Detection of ESKAPE Bacterial Pathogens at the Point of Care Using Isothermal DNA-Based Assays in a Portable Degas-Actuated Microfluidic Diagnostic Assay Platform

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2016 Dec 18

PMID 27986722

Citations 24

Authors

Lars D Renner

Jindong Zan

Linda I Hu

Manuel Martinez

Pedro J Resto

Adam C Siegel

Clint Torres

Sara B Hall

Tom R Slezak

Tuan H Nguyen

Douglas B Weibel

Affiliations

Soon will be listed here.

Abstract

Importance: This paper describes a portable system for rapidly identifying bacteria in resource-limited environments; we highlight the capabilities of the technology by detecting different pathogens within the ESKAPE collection, which cause nosocomial infections. The system is designed around isothermal DNA-based assays housed within an autonomous plastic cartridge that are designed with the end user in mind, who may have limited technological training. Displaying excellent sensitivity and specificity, the assay systems that we demonstrate may enable future diagnoses of bacterial infection to guide the development of effective chemotherapies and may have a role in areas beyond health where rapid detection is valuable, including in industrial processing and manufacturing, food security, agriculture, and water quality testing.

Citing Articles

Advances in plant pathogen detection: integrating recombinase polymerase amplification with CRISPR/Cas systems.

Anbazhagan P, Parameswari B, Anitha K, Chaitra G, Bajaru B, Rajashree A 3 Biotech. 2024; 14(9):214.

PMID: 39211481 PMC: 11349965. DOI: 10.1007/s13205-024-04055-x.

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.

Adewusi O, Waldner C, Hanington P, Hill J, Freeman C, Otto S J Vet Diagn Invest. 2024; 36(3):400-417.

PMID: 38456288 PMC: 11110769. DOI: 10.1177/10406387241235968.

Bridging Flocculation of a Sterically Stabilized Cationic Latex as a Biosensor for the Detection of Microbial DNA after Amplification via PCR.

Trinh E, Batt L, Yue Q, Du R, Jones S, Fielding L Biomacromolecules. 2024; 25(3):1629-1636.

PMID: 38361251 PMC: 10934273. DOI: 10.1021/acs.biomac.3c01187.

Applications of Lab on a Chip in Antimicrobial Susceptibility of : A Systematic Review.

Ardila C, Zuluaga-Gomez M, Vivares-Builes A Medicina (Kaunas). 2023; 59(10).

PMID: 37893437 PMC: 10608121. DOI: 10.3390/medicina59101719.

Multidimensional futuristic approaches to address the pandemics beyond COVID-19.

Kotwal S, Orekondey N, Saradadevi G, Priyadarshini N, Puppala N, Bhushan M Heliyon. 2023; 9(6):e17148.

PMID: 37325452 PMC: 10257889. DOI: 10.1016/j.heliyon.2023.e17148.

References

Piepenburg O, Williams C, Stemple D, Armes N . DNA detection using recombination proteins. PLoS Biol. 2006; 4(7):e204. PMC: 1475771. DOI: 10.1371/journal.pbio.0040204. View

Koressaar T, Remm M . Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007; 23(10):1289-91. DOI: 10.1093/bioinformatics/btm091. View

KIRBY W . EXTRACTION OF A HIGHLY POTENT PENICILLIN INACTIVATOR FROM PENICILLIN RESISTANT STAPHYLOCOCCI. Science. 1944; 99(2579):452-3. DOI: 10.1126/science.99.2579.452. View

Rice L . Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis. 2008; 197(8):1079-81. DOI: 10.1086/533452. View

Markham N, Zuker M . UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008; 453:3-31. DOI: 10.1007/978-1-60327-429-6_1. View

Barber M, ROZWADOWSKA-DOWZENKO M . Infection by penicillin-resistant staphylococci. Lancet. 1948; 2(6530):641-4. DOI: 10.1016/s0140-6736(48)92166-7. View

Chambers H, DeLeo F . Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat Rev Microbiol. 2009; 7(9):629-41. PMC: 2871281. DOI: 10.1038/nrmicro2200. View

Schmiemann G, Kniehl E, Gebhardt K, Matejczyk M, Hummers-Pradier E . The diagnosis of urinary tract infection: a systematic review. Dtsch Arztebl Int. 2010; 107(21):361-7. PMC: 2883276. DOI: 10.3238/arztebl.2010.0361. View

Sydnor E, Perl T . Hospital epidemiology and infection control in acute-care settings. Clin Microbiol Rev. 2011; 24(1):141-73. PMC: 3021207. DOI: 10.1128/CMR.00027-10. View

10.

Leekha S, Terrell C, Edson R . General principles of antimicrobial therapy. Mayo Clin Proc. 2011; 86(2):156-67. PMC: 3031442. DOI: 10.4065/mcp.2010.0639. View

11.

Asiello P, Baeumner A . Miniaturized isothermal nucleic acid amplification, a review. Lab Chip. 2011; 11(8):1420-30. DOI: 10.1039/c0lc00666a. View

12.

Shen F, Davydova E, Du W, Kreutz J, Piepenburg O, Ismagilov R . Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip. Anal Chem. 2011; 83(9):3533-40. PMC: 3101872. DOI: 10.1021/ac200247e. View

13.

Liang D, Tentori A, Dimov I, Lee L . Systematic characterization of degas-driven flow for poly(dimethylsiloxane) microfluidic devices. Biomicrofluidics. 2011; 5(2):24108. PMC: 3124517. DOI: 10.1063/1.3584003. View

14.

Cira N, Ho J, Dueck M, Weibel D . A self-loading microfluidic device for determining the minimum inhibitory concentration of antibiotics. Lab Chip. 2011; 12(6):1052-9. DOI: 10.1039/c2lc20887c. View

15.

Hysom D, Naraghi-Arani P, Elsheikh M, Carrillo A, Williams P, Gardner S . Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments. PLoS One. 2012; 7(4):e34560. PMC: 3317645. DOI: 10.1371/journal.pone.0034560. View

16.

Euler M, Wang Y, Otto P, Tomaso H, Escudero R, Anda P . Recombinase polymerase amplification assay for rapid detection of Francisella tularensis. J Clin Microbiol. 2012; 50(7):2234-8. PMC: 3405570. DOI: 10.1128/JCM.06504-11. View

17.

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B, Remm M . Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012; 40(15):e115. PMC: 3424584. DOI: 10.1093/nar/gks596. View

18.

Ho J, Cira N, Crooks J, Baeza J, Weibel D . Rapid identification of ESKAPE bacterial strains using an autonomous microfluidic device. PLoS One. 2012; 7(7):e41245. PMC: 3407151. DOI: 10.1371/journal.pone.0041245. View

19.

Pendleton J, Gorman S, Gilmore B . Clinical relevance of the ESKAPE pathogens. Expert Rev Anti Infect Ther. 2013; 11(3):297-308. DOI: 10.1586/eri.13.12. View

20.

Strotman L, OConnell R, Casavant B, Berry S, Sperger J, Lang J . Selective nucleic acid removal via exclusion (SNARE): capturing mRNA and DNA from a single sample. Anal Chem. 2013; 85(20):9764-70. PMC: 3897163. DOI: 10.1021/ac402162r. View