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.

A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension

“…Various multiplex SBE assays have been validated successfully for the analysis of mitochondrial DNA, autosomes, the Y‐chromosome, Duffy and ABO blood groups, bacteria and microbial eukaryotes (Araujo et al . 2015; Zeddeman et al . 2015; Chen et al .…”

SNaPBceBcon : a Practical Tool for Identification and Genotyping of Burkholderia cepacia and Burkholderia contaminans

“…It allows the simultaneous analysis of multiple polymorphisms following amplification and minisequencing reactions. The flexibility of the method allows the modification and addition of extra markers in case they prove to be relevant for the genotyping of specific populations (30). In this work, 7 extra markers (At66F, At248F, At359F, At443F, Gl313F, Gy218F, and Ph318F) were defined for B. cepacia and B. contaminans genotyping, in addition to 11 other markers previously defined for B. cenocepacia (13), suggesting that a set of well-characterized markers can be used to genotype Bcc species.…”