Abdou Mohamed MA, Kozlowski HN, Kim J, Zagorovsky K, Kantor M, Feld JJ, Mubareka S, Mazzulli T, Chan WCW (2021) Diagnosing antibiotic resistance using nucleic acid enzymes and gold nanoparticles. ACS Nano 15(6):9379–9390. https://doi.org/10.1021/acsnano.0c09902

Article  CAS  PubMed  Google Scholar 

Adzitey F, Huda N, Ali GR (2013) Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks. 3 Biotech 3(2):97–107. https://doi.org/10.1007/s13205-012-0074-4

Article  PubMed  Google Scholar 

Alipour F, Ahmadi M, Javadi S (2014) Evaluation of different methods to detect methicillin resistance in Staphylococcus aureus (MRSA). J Infect Public Health 7(3):186–191. https://doi.org/10.1016/j.jiph.2014.01.007

Article  PubMed  Google Scholar 

Alsulami TS, Zhu XY, Abdelhaseib MU, Singh AK, Bhunia AK (2018) Rapid detection and differentiation of Staphylococcus colonies using an optical scattering technology. Anal Bioanal Chem 410(22):5445–5454. https://doi.org/10.1007/s00216-018-1133-4

Article  CAS  PubMed  Google Scholar 

Ambriz-Avina V, Contreras-Garduno JA, Pedraza-Reyes M (2014) Applications of flow cytometry to characterize bacterial physiological responses. Biomed Res Int 2014:461941. https://doi.org/10.1155/2014/461941

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anjum MF, Zankari E, Hasman H (2017) Molecular methods for detection of antimicrobial resistance. Microbiol Spectr 5(6). https://doi.org/10.1128/microbiolspec.ARBA-0011-2017

Archer NK, Mazaitis MJ, Costerton JW, Leid JG, Powers ME, Shirtliff ME (2011) Staphylococcus aureus biofilms: properties, regulation, and roles in human disease. Virulence 2(5):445–459. https://doi.org/10.4161/viru.2.5.17724

Article  PubMed  PubMed Central  Google Scholar 

Bae E, Bai N, Aroonnual A, Bhunia AK, Hirleman ED (2011) Label-free identification of bacterial microcolonies via elastic scattering. Biotechnol Bioeng 108(3):637–644. https://doi.org/10.1002/bit.22980

Article  CAS  PubMed  Google Scholar 

Bae E, Patsekin V, Rajwa B, Bhunia AK, Holdman C, Davisson VJ, Hirleman ED, Robinson JP (2012a) Development of a microbial high-throughput screening instrument based on elastic light scatter patterns. Rev Sci Instrum 83(4):044304. https://doi.org/10.1063/1.3697853

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bae E, Ying D, Kramer D, Patsekin V, Rajwa B, Holdman C, Sturgis J, Davisson VJ, Robinson JP (2012b) Portable bacterial identification system based on elastic light scatter patterns. J Biol Eng 6(1):12. https://doi.org/10.1186/1754-1611-6-12

Article  PubMed  PubMed Central  Google Scholar 

Bae E, Kim H, Rajwa B, Thomas JG, Robinson JP (2016) Current status and future prospects of using advanced computer-based methods to study bacterial colonial morphology. Expert Rev Anti Infect Ther 14(2):207–218. https://doi.org/10.1586/14787210.2016.1122524

Article  CAS  PubMed  Google Scholar 

Bae E, Bai N, Aroonnual A, Robinson JP, Bhunia AK, Hirleman ED (2010) Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns. J Biomed Opt 15(4). https://doi.org/10.1117/1.3463003

Bagwell CB, Adams EG (1993) Fluorescence spectral overlap compensation for any number of flow cytometry parameters. Ann N Y Acad Sci 677(1):167–184. https://doi.org/10.1111/j.1749-6632.1993.tb38775.x

Article  CAS  PubMed  Google Scholar 

Baker CN, Stocker SA, Culver DH, Thornsberry C (1991) Comparison of the E test to agar dilution, broth microdilution, and agar diffusion susceptibility testing techniques by using a special challenge set of bacteria. J Clin Microbiol 29(3):533–538. https://doi.org/10.1128/jcm.29.3.533-538.1991

Article  CAS  PubMed  PubMed Central  Google Scholar 

Balouiri M, Sadiki M, Ibnsouda SK (2016) Methods for in vitro evaluating antimicrobial activity: a review. J Pharm Anal 6(2):71–79. https://doi.org/10.1016/j.jpha.2015.11.005

Article  PubMed  Google Scholar 

Baltekin O, Boucharin A, Tano E, Andersson DI, Elf J (2017) Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging. P Natl Acad Sci USA 114(34):9170–9175. https://doi.org/10.1073/pnas.1708558114

Article  CAS  Google Scholar 

Banada PP, Guo S, Bayraktar B, Bae E, Rajwa B, Robinson JP, Hirleman ED, Bhunia AK (2007) Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species. Biosens Bioelectron 22(8):1664–1671. https://doi.org/10.1016/j.bios.2006.07.028

Article  CAS  PubMed  Google Scholar 

Banada PP, Huff K, Bae E, Rajwa B, Aroonnual A, Bayraktar B, Adil A, Robinson JP, Hirleman ED, Bhunia AK (2009) Label-free detection of multiple bacterial pathogens using light-scattering sensor. Biosens Bioelectron 24(6):1685–1692. https://doi.org/10.1016/j.bios.2008.08.053

Article  CAS  PubMed  Google Scholar 

Barton MD (2000) Antibiotic use in animal feed and its impact on human healt. Nutr Res Rev 13(2):279–299. https://doi.org/10.1079/095442200108729106

Article  CAS  PubMed  Google Scholar 

Bayraktar B, Banada PP, Hirleman ED, Bhunia AK, Robinson JP, Rajwa B (2006) Feature extraction from light-scatter patterns of Listeria colonies for identification and classification. J Biomed Opt 11(3):34006. https://doi.org/10.1117/1.2203987

Article  PubMed  Google Scholar 

Bryson V, Szybalski W (1952) Microbial selection. Science 116(3003):45–51. https://doi.org/10.1126/science.116.3003.45

Article  PubMed  Google Scholar 

Burnett LC, Lunn G, Coico R (2009) Biosafety: guidelines for working with pathogenic and infectious microorganisms. Curr Protoc Microbiol Chapter 1(1). https://doi.org/10.1002/9780471729259.mc01a01s13 (Unit 1A 1)

Buzalewicz I, Suchwałko A, Trzciński P, Sas-Paszt L, Sumorok B, Kowal K, Kozera R, Wieliczko A, Podbielska H (2019) Integrated multi-channel optical system for bacteria characterization and its potential use for monitoring of environmental bacteria. Biomed Opt Express 10(3):1165–1183. https://doi.org/10.1364/BOE.10.001165

Article  PubMed  PubMed Central  Google Scholar 

Cangelosi GA, Meschke JS (2014) Dead or alive: molecular assessment of microbial viability. Appl Environ Microbiol 80(19):5884–5891. https://doi.org/10.1128/AEM.01763-14

Article  CAS  PubMed  PubMed Central  Google Scholar 

CDC (2019) Methicillin-resistant Staphylococcus aureus (MRSA)- Laboratory testing. PUblisher. https://www.cdc.gov/mrsa/lab/index.html

Cherkaoui A, Hibbs J, Emonet S, Tangomo M, Girard M, Francois P, Schrenzel J (2010) Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J Clin Microbiol 48(4):1169–1175. https://doi.org/10.1128/JCM.01881-09

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chong CW, Raveendran P, Mukundan R (2003) An efficient algorithm for fast computation of pseudo-zernike moments. Int J Pattern Recogn 17(6):1011–1023. https://doi.org/10.1142/S0218001403002769

Article  Google Scholar 

CLSI (2020) Performance standards for antimicrobial susceptibility testing M100. 30 edn CLSI, p 402. https://clsi.org/standards/products/microbiology/documents/m100/?gad_source=1&gclid=CjwKCAjw5ImwBhBtEiwAFHDZx5UgJvByxZcYpbUkJCU_cNZKiGcTnj9zgi0CWTQpUUQkrfACyUdwaxoCjSoQAvD_BwE

Davey HM, Kell DB (1996) Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiol Rev 60(4):641–696. https://doi.org/10.1128/mr.60.4.641-696.1996

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dietvorst J, Ferrer-Vilanova A, Iyengar SN, Russom A, Vigues N, Mas J, Vilaplana L, Marco MP, Guirado G, Munoz-Berbel X (2022) Bacteria detection at a single-cell Level through a cyanotype-based photochemical reaction. Anal Chem 94(2):787–792. https://doi.org/10.1021/acs.analchem.1c03326

Article  CAS  PubMed  Google Scholar 

Ferone M, Gowen A, Fanning S, Scannell AGM (2020) Microbial detection and identification methods: Bench top assays to omics approaches. Compr Rev Food Sci Food Saf 19(6):3106–3129. https://doi.org/10.1111/1541-4337.12618

Article  PubMed