A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections.

Nature Communications
Michael B MayhewTimothy E Sweeney

Abstract

Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we develop a generalizable host-gene-expression-based classifier for acute bacterial and viral infections. We use training data (N = 1069) from 18 retrospective transcriptomic studies. Using only 29 preselected host mRNAs, we train a neural-network classifier with a bacterial-vs-other area under the receiver-operating characteristic curve (AUROC) 0.92 (95% CI 0.90-0.93) and a viral-vs-other AUROC 0.92 (95% CI 0.90-0.93). We then apply this classifier, inflammatix-bacterial-viral-noninfected-version 1 (IMX-BVN-1), without retraining, to an independent cohort (N = 163). In this cohort, IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.86 (95% CI 0.77-0.93), and viral-vs.-other 0.85 (95% CI 0.76-0.93). In patients enrolled within 36 h of hospital admission (N = 70), IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.92 (95% CI 0.83-0.99), and viral-vs.-other 0.91 (95% CI 0.82-0.98). With further study, IMX-BVN-1 could provide a tool for assessing patients with suspected infection and sepsis at hospital admission.

References

Mar 1, 2006·BMC Bioinformatics·Sudhir Varma, Richard Simon
Apr 25, 2006·Biostatistics·W Evan JohnsonAriel Rabinovic
Sep 16, 2010·Critical Care : the Official Journal of the Critical Care Forum·Jesus F Bermejo-MartinDavid Kelvin
Jun 21, 2011·Critical Care : the Official Journal of the Critical Care Forum·Allison SutherlandDeon Venter
Jul 26, 2011·The Journal of Infection·Jan-Erik BerdalChristine M Jonassen
Aug 2, 2012·JAMA : the Journal of the American Medical Association·Bryan CoburnAllan S Detsky
Aug 18, 2012·Critical Care : the Official Journal of the Critical Care Forum·Grant P ParnellBenjamin M Tang
Apr 1, 2014·Journal of Cheminformatics·Damjan KrstajicSimon Thomas
May 20, 2014·JAMA : the Journal of the American Medical Association·Vincent LiuTheodore J Iwashyna
Jan 6, 2015·The Journal of Infection·Raquel AlmansaEduardo Tamayo
Jun 30, 2015·American Journal of Respiratory and Critical Care Medicine·Brendon P SciclunaTom van der Poll
Jul 15, 2015·The New England Journal of Medicine·Seema JainUNKNOWN CDC EPIC Study Team
Jul 29, 2015·Intensive Care Medicine Experimental·Marie-Angélique CazalisGuillaume Monneret
Sep 29, 2015·American Journal of Respiratory and Critical Care Medicine·Carolin FleischmannUNKNOWN International Forum of Acute Care Trialists
Feb 24, 2016·JAMA : the Journal of the American Medical Association·Mervyn SingerDerek C Angus
Feb 26, 2016·The Lancet. Respiratory Medicine·Timothy E SweeneyPurvesh Khatri
Jul 8, 2016·Science Translational Medicine·Timothy E SweeneyPurvesh Khatri
Sep 30, 2016·Critical Care Medicine·Timothy E Sweeney, Purvesh Khatri
Dec 31, 2016·American Journal of Respiratory and Critical Care Medicine·Katie L BurnhamJulian C Knight
May 17, 2017·Critical Care Medicine·Timothy E Sweeney, Purvesh Khatri
Jun 13, 2017·JAMA Internal Medicine·Pranita D TammaSara E Cosgrove
Feb 17, 2018·Nature Communications·Timothy E SweeneyRaymond J Langley
Apr 28, 2018·Scientific Reports·Shayan Tabe-BordbarSaurabh Sinha
Jun 26, 2018·Expert Review of Molecular Diagnostics·Emily C LydonEphraim L Tsalik
Apr 4, 2019·The New England Journal of Medicine·Angela X ChenDaniel J Pallin
Apr 26, 2019·Intensive Care Medicine·Benjamin M TangAnthony S McLean

❮ Previous
Next ❯

Citations

Jun 13, 2020·Expert Review of Molecular Diagnostics·Ellen HaagPhilipp Schuetz
Jul 25, 2020·JCI Insight·Jennifer G WilsonAngela J Rogers
Nov 18, 2020·Critical Care Medicine·Timothy E SweeneyEvangelos J Giamarellos-Bourboulis
Jan 30, 2021·Patterns·Adriana TomicMark M Davis
Feb 19, 2021·Nature Communications·Micah T McClainChristopher W Woods
Feb 19, 2021·Nature Communications·William YuanIsaac S Kohane
May 1, 2021·Microorganisms·Ricarda MichelsCihan Papan
Jun 4, 2021·Frontiers in Immunology·Judith ZandstraTaco W Kuijpers
Jun 1, 2021·Frontiers in Medicine·Miao WuJie Wei
Jun 16, 2021·Pediatric Research·Hector R Wong
Jun 19, 2021·Intensive Care Medicine Experimental·Asimina SafarikaEvangelos J Giamarellos-Bourboulis
Jun 14, 2021·European Journal of Clinical Investigation·Raquel AlmansaUNKNOWN PREVISE Study Group
Jan 20, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Rachael E MahleEphraim L Tsalik
May 4, 2021·Critical Care Medicine·Ephraim L TsalikUNKNOWN Antibacterial Resistance Leadership Group
Sep 17, 2021·Critical Care Medicine·Caitlyn Vlasschaert, Michael J Rauh
Oct 22, 2021·Critical Care Explorations·Scott C BrakenridgeLyle L Moldawer

❮ Previous
Next ❯

Software Mentioned

IMX
BVN
LOSO CV
XGBoost
COmbat CO - Normalization Using conTrols ( COCONUT )
NanoString nCounter
HiCV
COCONUT

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.