Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

doi:10.1371/journal.pone.0117617

Title: Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

Journal Article · Fri Feb 06 04:00:00 UTC 2015 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0117617 · OSTI ID:1212477

Srinivasan, Ramya ^[1]; Karaoz, Ulas ^[2]; Volegova, Marina ^[3]; MacKichan, Joanna ^[4]; Kato-Maeda, Midori ^[5]; Miller, Steve ^[6]; Nadarajan, Rohan ^[6]; Brodie, Eoin L. ^[2]; Lynch, Susan V. ^[1]; Heimesaat, Markus M. ^[7]

Univ. of California San Francisco, San Francisco, CA (United States). Dept. of Medicine
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Div.
Univ. of California, Berkeley, CA (United States)
Victoria Univ. of Wellington, Wellington (New Zealand). School of BIological Sciences
San Francisco General Hospital, San Francisco, CA (United States). Dept. of Medicine
Univ. of California San Francisco, San Francisco, CA (United States). Clinical Microbiology Lab.
Charité, Campus Benjamin Franklin, Berlin (Germany)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Institute of Health

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1212477

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 2 Vol. 10; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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