Application of minimal sequence quality values prevents misidentification of the blaSHV type in single bacterial isolates carrying different SHV extended-spectrum beta-lactamase genes

Abstract

Nucleotide sequencing is the standard molecular method for determination of the beta-lactamase gene present in an isolate. Using minimal sequence quality values prevents misidentification of bla(SHV) genes, as illustrated by three strains of three different species that each contained two different bla(SHV) alleles, SHV-2 and SHV-12.

FIG. 1.

Graphic representation of Phred quality values for the contig assembled from four separate trace files for one of the bla_SHV PCR products. The quality value scale is logarithmic: a Phred value of 20 means a 1/100 likelihood of error, a Phred value of 40 means 1/10,000, and so on. The low-quality values for nucleotide positions 92, 402, and 703 are indicated.

FIG. 2.

Low-quality positions in sequence traces of a bla_SHV PCR product. (A to C) Electropherograms of the regions containing nucleotide positions 92, 402, and 703. (A) Double signals in the PCR amplicon. (B) Signals in one class of clones, T₉₂A₄₀₂G₇₀₃, corresponding to SHV-12. (C) Signals in the other class of clones, A₉₂G₄₀₂A₇₀₃, corresponding to SHV-2.