A diagnostic platform that can simultaneously screen for all known human pathogenic bacteria as well as markers for virulence and antibiotic resistance has been developed by scientists from the Columbia University Mailman School of Public Health. According to the team, BacCapSeq has the potential to reduce morbidity and mortality, health care costs, and the inappropriate use of antibiotics.
"Once approved for clinical use, BacCapSeq will give physicians a powerful tool to quickly and precisely screen for all known pathogenic bacteria, including those that cause sepsis, the third leading cause of death in the United States," says first author Orchid M. Allicock, Ph.D., a post-doctoral researcher at the Center for Infection and Immunity (CII) at Columbia. "This platform is 1,000 times more sensitive than traditional unbiased testing, at a level comparable to tests that screen one bacterium at a time."
Currently, the most common method used to test for sepsis can take as long as three days, and even longer to provide information on antibiotic resistance. BacCapSeq provides results in 70 hours, but the researchers believe that the platform will become faster with advances in computing power.
BacCapSeq, which is described in detail in an mBio paper published today, contains 4.2 million genetic probes used to detect the signature DNA of all 307 pathogenic bacteria, as well as biomarkers for antibiotic resistance and virulence. Each probe binds to a corresponding sequence; when a particular bacterium and biomarker is present in a sample, a magnetic process "pulls out" its unique sequences, which can then be used to identify the bacterium and its characteristics.
In the study, the researchers assess the performance of BacCapSeq in several ways: using nucleic acid from blood spiked with DNA from several different bacteria, blood spiked with bacterial cells, blood culture samples, and blood samples from patients with unexplained sepsis. In each case, the platform performance exceeded traditional methods, sometimes detecting infections that were missed by the alternative method.
BacCapSeq is a complement to VirCapSeq, a similar test developed at CII that screens for all known human viral infections.
"Microbiological intelligence must be an integral component of precision medicine," says W. Ian Lipkin, M.D., director of CII. "Accurate, early differential diagnosis of infectious diseases and knowledge of drug sensitivity profiles will reduce mortality, morbidity, and health care costs."