Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens

Abstract

According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.

Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group

“…In some instances, 16S rRNA gene sequencing continues to outperform traditional culturebased methods or non-16S molecular methods for identification of clinically relevant bacterial pathogens (23). Recently, a clinically validated next-generation sequencing-based approach that uses targeted 16S rRNA gene sequencing for the diagnostic identification of bacterial species directly from clinical samples was described (24).…”

Microbiota sampled from a polluted stream in Recife-PE, Brazil and its importance to public health

“…The 16S rRNA gene is widely used as phylogenetic marker, and it has been sequenced for a large number of bacterial lineages (Srinivasan et al, 2015). Most of these sequences are deposited in the GenBank database (Benson et al, 2012), and can therefore be compared with sequences of new isolates.…”

“…Among these, methods using 16S rRNA gene sequencing are predominant. This gene is used as a phylogenetic marker because its sequences are highly conserved (Srinivasan et al, 2015).…”

SPECIES IDENTIFICATION INFERRED THROUGH MITOCHONDRIAL 16S rRNA GENE SEQUENCE BETWEEN FRESHWATER TESTUDINES - LISSEMYS PUNCTATA AND MELANOCHELYS TRIJUGA.

“…In later years there was immense study of 16S rRNA gene in various organisms; especially the contribution was significant from the field of microbiology. Microbes causing infectious and deadly diseases in animals are clinically identified based on 16S rRNA sequences and has grown into popular molecular marker for unbiased identification of pathogens compared to conventional culture based methods (Srinivasan et al, 2015).…”