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Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system.
Cordovana, Miriam; Mauder, Norman; Join-Lambert, Olivier; Gravey, François; LeHello, Simon; Auzou, Michel; Pitti, Monica; Zoppi, Simona; Buhl, Michael; Steinmann, Joerg; Frickmann, Hagen; Dekker, Denise; Funashima, Yumiko; Nagasawa, Zenzo; Soki, József; Orosz, László; Veloo, Alida C; Justesen, Ulrik S; Holt, Hanne M; Liberatore, Andrea; Ambretti, Simone; Pongolini, Stefano; Soliani, Laura; Wille, Andreas; Rojak, Sandra; Hagen, Ralf Matthias; May, Jürgen; Pranada, A B; Kostrzewa, Markus.
Afiliación
  • Cordovana M; Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany. Electronic address: miriam.cordovana@bruker.com.
  • Mauder N; Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany. Electronic address: norman.mauder@bruker.com.
  • Join-Lambert O; Université de Caen, Normandie, 14032, Cedex 5, Caen, France. Electronic address: olivier.join-lambert@unicaen.fr.
  • Gravey F; Université de Caen, Normandie, 14032, Cedex 5, Caen, France.
  • LeHello S; Université de Caen, Normandie, 14032, Cedex 5, Caen, France. Electronic address: Lehello-s@chu-caen.fr.
  • Auzou M; Université de Caen, Normandie, 14032, Cedex 5, Caen, France. Electronic address: auzou-m@chu-caen.fr.
  • Pitti M; Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, (SS Patologia Animale - Simona; SS Microbiologia Comparativa Specialistica - Centro di Riferimento Tipizzazione delle Salmonelle (CeRTiS) - Monica), via Bologna 148,Torino, Italy. Electronic address: monica.pitti@izsto.it.
  • Zoppi S; Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, (SS Patologia Animale - Simona; SS Microbiologia Comparativa Specialistica - Centro di Riferimento Tipizzazione delle Salmonelle (CeRTiS) - Monica), via Bologna 148,Torino, Italy. Electronic address: simona.zoppi@izsto.it.
  • Buhl M; Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany. Electronic address: Michael.Buhl@klinikum-nuernberg.de.
  • Steinmann J; Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Nuremberg, Germany. Electronic address: Joerg.Steinmann@klinikum-nuernberg.de.
  • Frickmann H; Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany. Electronic address: frickmann@bnitm.de.
  • Dekker D; Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany. Electronic address: dekker@bnitm.de.
  • Funashima Y; Department of Medical Technology and Sciences, School of Health Sciences, Fukuoka International University of Health and Welfare, 137-1 Enokizu, Okawa, Fukuoka, Japan. Electronic address: funashima@iuhw.ac.jp.
  • Nagasawa Z; Department of Medical Technology and Sciences, School of Health Sciences, Fukuoka International University of Health and Welfare, 137-1 Enokizu, Okawa, Fukuoka, Japan. Electronic address: nagasa@iuhw.ac.jp.
  • Soki J; Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary. Electronic address: soki.jozsef@med.u-szeged.hu.
  • Orosz L; Institute of Medical Microbiology, Albert Szent-Györgyi Health Centre and Medical School, University of Szeged, Szeged, Hungary. Electronic address: orosz.laszlo@med.u-szeged.hu.
  • Veloo AC; Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 AB Groningen, the Netherlands. Electronic address: a.c.m.veloo@umcg.nl.
  • Justesen US; Department of Clinical Microbiology, Odense University Hospital, 5000 Odense C, Denmark. Electronic address: Ulrik.Stenz.Justesen@rsyd.dk.
  • Holt HM; Department of Clinical Microbiology, Odense University Hospital, 5000 Odense C, Denmark. Electronic address: Hanne.Holt@rsyd.dk.
  • Liberatore A; Operative Unit of Microbiology, IRCCS-Azienda Ospedaliero Policlinico Sant'Orsola-Universitaria di Bologna, 40138 Bologna, Italy. Electronic address: andrea.liberatore@studio.unibo.it.
  • Ambretti S; Operative Unit of Microbiology, IRCCS-Azienda Ospedaliero Policlinico Sant'Orsola-Universitaria di Bologna, 40138 Bologna, Italy. Electronic address: simone.ambretti@aosp.bo.it.
  • Pongolini S; Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, 43126, Italy. Electronic address: stefano.pongolini@izsler.it.
  • Soliani L; Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, 43126, Italy. Electronic address: laura.soliani@izsler.it.
  • Wille A; Institute for Hygiene and Environment, City of Hamburg, 20539 Hamburg, Germany. Electronic address: andreas.wille@hu.hamburg.de.
  • Rojak S; Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany. Electronic address: sandrarojak@bundeswehr.org.
  • Hagen RM; Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany. Electronic address: ralfmatthiashagen@bundeswehr.org.
  • May J; Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany; University Medical Center Hamburg-Eppendorf (UKE), Tropical Medicine II, Hamburg, Germany. Electronic address: may@bnitm.de.
  • Pranada AB; Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Balkenstrasse 17-19, 44137 Dortmund, Germany. Electronic address: apranada@labmed.de.
  • Kostrzewa M; Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany. Electronic address: markus.kostrzewa@bruker.com.
J Microbiol Methods ; 201: 106564, 2022 10.
Article en En | MEDLINE | ID: mdl-36084763
BACKGROUND: Salmonella enterica is among the major burdens for public health at global level. Typing of salmonellae below the species level is fundamental for different purposes, but traditional methods are expensive, technically demanding, and time-consuming, and therefore limited to reference centers. Fourier transform infrared (FTIR) spectroscopy is an alternative method for bacterial typing, successfully applied for classification at different infra-species levels. AIM: This study aimed to address the challenge of subtyping Salmonella enterica at O-serogroup level by using FTIR spectroscopy. We applied machine learning to develop a novel approach for S. enterica typing, using the FTIR-based IR Biotyper® system (IRBT; Bruker Daltonics GmbH & Co. KG, Germany). We investigated a multicentric collection of isolates, and we compared the novel approach with classical serotyping-based and molecular methods. METHODS: A total of 958 well characterized Salmonella isolates (25 serogroups, 138 serovars), collected in 11 different centers (in Europe and Japan), from clinical, environmental and food samples were included in this study and analyzed by IRBT. Infrared absorption spectra were acquired from water-ethanol bacterial suspensions, from culture isolates grown on seven different agar media. In the first part of the study, the discriminatory potential of the IRBT system was evaluated by comparison with reference typing method/s. In the second part of the study, the artificial intelligence capabilities of the IRBT software were applied to develop a classifier for Salmonella isolates at serogroup level. Different machine learning algorithms were investigated (artificial neural networks and support vector machine). A subset of 88 pre-characterized isolates (corresponding to 25 serogroups and 53 serovars) were included in the training set. The remaining 870 samples were used as validation set. The classifiers were evaluated in terms of accuracy, error rate and failed classification rate. RESULTS: The classifier that provided the highest accuracy in the cross-validation was selected to be tested with four external testing sets. Considering all the testing sites, accuracy ranged from 97.0% to 99.2% for non-selective media, and from 94.7% to 96.4% for selective media. CONCLUSIONS: The IRBT system proved to be a very promising, user-friendly, and cost-effective tool for Salmonella typing at serogroup level. The application of machine learning algorithms proved to enable a novel approach for typing, which relies on automated analysis and result interpretation, and it is therefore free of potential human biases. The system demonstrated a high robustness and adaptability to routine workflows, without the need of highly trained personnel, and proving to be suitable to be applied with isolates grown on different agar media, both selective and unselective. Further tests with currently circulating clinical, food and environmental isolates would be necessary before implementing it as a potentially stand-alone standard method for routine use.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Salmonella enterica Tipo de estudio: Clinical_trials Límite: Humans Idioma: En Revista: J Microbiol Methods Año: 2022 Tipo del documento: Article Pais de publicación: Países Bajos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Salmonella enterica Tipo de estudio: Clinical_trials Límite: Humans Idioma: En Revista: J Microbiol Methods Año: 2022 Tipo del documento: Article Pais de publicación: Países Bajos