RNA Sequencing of Sepsis Patients Informs Tests to Quickly Diagnose Pathogens and Resistance DOI Creative Commons
Sean F. Monaghan, Jaewook Shin, Brandon E. Armstead

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

Abstract Diagnosis of infection in patients with sepsis takes days via culture and appropriate treatment pathogens are delayed awaiting results. A faster diagnosis the pathogen resistance RNA sequencing informed PCR will improve outcomes. We hypothesize that we can use from to identify novel targets for future nucleic acid-based tests. This cohort study 46 admitted ICU samples taken on 0, 1, 3, 7 follow up through hospital stay during 2021–2022. All had sequencing, depth > 100 million reads, conducted a single center medical intensive care unit. Patients were sepsis. or surrogates approached consecutively those who consented enrolled. peripheral blood was performed pathogens. data did not map human genome then aligned genes genomes used design These tests correlated clinical Forty-six (mean age 62.2, 48% female) enrolled 87 time points collected. resulted 8.6 billion reads RNA. target discovery this focused positive cultures (n = 40) due Escherichia coli (5), Staphylococcus aureus (6), Pseudomonas aeruginosa (3) as well identification genes. From these 40 defined tested by quantitative PCR. In 9) some proposed PCRs identified all cases (Pseudomonas aureus, no cohort). causing infection. be primers cultures. Translation microbiology machines is next step allow than culture.

Language: Английский

Recent advances in dynamic single-molecule analysis platforms for diagnostics: advantages over bulk assays and miniaturization approaches DOI
Dang Du Nguyen, Fedor A. Shuklin, Elena Barulina

et al.

Biosensors and Bioelectronics, Journal Year: 2025, Volume and Issue: 278, P. 117361 - 117361

Published: March 10, 2025

Language: Английский

Citations

0
Digital PCR characterizes epithelial cell populations in murine duodenal organoids DOI Creative Commons
Karla Acosta‐Virgen, Hugo González-Conchillos,

Gabriela Vallejo-Flores

et al.

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(3), P. e0319701 - e0319701

Published: March 13, 2025

Three-dimensional cultures are powerful tools to recapitulate animal and human tissues. Under the influence of specific growth factors, adult stem cells differentiate organize into 3D named organoids. The molecular phenotyping these structures is an essential step for validating organoid model. However, limited number organoids generated in culture yields very low amounts genetic material, making difficult. Recently, digital PCR (dPCR) techniques have become available highly sensitive detection material at concentrations. aim this work was apply dPCR identification various cell populations expected be present murine duodenal Results show potential use as a characterization tool

Language: Английский

Citations

0
A Quadruplex Digital PCR Assay for the Simultaneous Detection of Four Intestinal Bacterial Pathogens and Its Application in Wastewater Samples DOI
Huihui Sun, Qingzhen Yao,

Xiangang Zhao

et al.

Deleted Journal, Journal Year: 2025, Volume and Issue: 7(12), P. 393 - 399

Published: Jan. 1, 2025

Language: Английский

Citations

0
Quantification of Salmonella in raw poultry using Droplet Digital PCR with a Whole Cell, Enrichment-free Approach DOI Creative Commons
Cheryl M. Armstrong, Chin‐Yi Chen, Yicheng Xie

et al.

Journal of Food Protection, Journal Year: 2025, Volume and Issue: unknown, P. 100498 - 100498

Published: March 1, 2025

Language: Английский

Citations

0
Mycoplasma bovis : A review of vaccination and diagnostic initiatives DOI

Isaac Dayo Olorunshola,

Kabiru Ahmad, A.R. Peters

et al.

CABI Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Abstract Mycoplasma bovis infections in cattle constitute a worldwide problem with significant detrimental economic impacts on industry. Mastitis, pneumonia, arthritis, keratoconjunctivitis, otitis media and genital disorders are its clinical manifestations. Presently, no vaccines commercially available; antimicrobial resistance is increasing; diagnostic sensitivity testing needs to be improved; new rapid diagnosis kits eminent for implementation of treatment antimicrobials. We conducted systematic search databases such as PubMed, Scopus, Web Science, Google Scholar, AGRIS African Journals Online (AJOL), from 1995 2024. Searched keywords, as, bovis, M : vaccine development, techniques strain variability using the predefined criteria were used address review objectives. Although they have preventative function, – killed, live attenuated, subunit types face difficulties because M. strains vary widely. Every approach has own set benefits drawbacks, those that been studies include conventional culture identification, serological testing, immunohistochemical demonstration tissues, sophisticated molecular like PCR, qPCR, next-generation sequencing. For early detection, successful treatment, vaccination efficacy monitoring, accurate crucial. Future directions managing -associated diseases improving accessibility creating broad-spectrum vaccinations. By incorporating these developments, it may possible enhance health cattle, promote sustainability livestock production, increase food security. This points urgent need further research innovation advancement support

Language: Английский

Citations

0
Bringing Attomolar Detection to the Point-of-Care with Nanopatterned DNA Origami Nanoantennas DOI Creative Commons
Renukka Yaadav, Kateryna Trofymchuk, Mihir Dass

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

Abstract Creating increasingly sensitive and cost-effective nucleic acid detection methods is critical for enhancing point-of-care (POC) applications. This involves capturing all desired biomarkers in a sample with high specificity transducing the capture events to detector. However, signal from present at extremely low amounts often falls below limit of typical fluorescence-based methods, making molecular amplification necessary step. Here, we assay 151-nucleotide sequence specific antibiotics-resistant Klebsiella pneumoniae , based on single-molecule fluorescence non-amplified DNA down attomolar level, using Trident NanoAntennas Cleared HOtSpots (NACHOS). Our NACHOS-diagnostics leverages compact microscope large field-of-view cost-efficient components, including microfluidic flow enhance efficiency. Fluorescence enhancement provided by origami NanoAntennas, arranged dense array combination nanosphere lithography site-specific placement. method can detect 200 ± 50 out 600 molecules 100 µL volume within an hour. represents number pathogens clinical samples commonly detected Polymerase Chain Reaction but without need amplification. We achieve similar sensitivity untreated human blood plasma, practical applicability system. platform be adapted shorter fragments that are not compatible traditional amplification-based technologies. broadens its potential diverse diagnostic healthcare applications, providing robust scalable solution various settings.

Language: Английский

Citations

1
RNA Sequencing of Sepsis Patients Informs Tests to Quickly Diagnose Pathogens and Resistance DOI Creative Commons
Sean F. Monaghan, Jaewook Shin, Brandon E. Armstead

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 25, 2024

Abstract Diagnosis of infection in patients with sepsis takes days via culture and appropriate treatment pathogens are delayed awaiting results. A faster diagnosis the pathogen resistance RNA sequencing informed PCR will improve outcomes. We hypothesize that we can use from to identify novel targets for future nucleic acid-based tests. This cohort study 46 admitted ICU samples taken on 0, 1, 3, 7 follow up through hospital stay during 2021–2022. All had sequencing, depth > 100 million reads, conducted a single center medical intensive care unit. Patients were sepsis. or surrogates approached consecutively those who consented enrolled. peripheral blood was performed pathogens. data did not map human genome then aligned genes genomes used design These tests correlated clinical Forty-six (mean age 62.2, 48% female) enrolled 87 time points collected. resulted 8.6 billion reads RNA. target discovery this focused positive cultures (n = 40) due Escherichia coli (5), Staphylococcus aureus (6), Pseudomonas aeruginosa (3) as well identification genes. From these 40 defined tested by quantitative PCR. In 9) some proposed PCRs identified all cases (Pseudomonas aureus, no cohort). causing infection. be primers cultures. Translation microbiology machines is next step allow than culture.

Language: Английский

Citations

0