title: Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses.
abstract: Practical schemes based on single nucleotide polymorphisms (SNP) have been proposed as alternatives to simplify and replace the molecular methodologies based on the extensive sequencing analysis of genes. SNaPshot mini-sequencing has been progressively experienced during the last decade and represents a fast and robust strategy to analyze critical polymorphisms. Such assays have been proposed to characterize some bacteria and microbial eukaryotes, and its feasibility was now reviewed in the present manuscript. The mini-sequencing schemes showed high discriminatory power and competence for identification of microorganisms, but some specificity errors were still found, particularly for species of the Burkholderia cepacia complex and mycobacteria. SNP assays designed for other goals, e.g., comparison of strains, detection of serotypes, virulence, epidemic, and phylogenetic-related subgroups of isolates, can be very useful by facilitating the investigation of large collections of isolates. The next-generation of SNP assays might consider the inclusion of large number of markers to fully characterize microbial taxonomy and strains; nevertheless, these new technologies are still prone to errors and can largely benefit from integration with well-established mini-sequencing assays. Newly proposed molecular tools should be systematically tested in collections of isolates with high indexes of diversity and guarantee interlaboratorial validation.
authors: IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal, ricjparaujo@yahoo.com.
authors: Ricardo
authors: R
authors: Araujo
authors: Nadia
authors: N
authors: Eusebio
authors: Rita
authors: R
authors: Caramalho
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D042602:Burkholderia cepacia complex / Q000145:classification / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D023281:Genomics; D060005:Genotyping Techniques; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial