We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
LGC Clinical Diagnostics

Download Mobile App




New Liquid Biopsy Assay Reveals Host-Pathogen Interactions

By LabMedica International staff writers
Posted on 09 Sep 2019
Print article
Image: A micrograph of a urine cytology specimen showing a polyomavirus infected cell (Photo courtesy of Wikimedia Commons).
Image: A micrograph of a urine cytology specimen showing a polyomavirus infected cell (Photo courtesy of Wikimedia Commons).
A sensitive new assay employs high-throughput DNA sequencing to identify a large range of viral and bacterial pathogens in clinical samples, distinguish them from host DNA, and determine the degree of host tissue injury due to interaction with the pathogens.

While high-throughput DNA sequencing offers an unbiased approach to identify pathogens in clinical samples, this method does not take into account information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease.

To provide more information about the host-pathogen relationship, investigators at Cornell University (Ithaca, NY, USA) developed a liquid biopsy technique to map cell-free DNA (cfDNA) from clinical samples such as blood and urine. This assay simultaneously quantified the abundance of a large range of viral and bacterial pathogens as well as the degree of host tissue injury from host–microorganism interaction. This was accomplished with a genome-wide measurement of cell-free DNA methylation marks via bisulfite sequencing, a process in which the cell-free DNA was treated with salt to reveal methylation marks.

Bisulfite sequencing to determine the pattern of methylation was performed following treatment of DNA with bisulfite. Treatment of DNA with bisulfite converted cytosine residues to uracil, but left 5-methylcytosine residues unaffected. Therefore, DNA that had been treated with bisulfite retained only methylated cytosines. Bisulfite treatment introduced specific changes in the DNA sequence that depended on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA.

The investigators applied the new assay technique to analyze 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. They found that the cell and tissue types of origin of urinary cfDNA could be derived from its genome-wide profile of methylation marks, and strongly depended on infection status. Furthermore, they found evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional DNA sequencing as well as clinical tests of infection, they found that this assay accurately captured the bacterial and viral composition of the sample.

In particular, the investigators demonstrated that kidney-specific urine cell-free DNA was higher in individuals with BK polyomavirus (BKV nephropathy) as compared to those with BKV replication alone and those with no BKV replication, suggesting a role for this assay to monitor kidney damage in the face of active viral replication and infection.

Senior author Dr. Iwijn De Vlaminck, professor of biomedical engineering at Cornell University, said, "So we developed an assay that would simultaneously inform us about the presence or absence of a wide range of pathogens, but at the same time would also tell us about the injury of different host tissues. The combined information enables us to more definitively say whether a person is dealing with disease or not. But there was still a big gap to assess whether that organism is actually causing disease. That is really a critical question, because some organisms are just commensals, they live side by side with the host. Our guts are filled with microbes, but those microbes may not be the reason you are suffering from disease. In a way, you are infected. You are colonized, but that is just part of normal biology."

The new assay method was described in the August 26, 2019, online edition of the journal Proceedings of the [U.S.] National Academy of Sciences.

Related Links:
Cornell University

Platinum Member
COVID-19 Rapid Test
OSOM COVID-19 Antigen Rapid Test
One Step HbA1c Measuring System
GREENCARE A1c
Anti-Cyclic Citrullinated Peptide Test
GPP-100 Anti-CCP Kit
New
Gold Member
Reagent Reservoirs
Reagent Reservoirs

Print article

Channels

Clinical Chemistry

view channel
Image: Wireless Point-of-Care Testing for Hepatitis B Virus (Photo courtesy of Chulalongkorn University)

Wireless Hepatitis B Test Kit Completes Screening and Data Collection in One Step

Hepatitis B, a significant global health concern, is responsible for chronic liver diseases like cirrhosis and liver cancer which is one of the most common cancers worldwide. The challenge with hepatitis... Read more

Molecular Diagnostics

view channel
Image: Aptiva utilizes particle-based multi-analyte technology (PMAT) (Photo courtesy of Werfen)

Novel Immunoassays Enable Early Diagnosis of Antiphospholipid Syndrome

Antiphospholipid syndrome (APS) is an autoimmune disorder that typically presents as venous or arterial thrombosis and/or pregnancy loss. Diagnosing APS can be difficult as its symptoms often resemble... Read more

Hematology

view channel
Image: The Gazelle Hb Variant Test (Photo courtesy of Hemex Health)

First Affordable and Rapid Test for Beta Thalassemia Demonstrates 99% Diagnostic Accuracy

Hemoglobin disorders rank as some of the most prevalent monogenic diseases globally. Among various hemoglobin disorders, beta thalassemia, a hereditary blood disorder, affects about 1.5% of the world's... Read more

Pathology

view channel
Image: The photoacoustic spectral response sensing instrument is based on low-cost laser diodes (Photo courtesy of Khan et al., doi 10.1117/1.JBO.29.1.017002)

Compact Photoacoustic Sensing Instrument Enhances Biomedical Tissue Diagnosis

The pursuit of precise and efficient diagnostic methods is a top priority in the constantly evolving field of biomedical sciences. A promising development in this area is the photoacoustic (PA) technique.... Read more

Industry

view channel
Image: The companies will develop genetic testing systems based on capillary electrophoresis sequencers (Photo courtesy of 123RF)

Sysmex and Hitachi Collaborate on Development of New Genetic Testing Systems

Sysmex Corporation (Kobe, Japan) and Hitachi High-Tech Corporation (Tokyo, Japan) have entered into a collaboration for the development of genetic testing systems using capillary electrophoresis sequencers... Read more
Copyright © 2000-2024 Globetech Media. All rights reserved.