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Article ; Online: Identification of a clonal population of Aspergillus flavus by MALDI-TOF mass spectrometry using deep learning.

Normand, Anne-Cécile / Chaline, Aurélien / Mohammad, Noshine / Godmer, Alexandre / Acherar, Aniss / Huguenin, Antoine / Ranque, Stéphane / Tannier, Xavier / Piarroux, Renaud

Scientific reports

2022 Volume 12, Issue 1, Page(s) 1575

Abstract: The spread of fungal clones is hard to detect in the daily routines in clinical laboratories, and there is a need for new tools that can facilitate clone detection within a set of strains. Currently, Matrix Assisted Laser Desorption-Ionization Time-of- ... ...

Abstract	The spread of fungal clones is hard to detect in the daily routines in clinical laboratories, and there is a need for new tools that can facilitate clone detection within a set of strains. Currently, Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry is extensively used to identify microbial isolates at the species level. Since most of clinical laboratories are equipped with this technology, there is a question of whether this equipment can sort a particular clone from a population of various isolates of the same species. We performed an experiment in which 19 clonal isolates of Aspergillus flavus initially collected on contaminated surgical masks were included in a set of 55 A. flavus isolates of various origins. A simple convolutional neural network (CNN) was trained to detect the isolates belonging to the clone. In this experiment, the training and testing sets were totally independent, and different MALDI-TOF devices (Microflex) were used for the training and testing phases. The CNN was used to correctly sort a large portion of the isolates, with excellent (> 93%) accuracy for two of the three devices used and with less accuracy for the third device (69%), which was older and needed to have the laser replaced.
MeSH term(s)	Aspergillus flavus
Language	English
Publishing date	2022-01-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-05647-4
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Article: Improving the Detection of Epidemic Clones in

Mohammad, Noshine / Normand, Anne-Cécile / Nabet, Cécile / Godmer, Alexandre / Brossas, Jean-Yves / Blaize, Marion / Bonnal, Christine / Fekkar, Arnaud / Imbert, Sébastien / Tannier, Xavier / Piarroux, Renaud

Microorganisms

2023 Volume 11, Issue 4

Abstract: Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to ... ...

Abstract	Identifying fungal clones propagated during outbreaks in hospital settings is a problem that increasingly confronts biologists. Current tools based on DNA sequencing or microsatellite analysis require specific manipulations that are difficult to implement in the context of routine diagnosis. Using deep learning to classify the mass spectra obtained during the routine identification of fungi by MALDI-TOF mass spectrometry could be of interest to differentiate isolates belonging to epidemic clones from others. As part of the management of a nosocomial outbreak due to
Language	English
Publishing date	2023-04-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11041071
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Article ; Online: Investigation of a

Faury, Hélène B / Awad, Zeina / Jolivet, Sarah / Le Neindre, Killian / Couturier, Jeanne / Godmer, Alexandre / Colle, Raphaël / Levi, Laura I / Cambau, Emmanuelle / Barbut, Frédéric

Infection control and hospital epidemiology

2023 Volume 44, Issue 8, Page(s) 1342–1344

Abstract: We describe a case of healthcare-associated bloodstream infection due ... ...

Abstract	We describe a case of healthcare-associated bloodstream infection due to
MeSH term(s)	Humans ; Mycobacterium fortuitum ; Mycobacterium Infections, Nontuberculous/diagnosis ; Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; Cross Infection/microbiology ; Water ; Sepsis ; Catheters
Chemical Substances	Water (059QF0KO0R)
Language	English
Publishing date	2023-02-20
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	639378-0
ISSN	1559-6834 ; 0195-9417 ; 0899-823X
ISSN (online)	1559-6834
ISSN	0195-9417 ; 0899-823X
DOI	10.1017/ice.2022.263
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Article ; Online: Revisiting Species Identification within the Enterobacter cloacae Complex by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Godmer, Alexandre / Benzerara, Yahia / Normand, Anne Cécile / Veziris, Nicolas / Gallah, Salah / Eckert, Catherine / Morand, Philipe / Piarroux, Renaud / Aubry, Alexandra

Microbiology spectrum

2021 Volume 9, Issue 1, Page(s) e0066121

Abstract: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) ... ...

Abstract	Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify pathogens, despite some limitations of the technique. The Enterobacter cloacae complex (ECC) taxonomy has recently been expanded, leading to uncertain identification of some species within the ECC when commercial MALDI-TOF MS is used. This technique is especially unsuited in the case of
MeSH term(s)	Algorithms ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacterial Typing Techniques/methods ; Databases, Factual ; Enterobacter cloacae/chemistry ; Enterobacter cloacae/genetics ; Enterobacter cloacae/isolation & purification ; Enterobacter cloacae/metabolism ; Enterobacteriaceae Infections/microbiology ; Humans ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2021-08-11
Publishing country	United States
Document type	Evaluation Study ; Journal Article
ISSN	2165-0497
ISSN (online)	2165-0497
DOI	10.1128/Spectrum.00661-21
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Article ; Online: Four-Hour Immunochromatographic Detection of Intestinal Carriage of Carbapenemase-Producing

Gallah, Salah / Villageois-Tran, Khanh / Godmer, Alexandre / Arlet, Guillaume / Rottman, Martin / Benzerara, Yahia / Garnier, Marc

Journal of clinical microbiology

2021 Volume 59, Issue 6

Abstract: The increasing incidence of carbapenemase-producing Gram-negative bacilli (C-PGNB) represents a major public health challenge. Rapid detection of digestive colonization with C-PGNB is fundamental to control their spread. We performed the validation of a ... ...

Abstract	The increasing incidence of carbapenemase-producing Gram-negative bacilli (C-PGNB) represents a major public health challenge. Rapid detection of digestive colonization with C-PGNB is fundamental to control their spread. We performed the validation of a rapid protocol for C-PGNB detection directly on rectal swabs. We developed a protocol combining enrichment by a rapid selective subculture of the rectal swab medium and realization of a Resist-4 O.K.N.V. K-SeT test on the bacterial pellet obtained. The limit of detection and performances of this protocol were validated
MeSH term(s)	Bacterial Proteins ; Carbapenem-Resistant Enterobacteriaceae ; Chromatography, Affinity ; Enterobacteriaceae Infections/diagnosis ; Gram-Negative Bacteria ; Humans ; Sensitivity and Specificity ; beta-Lactamases
Chemical Substances	Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2021-05-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02973-20
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Article ; Online: Differential Performance of the FilmArray Meningitis/Encephalitis Assay To Detect Bacterial and Viral Pathogens in Both Pediatric and Adult Populations.

Schnuriger, Aurélie / Vimont, Sophie / Godmer, Alexandre / Gozlan, Joël / Gallah, Salah / Macé, Muriel / Lalande, Valérie / Saloum, Kenda / Perrier, Marine / Veziris, Nicolas / Morand-Joubert, Laurence

Microbiology spectrum

2022 Volume 10, Issue 2, Page(s) e0277421

Abstract: Meningitis/encephalitis (ME) syndromic diagnostic assays can be applied for the rapid one-step detection of the most common pathogens in cerebrospinal fluid (CSF). However, the comprehensive performance of multiplex assays is still under evaluation. In ... ...

Abstract	Meningitis/encephalitis (ME) syndromic diagnostic assays can be applied for the rapid one-step detection of the most common pathogens in cerebrospinal fluid (CSF). However, the comprehensive performance of multiplex assays is still under evaluation. In our multisite university hospital of eastern Paris, France, ME syndromic testing has been gradually implemented since 2017 for patients with neurological symptoms presenting to an adult or pediatric emergency unit. We analyzed the results from the BioFire FilmArray ME panel versus standard routine bacteriology and virology techniques, together with CSF cytology and clinical data, over a 2.5-year period to compare the diagnostic accuracy of the FilmArray ME panel to that of the reference methods. In total, 1,744 CSF samples from 1,334 pediatric and 336 adult patients were analyzed. False-positive (mostly bacterial) and false-negative (mostly viral) cases were deciphered with the help of clinical data. The performance of the FilmArray ME panel in our study was better for bacterial detection (specificity >99%, sensitivity 100%) than viral detection (specificity >99%, sensitivity 75% for herpes simplex virus 1 [HSV-1] and 89% for enterovirus), our study being one of the largest, to date, concerning enteroviruses. The use of a threshold of 10 leukocytes/mm
MeSH term(s)	Adult ; Bacteria ; Child ; Encephalitis/diagnosis ; Enterovirus ; Enterovirus Infections ; Humans ; Meningitis/diagnosis ; Meningitis/microbiology ; Multiplex Polymerase Chain Reaction/methods
Language	English
Publishing date	2022-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02774-21
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Article ; Online: Diagnosis of mucormycosis using an intercalating dye-based quantitative PCR.

Bigot, Jeanne / Godmer, Alexandre / Prudenté, Lysa / Angebault, Cécile / Brissot, Eolia / Bige, Naike / Voiriot, Guillaume / Leger, Pierre-Louis / Petit-Hoang, Camille / Atallah, Sarah / Gouache, Elodie / Senghor, Yaye / Valot, Stéphane / Hennequin, Christophe / Guitard, Juliette

Medical mycology

2022 Volume 60, Issue 4

Abstract: PCR-based methods applied to various body fluids emerged in recent years as a promising approach for the diagnosis of mucormycosis. In this study, we set up and assess the value of a qPCR to detect a wide variety of Mucorales species in a single tube. A ... ...

Abstract	PCR-based methods applied to various body fluids emerged in recent years as a promising approach for the diagnosis of mucormycosis. In this study, we set up and assess the value of a qPCR to detect a wide variety of Mucorales species in a single tube. A pair of degenerated primers targeting the rDNA operon was used in a qPCR utilizing an intercalating fluorescent dye. Analytical assessment, using a wide variety of both Mucorales strains (8 genera, 11 species) and non-Mucorales strains (9 genera, 14 species), showed 100% sensitivity and specificity rates with a limit of detection at 3 rDNA copy/qPCR reaction. Subsequently, 364 clinical specimens from 166 at-risk patients were prospectively tested with the assay. All the seven patients classified as proven/probable mucormycosis using the EORTC-MSG criteria had a positive qPCR as well as a patient with a proven uncharacterized invasive mold infection. In addition, three out of seven patients with possible mold invasive infections had at least one positive qPCR test. Sensitivity was calculated between 73.33 and 100% and specificity between 98.10 and 100%. The qPCR method proposed showed excellent performances and would be an important adjunctive tool for the difficult diagnosis of mucormycosis diagnosis. Lay abstract: qPCR-based diagnosis is the most reliable approach for mucormycosis. We set up a pan-Mucorales qPCR able to detect in a single reaction not less than 11 different species. Both analytical and clinical performances support its use in the clinical setting.
MeSH term(s)	Animals ; DNA Primers ; DNA, Fungal/genetics ; Mucorales/genetics ; Mucormycosis/diagnosis ; Mucormycosis/veterinary ; Real-Time Polymerase Chain Reaction/veterinary
Chemical Substances	DNA Primers ; DNA, Fungal
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1421796-x
ISSN	1460-2709 ; 1369-3786
ISSN (online)	1460-2709
ISSN	1369-3786
DOI	10.1093/mmy/myac015
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Article ; Online: Activity of mecillinam against carbapenem-resistant Enterobacterales.

Emeraud, Cécile / Godmer, Alexandre / Girlich, Delphine / Vanparis, Océane / Mahamdi, Fériel / Creton, Elodie / Jousset, Agnès B / Naas, Thierry / Bonnin, Rémy A / Dortet, Laurent

The Journal of antimicrobial chemotherapy

2022 Volume 77, Issue 10, Page(s) 2835–2839

Abstract: Background: Despite the fact that carbapenem-resistant Enterobacterales (CRE) mostly cause urinary tract infections (UTIs), only few studies have focused on the efficacity of mecillinam against these CRE.: Objectives: To evaluate the mecillinam ... ...

Abstract	Background: Despite the fact that carbapenem-resistant Enterobacterales (CRE) mostly cause urinary tract infections (UTIs), only few studies have focused on the efficacity of mecillinam against these CRE. Objectives: To evaluate the mecillinam susceptibility of a huge collection of CRE, including carbapenemase-producing Enterobacterales (CPE) and non-CPE (ESBL and AmpC producers with decreased permeability of the outer membrane). Methods: A total of 8310 non-duplicate clinical CRE, including 4042 OXA-48-like producers, 1094 NDM producers, 411 VIM producers, 174 KPC producers, 42 IMI producers, 153 multiple-carbapenemase producers and 45 isolates producing other types of carbapenemases (such as IMP-like enzymes or GES-5), were included in the study. WGS was performed on all CPE using Illumina technology. Categorization of susceptibility to mecillinam was performed using disc diffusion (mecillinam discs at 10 μg; I2A, France) according to EUCAST recommendations. The results were interpreted according to EUCAST guidelines (S ≥15 mm). Results: Significantly higher susceptibility rates were observed for carbapenem-resistant Proteus spp. (85%) and carbapenem-resistant Escherichia coli (84%), which are the two most common species responsible for UTIs, than for Klebsiella pneumoniae (67%), Enterobacter cloacae complex (75%), Citrobacter spp. (65%), Serratia spp. (34%) and Morganella morganii (12%). Susceptibility rates were 84%, 71% and 91% for OXA-48-like, NDM and IMI producers and 70% for non-CPE CRE. Mecillinam was less active against VIM and KPC producers (14% and 0%, respectively). Conclusions: Mecillinam might be an alternative for the treatment of infections due to CRE, particularly UTIs, except for VIM and KPC producers and for M. morganii and Serratia spp species.
MeSH term(s)	Amdinocillin/therapeutic use ; Bacterial Proteins ; Carbapenems/pharmacology ; Carbapenems/therapeutic use ; Enterobacteriaceae Infections/drug therapy ; Escherichia coli ; Humans ; Inosine Monophosphate ; Microbial Sensitivity Tests ; Urinary Tract Infections/drug therapy ; beta-Lactamases
Chemical Substances	Bacterial Proteins ; Carbapenems ; Inosine Monophosphate (131-99-7) ; beta-Lactamases (EC 3.5.2.6) ; Amdinocillin (V10579P3QZ)
Language	English
Publishing date	2022-07-19
Publishing country	England
Document type	Journal Article
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkac226
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Zs.A 1197: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Stability of Routine Biochemical Analytes in Whole Blood and Plasma From Lithium Heparin Gel Tubes During 6-hr Storage.

Monneret, Denis / Godmer, Alexandre / Le Guen, Ronan / Bravetti, Clotilde / Emeraud, Cecile / Marteau, Anthony / Alkouri, Rana / Mestari, Fouzi / Dever, Sylvie / Imbert-Bismut, Françoise / Bonnefont-Rousselot, Dominique

Journal of clinical laboratory analysis

2016 Volume 30, Issue 5, Page(s) 602–609

Abstract: Background: The stability of biochemical analytes has already been investigated, but results strongly differ depending on parameters, methodologies, and sample storage times. We investigated the stability for many biochemical parameters after different ... ...

Abstract	Background: The stability of biochemical analytes has already been investigated, but results strongly differ depending on parameters, methodologies, and sample storage times. We investigated the stability for many biochemical parameters after different storage times of both whole blood and plasma, in order to define acceptable pre- and postcentrifugation delays in hospital laboratories. Methods: Twenty-four analytes were measured (Modular® Roche analyzer) in plasma obtained from blood collected into lithium heparin gel tubes, after 2-6 hr of storage at room temperature either before (n = 28: stability in whole blood) or after (n = 21: stability in plasma) centrifugation. Variations in concentrations were expressed as mean bias from baseline, using the analytical change limit (ACL%) or the reference change value (RCV%) as acceptance limit. Results: In tubes stored before centrifugation, mean plasma concentrations significantly decreased after 3 hr for phosphorus (-6.1% [95% CI: -7.4 to -4.7%]; ACL 4.62%) and lactate dehydrogenase (LDH; -5.7% [95% CI: -7.4 to -4.1%]; ACL 5.17%), and slightly decreased after 6 hr for potassium (-2.9% [95% CI: -5.3 to -0.5%]; ACL 4.13%). In plasma stored after centrifugation, mean concentrations decreased after 6 hr for bicarbonates (-19.7% [95% CI: -22.9 to -16.5%]; ACL 15.4%), and moderately increased after 4 hr for LDH (+6.0% [95% CI: +4.3 to +7.6%]; ACL 5.17%). Based on RCV, all the analytes can be considered stable up to 6 hr, whether before or after centrifugation. Conclusion: This study proposes acceptable delays for most biochemical tests on lithium heparin gel tubes arriving at the laboratory or needing to be reanalyzed.
MeSH term(s)	Blood Specimen Collection/instrumentation ; Blood Specimen Collection/methods ; Cell-Free System ; Centrifugation ; Heparin/chemistry ; Humans ; L-Lactate Dehydrogenase/blood ; Plasma/chemistry ; Reference Values ; Time Factors ; Triglycerides/blood ; gamma-Glutamyltransferase/blood
Chemical Substances	Triglycerides ; Heparin (9005-49-6) ; L-Lactate Dehydrogenase (EC 1.1.1.27) ; gamma-Glutamyltransferase (EC 2.3.2.2)
Language	English
Publishing date	2016-02-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	645095-7
ISSN	1098-2825 ; 0887-8013
ISSN (online)	1098-2825
ISSN	0887-8013
DOI	10.1002/jcla.21909
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