Microfluidic technologies for advanced antimicrobial susceptibility testing

Abstract

Antimicrobial resistance is getting serious and becoming a threat to public health worldwide. The improper and excessive use of antibiotics is responsible for this situation. The standard methods used in clinical laboratories, to diagnose bacterial infections, identify pathogens, and determine susceptibility profiles, are time-consuming and labor-intensive, leaving the empirical antimicrobial therapy as the only option for the first treatment. To prevent the situation from getting worse, evidence-based therapy should be given. The choosing of effective drugs requires powerful diagnostic tools to provide comprehensive information on infections. Recent progress in microfluidics is pushing infection diagnosis and antimicrobial susceptibility testing (AST) to be faster and easier. This review summarizes the recent development in microfluidic assays for rapid identification and AST in bacterial infections. Finally, we discuss the perspective of microfluidic-AST to develop the next-generation infection diagnosis technologies.

FIG. 1.

Microfluidic devices for bacterial purification from raw samples. (a) Two-layered inertial microfluidic chip for sorting the bacteria in urine. [Reproduced with permission from Wu et al., Anal. Chem. 94(51), 17853–17860 (2022). Copyright 2022 American Chemical Society]. (b) Acoustic powered bacteria separation system. [Reproduced with permission from Ohlsson et al., Anal. Chem. 88(19), 9403–9411 (2016). Copyright 2016 American Chemical Society]. (c) Antibody functionalized microchannel for specific bacteria capture. [Reproduced with permission from Safavieh et al., ACS Appl. Mater. Interfaces 9(14), 12832–12840 (2017). Copyright 2017 American Chemical Society].

FIG. 2.

Microfluidic gradient generators. (a) Integrated AST platform with Christmas tree gradient generator. [Reproduced with permission from Chan et al., Biosens. Bioelectron. 192, 113516 (2021). Copyright 2022 Elsevier]. (b) Diffusion-based AST chip. [Reproduced with permission from Wistrand-Yuen et al., mBio 11, 03109–03119 (2020). Copyright 2020 Wistrand-Yuen et al.]. (c) Multiplexed gradient microfluidic platform. [Reproduced with permission from Liu et al., Chem. Plus Chem. 82(5), 792–801 (2017). Copyright 2017 Wiley-VCH]. (d) Gradient generation chip with asymmetrical source channel. [Reproduced with permission from Shi et al. Chem. Eng. J. 359, 1327–1338 (2019). Copyright 2021 Elsevier]. (e) Pneumatic valves-based PDMS device for antibiotic dilution and AST. [Reproduced with permission from Dai et al. Biotechnol. J. 10, 1783–1791(2015). Copyright 2015 Wiley-VCH].

FIG. 3.

AST in microchannel devices. (a) AST using high surface-to-volume ratio microchannels. (i) Microchannel with a large depth. The oxygen level is insufficient for rapid cell growth. (ii) Microchannel with a small depth. The large s/v ratio contributes to a high oxygen content during bacterial growth. [Reproduced with permission from Chen et al., Anal. Chem. 82, 1012–1019 (2010). Copyright 2010 American Chemical Society]. (b) Cell tracking in microchannel for AST. (i) Configuration of the microchannel chip with thin imaging channels. (ii) Observation of cells confined by thin microchannels. (iii) Differential image of cell positions. [Reproduced with permission from Radonicic et al., Fermentation 8, 195–208 (2022). Copyright 2020 The Authors]. (c) Enzymatic stress-induced AST on a microchannel device. [Reproduced with permission from Kalashnikov et al., Lab Chip 12(21), 4523–4532 (2012). Copyright 2012 Royal Society of Chemistry]. (d) Sieve-like microchannel chip for susceptibility determination and probe-based species identification. (i) Bacteria are trapped in the sieve-like microchannel for monitoring cell growth in the presence of antibiotic at the single-cell level. (ii) Multiplex pathogen identification by combinatory fluorescent probes. [Reproduced with permission from Baltekin et al., Proc. Natl. Acad. Sci. U.S.A. 114(34), 9170–9175 (2017). Copyright 2017 National Academy of Sciences and from Kandavalli et al., Nat. Commun. 13(1), 6215 (2022). Copyright 2022 Nature Portfolio]. (e) Monitoring of the bacterial growth in microchannel with an on-chip electrical resistance meter. [Reproduced with permission from Yang et al., Proc. Natl. Acad. Sci. U.S.A. 117(20), 10639–10644 (2020). Copyright 2020 National Academy of Sciences]. (f) Impendence cytometry for susceptibility determination. [Reproduced with permission from Troiano et al., ACS Sens. 8, 2572−2582 (2023). Copyright 2023 The Authors].

FIG. 4.

Microwell array-based ASTs. (a) Rapid AST using nanoliter microwell arrays. [Reproduced with permission from Avesar et al., Proc. Natl. Acad. Sci. U.S.A. 114(29), E5787–E5795 (2017). Copyright 2017 National Academy of Sciences]. (b) MIC determination by a self-loaded chip with colorimetric chemicals. [Reproduced with permission from Cira et al., Lab Chip 12(6), 1052–1059 (2012). Copyright 2012 Royal Society of Chemistry]. (c) Principle of single-cell AST in microwell array for alleviating inoculum effect. (d) 3D-MAC with capillary valve-based flow distributor. Insets show the capillary valves-based flow distributor (i) and 3D arrangement of microwells (ii). [Reproduced with permission from Wu et al., Lab Chip 23(10), 2399–2410 (2023). Copyright 2023 Royal Society of Chemistry]. (e) AST reagents pre-loading for one-step AST. (i) Chip degassing, (ii) reagent preloading, (iii) lyophilization, and (iv) sample loading and AST initiation. [Reproduced with permission from Wu et al., Lab Chip 23(10), 2399–2410 (2023). Copyright 2023 Royal Society of Chemistry]. (f) Pheno-molecular AST with pathogen identification by digital PCR and high-resolution melt on a microwell array chip. [Reproduced with permission from Athamanolap et al., Anal. Chem. 91(20), 12784–12792 (2019). Copyright 2019 American Chemical Society].

FIG. 5.

Novel droplet-based platforms for rapid AST. (a) Droplet generation at the tip of a vibrating capillary. [Reproduced with permission from Ding et al., Sens. Actuators, B 380, 133254 (2023). Copyright 2023 Elsevier]. (b) Gravity-driven step emulsification device. [Reproduced with permission from Kao et al., Lab Chip 20(1), 54–63 (2020). Copyright 2020 Royal Society of Chemistry]. (c) Immobilized droplet array generated on a plasma patterned glass slide. [Reproduced with permission from Li et al., Lab Chip 23(8), 2005–2015 (2023). Copyright 2023 Royal Society of Chemistry]. (d) An integrated Slipchip for direct AST from blood sample. [Reproduced with permission from Yi et al., Biosens. Bioelectron. 135, 200–207 (2019). Copyright 2019 Elsevier]. (e) Pathogen-specific AST on the pathogen in urine using Slipchip-based digital LAMP. [Reproduced with permission from Schoepp et al., Sci. Transl. Med. 9, eaal3693(2017). Copyright 2017 AAAS].

FIG. 6.

Droplet AST against multiple drug conditions. (a) Droplets with different drug conditions generated by on-line injecting the difference volumes of antibiotic into nanoplugs. [Reproduced with permission from Zhang et al., Small Methods 6, 2101254 (2022), Copyright 2022 Wiley]. (b) Color-coded droplets for multi-condition AST. [Reproduced with permission from Jeong et al., Biosensors 11(8), 238 (2021). Copyright 2021 MDPI].

FIG. 7.

Other microfluidic devices for portable AST. (a) Illustration of digital microfluidic system. [Reproduced with permission from Qiu et al., ACS Sens 6(3), 1147–1156 (2021). Copyright 2021 American Chemistry Society]. (b) AST assay and biochemical reactions for pathogen classification. [Reproduced with permission from Sklavounos et al., Lab Chip 21(21), 4208–4222 (2021). Copyright 2021 Royal Society of Chemistry]. (c) Phenotypic susceptibility determination by probe-hybridization on a compact centrifugal microfluidic system. [Reproduced with permission from Perebikovsky et al., Lab Chip 21(3), 534–545 (2021). Copyright 2021 Royal Society of Chemistry]. (d) Portable AST assay on a paper-based device. [Reproduced with permission from Deiss et al., Lab Chip 14(1), 167–171 (2014). Copyright 2014 Royal Society of Chemistry].