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Nakayama A, Morinaga Y, Izuno R, Morikane K, Yanagihara K. Evaluation of MALDI-TOF mass spectrometry coupled with ClinProTools as a rapid tool for toxin-producing Clostridioides difficile. J Infect Chemother 2024; 30:847-852. [PMID: 38423297 DOI: 10.1016/j.jiac.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION The performance of MALDI-TOF MS combined with analysis platform for identification of toxin-producing Clostridiodes difficile is yet to be known. METHODS Between August 2018 and September 2020, 61 isolates from stool specimens of patients with C. difficile-associated diarrhea were analyzed using the MALDI Biotyper system. A C. difficile toxin-producer detection model was developed using ClinProTools. The model was validated using 28 known strains that differed from the isolates used to develop the model. RESULTS The sensitivity and specificity of the Genetic Algorithm (GA) model using isolates grown on Brucella with hemin and vitamin K (BHK) agar plates were 91.7% and 44.4%, respectively. When isolates grown on cycloserine-cefoxitin mannitol agar were analyzed by the model, sensitivity and specificity were 6.3% and 100%, respectively. The GA model using BHK medium showed the highest discriminatory performance in detection of toxin-producing C. difficile. However, a discrepancy in detection of toxin-producing C. difficile was observed in the results generated when the model was being developed and when the model was validated which suggests that incubation conditions may have affected the results. CONCLUSION MALDI-TOF analysis using ClinProTools has a potential to be a cost-effective tool for rapid diagnosis and contribute to antimicrobial stewardship by differentiating toxin-producing C. difficile from non-producers.
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Affiliation(s)
- Asami Nakayama
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Laboratory Medicine, Tohoku University Hospital, Miyagi, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan; Center for Advanced Antibody Drug Development, University of Toyama, Toyama, Japan; Clinical and Research Center for Infectious Diseases, Toyama University Hospital, Toyama, Japan.
| | - Ryota Izuno
- Department of Laboratory Medicine, Yamagata University Hospital, Yamagata, Japan
| | - Keita Morikane
- Department of Laboratory Medicine, Yamagata University Hospital, Yamagata, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Godmer A, Giai Gianetto Q, Le Neindre K, Latapy V, Bastide M, Ehmig M, Lalande V, Veziris N, Aubry A, Barbut F, Eckert C. Contribution of MALDI-TOF mass spectrometry and machine learning including deep learning techniques for the detection of virulence factors of Clostridioides difficile strains. Microb Biotechnol 2024; 17:e14478. [PMID: 38850267 PMCID: PMC11162102 DOI: 10.1111/1751-7915.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 06/10/2024] Open
Abstract
Clostridioides difficile (CD) infections are defined by toxins A (TcdA) and B (TcdB) along with the binary toxin (CDT). The emergence of the 'hypervirulent' (Hv) strain PR 027, along with PR 176 and 181, two decades ago, reshaped CD infection epidemiology in Europe. This study assessed MALDI-TOF mass spectrometry (MALDI-TOF MS) combined with machine learning (ML) and Deep Learning (DL) to identify toxigenic strains (producing TcdA, TcdB with or without CDT) and Hv strains. In total, 201 CD strains were analysed, comprising 151 toxigenic (24 ToxA+B+CDT+, 22 ToxA+B+CDT+ Hv+ and 105 ToxA+B+CDT-) and 50 non-toxigenic (ToxA-B-) strains. The DL-based classifier exhibited a 0.95 negative predictive value for excluding ToxA-B- strains, showcasing accuracy in identifying this strain category. Sensitivity in correctly identifying ToxA+B+CDT- strains ranged from 0.68 to 0.91. Additionally, all classifiers consistently demonstrated high specificity (>0.96) in detecting ToxA+B+CDT+ strains. The classifiers' performances for Hv strain detection were linked to high specificity (≥0.96). This study highlights MALDI-TOF MS enhanced by ML techniques as a rapid and cost-effective tool for identifying CD strain virulence factors. Our results brought a proof-of-concept concerning the ability of MALDI-TOF MS coupled with ML techniques to detect virulence factor and potentially improve the outbreak's management.
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Affiliation(s)
- Alexandre Godmer
- U1135, Centre d'Immunologie et Des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
| | - Quentin Giai Gianetto
- Institut PasteurUniversité Paris Cité, Bioinformatics and Biostatistics HUBParisFrance
- Institut PasteurUniversité Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024ParisFrance
| | - Killian Le Neindre
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides DifficileParisFrance
| | - Valentine Latapy
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
| | - Mathilda Bastide
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
| | - Muriel Ehmig
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides DifficileParisFrance
| | - Valérie Lalande
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides DifficileParisFrance
| | - Nicolas Veziris
- U1135, Centre d'Immunologie et Des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
| | - Alexandra Aubry
- U1135, Centre d'Immunologie et Des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- Centre National de Référence Des Mycobactéries et de la Résistance Des Mycobactéries Aux AntituberculeuxAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Hôpital Pitié SalpêtrièreParisFrance
| | - Frédéric Barbut
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides DifficileParisFrance
- INSERM 1139Université Paris CitéParisFrance
- Paris Center for Microbiome Medicine (PaCeMM) FHUParisFrance
| | - Catherine Eckert
- U1135, Centre d'Immunologie et Des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- Département de BactériologieAP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint‐AntoineParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides DifficileParisFrance
- Paris Center for Microbiome Medicine (PaCeMM) FHUParisFrance
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Calderaro A, Chezzi C. MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory. Microorganisms 2024; 12:322. [PMID: 38399726 PMCID: PMC10892259 DOI: 10.3390/microorganisms12020322] [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: 01/14/2024] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses' identification were also reported, seeking further studies before adapting this tool to the virus's diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
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Ebersbach JC, Sato MO, de Araújo MP, Sato M, Becker SL, Sy I. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for differential identification of adult Schistosoma worms. Parasit Vectors 2023; 16:20. [PMID: 36658630 PMCID: PMC9854196 DOI: 10.1186/s13071-022-05604-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/30/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Schistosomiasis is a major neglected tropical disease that affects up to 250 million individuals worldwide. The diagnosis of human schistosomiasis is mainly based on the microscopic detection of the parasite's eggs in the feces (i.e., for Schistosoma mansoni or Schistosoma japonicum) or urine (i.e., for Schistosoma haematobium) samples. However, these techniques have limited sensitivity, and microscopic expertise is waning outside endemic areas. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has become the gold standard diagnostic method for the identification of bacteria and fungi in many microbiological laboratories. Preliminary studies have recently shown promising results for parasite identification using this method. The aims of this study were to develop and validate a species-specific database for adult Schistosoma identification, and to evaluate the effects of different storage solutions (ethanol and RNAlater) on spectra profiles. METHODS Adult worms (males and females) of S. mansoni and S. japonicum were obtained from experimentally infected mice. Species identification was carried out morphologically and by cytochrome oxidase 1 gene sequencing. Reference protein spectra for the creation of an in-house MALDI-TOF MS database were generated, and the database evaluated using new samples. We employed unsupervised (principal component analysis) and supervised (support vector machine, k-nearest neighbor, Random Forest, and partial least squares discriminant analysis) machine learning algorithms for the identification and differentiation of the Schistosoma species. RESULTS All the spectra were correctly identified by internal validation. For external validation, 58 new Schistosoma samples were analyzed, of which 100% (58/58) were correctly identified to genus level (log score values ≥ 1.7) and 81% (47/58) were reliably identified to species level (log score values ≥ 2). The spectra profiles showed some differences depending on the storage solution used. All the machine learning algorithms classified the samples correctly. CONCLUSIONS MALDI-TOF MS can reliably distinguish adult S. mansoni from S. japonicum.
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Affiliation(s)
- Jurena Christiane Ebersbach
- grid.11749.3a0000 0001 2167 7588Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Marcello Otake Sato
- grid.255137.70000 0001 0702 8004Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi Japan
| | - Matheus Pereira de Araújo
- grid.255137.70000 0001 0702 8004Laboratory of Tropical Medicine and Parasitology, Dokkyo Medical University, Mibu, Tochigi Japan
| | - Megumi Sato
- grid.260975.f0000 0001 0671 5144Graduate School of Health Sciences, Niigata University, Niigata, Japan
| | - Sören L. Becker
- grid.11749.3a0000 0001 2167 7588Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany ,grid.416786.a0000 0004 0587 0574Swiss Tropical and Public Health Institute, Allschwil, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, Basel, Switzerland
| | - Issa Sy
- grid.11749.3a0000 0001 2167 7588Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
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Calderaro A, Buttrini M, Farina B, Montecchini S, Martinelli M, Arcangeletti MC, Chezzi C, De Conto F. Characterization of Clostridioides difficile Strains from an Outbreak Using MALDI-TOF Mass Spectrometry. Microorganisms 2022; 10:microorganisms10071477. [PMID: 35889196 PMCID: PMC9320467 DOI: 10.3390/microorganisms10071477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
The epidemiology of Clostridioides difficile infection (CDI) has changed over the last two decades, due to the emergence of C. difficile strains with clinical relevance and responsible for nosocomial outbreaks with severe outcomes. This study reports an outbreak occurred in a Long-term Care Unit from February to March 2022 and tracked by using a Matrix-Assisted Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) typing approach (T-MALDI); subsequently, a characterization of the toxigenic and antimicrobial susceptibility profiles of the C. difficile isolates was performed. A total of 143 faecal samples belonging to 112 patients was evaluated and C. difficile DNA was detected in 51 samples (46 patients). Twenty-nine C. difficile isolates were obtained, and three different clusters were revealed by T-MALDI. The most representative cluster accounted 22 strains and was considered to be epidemic, in agreement with PCR-Ribotyping. Such epidemic strains were susceptible to vancomycin (MIC ≤ 0.5 mg/mL) and metronidazole (MIC ≤ 1 mg/mL), but not to moxifloxacin (MIC > 32 mg/mL). Moreover, they produced only the Toxin A and, additionally, the binary toxin. To our knowledge, this is the first reported outbreak referable to a tcdA+/tcdB-/cdt+ genotypic profile. In light of these results, T-MALDI is a valid and rapid approach for discovering and tracking outbreaks.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
- Correspondence: ; Tel.: +39-0521-033499; Fax: +39-0521-993620
| | - Mirko Buttrini
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Benedetta Farina
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Sara Montecchini
- Unit of Clinical Virology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
| | - Monica Martinelli
- Unit of Clinical Microbiology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
| | - Maria Cristina Arcangeletti
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Carlo Chezzi
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
| | - Flora De Conto
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (M.B.); (B.F.); (M.C.A.); (C.C.); (F.D.C.)
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Giles J, Roberts A. Clostridioides difficile: Current overview and future perspectives. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 129:215-245. [PMID: 35305720 DOI: 10.1016/bs.apcsb.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The most common world-wide cause of antibiotic-associated infectious diarrhea and colitis is the toxin producing bacterium, Clostridioides difficile (C. difficile). Here we review the background and characteristics of the bacterium and the toxins produced together with the epidemiology and the complex pathogenesis that leads to a broad clinical spectrum of disease. The review describes the difficulties faced in obtaining a quick and accurate diagnosis despite the range of sensitive and specific diagnostic tools available. We also discuss the problem of disease recurrence and the importance of disease prevention. The high rates of infection recurrence mean that treatment strategies are constantly under review and we outline the diverse treatment options that are currently in use and explore the emerging treatment options of pulsed antibiotic use, microbial replacement therapies and the use of monoclonal antibodies. We summarize the future direction of treatment strategies which include the development of novel antibiotics, the administration of oral polyclonal antibody formulations, the use of vaccines, the administration of competitive non-toxigenic spores and the neutralization of antibiotics at the microbiota level. Future successful treatments will likely involve a combination of therapies to provide the most effective and robust approach to C. difficile management.
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Affiliation(s)
- Joanna Giles
- MicroPharm Ltd, Newcastle Emlyn, United Kingdom.
| | - April Roberts
- Toxins Group, National Infection Service, Public Health England, Porton Down, United Kingdom
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OUP accepted manuscript. J AOAC Int 2022; 105:1468-1474. [DOI: 10.1093/jaoacint/qsac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022]
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Detection of potential enteric pathogens in children with severe acute gastroenteritis using the filmarray: Results from a three - years hospital-based survey in Northern Italy. Diagn Microbiol Infect Dis 2021; 102:115611. [PMID: 34953368 DOI: 10.1016/j.diagmicrobio.2021.115611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022]
Abstract
Acute gastroenteritis (AGE) are leading causes of morbidity and mortality in children. Therefore, rapid pathogens identification is needed. The AGE aetiology was investigated from 2018 to 2020 in 2,066 children in Parma (Italy) by FilmArray Gastrointestinal Panel and Enterovirus-targeting RT-PCR. Pathogens were detected in 1,162 (56.2%) stool samples from as many children; 798 (68.7%) were single and 364 (31.3%) mixed infections (68.7% vs 31.3%, P < 0.0001). Children aged 0-5 years showed the highest infection incidence (66.1%). The most frequent pathogens were Enteropathogenic Escherichia coli (EPEC; 19.14%), Clostridioides difficile (10.42%), Norovirus (10.36%), Enterovirus (9.44%), and Campylobacter (9.21%). EPEC, Campylobacter, enteroaggregative E. coli, Norovirus, and Rotavirus showed seasonality. The incidence of pathogens detected decreased between 2018 and 2020 (42.7% vs 20.8%, P < 0.0001), seemingly for the preventive measures imposed by the severe acute respiratory syndrome coronavirus-2 pandemic. A putative aetiology in half the children examined and an estimate of enteric pathogens epidemiology were assessed.
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Rapid Identification of Escherichia coli Colistin-Resistant Strains by MALDI-TOF Mass Spectrometry. Microorganisms 2021; 9:microorganisms9112210. [PMID: 34835336 PMCID: PMC8623207 DOI: 10.3390/microorganisms9112210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/11/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022] Open
Abstract
Colistin resistance is one of the major threats for global public health, requiring reliable and rapid susceptibility testing methods. The aim of this study was the evaluation of a MALDI-TOF mass spectrometry (MS) peak-based assay to distinguish colistin resistant (colR) from susceptible (colS) Escherichia coli strains. To this end, a classifying algorithm model (CAM) was developed, testing three different algorithms: Genetic Algorithm (GA), Supervised Neural Network (SNN) and Quick Classifier (QC). Among them, the SNN- and GA-based CAMs showed the best performances: recognition capability (RC) of 100% each one, and cross validation (CV) of 97.62% and 100%, respectively. Even if both algorithms shared similar RC and CV values, the SNN-based CAM was the best performing one, correctly identifying 67/71 (94.4%) of the E. coli strains collected: in point of fact, it correctly identified the greatest number of colS strains (42/43; 97.7%), despite its lower ability in identifying the colR strains (15/18; 83.3%). In conclusion, although broth microdilution remains the gold standard method for testing colistin susceptibility, the CAM represents a useful tool to rapidly screen colR and colS strains in clinical practice.
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