Assessment of Poliovirus Eradication in Japan: Genomic Analysis of Polioviruses Isolated from River Water and Sewage in Toyama Prefecture

ABSTRACT Seventy-eight poliovirus strains isolated from river water and sewage in Toyama Prefecture, Japan, during 1993 to 1995 were characterized by the PCR-restriction fragment length polymorphism (RFLP) method and by partially sequencing the VP3 and VP1 regions of the viral genome. Of these isolates, 36 were identified as Sabin vaccine strains, and 42 were identified as vaccine variant strains that had less than 1.4% nucleotide divergence from the Sabin strains, including 7 isolates with patterns different from those of Sabin strains as determined by PCR-RFLP analysis. These findings suggest that wild-type poliovirus was not circulating in Toyama Prefecture.

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Characterisation of avian Pasteurella multocida strains with PCR-RFLP analysis of the ompH gene

Acta Veterinaria Hungarica ◽

10.1556/avet.2012.048 ◽

2013 ◽

Vol 61 (1) ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Boglárka Sellyei ◽

Éva Ivanics ◽

Tibor Magyar

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Pasteurella Multocida ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

The Other ◽

Pcr Rflp ◽

H Gene ◽

Geographic Regions ◽

Type Strains ◽

Restriction Fragment Length

The 16 somatic serotype type strains and 60 field isolates of Pasteurella multocida, representing various avian species and geographic regions in Hungary, were characterised by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the ompH gene with DraI restriction endonuclease. The type strains yielded eight different (I-VIII) profiles. Strains whose PCR fragment was uncut by DraI (profile IV) could be differentiated with HindIII and PvuII restriction endonucleases. Five of the eight PCR-RFLP profiles (I, III, V, VI and VII) were detected among the field strains. Only a correlation of limited strength was found between the classical somatic serotypes and the PCR-RFLP profiles. However, the results confirmed that molecular methods could confidently distinguish serotype A:1 strains from the other serotypes. Moreover, the specific relationship between somatic serotypes and PCR-RFLP types among isolates from turkey raises the possibility of the existence of host-specific clones within the P. multocida population.

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Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽

10.3390/diagnostics9040196 ◽

2019 ◽

Vol 9 (4) ◽

pp. 196 ◽

Cited By ~ 1

Author(s):

García-Suárez ◽

González-Rodríguez ◽

Cima-Cabal ◽

Yuste ◽

Vazquez ◽

...

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Restriction Fragment ◽

Length Polymorphism ◽

Dna Sequences ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Restriction Enzymes ◽

Pcr Rflp ◽

Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

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PCR–Restriction Fragment Length Polymorphism and Pulsed-Field Gel Electrophoresis Characterization of Listeria monocytogenes Isolates from Ready-to-Eat Foods, the Food Processing Environment, and Clinical Samples in South Africa

Journal of Food Protection ◽

10.4315/0362-028x.jfp-19-301 ◽

2020 ◽

Vol 83 (3) ◽

pp. 518-533

Author(s):

DIANE RIP ◽

PIETER A. GOUWS

Keyword(s):

South Africa ◽

Listeria Monocytogenes ◽

Restriction Fragment Length Polymorphism ◽

Length Polymorphism ◽

Food Processing ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Pcr Rflp ◽

Restriction Fragment Length ◽

Food Processing Environment

ABSTRACT Listeria monocytogenes is a ubiquitous, intracellular foodborne pathogen that is responsible for invasive listeriosis. The ability of L. monocytogenes to cause disease has some correlation with the serotypes of a specific lineage group, making the identification of lineage groups important for epidemiological analysis. The development of typing methods to link the strains of L. monocytogenes to an outbreak of listeriosis would help minimize the spread of the disease. The aim of this study was to design a PCR–restriction fragment length polymorphism (RFLP) method to differentiate between the lineage groups of L. monocytogenes. PCR-amplified fragments of the hly gene for 12 serotypes of L. monocytogenes were sequenced, aligned, and analyzed with the BioEdit program, and single nucleotide polymorphisms (SNPs) within regions of this gene were identified. Because of the difficulty in acquiring a serotype 4ab reference strain, this serotype was not included in this study. We tested the specificity and accuracy of the PCR-RFLP method on these L. monocytogenes reference strains and validated the method with 172 L. monocytogenes strains recovered from humans, food, and the food processing environment in 2000 to 2002 and 2008 to 2010 from regions within South Africa. PCR-RFLP analysis applied in this study placed L. monocytogenes serotypes into one of three lineage groups based on the sequence differences and SNPs within each lineage group. The SNPs were conserved in a region where RFLP analysis could be applied for a distinction between L. monocytogenes lineage groups. HIGHLIGHTS

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Diversity of “Candidatus Liberibacter asiaticus,” Based on the omp Gene Sequence

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6473-6478.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6473-6478 ◽

Cited By ~ 43

Author(s):

C. Bastianel ◽

M. Garnier-Semancik ◽

J. Renaudin ◽

J. M. Bové ◽

S. Eveillard

Keyword(s):

Restriction Fragment Length Polymorphism ◽

Gene Sequence ◽

Fragment Length Polymorphism ◽

Rflp Analysis ◽

Candidatus Liberibacter Asiaticus ◽

Simple Method ◽

Pcr Rflp ◽

Candidatus Liberibacter ◽

Liberibacter Asiaticus ◽

Restriction Fragment Length

ABSTRACT Huanglongbing (yellow dragon disease) is a destructive disease of citrus. The etiological agent is a noncultured, phloem-restricted alpha-proteobacterium, “Candidatus Liberibacter africanus” in Africa and “Candidatus Liberibacter asiaticus” in Asia. In this study, we used an omp-based PCR-restriction fragment length polymorphism (RFLP) approach to analyze the genetic variability of “Ca. Liberibacter asiaticus” isolates. By using five different enzymes, each the 10 isolates tested could be associated with a specific combination of restriction profiles. The results indicate that the species “Ca. Liberibacter asiaticus,” even within a given region, may comprise several different variants. Thus, omp-based PCR-RFLP analysis is a simple method for detecting and differentiating “Ca. Liberibacter asiaticus” isolates.

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