{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T16:20:32Z","timestamp":1776961232337,"version":"3.51.4"},"reference-count":35,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T00:00:00Z","timestamp":1535068800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tokyo Metropolitan Small and Medium Enterprise Support Center","award":["NA"],"award-info":[{"award-number":["NA"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Sensors"],"abstract":"<jats:p>Detection and discrimination of bacteria are crucial in a wide range of industries, including clinical testing, and food and beverage production. Staphylococcus species cause various diseases, and are frequently detected in clinical specimens and food products. In particular, S. aureus is well known to be the most pathogenic species. Conventional phenotypic and genotypic methods for discrimination of Staphylococcus spp. are time-consuming and labor-intensive. To address this issue, in the present study, we applied a novel discrimination methodology called colony fingerprinting. Colony fingerprinting discriminates bacterial species based on the multivariate analysis of the images of microcolonies (referred to as colony fingerprints) with a size of up to 250 \u03bcm in diameter. The colony fingerprints were obtained via a lens-less imaging system. Profiling of the colony fingerprints of five Staphylococcus spp. (S. aureus, S. epidermidis, S. haemolyticus, S. saprophyticus, and S. simulans) revealed that the central regions of the colony fingerprints showed species-specific patterns. We developed 14 discriminative parameters, some of which highlight the features of the central regions, and analyzed them by several machine learning approaches. As a result, artificial neural network (ANN), support vector machine (SVM), and random forest (RF) showed high performance for discrimination of theses bacteria. Bacterial discrimination by colony fingerprinting can be performed within 11 h, on average, and therefore can cut discrimination time in half compared to conventional methods. Moreover, we also successfully demonstrated discrimination of S. aureus in a mixed culture with Pseudomonas aeruginosa. These results suggest that colony fingerprinting is useful for discrimination of Staphylococcus spp.<\/jats:p>","DOI":"10.3390\/s18092789","type":"journal-article","created":{"date-parts":[[2018,8,24]],"date-time":"2018-08-24T11:13:45Z","timestamp":1535109225000},"page":"2789","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Colony Fingerprint-Based Discrimination of Staphylococcus species with Machine Learning Approaches"],"prefix":"10.3390","volume":"18","author":[{"given":"Yoshiaki","family":"Maeda","sequence":"first","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yui","family":"Sugiyama","sequence":"additional","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atsushi","family":"Kogiso","sequence":"additional","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tae-Kyu","family":"Lim","sequence":"additional","affiliation":[{"name":"Malcom Co., Ltd., 4-15-10, Honmachi, Shibuya-ku, Tokyo 151-0071, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manabu","family":"Harada","sequence":"additional","affiliation":[{"name":"Malcom Co., Ltd., 4-15-10, Honmachi, Shibuya-ku, Tokyo 151-0071, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomoko","family":"Yoshino","sequence":"additional","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tadashi","family":"Matsunaga","sequence":"additional","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"},{"name":"Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2601-2256","authenticated-orcid":false,"given":"Tsuyoshi","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2018,8,24]]},"reference":[{"key":"ref_1","unstructured":"Schleifer, K.-H., and Bell, J.A. (2009). Staphylococcaceae, Springer."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1111\/j.1574-6976.2011.00311.x","article-title":"Staphylococcus aureus and its food poisoning toxins: Characterization and outbreak investigation","volume":"36","author":"Hennekinne","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Asperger, H., and Zangerl, P. (2003). Staphylococcus aureus, Academic Press.","DOI":"10.1016\/B0-12-227235-8\/00471-5"},{"key":"ref_4","first-page":"443","article-title":"Growth characterisation of Staphylococcus aureus in milk: A quantitative approach","volume":"27","year":"2009","journal-title":"Czech J. Food Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Medve\u010fov\u00e1, A., and Val\u00edk, \u013d. (2012). Staphylococcus aureus: Characterisation and quantitative growth description in milk and artisanal raw milk cheese production. Structure and Function of Food Engineering, InTech.","DOI":"10.5772\/48175"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1128\/jb.50.2.201-203.1945","article-title":"The significance of sodium chloride in studies of Staphylococci","volume":"50","author":"Chapman","year":"1945","journal-title":"J. Bacteriol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1128\/am.29.4.502-505.1975","article-title":"Interpretation of the tube coagulase test for identification of Staphylococcus aureus","volume":"29","author":"Sperber","year":"1975","journal-title":"Appl. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.syapm.2010.11.013","article-title":"Applications of whole-cell matrix-assisted laser-desorption\/ionization time-of-flight mass spectrometry in systematic microbiology","volume":"34","author":"Welker","year":"2011","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1002\/mas.21359","article-title":"MALDI TOF MS profiling of bacteria at the strain level: A review","volume":"32","author":"Sandrin","year":"2013","journal-title":"Mass Spectrom. Rev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/jrs.4844","article-title":"The application of Raman spectroscopy for the detection and identification of microorganisms","volume":"47","author":"Kirchhoff","year":"2016","journal-title":"J. Raman Spectrosc."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1002\/bit.22980","article-title":"Label-free identification of bacterial microcolonies via elastic scattering","volume":"108","author":"Bae","year":"2011","journal-title":"Biotechnol. Bioeng."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1016\/j.bios.2006.07.028","article-title":"Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species","volume":"22","author":"Banada","year":"2007","journal-title":"Biosens. Bioelectron."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1016\/j.bios.2008.08.053","article-title":"Label-free detection of multiple bacterial pathogens using light-scattering sensor","volume":"24","author":"Banada","year":"2009","journal-title":"Biosens. Bioelectron."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1111\/j.1751-7915.2012.00349.x","article-title":"Light-scattering sensor for real-time identification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae colonies on solid agar plate","volume":"5","author":"Huff","year":"2012","journal-title":"Microb. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Tang, Y., Kim, H., Singh, A.K., Aroonnual, A., Bae, E., Rajwa, B., Fratamico, P.M., and Bhunia, A.K. (2014). Light scattering sensor for direct identification of colonies of Escherichia coli serogroups O26, O45, O103, O111, O121, O145 and O157. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0105272"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Maeda, Y., Dobashi, H., Sugiyama, Y., Saeki, T., Lim, T.K., Harada, M., Matsunaga, T., Yoshino, T., and Tanaka, T. (2017). Colony fingerprint for discrimination of microbial species based on lensless imaging of microcolonies. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0174723"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1016\/j.bios.2010.07.081","article-title":"High-content analysis of single cells directly assembled on CMOS sensor based on color imaging","volume":"26","author":"Tanaka","year":"2010","journal-title":"Biosens. Bioelectron."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1039\/B713695A","article-title":"Ultra wide-field lens-free monitoring of cells on-chip","volume":"8","author":"Ozcan","year":"2008","journal-title":"Lab Chip"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"21473","DOI":"10.1038\/srep21473","article-title":"Real-time bacterial microcolony counting using on-chip microscopy","volume":"6","author":"Jung","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Saeki, T., Hosokawa, M., Lim, T.K., Harada, M., Matsunaga, T., and Tanaka, T. (2014). Digital cell counting device integrated with a single-cell array. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0089011"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1039\/c0lc00039f","article-title":"Single-cell detection using a thin film transistor photosensor with micro-partitions","volume":"10","author":"Tanaka","year":"2010","journal-title":"Lab Chip"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aca.2017.03.030","article-title":"Rapid imaging and detection of circulating tumor cells using a wide-field fluorescence imaging system","volume":"969","author":"Yoshino","year":"2017","journal-title":"Anal. Chim. Acta"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.bios.2014.08.051","article-title":"Simple and rapid CD4 testing based on large-field imaging system composed of microcavity array and two-dimensional photosensor","volume":"67","author":"Saeki","year":"2015","journal-title":"Biosens. Bioelectron."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_25","first-page":"23","article-title":"A threshold selection method from gray-level histograms","volume":"11","author":"Otsu","year":"1975","journal-title":"Automatica"},{"key":"ref_26","unstructured":"R. Development Core Team (2018, August 19). R: A Language and Environment for Statistical Computing. Available online: http:\/\/softlibre.unizar.es\/manuales\/aplicaciones\/r\/fullrefman.pdf."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1039\/c0lc00684j","article-title":"Holographic pixel super-resolution in portable lensless on-chip microscopy using a fiber-optic array","volume":"11","author":"Bishara","year":"2011","journal-title":"Lab Chip"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1039\/C4LC01131G","article-title":"Three-part differential of unlabeled leukocytes with a compact lens-free imaging flow cytometer","volume":"15","author":"Vercruysse","year":"2015","journal-title":"Lab Chip"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"26312","DOI":"10.1364\/OE.22.026312","article-title":"Bacteria identification in an optical system with optimized diffraction pattern registration condition supported by enhanced statistical analysis","volume":"22","author":"Suchwalko","year":"2014","journal-title":"Opt. Express"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"26493","DOI":"10.1364\/OE.21.026493","article-title":"Degeneration of Fraunhofer diffraction on bacterial colonies due to their light focusing properties examined in the digital holographic microscope system","volume":"21","author":"Buzalewicz","year":"2013","journal-title":"Opt. Express"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Su, P.T., Liao, C.T., Roan, J.R., Wang, S.H., Chiou, A., and Syu, W.J. (2012). Bacterial colony from two-dimensional division to three-dimensional development. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0048098"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Rosenstein, R., and G\u00f6tz, F. (2012). What distinguishes highly pathogenic staphylococci from medium-and non-pathogenic?. Between Pathogenicity and Commensalism, Springer.","DOI":"10.1007\/82_2012_286"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1007\/s10295-017-1943-y","article-title":"Discrimination of wine lactic acid bacteria by Raman spectroscopy","volume":"44","author":"Rodriguez","year":"2017","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.syapm.2010.11.003","article-title":"Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning","volume":"34","author":"Slabbinck","year":"2011","journal-title":"Syst. Appl. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"6416","DOI":"10.1002\/pmic.200600335","article-title":"Discrimination of intact mycobacteria at the strain level: A combined MALDI-TOF MS and biostatistical analysis","volume":"6","author":"Hettick","year":"2006","journal-title":"Proteomics"}],"container-title":["Sensors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8220\/18\/9\/2789\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:20:54Z","timestamp":1760196054000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8220\/18\/9\/2789"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,24]]},"references-count":35,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2018,9]]}},"alternative-id":["s18092789"],"URL":"https:\/\/doi.org\/10.3390\/s18092789","relation":{},"ISSN":["1424-8220"],"issn-type":[{"value":"1424-8220","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,24]]}}}