Exploiting open source 3D printer architecture for laboratory robotics to automate high-throughput time-lapse imaging for analytical microbiology


Autoři: Sarah H. Needs aff001;  Tai The Diep aff001;  Stephanie P. Bull aff001;  Anton Lindley-Decaire aff002;  Partha Ray aff003;  Alexander D. Edwards aff001
Působiště autorů: Reading School of Pharmacy, University of Reading, Whiteknights, Reading, United Kingdom aff001;  Centre for Electronic Imaging, The Open University, Milton Keynes, United Kingdom aff002;  Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: 10.1371/journal.pone.0224878

Souhrn

Growth in open-source hardware designs combined with the low-cost of high performance optoelectronic and robotics components has supported a resurgence of in-house custom lab equipment development. We describe a low cost (below $700), open-source, fully customizable high-throughput imaging system for analytical microbiology applications. The system comprises a Raspberry Pi camera mounted on an aluminium extrusion frame with 3D-printed joints controlled by an Arduino microcontroller running open-source Repetier Host Firmware. The camera position is controlled by simple G-code scripts supplied from a Raspberry Pi singleboard computer and allow customized time-lapse imaging of microdevices over a large imaging area. Open-source OctoPrint software allows remote access and control. This simple yet effective design allows high-throughput microbiology testing in multiple formats including formats for bacterial motility, colony growth, microtitre plates and microfluidic devices termed ‘lab-on-a-comb’ to screen the effects of different culture media components and antibiotics on bacterial growth. The open-source robot design allows customization of the size of the imaging area; the current design has an imaging area of ~420 × 300mm, which allows 29 ‘lab-on-a-comb’ devices to be imaged which is equivalent 3480 individual 1μl samples. The system can also be modified for fluorescence detection using LED and emission filters embedded on the PiCam for more sensitive detection of bacterial growth using fluorescent dyes.

Klíčová slova:

3D printing – Antibiotics – Antimicrobial resistance – Cameras – Fluorescence imaging – Microfluidics – Milk – Open source hardware


Zdroje

1. Bourbeau PP, Ledeboer NA. Automation in Clinical Microbiology. Journal of Clinical Microbiology. 2013;51(6):1658. doi: 10.1128/JCM.00301-13 23515547

2. Burckhardt I. Laboratory Automation in Clinical Microbiology. Bioengineering (Basel, Switzerland). 2018;5(4):102.

3. Tillich UM, Wolter N, Schulze K, Kramer D, Brödel O, Frohme M. High-throughput cultivation and screening platform for unicellular phototrophs. BMC Microbiology. 2014;14(1):239.

4. Li B, Webster TJ. Bacteria antibiotic resistance: New challenges and opportunities for implant-associated orthopedic infections. Journal of orthopaedic research: official publication of the Orthopaedic Research Society. 2018;36(1):22–32.

5. Machowska A, Stålsby Lundborg C. Drivers of Irrational Use of Antibiotics in Europe. International journal of environmental research and public health. 2018;16(1):27.

6. Ab Rahman N, Teng CL, Sivasampu S. Antibiotic prescribing in public and private practice: a cross-sectional study in primary care clinics in Malaysia. BMC infectious diseases. 2016;16:208-. doi: 10.1186/s12879-016-1530-2 27188538

7. Darboe F, Mbandi SK, Naidoo K, Yende-Zuma N, Lewis L, Thompson EG, et al. Detection of Tuberculosis Recurrence, Diagnosis and Treatment Response by a Blood Transcriptomic Risk Signature in HIV-Infected Persons on Antiretroviral Therapy. 2019(1664-302X (Print)).

8. Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. 2019(1879–0364 (Electronic)).

9. Kang WA-Ohoo, Sarkar S, Lin ZS, McKenney S, Konry T. Ultrafast Parallelized Microfluidic Platform for Antimicrobial Susceptibility Testing of Gram Positive and Negative Bacteria. 2019(1520–6882 (Electronic)).

10. Gao J, Li H, Torab P, Mach KE, Craft DW, Thomas NJ, et al. Nanotube assisted microwave electroporation for single cell pathogen identification and antimicrobial susceptibility testing. Nanomedicine: Nanotechnology, Biology and Medicine. 2019;17:246–53.

11. Kim SA-O, Lee SA-O, Kim JA-O, Chung Hj Auid- Orcid: —902X Fau—Jeon JS, Jeon JA-O. Microfluidic-based observation of local bacterial density under antimicrobial concentration gradient for rapid antibiotic susceptibility testing. 2019(1932–1058 (Print)).

12. Reis NM, Pivetal J Fau—Loo-Zazueta AL, Loo-Zazueta Al Fau—Barros JMS, Barros Jm Fau—Edwards AD, Edwards AD. Lab on a stick: multi-analyte cellular assays in a microfluidic dipstick. Lab On a Chip. 2016(1473–0189 (Electronic)).

13. Reis NM, Pivetal J, Loo-Zazueta AL, Barros JMS, Edwards AD. Lab on a stick: multi-analyte cellular assays in a microfluidic dipstick. Lab on a Chip. 2016;16(15):2891–9. doi: 10.1039/c6lc00332j 27374435

14. Pearce JM. Impacts of Open Source Hardware in Science and Engineering. The Bridge. 2017;47(3).

15. Kim K, Kim HK, Lim H, Myung H. A Low Cost/Low Power Open Source Sensor System for Automated Tuberculosis Drug Susceptibility Testing. Sensors (Basel, Switzerland). 2016;16(6):942.

16. Nejatimoharrami F, Faina A, Stoy K. New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot. 2017(2472–6311 (Electronic)).

17. Nunez I, Matute T, Herrera R, Keymer J, Marzullo T, Rudge T, et al. Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering. 2017(1932–6203 (Electronic)).

18. Steffens S, Nüßer L, Seiler T-B, Ruchter N, Schumann M, Döring R, et al. A versatile and low-cost open source pipetting robot for automation of toxicological and ecotoxicological bioassays. PLOS ONE. 2017;12(6):e0179636. doi: 10.1371/journal.pone.0179636 28622373

19. Lu Q, Liu G, Xiao C, Hu C, Zhang S, Xu RX, et al. A modular, open-source, slide-scanning microscope for diagnostic applications in resource-constrained settings. PLOS ONE. 2018;13(3):e0194063. doi: 10.1371/journal.pone.0194063 29543835

20. Maia Chagas A, Prieto-Godino LL, Arrenberg AB, Baden T. The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans. PLoS biology. 2017;15(7):e2002702–e. doi: 10.1371/journal.pbio.2002702 28719603

21. James P. Sharkey DCWF, Kabla Alexandre, Baumberg Jeremy J., Richard W. Bowman. A one-piece 3D printed flexure translation stage for open-source microscopy. Review of Sceintific Instruments 2016;87(2).

22. Jones R, Haufe P, Sells E, Iravani P, Olliver V, Palmer C, et al. RepRap–the replicating rapid prototyper. Robotica. 2011;29(1):177–91.

23. Solanki R, Gosling R, Rammohan V, Hose R, Lawford P, Gunn J, et al. 16 Assessing the accuracy of a novel in silico imaging tool for the 3D reconstruction of coronary vasculature in the context of virtual fractional flow reserve. Heart. 2019;105(Suppl 6):A14.

24. Aw YY, Yeoh CK, Idris MA, Teh PL, Elyne WN, Hamzah KA, et al. Influence of Filler Precoating and Printing Parameter on Mechanical Properties of 3D Printed Acrylonitrile Butadiene Styrene/Zinc Oxide Composite. Polymer-Plastics Technology and Materials. 2019;58(1):1–13.

25. Pereira VR, Hosker BS. Low-cost (<€5), open-source, potential alternative to commercial spectrophotometers. PLOS Biology. 2019;17(6):e3000321. doi: 10.1371/journal.pbio.3000321 31188818

26. Biolog U. 2019 [Available from: https://www.toshindia.com/products/bacteria-yeast-and-fungi-identification-system.

27. OpenBuilds. [Internet] https://openbuildspartstore.com/v-slot-mini-v-linear-actuator-bundle/.

28. GitLab. [Internet] https://gitlab.com/AlEdwards/polir

29. Thingiverse. [Internet] https://www.thingiverse.com.

30. Reis NM, Pivetal J, Loo-Zazueta AL, Barros JM, Edwards AD. Lab on a stick: multi-analyte cellular assays in a microfluidic dipstick. Lab Chip. 2016;16(15):2891–9. doi: 10.1039/c6lc00332j 27374435

31. Pivetal J, Pereira F, Barbosa AI, Castanheira AP, Reis NM, Edwards AD. Covalent immobilisation of antibodies in Teflon-FEP microfluidic devices for sensitive quantification of clinically relevant protein biomarkers. Analyst. 2017.

32. Andrews J. BSAC standardized disc susceptibility testing method (version 4). Journal of Antimicrobial Chemotherapy. 2005;56(1):60–76. doi: 10.1093/jac/dki124 15911553

33. Jorgensen JH, Turnidge JD. Susceptibility test methods: dilution and disk diffusion methods. Manual of Clinical Microbiology, Eleventh Edition: American Society of Microbiology; 2015. p. 1253–73.

34. RepRap. [Internet] https://reprap.org/wiki/CoreXY.

35. Roncarati D, Danielli A Fau—Spohn G, Spohn G Fau—Delany I, Delany I Fau—Scarlato V, Scarlato V. Transcriptional regulation of stress response and motility functions in Helicobacter pylori is mediated by HspR and HrcA. 2007(0021–9193 (Print)).

36. Butler CC, Francis NA, Thomas-Jones E, Longo M, Wootton M, Llor C, et al. Point-of-care urine culture for managing urinary tract infection in primary care: a randomised controlled trial of clinical and cost-effectiveness. The British journal of general practice: the journal of the Royal College of General Practitioners. 2018;68(669):e268–e78.

37. Yodoshi T, Matsushima M, Taniguchi T, Kinjo S. Utility of point-of-care Gram stain by physicians for urinary tract infection in children ≤36 months. Medicine. 2019;98(14):e15101–e. doi: 10.1097/MD.0000000000015101 30946373

38. Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang T-H, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nature reviews Urology. 2017;14(5):296–310. doi: 10.1038/nrurol.2017.20 28248946

39. Kromker V, Leimbach S. Mastitis treatment-Reduction in antibiotic usage in dairy cows. Reproduction in domestic animals = Zuchthygiene. 2017;52 Suppl 3:21–9.

40. Kempf F, Slugocki C, Blum SE, Leitner G, Germon P. Genomic Comparative Study of Bovine Mastitis Escherichia coli. PloS one. 2016;11(1):e0147954–e. doi: 10.1371/journal.pone.0147954 26809117

41. Dahm DJ. Explaining Some Light Scattering Properties of Milk Using Representative Layer Theory. J Near Infrared Spectrosc. 2013;21(5):323–39.

42. Natto MJ, Savioli F, Quashie NB, Dardonville C, Rodenko B, de Koning HP. Validation of novel fluorescence assays for the routine screening of drug susceptibilities of Trichomonas vaginalis. The Journal of antimicrobial chemotherapy. 2012;67(4):933–43. doi: 10.1093/jac/dkr572 22258922

43. Mishra P, Singh D, Mishra KP, Kaur G, Dhull N, Tomar M, et al. Rapid antibiotic susceptibility testing by resazurin using thin film platinum as a bio-electrode. Journal of microbiological methods. 2019;162:69–76. doi: 10.1016/j.mimet.2019.05.009 31103460

44. Germ J, Poirel L, Kisek TC, Spik VC, Seme K, Premru MM, et al. Evaluation of resazurin-based rapid test to detect colistin resistance in Acinetobacter baumannii isolates. European journal of clinical microbiology & infectious diseases: official publication of the European Society of Clinical Microbiology. 2019.


Článek vyšel v časopise

PLOS One


2019 Číslo 11