High density whole genome fingerprinting of methicillin-resistant and -susceptible strains of Staphylococcus aureus in search of phenotype-specific molecular determinants

Size-selective separation and overall-amplification of cell-free fetal DNA fragments using PCR-based enrichment

This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification). Finally, we used an optimum temperature range to amplify cffDNA selectively. Amplification results were validated by electrophoresis and real-time quantitative PCR. Our PCR-based enrichment efficiently amplified all DNA fragments with differing lengths within a single reaction system, as well as preserving the integrity of the DNA fragments. cffDNA was significantly amplified along with the selective amplification of small fragment maternal plasma DNA in an appropriate range of denaturation temperatures. We have established a PCR-based method for the simultaneous enrichment and amplification of cffDNA in order to meet the requirements of high cffDNA quantity for routine non-invasive prenatal testing.

Mapping the genetic diversity within major clonal complexes of meticillin-resistant Staphylococcus aureus utilizing genome-wide fluorescent amplified fragment length polymorphism markers

The genetic diversity between major meticillin-resistant Staphylococcus aureus (MRSA) lineages was probed using fluorescent amplified fragment length polymorphism (FAFLP) as a random genome sampling tool. Genomic DNA was digested with endonucleases BglII and Csp6I and a subset of the restricted fragments were amplified using the primer pair BglII+A and Csp6I+0. Sixty-seven FAFLP profiles consisting of 46-68 amplified fragments ranging in size from 50 to 600 bp were exhibited amongst the 71 isolates analysed. Cluster analysis of FAFLP data revealed concordance with spa typing and MLST clonal complexes (CC), with isolates of each CC grouping in the same FAFLP cluster. Furthermore, FAFLP could differentiate subtypes within the homogeneous CC22 isolates and also between MLST sequence types 8 and 239. The discriminatory power of FAFLP was 0.998 compared to values of 0.975 and 0.909 for spa typing and MLST, respectively. Thus, FAFLP analysis proved to be a rapid, reproducible and high-resolution tool that displayed the microheterogeneity within MRSA lineages. Using FAFLP data, lineage-specific fragments were identified and sequenced; these encoded toxins, antibiotic resistance determinants and bacteriophage resistance factors. Lineage-specific sequence variations were observed, which may provide insights into the evolution and fitness of successful lineages. This will also aid in the development of rapid and high-throughput diagnostic PCR-based assays for the identification of MRSA lineages in resource-poor settings.

Amplified fragment-length polymorphism analysis

Amplified fragment length polymorphism (AFLP) analysis is a universal polymerase chain reaction (PCR)-based DNA fingerprinting technique comprising three main stages: (i) digestion of genomic DNA with restriction endonucleases and ligation to double-stranded adaptors (each comprised of two oligonucleotides), thus creating restriction fragments with identical known adaptor sequences; (ii) specific amplification of a subset of these DNA fragments using primers (one labeled) targeting the adaptor sequences and additional selected bases within the unknown genomic DNA; and (iii) analysis of the patterns (usually automated). Differences or polymorphisms between samples are revealed by separation of the labeled fragments by electrophoresis (standard agarose, high-resolution denaturing acrylamide, or capillary gels). Comparison of banding patterns is typically achieved using dedicated fingerprinting analysis software. The advantages of AFLP analysis include the ability to use a universal protocol in combination with different restriction endonucleases and the choice of adding one or more selective nucleotides in the PCR -primers to achieve optimal results relatively quickly without prior knowledge of DNA sequences from a large variety of (micro)organisms. The method also has the potential for high-throughput and local electronic database pattern storage with relatively low cost. Disadvantages include variation in the precision of sizing of fragments, leading to suboptimal reproducibility, particularly across different platforms.