Center for Health Policy and Research (CHPR) Publications

UMMS Affiliation

Massachusetts Supranational Tuberculosis Reference Laboratory; Center for Health Policy and Research

Publication Date


Document Type



Anti-Bacterial Agents; Bacteria; Cells, Cultured; Erythrocytes; Fungi; HEK293 Cells; HeLa Cells; Herpesvirus 1, Human; Herpesvirus 2, Human; Humans; Microbial Sensitivity Tests; Plasmodium falciparum; RNA; Reproducibility of Results; Species Specificity; Urine


Bacterial Infections and Mycoses | Genetics and Genomics | Immunology and Infectious Disease | Medical Sciences | Public Health | Respiratory Tract Diseases


With rising rates of drug-resistant infections, there is a need for diagnostic methods that rapidly can detect the presence of pathogens and reveal their susceptibility to antibiotics. Here we propose an approach to diagnosing the presence and drug-susceptibility of infectious diseases based on direct detection of RNA from clinical samples. We demonstrate that species-specific RNA signatures can be used to identify a broad spectrum of infectious agents, including bacteria, viruses, yeast, and parasites. Moreover, we show that the behavior of a small set of bacterial transcripts after a brief antibiotic pulse can rapidly differentiate drug-susceptible and -resistant organisms and that these measurements can be made directly from clinical materials. Thus, transcriptional signatures could form the basis of a uniform diagnostic platform applicable across a broad range of infectious agents.

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DOI of Published Version



Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6217-22. doi: 10.1073/pnas.1119540109. Epub 2012 Apr 2. Link to article on publisher's site

Journal/Book/Conference Title

Proceedings of the National Academy of Sciences of the United States of America

Related Resources

Link to Article in PubMed