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Abu-Aqil G, Suleiman M, Sharaha U, Nesher L, Lapidot I, Salman A, Huleihel M. Detection of extended-spectrum β-lactamase-producing bacteria isolated directly from urine by infrared spectroscopy and machine learning. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 295:122634. [PMID: 36944279 DOI: 10.1016/j.saa.2023.122634] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Resistant bacteria have become one of the leading health threats in the last decades. Extended-spectrum β-lactamase (ESBL) producing bacteria, including Escherichia (E.) coli and Klebsiella (K.) pneumoniae (the most frequent ones), are a significant class out of all resistant infecting bacteria. Due to the widespread and ongoing development of ESBL-producing (ESBL+) resistant bacteria, many routinely used antibiotics are no longer effective against them. However, an early and reliable ESBL+ bacteria detection method will improve the efficiency of treatment and limit their spread. In this work, we investigated the capability of infrared (IR) spectroscopy based machine learning tools [principal component analysis (PCA) and Random Forest (RF) classifier] for the rapid detection of ESBL+ bacteria isolated directly from patients' urine. For that, we examined 1881 E. coli samples (416 ESBL+ and 1465 ESBL-) and 609 K. pneumoniae samples (237 ESBL+ and 372 ESBL-). All samples were isolated directly from the urine of midstream patients. This study revealed that within 40 min of receiving the patient urine it is possible to determine the infecting bacterium as E. coli or K. pneumoniae with 95% success rate while it was possible to determine the ESBL+E. coli and ESBL+K. pneumoniae with 83% and 78% accuracy rates, respectively.
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Affiliation(s)
- George Abu-Aqil
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Manal Suleiman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; Department of Biology, Science and Technology College, Hebron University, Hebron P760, Palestine
| | - Lior Nesher
- Infectious Disease Institute, Soroka University Medical Center, Beer-Sheva, Israel; Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel; LIA Avignon Université, 339 Chemin des Meinajaries, 84000 Avignon, France
| | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel.
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Kavitha A, Doss A, Praveen Pole R, Pushpa Rani TK, Prasad R, Satheesh S. A mini review on plant-mediated zinc oxide nanoparticles and their antibacterial potency. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Abu-Aqil G, Suleiman M, Sharaha U, Riesenberg K, Lapidot I, Huleihel M, Salman A. Fast identification and susceptibility determination of E. coli isolated directly from patients' urine using infrared-spectroscopy and machine learning. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121909. [PMID: 36170776 DOI: 10.1016/j.saa.2022.121909] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/18/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
For effective treatment, it is crucial to identify the infecting bacterium at the species level and to determine its antimicrobial susceptibility. This is especially true now, when numerous bacteria have developed multidrug resistance to most commonly used antibiotics. Currently used methods need ∼ 48 h to identify a bacterium and determine its susceptibility to specific antibiotics. This study reports the potential of using infrared spectroscopy with machine learning algorithms to identify E. coli isolated directly from patients' urine while simultaneously determining its susceptibility to antibiotics within ∼ 40 min after receiving the patient's urine sample. For this goal, 1,765 E. coli isolates purified directly from urine samples were collected from patients with urinary tract infections (UTIs). After collection, the samples were tested by infrared microscopy and analyzed by machine learning. We achieved success rates of ∼ 96% in isolate level identification and ∼ 84% in susceptibility determination.
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Affiliation(s)
- George Abu-Aqil
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Manal Suleiman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Klaris Riesenberg
- Director of Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel.
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Tokunaga Y, Yamaguchi N. Rapid quantification of
Escherichia coli
O157
:
H7
in lettuce and beef using an on‐chip staining microfluidic device. J Food Saf 2020. [DOI: 10.1111/jfs.12851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yusuke Tokunaga
- Division of Hygienic Chemistry Osaka Institute of Public Health Osaka Japan
| | - Nobuyasu Yamaguchi
- Division of Hygienic Chemistry Osaka Institute of Public Health Osaka Japan
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Sharaha U, Rodriguez-Diaz E, Sagi O, Riesenberg K, Salman A, Bigio IJ, Huleihel M. Fast and reliable determination of Escherichia coli susceptibility to antibiotics: Infrared microscopy in tandem with machine learning algorithms. JOURNAL OF BIOPHOTONICS 2019; 12:e201800478. [PMID: 30916881 DOI: 10.1002/jbio.201800478] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/12/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Antimicrobial drugs have an important role in controlling bacterial infectious diseases. However, the increasing resistance of bacteria to antibiotics has become a global health care problem. Rapid determination of antimicrobial susceptibility of clinical isolates is often crucial for the optimal antimicrobial therapy. The conventional methods used in medical centers for susceptibility testing are time-consuming (>2 days). Two bacterial culture steps are needed, the first is used to grow the bacteria from urine on agar plates to determine the species of the bacteria (~24 hours). The second culture is used to determine the susceptibility by growing colonies from the first culture for another 24 hours. Here, the main goal is to examine the potential of infrared microscopy combined with multivariate analysis, to reduce the time it takes to identify Escherichia coli susceptibility to antibiotics and to determine the optimum choice of antibiotic to which the bacteria will respond. E coli colonies of the first culture from patients with urinary tract infections (UTI) were examined for the bacterial susceptibility using Fourier-transform infrared (FTIR). Our results show that it is possible to determine the optimum choice of antibiotic with better than 89% sensitivity, in the time span of few minutes, following the first culture.
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Affiliation(s)
- Uraib Sharaha
- Department of Microbiology, Immunology and Genetic, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eladio Rodriguez-Diaz
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
- Section of Gastroenterology, VA Boston Healthcare System, Boston, Massachusetts
| | - Orli Sagi
- Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Klaris Riesenberg
- Infectious Diseases Department, Soroka University Medical Center, Beer-Sheva, Israel
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering, Beer-Sheva, Israel
| | - Irving J Bigio
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
- Department of Electrical & Computer Engineering, Boston University, Boston, Massachusetts
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetic, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Sharaha U, Rodriguez-Diaz E, Sagi O, Riesenberg K, Lapidot I, Segal Y, Bigio IJ, Huleihel M, Salman A. Detection of Extended-Spectrum β-Lactamase-Producing Escherichia coli Using Infrared Microscopy and Machine-Learning Algorithms. Anal Chem 2019; 91:2525-2530. [DOI: 10.1021/acs.analchem.8b05497] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
| | | | - Orli Sagi
- Director of Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva 84105, Israel
| | | | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
| | | | | | | | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel
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Faghihzadeh F, Anaya NM, Schifman LA, Oyanedel-Craver V. Fourier transform infrared spectroscopy to assess molecular-level changes in microorganisms exposed to nanoparticles. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s41204-016-0001-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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8
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Lu X, Rasco BA. Determination of Antioxidant Content and Antioxidant Activity in Foods using Infrared Spectroscopy and Chemometrics: A Review. Crit Rev Food Sci Nutr 2012; 52:853-75. [DOI: 10.1080/10408398.2010.511322] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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Davis R, Deering A, Burgula Y, Mauer L, Reuhs B. Differentiation of live, dead and treated cells of Escherichia coli O157:H7 using FT-IR spectroscopy. J Appl Microbiol 2012; 112:743-51. [DOI: 10.1111/j.1365-2672.2011.05215.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Lu X, Liu Q, Wu D, Al-Qadiri HM, Al-Alami NI, Kang DH, Shin JH, Tang J, Jabal JM, Aston ED, Rasco BA. Using of infrared spectroscopy to study the survival and injury of Escherichia coli O157:H7, Campylobacter jejuni and Pseudomonas aeruginosa under cold stress in low nutrient media. Food Microbiol 2011; 28:537-46. [DOI: 10.1016/j.fm.2010.11.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 10/31/2010] [Accepted: 11/02/2010] [Indexed: 11/30/2022]
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Davis R, Burgula Y, Deering A, Irudayaraj J, Reuhs B, Mauer L. Detection and differentiation of live and heat-treated Salmonella enterica serovars inoculated onto chicken breast using Fourier transform infrared (FT-IR) spectroscopy. J Appl Microbiol 2010; 109:2019-31. [DOI: 10.1111/j.1365-2672.2010.04832.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Davis R, Irudayaraj J, Reuhs BL, Mauer LJ. Detection of E. coli O157:H7 from Ground Beef Using Fourier Transform Infrared (FT-IR) Spectroscopy and Chemometrics. J Food Sci 2010; 75:M340-6. [DOI: 10.1111/j.1750-3841.2010.01686.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Ravindranath SP, Mauer LJ, Deb-Roy C, Irudayaraj J. Biofunctionalized Magnetic Nanoparticle Integrated Mid-Infrared Pathogen Sensor for Food Matrixes. Anal Chem 2009; 81:2840-6. [PMID: 19281189 DOI: 10.1021/ac802158y] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sandeep P. Ravindranath
- Department of Agricultural and Biological Engineering and Bindley Bioscience Center, Purdue University, 225 South University Street, West Lafayette, Indiana 47907, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, and E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lisa J. Mauer
- Department of Agricultural and Biological Engineering and Bindley Bioscience Center, Purdue University, 225 South University Street, West Lafayette, Indiana 47907, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, and E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Chitrita Deb-Roy
- Department of Agricultural and Biological Engineering and Bindley Bioscience Center, Purdue University, 225 South University Street, West Lafayette, Indiana 47907, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, and E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering and Bindley Bioscience Center, Purdue University, 225 South University Street, West Lafayette, Indiana 47907, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, and E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
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BURGULA Y, KHALI D, KIM S, KRISHNAN S, COUSIN M, GORE J, REUHS B, MAUER L. REVIEW OF MID-INFRARED FOURIER TRANSFORM-INFRARED SPECTROSCOPY APPLICATIONS FOR BACTERIAL DETECTION. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1745-4581.2007.00078.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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