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; Bühl, Michæl; Steinmann, Joerg; Frickmann, Hagen; Dekker, Denise; Funashima, Yumiko; Nagasawa, Zenzo; Soki, József; Orosz, László; Veloo, Alida; Justesen, Ulrik Stenz; Holt, Hanne Marie; Liberatore, Andrea; Ambretti, Simone; Pongolini, Stefano; Soliani, Laura; Wille, Andreas; Rojak, Sandra; Hagen, Ralf Matthias; May, Jürgen; Pranada, Arthur B.; Kostrzewa, Markus

doi:10.1016/j.mimet.2022.106564

Cited by 8 publications

(9 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous studies have already shown the successful discrimination of Salmonella enterica serogroups ( Cordovana et al, 2022 ) and (para-) typhoid ( Cordovana et al, 2021 ) by FT-IR spectroscopy and machine learning and the same was recently explored for the serotyping of each of the L. pneumophila serogroups and the exploratory differentiation of L. pneumophila sg. 1 from sg.…”

Section: Discussionmentioning

confidence: 99%

“…Since the different functional groups of these compounds absorb IR light at different wavenumber ranges, FT-IR spectroscopy generates infrared absorption spectra that turn in a highly specific fingerprint of each microorganism ( Novais et al, 2019 ). In the past, FT-IR spectroscopy was already proposed for the screening of both Gram-positive and Gram-negative bacteria including Listeria monocytogenes , Streptococcus pneumoniae , and Salmonella in clinical and food fields ( Kim et al, 2005 ; Davis and Mauer, 2011 ; Cordovana et al, 2021 ; Deidda et al, 2021 ; Cordovana et al, 2022 ; Pascale et al, 2022 ; Passaris et al, 2022 ). The technique showed good potentials in the serotyping of Escherichia coli ( Beutin et al, 2007 ; Mora et al, 2011 ) , Yersinia enterocolitica ( Kuhm et al, 2009 ) , Staphylococcus aureus ( Grunert et al, 2013 ) and L. pneumophila ( Pascale et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

et al. 2023

Self Cite

View full text Add to dashboard Cite

This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO2) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

et al. 2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…Fourier transform infrared (FTIR) spectroscopy is a robust alternative to whole genome sequencing for the discernment of bacteria at varying taxonomic levels 1–4 . A previously validated FTIR approach utilizing the IR Biotyper (Bruker) was utilized for the precise differentiation of Salmonella strains belonging to different serogroups (B, C, D and E) and clinically relevant serotypes ( S. Enteritidis , S. Infantis , S. Agona and S. Dublin ) 5–10 . Based on cluster analysis of the Salmonella spp.…”

Section: Epidemiology Investigationmentioning

confidence: 99%

“…[1][2][3][4] A previously validated FTIR approach utilizing the IR Biotyper (Bruker) was utilized for the precise differentiation of Salmonella strains belonging to different serogroups (B, C, D and E) and clinically relevant serotypes (S. Enteritidis, S. Infantis, S. Agona and S. Dublin). [5][6][7][8][9][10] Based on cluster analysis of the Salmonella spp. (n = 9), the IR Biotyper effectively separated the different serovars based on their respective O antigen-groups (B, C1 and D) (Figure 1).…”

Section: Epidemiology Investigationmentioning

confidence: 99%

Successful autologous hematopoietic stem cell transplants using Salmonella positive products collected from asymptomatic donors

et al. 2023

View full text Add to dashboard Cite

Background Bacterial contamination of hematopoietic stem cell (HSC) products is most commonly due to normal skin flora. Salmonella in HSC products is rare, and to our knowledge safe administration of an autologous HSC product containing Salmonella has not been reported. Study Design and Methods We describe two patients undergoing autologous HSC transplant: peripheral blood HSC collection was performed by leukapheresis, and samples were cultured according to standard institutional protocol. Subsequent microorganism identification was performed using MALDI‐TOF (Bruker Biotyper). Strain‐relatedness was investigated by infrared spectroscopy using the IR Biotyper (Bruker). Results The patients were asymptomatic throughout the collection process; however, HSC products collected on two consecutive days from each patient were positive for Salmonella. Isolates from both cultures were further characterized as Salmonella enterica serovar Dublin by the local public health department. Antibiotic susceptibility testing revealed different sensitivity patterns for the two strains. IR Biotyper demonstrated significant discriminatory power among the clinically significant Salmonella enterica subspecies, serogroups B, C1, and D. The patient strains were similar as both belonged to Group D Salmonella enterica serovar Dublin but were not identical. The Salmonella positive autologous HSC products were infused to both patients following administration of empiric antibiotic therapy. Both patients successfully engrafted and did well. Conclusion Salmonella is rarely seen in cellular therapy products and positivity may be the result of asymptomatic bacteremia at the time of collection. We present two instances of autologous HSC products containing Salmonella that were infused, along with prophylactic antimicrobial therapy without significant adverse clinical effects.

show abstract

“…FTIR spectroscopy has recently become an alternative to bacterial typing due to its ease of use and high discriminatory power in recognizing clonal relationships among bacterial isolates [ 11 ]. The IR Biotyper® system (IRBT, Bruker Daltonics GmbH & Co. KG, Bremen, Germany), based on FTIR technology, is a device that enables easy and fast strain typing [ 12 ]. For example, following species-level identification using the MALDI Biotyper® (Bruker Daltonics GmbH & Co. Billerica, MA, USA), the strains can be typed and grouped by measuring their specific molecular vibration fingerprints [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Strain typing and antimicrobial susceptibility of Salmonella enterica Albany isolates from duck farms in South Korea

Han,

Chae,

Lee

et al. 2024

Heliyon

View full text Add to dashboard Cite

Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system

Cited by 8 publications

References 40 publications

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

Successful autologous hematopoietic stem cell transplants using Salmonella positive products collected from asymptomatic donors

Strain typing and antimicrobial susceptibility of Salmonella enterica Albany isolates from duck farms in South Korea

Contact Info

Product

Resources

About