Research Article: BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections, 2018, Allicock et al

[Andy]

ABSTRACT
We report a platform that increases the sensitivity of high-throughput sequencing for detection and characterization of bacteria, virulence determinants, and antimicrobial resistance (AMR) genes. The system uses a probe set comprised of 4.2 million oligonucleotides based on the Pathosystems Resource Integration Center (PATRIC) database, the Comprehensive Antibiotic Resistance Database (CARD), and the Virulence Factor Database (VFDB), representing 307 bacterial species that include all known human-pathogenic species, known antimicrobial resistance genes, and known virulence factors, respectively.

The use of bacterial capture sequencing (BacCapSeq) resulted in an up to 1,000-fold increase in bacterial reads from blood samples and lowered the limit of detection by 1 to 2 orders of magnitude compared to conventional unbiased high-throughput sequencing, down to a level comparable to that of agent-specific real-time PCR with as few as 5 million total reads generated per sample. It detected not only the presence of AMR genes but also biomarkers for AMR that included both constitutive and differentially expressed transcripts.

IMPORTANCE BacCapSeq is a method for differential diagnosis of bacterial infections and defining antimicrobial sensitivity profiles that has the potential to reduce morbidity and mortality, health care costs, and the inappropriate use of antibiotics that contributes to the development of antimicrobial resistance.

Open access at https://mbio.asm.org/content/9/5/e02007-18

Article based on the above

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, PhD, 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.”

https://www.mailman.columbia.edu/pu...h-test-screens-all-known-bacterial-infections

 

[Kalliope]

 

[Andy]

A better method of identifying bacteria and their drug susceptibility would help in the treatment of sepsis and other serious illnesses caused by bacterial infections. It would also help combat the growing problem of antibiotic resistance.

A research team led by Drs. Thomas Briese and W. Ian Lipkin of Columbia University set out to develop a more effective method of diagnosing bacterial infections. Their work was supported by NIH’s National Institute of Allergy and Infectious Diseases (NIAID) and published in mBio on October 23, 2018.

The team created a set of more than 4 million probes, which can bind to bacterial gene sequences in a blood sample. To do this, they combined several databases to obtain sequences for 307 bacterial species, more than 30,000 virulence factors, and more than 2,000 antibiotic resistance genes. When a test is run, the resulting data are analyzed by a computer to identify bacteria.

https://www.nih.gov/news-events/nih-research-matters/method-identifies-disease-causing-bacteria