Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases

Abstract

The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. Comparison of the bacterial 16S rRNA gene sequence has emerged as a preferred genetic technique. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories.

FIG. 1.

Universal phylogenetic tree based on the 16S rRNA gene sequence comparisons. Reprinted from reference with permission of the publisher.

FIG. 2.

Dendrogram showing the genetic relationships of many of the major groups of clinically important organisms based on the 500-bp 16S rRNA gene sequence. Most sequences are of type strains from the MicroSeq database. The Leptotrichia buccalis sequence was downloaded from GenBank, and the sequence for clinical strain Unknownsp01M1398 was generated in our laboratory.

FIG. 3.

A comparison of dendrograms generated using either the 1,500-bp 16S rRNA gene sequence (left) or the 500-bp 16S rRNA gene sequence (right) of a group of clinical and type strains of Brevibacterium.

FIG. 4.

Importance of an appropriate outgroup and a concise comparison of strains. (A and B) Chlamydia trachomata (A) is too distantly related to allow differences easily seen using S. anginosus as outgroup (B). (C) Exact base pair differences between strains seen in panel B in concise alignment form. The numbers at the top of the figure are the base position in the sequence and are to be read vertically; for example, strain VAMC5210 differs from S7745 at positions 137, 274, and 487.