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Ganasala P. Maximally stable extremal regions-based algorithm for automatic interpretation of disc-diffusion antibiotic sensitivity test. J Med Eng Technol 2024:1-10. [PMID: 38856991 DOI: 10.1080/03091902.2024.2356622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/12/2024] [Indexed: 06/11/2024]
Abstract
Antibiotic resistance causes a major threat to patients suffering from infectious diseases. Accurate and timely assessment of Antibiotic Susceptibility Test (AST) is of great importance to ensure adequate treatment for patients and for epidemiological monitoring. Disc Diffusion Test (DDT) is a standard and widely used method for AST. Manual interpretation of DDT results is a tedious task and susceptible to human errors. Computer vision-based automated interpretation of DDT results will speed up the process and reduces the manpower requirement. This would assist the physician to initiate the antibiotic treatment for the patients on time and results in saving the patient's life. The crucial step in automatic interpretation of DDT result is to measure and present the diameter of zone of inhibition without manual intervention. The existing methods require manual interventions at various stages during inhibition zone diameter measurement for some typical cases. This issue is addressed in the present work through maximally stable extremal regions (MSER) based algorithm. Dataset consisting of 60 agar plate images that includes different agar medium, images having different resolution and visual quality is used to validate the proposed method. Experimental results demonstrated that there is a strong correlation between standard method and the proposed method.
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Affiliation(s)
- Padma Ganasala
- Department of ECE, Gayatri Vidya Parishad College of Engineering, Visakhapatnam, Andhra Pradesh, India
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Rivera A, Viñado B, Benito N, Docobo-Pérez F, Fernández-Cuenca F, Fernández-Domínguez J, Guinea J, López-Navas A, Moreno MÁ, Larrosa MN, Oliver A, Navarro F. Recommendations of the Spanish Antibiogram Committee (COESANT) for in vitro susceptibility testing of antimicrobial agents by disk diffusion. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2023; 41:571-576. [PMID: 36610835 DOI: 10.1016/j.eimce.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2022] [Indexed: 01/07/2023]
Abstract
Disk diffusion is a well standardized method that provides reliable categorical results to guide antimicrobial therapy in numerous types of infections. Based on the guidelines of the European Committee on Antimicrobial Susceptibility Testing (EUCAST), which are widely implemented in Spain, the Spanish Antibiogram Committee (COESANT) has drawn up recommendations for antimicrobial selection by the disk diffusion technique, including selective reporting and its use for the detection of resistance mechanisms. Factors affecting disk diffusion results, along with advantages and shortcomings of the method, are also discussed.
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Affiliation(s)
- Alba Rivera
- Servicio de Microbiología, Hospital de la Santa Creu i Sant Pau, Departamento de Genética y de Microbiología de la Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica de Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Belén Viñado
- Servicio de Microbiología, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Natividad Benito
- Unidad de Enfermedades Infecciosas, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica de Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Fernando Docobo-Pérez
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain; Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Felipe Fernández-Cuenca
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Sevilla, Spain; Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena/CSIC/Universidad de Sevilla, Sevilla, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Fernández-Domínguez
- Servicio de Microbiología, Hospital Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Guinea
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Antonio López-Navas
- Agencia Española de Medicamentos y Productos Sanitarios (AEMPS), Madrid, Spain
| | - Miguel Ángel Moreno
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - María Nieves Larrosa
- Servicio de Microbiología, Hospital Universitario Vall d'Hebron, Universitat Autònoma de Barcelona, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Antonio Oliver
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain; Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Ferran Navarro
- Servicio de Microbiología, Hospital de la Santa Creu i Sant Pau, Departamento de Genética y de Microbiología de la Universitat Autònoma de Barcelona, Institut d'Investigació Biomèdica de Sant Pau (IIB Sant Pau), Barcelona, Spain.
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Salam MA, Al-Amin MY, Pawar JS, Akhter N, Lucy IB. Conventional methods and future trends in antimicrobial susceptibility testing. Saudi J Biol Sci 2023; 30:103582. [PMID: 36852413 PMCID: PMC9958398 DOI: 10.1016/j.sjbs.2023.103582] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/07/2023] [Accepted: 01/29/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial susceptibility testing is an essential task for selecting appropriate antimicrobial agents to treat infectious diseases. Constant evolution has been observed in methods used in the diagnostic microbiology laboratories. Disc diffusion or broth microdilution are classical and conventional phenotypic methods with long turnaround time and labour-intensive but still widely practiced as gold-standard. Scientists are striving to develop innovative, novel and faster methods of antimicrobial susceptibility testing to be applicable for routine microbiological laboratory practice and research. To meet the requirements, there is an increasing trend towards automation, genotypic and micro/nano technology-based innovations. Automation in detection systems and integration of computers for online data analysis and data sharing are giant leaps towards versatile nature of automated methods currently in use. Genotypic methods detect a specific genetic marker associated with resistant phenotypes using molecular amplification techniques and genome sequencing. Microfluidics and microdroplets are recent addition in the continuous advancement of methods that show great promises with regards to safety and speed and have the prospect to identify and monitor resistance mechanisms. Although genotypic and microfluidics methods have many exciting features, however, their applications into routine clinical laboratory practice warrant extensive validation. The main impetus behind the evolution of methods in antimicrobial susceptibility testing is to shorten the overall turnaround time in obtaining the results and to enhance the ease of sample processing. This comprehensive narrative review summarises major conventional phenotypic methods and automated systems currently in use, and highlights principles of some of the emerging genotypic and micro/nanotechnology-based methods in antimicrobial susceptibility testing.
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Key Words
- ADR, Adverse drug reaction
- AMR, Antimicrobial resistance
- AST, Antimicrobial susceptibility testing
- ATCC, American Type Culture Collection
- Advantages and disadvantages
- Antimicrobial susceptibility testing
- Automations
- CFU, Colony forming units
- CLSI, Clinical & Laboratory Standards Institute
- Conventional methods
- DOT-MGA, Direct-On-Target Microdroplet Growth Assay
- EUCAST, European Committee on Antimicrobial Susceptibility Testing
- Etest, Epsilometer testing
- Genotypic methods
- ID, Identification
- MALDI-TOF MS, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
- MBC, Minimum bactericidal concentration
- MDR, Multi drug resistant
- MHA, Muller Hinton Agar
- MIC, Minimum inhibitory concentration
- Micro/nanotechnology-based techniques
- NAAT, Nucleic Acid Amplification Test
- PCR, Polymerase chain reaction
- PMF, Peptide mass fingerprint
- POC, Point of care
- WGS, Whole Genome Sequencing
- ZOI, Zone of inhibition
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Affiliation(s)
- Md. Abdus Salam
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University, Malaysia
| | - Md. Yusuf Al-Amin
- Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN, USA,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jogendra Singh Pawar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Naseem Akhter
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Irine Banu Lucy
- Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh,Corresponding author at: Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh.
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Rivera A, Viñado B, Benito N, Docobo-Pérez F, Fernández-Cuenca F, Fernández-Domínguez J, Guinea J, López-Navas A, Moreno MÁ, Larrosa MN, Oliver A, Navarro F. Recommendations of the Spanish Antibiogram Committee (COESANT) for in vitro susceptibility testing of antimicrobial agents by disk diffusion. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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5
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kaprou GD, Bergšpica I, Alexa EA, Alvarez-Ordóñez A, Prieto M. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel) 2021; 10:209. [PMID: 33672677 PMCID: PMC7924329 DOI: 10.3390/antibiotics10020209] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most challenging threats in public health; thus, there is a growing demand for methods and technologies that enable rapid antimicrobial susceptibility testing (AST). The conventional methods and technologies addressing AMR diagnostics and AST employed in clinical microbiology are tedious, with high turnaround times (TAT), and are usually expensive. As a result, empirical antimicrobial therapies are prescribed leading to AMR spread, which in turn causes higher mortality rates and increased healthcare costs. This review describes the developments in current cutting-edge methods and technologies, organized by key enabling research domains, towards fighting the looming AMR menace by employing recent advances in AMR diagnostic tools. First, we summarize the conventional methods addressing AMR detection, surveillance, and AST. Thereafter, we examine more recent non-conventional methods and the advancements in each field, including whole genome sequencing (WGS), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) spectrometry, Fourier transform infrared (FTIR) spectroscopy, and microfluidics technology. Following, we provide examples of commercially available diagnostic platforms for AST. Finally, perspectives on the implementation of emerging concepts towards developing paradigm-changing technologies and methodologies for AMR diagnostics are discussed.
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Affiliation(s)
- Georgia D. Kaprou
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Ieva Bergšpica
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia
| | - Elena A. Alexa
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, University of León, 24071 León, Spain; (I.B.); (E.A.A.); (A.A.-O.); (M.P.)
- Institute of Food Science and Technology, University of León, 24071 León, Spain
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Benkova M, Soukup O, Marek J. Antimicrobial susceptibility testing: currently used methods and devices and the near future in clinical practice. J Appl Microbiol 2020; 129:806-822. [DOI: 10.1111/jam.14704] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- M. Benkova
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
| | - O. Soukup
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
- Department of Toxicology and Military Pharmacy Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
| | - J. Marek
- Department of Epidemiology Faculty of Military Health Sciences University of Defence Hradec Kralove Czech Republic
- Biomedical Research Center University Hospital Hradec Kralove Hradec Kralove Czech Republic
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8
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Strauss M, Zoabi K, Sagas D, Reznik-Gitlitz B, Colodner R. Evaluation of Bio-Rad® discs for antimicrobial susceptibility testing by disc diffusion and the ADAGIO™ system for the automatic reading and interpretation of results. Eur J Clin Microbiol Infect Dis 2019; 39:375-384. [PMID: 31720945 DOI: 10.1007/s10096-019-03735-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022]
Abstract
The disc diffusion test is used for antimicrobial susceptibility testing worldwide. In this study, the performance of both Bio-Rad® antibiotic discs (as compared with Oxoid® discs) and the ADAGIO™ automated system for the reading of disc diffusion test results was evaluated with American Type Culture Collection (ATCC) quality control (QC) and wild strains of bacteria. Inhibition zones of both disc brands were read manually and through use of the ADAGIO™ system. Categorized interpretation of the results for each strain and antibiotic combination was summarized according to the Clinical Laboratory Standards Institute MS-100 (2017 update) manual and ADAGIO™ readings. Eight ATCC QC strains and 120 different wild strains were evaluated, to give a total of 1226 antibiotic/bacteria combinations and 2486 manual readings. One major error and four minor errors (0.08% and 0.34%, respectively) were detected via manual readings of the Bio-Rad® discs as compared with the Oxoid® discs. For the same number of antibiotic/bacteria combinations, five minor errors and one major error (0.42% and 0.08%, respectively) were detected with the Bio-Rad® discs read by the ADAGIO™ system. In addition, the number of times the automatic reading needed manual edition with Bio-Rad® discs was statistically lower than it did with Oxoid® discs (3.7% vs. 5.7%, p < 0.05). These findings support the hypothesis that Bio-Rad discs are not inferior to Oxoid® discs, and the performance of the ADAGIO™ system is comparable to that of manual readings with both disc brands.
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Affiliation(s)
- Merav Strauss
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Kariman Zoabi
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | - Dana Sagas
- Microbiology Laboratory, Emek Medical Center, Afula, Israel
| | | | - Raul Colodner
- Microbiology Laboratory, Emek Medical Center, Afula, Israel.
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Badger S, Abraham S, Stryhn H, Trott DJ, Jordan D, Caraguel CGB. Intra- and inter-laboratory agreement of the disc diffusion assay for assessing antimicrobial susceptibility of porcine Escherichia coli. Prev Vet Med 2019; 172:104782. [PMID: 31586718 DOI: 10.1016/j.prevetmed.2019.104782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Reliable assessment of the susceptibility of animal bacterial pathogens to antimicrobials is of paramount importance in the fight against antimicrobial resistance. This work aims to estimate the repeatability (intra-laboratory agreement) and reproducibility (inter-laboratory agreement) of the disc diffusion assay in veterinary laboratories to understand further if the assay has a role in the surveillance of antimicrobial resistance in animals. Seven major veterinary laboratories from all States in Australia participated, and each tested the same panel of isolates five times at three to four-week intervals, against six antimicrobial agents using Clinical and Laboratory Standards Institute protocols. The panel consisted of twenty different isolates from porcine Escherichia coli from clinical cases and a single reference strain (ATCC 25922). Laboratories were blinded to the identity of the isolates, replicates, and to each other. In total, 4200 inhibition zone diameters (mm) were collected, and analysed descriptively, graphically, and with linear mixed models. Regardless of the laboratories and isolate/antimicrobial combinations, the overall very major error rate (proportion of isolates classified as susceptible when actual status is resistant) was 1.6%; the major error rate (proportion of isolates classified as resistant when actual status is susceptible) was 1.6%; and the 'minor error' rate (proportion of isolates with intermediate susceptibility that measure fully susceptible or resistant or vice versa) was 2.4%. The variation between repeated measurements ranged between 4.4-7.2 mm depending on the antimicrobial agent assessed. The reproducibility was always more variable than the repeatability, which suggested some laboratory effects. The repeatability coefficient of disc diffusion was lowest for tetracycline (4.4 mm, 95% CI: 3.8-5.0 mm) and ampicillin (4.6 mm, 95% CI: 4.2-5.2 mm) and highest for trimethoprim-sulfamethoxazole (6.6 mm, 95% CI: 5.9-7.4 mm). The reproducibility coefficient of disc diffusion was lowest for gentamicin (5.4, 95% CI: 4.0-7.2) and highest for trimethoprim-sulfamethoxazole (7.2 mm, 95%CI: 4.5-11.7 mm). The precision of the disc diffusion assay was deemed satisfactory for use in a national surveillance program for clinical porcine E. coli isolates. However, measurement variation of the disc diffusion assay is of concern for isolates with marginal susceptibility or resistance due to increased risk of misclassification.
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Affiliation(s)
- Skye Badger
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia; Antimicrobial Resistance and Infectious Diseases Laboratory, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia.
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia.
| | - Henrik Stryhn
- Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Darren J Trott
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
| | - David Jordan
- Antimicrobial Resistance and Infectious Diseases Laboratory, School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Western Australia, 6150, Australia; Wollongbar Primary Industries Institute, NSW Department of Primary Industries, 1243 Bruxner Highway, Wollongbar, New South Wales, 2477, Australia.
| | - Charles G B Caraguel
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, 5371, Australia.
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Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 2019; 20:356-370. [PMID: 30886350 PMCID: PMC6525649 DOI: 10.1038/s41576-019-0108-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial resistance identification and characterization methods, from traditional antimicrobial susceptibility testing to recent deep-learning methods. We focus on sequencing-based resistance discovery and discuss tools and databases used in antimicrobial resistance studies.
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Affiliation(s)
- Manish Boolchandani
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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Alonso CA, Domínguez C, Heras J, Mata E, Pascual V, Torres C, Zarazaga M. Antibiogramj: A tool for analysing images from disk diffusion tests. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2017; 143:159-169. [PMID: 28391814 DOI: 10.1016/j.cmpb.2017.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/06/2017] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND AND OBJECTIVES Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. METHODS Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. RESULTS We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. CONCLUSIONS AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory.
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Affiliation(s)
- C A Alonso
- Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
| | - C Domínguez
- Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
| | - J Heras
- Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
| | - E Mata
- Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
| | - V Pascual
- Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
| | - C Torres
- Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
| | - M Zarazaga
- Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain
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