strain, and two Campylobacter coli strains for this purpose. Gene targets were selected on the basis of distribution in multiple genomes or plasmids, and known or putative status as an epidemicity factor. Strains were examined with Penner serotyping, pulsed-field gel electrophoresis (PFGE; using SmaI and KpnI enzymes), and multilocus sequence typing (MLST) approaches for comparison. P-BIT provided 100% typeability for strains and gave a diversity index of 98.5%, compared with 97.0% for SmaI PFGE, 99.4% for KpnI PFGE, 96.1% for MLST, and 92.8% for serotyping. Numerical analysis of the P-BIT data clearly distinguished strains of the three Campylobacter species examined and correlated somewhat with MLST clonal complex assignations and with previous classifications of “high” and “low” risk. We identified 18 gene targets that conferred the same level of discrimination as the 68 initially examined. We conclude that P-BIT is a useful approach for subtyping, offering advantages of speed, cost, and potential for strain risk ranking unavailable from current molecular typing schema for Campylobacter spp.
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Cereda, Rosangela F., Ana C. Gales, Suzane Silbert, Ronald N. Jones, and Helio S. Sader. "Molecular Typing and Antimicrobial Susceptibility of Vancomycin-ResistantEnterococcus faeciumin Brazil." Infection Control & Hospital Epidemiology 23, no. 1 (January 2002): 19–22. http://dx.doi.org/10.1086/501962.

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AbstractObjectives:To characterize vancomycin-resistant enterococci (VRE) isolates and to evaluate the mode of dissemination of this pathogen in Brazil.Design:We collected 22 vancomycin-resistantEnterococcus faeciumisolates from 6 medical centers in Sao Paulo, Brazil, and 1 isolate from a medical center in Curitiba, Brazil.Participants:All Brazilian hospitals that had identified vancomycin-resistantE. faeciumup to the beginning of this study (late 1999) contributed isolates to the study.Methods:The isolates were susceptibility tested using the broth microdilution method and the E-test. The presence of vancomycin resistance genes (vanA,vanB,vanC1,vanC2-3, andvanD) was evaluated by polymerase chain reaction; molecular typing was performed by pulsed-field gel electrophoresis (PFGE).Results:ThevanA gene was demonstrated in all vancomycin-resistantE. faecium, except for 1 isolate. None of the vancomycin resistance genes cited above was detected in the isolate from Curitiba, which was the first vancomycin-resistantE. faeciumdescribed in Brazil. All isolates were resistant to ampicillin and teicoplanin. The main clone remains susceptible to doxycycline and chloramphenicol, but intermediate to quinupristin-dalfopristin. PFGE analysis demonstrated 7 major PFGE patterns. A unique PFGE pattern with 4 subtypes was detected in 17 isolates from 4 different hospitals.Conclusion:The results of our study indicate the occurrence of intra- and interhospital dissemination of VRE in Sao Paulo, Brazil.
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Brossier, Florence, Maïté Micaelo, Charles-Edouard Luyt, Qin Lu, Jean Chastre, Charlotte Arbelot, Jean-Louis Trouillet, et al. "Could the DiversiLab® semi-automated repetitive-sequence-based PCR be an acceptable technique for typing isolates ofPseudomonas aeruginosa? An answer from our experience and a review of the literature." Canadian Journal of Microbiology 61, no. 12 (December 2015): 903–12. http://dx.doi.org/10.1139/cjm-2015-0372.

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Recently the DiversiLab® (DL) system (bioMérieux) was developed as an automated platform that uses repetitive element polymerase chain reaction (rep-PCR) technology for standardized, reproducible DNA fingerprinting of bacteria. The purpose of this study was to evaluate the usefulness of DL rep-PCR for typing Pseudomonas aeruginosa isolates. The performance of DL rep-PCR was compared with that of pulsed-field gel electrophoresis (PFGE) in a prospective multicenter study of patients with ventilator-associated pneumonia due to P. aeruginosa, conducted in 3 intensive care units over a 31-month period. In total, 203 P. aeruginosa isolates from 66 patients, from whom at least 2 consecutive respiratory samples each were collected more than 48 h apart, were typed using DL rep-PCR. Forty isolates (corresponding to 20 patients) were also typed using PFGE of SpeI-digested DNA. The typeability was 100% with DL rep-PCR and 95% with PFGE. The discriminatory power was close for DL rep-PCR and for PFGE (Simpson’s diversity indices of 0.901 and 0.947, respectively). Insufficient agreement between DL rep-PCR and PFGE typing results was observed for the 40 selected isolates (adjusted Rand coefficient of 0.419), mostly due to isolates of the same DL rep-PCR type but of different PFGE types (adjusted Wallace coefficients of 0.306 for DL rep-PCR with PFGE, and of 0.667 for PFGE with DL rep-PCR). Considered together with published data, DL rep-PCR results should be interpreted with caution for the investigation of outbreaks caused by P. aeruginosa and evaluated in conjunction with epidemiological data.
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