Amplificationfragmentlengthpolymorphism (AFLP;amplifiedsequencepolymorphism, ASP; amplified fragment length polymorphism, AMP-FLP, PCR-RFLP)

Amplified-fragment length polymorphism (AFLP) analysis with the endonucleases BglII and MfeI was used to genotype 91 Campylobacter jejuni subsp. jejunistrains from outbreaks and sporadic cases. AFLP-generated fragments were labeled with fluorescent dye and separated by capillary electrophoresis. The software packages GeneScan and GelCompar II were used to calculate AFLP pattern similarities and to investigate phylogenetic relationships among the genotyped strains. The AFLP method was compared with two additional DNA-based typing methods, pulsed-field gel electrophoresis (PFGE) using SmaI and restriction fragment length polymorphism analysis on PCR products (PCR-RFLP) of theflaA and flaB genes. We found that AFLP analysis of C. jejuni strains is a rapid method that offers better discriminatory power than do both PFGE and PCR-RFLP. AFLP and, to a lesser extent, PCR-RFLP could differentiate strains within the same PFGE profiles, which also makes PCR-RFLP an alternative to PFGE. We were able to clearly distinguish 9 of 10 recognized outbreaks by AFLP and to identify similarities among outbreak and sporadic strains. Therefore, AFLP is suitable for epidemiological surveillance ofC. jejuni and will be an excellent tool for source identification in outbreak situations.

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Genotypic Characterization of Bradyrhizobium Strains Nodulating Small Senegalese Legumes by 16S-23S rRNA Intergenic Gene Spacers and Amplified Fragment Length Polymorphism Fingerprint Analyses

Applied and Environmental Microbiology ◽

10.1128/aem.66.9.3987-3997.2000 ◽

2000 ◽

Vol 66 (9) ◽

pp. 3987-3997 ◽

Cited By ~ 61

Author(s):

Florence Doignon-Bourcier ◽

Anne Willems ◽

Renata Coopman ◽

Gisele Laguerre ◽

Monique Gillis ◽

...

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Restriction Analysis ◽

Intergenic Spacer ◽

Amplified Fragment Length Polymorphism ◽

Rrna Genes ◽

Leguminous Plant ◽

23S Rrna ◽

Pcr Rflp

ABSTRACT We examined the genotypic diversity of 64Bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in Senegal (West Africa) belonging to the genera Abrus, Alysicarpus,Bryaspis, Chamaecrista, Cassia,Crotalaria, Desmodium, Eriosema,Indigofera, Moghania, Rhynchosia,Sesbania, Tephrosia, and Zornia, which play an ecological role and have agronomic potential in arid regions. The strains were characterized by intergenic spacer (between 16S and 23S rRNA genes) PCR and restriction fragment length polymorphism (IGS PCR-RFLP) and amplified fragment length polymorphism (AFLP) fingerprinting analyses. Fifty-three reference strains of the different Bradyrhizobium species and described groups were included for comparison. The strains were diverse and formed 27 groups by AFLP and 16 groups by IGS PCR-RFLP. The sizes of the IGS PCR products from the Bradyrhizobium strains that were studied varied from 780 to 1,038 bp and were correlated with the IGS PCR-RFLP results. The grouping of strains was consistent by the three methods AFLP, IGS PCR-RFLP, and previously reported 16S amplified ribosomal DNA restriction analysis. For investigating the whole genome, AFLP was the most discriminative technique, thus being of particular interest for future taxonomic studies in Bradyrhizobium, for which DNA is difficult to obtain in quantity and quality to perform extensive DNA:DNA hybridizations.

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Genotyping of Epidemic Methicillin-ResistantStaphylococcus aureus Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

Journal of Clinical Microbiology ◽

10.1128/jcm.37.10.3198-3203.1999 ◽

1999 ◽

Vol 37 (10) ◽

pp. 3198-3203 ◽

Cited By ~ 21

Author(s):

Ruth Grady ◽

Meeta Desai ◽

Gael O’Neill ◽

Barry Cookson ◽

John Stanley

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Phage Type ◽

Amplified Fragment Length Polymorphism ◽

Group Method ◽

Polymorphism Analysis ◽

Methicillin Resistant ◽

Hospital Infection Control ◽

Pcr Rflp

Fluorescent amplified-fragment length polymorphism (FAFLP) analysis was investigated for its ability to identify and subtype isolates of an epidemic methicillin-resistant phage type of Staphylococcus aureus, EMRSA-15. These isolates were also characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) of the coagulase gene and pulsed-field gel electrophoresis (PFGE). For FAFLP, DNA was double digested with restriction enzymes ApaI plusTaqI or EcoRI plus MseI. Site-specific adaptors were ligated to one or the other set of restriction fragments, and PCR amplification was carried out with adaptor-specific primers. Amplified fragments separated on an ABI 377 automated sequencer and analyzed with Genescan version 2.1 software generated FAFLP profiles for all the isolates. The presence or absence of fragments was scored, similarity coefficients were calculated, and UPGMA (unweighted pair group method using arithmatic averages) cluster analysis was performed. Either enzyme-primer combination readily differentiated EMRSA-15 from other methicillin-resistant S. aureus (MRSA) isolates and also revealed heterogeneity within the phage type. The discriminatory power of FAFLP was high. By combining both enzyme-primer data sets, 24 isolates were divided into 11 profiles. PCR-RFLP did not discriminate among these EMRSA-15 isolates. PFGE could discriminate well between isolates but was not as reproducible as FAFLP. All S. aureus and MRSA isolates in this study were typeable by FAFLP, which was easy to perform, robust, and reproducible, with evident potential to subtype MRSA for purposes of hospital infection control.

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