Breakthrough test screens for all known bacterial infections

October 23, 2018, Columbia University's Mailman School of Public Health
Credit: CC0 Public Domain

Scientists at the Center for Infection and Immunity (CII) in the Columbia University Mailman School of Public Health have developed the first diagnostic platform that can simultaneously screen for all known human pathogenic bacteria as well as markers for virulence and antibiotic resistance. A study in the journal mBio provides details on the performance of the BacCapSeq platform.

"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 CII. "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. While physicians wait for a result, they usually prescribe , a practice that contributes to the growth of antibiotic resistance. BacCapSeq provides results in 70 hours, but the researchers believe that the platform will become faster with advances in computing power.

Each year, antibiotic-resistant infections claim 100,000 lives in the United States, and 700,000 globally, with the highest burden in the developing world, according to World Economic Forum estimates. The direct annual impact of antibiotic resistance in the U.S. is $20-35 billion with an additional $35 billion in lost productivity, according to the U.S. Center for Disease Control and Prevention. Absent an effective response to limit further growth in , the challenge will continue to increase. The World Bank issued a report in 2017 projecting an impact on the GDP between $1.1 trillion and $3.4 trillion.

BacCapSeq contains 4.2 million genetic probes used to detect the signature DNA of all 307 pathogenic bacteria, as well as biomarkers for 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. To date, even the most advanced multiplexed polymerase chain reaction systems are only able to screen for up to 19 , and none can assess virulence and antimicrobial .

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. In one case, the test implicated the bacterium Gardnerella vaginalis, which is only rarely associated with significant disease, as the cause of unexplained sepsis in an individual with HIV/AIDS.

BacCapSeq is a complement to VirCapSeq, a similar test developed at CII that screens for all known human viral infections. Recent published studies have reported on that test's performance in Tanzania and Uganda. A test for differential diagnosis of fungal infections is in development.

"Microbiological intelligence must be an integral component of precision medicine,"says W. Ian Lipkin, MD, director of CII and the John Snow Professor of Epidemiology at Columbia Public Health. "Accurate, early differential diagnosis of infectious diseases and knowledge of drug sensitivity profiles will reduce mortality, morbidity, and health care costs."

Explore further: Pinpointing mutations that cause bacterial antibiotic resistance

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rrwillsj
5 / 5 (2) Oct 23, 2018
First broad-band detection of viral infections. Now the capability for detecting the spectrum of bacterial infections. With the promise of next using these techniques to detect fungal infections?

A trifecta of disease control that cam alleviate a whole lot of Juman suffering. And, I would speculate, these procedures could be used to monitor and protect animals and plants.
michael_frishberg
1 / 5 (2) Oct 23, 2018
"alleviate a whole lot of human suffering" (allowing us to further ignore our ever burgeoning population's impact on the rest of life on earth).

We've already cut off any chance of humanity surviving to the year 2100. Sayonara

vhemt.org - the only moral choice, remain childfree.
rrwillsj
not rated yet Oct 24, 2018
mike I agree with your comments in general. However do you intend to "bell that cat"? To convince a large enough number of individuals in the reproductive demograph to voluntarily avoid reproducing?

Especially considering the social pressures on the present fertile generation from their own families demanding grandchildren? And they mean, Right Now!

It seems an easy choice, a "simple solution" to allow rampant disease and starvation and wars to cull a burgeoning population. But the reality is the opposite effect.

Where there is voluntary, widespread & successful population control? Is in prosperous countries with a well-educated population. Freely permitted access to extensive Public Health Services.

It is no accident that repression of publicly accessible birth control options, Pre & Post Natal health care are denied by the tyranny of religious fanatics, right fascist and left fascist regimes and other fake conservatives and fraudulent libertarian autocracies.
torbjorn_b_g_larsson
not rated yet Nov 11, 2018
[qWe've already cut off any chance of humanity surviving to the year 2100. ...
vhemt.org - the only moral choice, remain childfree.

Not relevant, not in evidence. In fact, this week the news was that many nations have or will drop under sustained populations, so the problem will be different (ageing pops, decreasing pops).

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