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Article ; Online: Mycoplasma pneumoniae is back! Is it the next pandemic?

Larcher, Romaric / Boudet, Agathe / Roger, Claire / Villa, Fanny / Loubet, Paul

Anaesthesia, critical care & pain medicine

2023 Volume 43, Issue 1, Page(s) 101338

MeSH term(s)	Humans ; Mycoplasma pneumoniae ; Pandemics/prevention & control ; Disease Outbreaks ; Pneumonia, Mycoplasma/epidemiology
Language	English
Publishing date	2023-12-10
Publishing country	France
Document type	Letter
ISSN	2352-5568
ISSN (online)	2352-5568
DOI	10.1016/j.accpm.2023.101338
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Article: Dynamics of community-acquired meningitis syndrome outbreaks in southern France.

Morsli, Madjid / Salipante, Florian / Kerharo, Quentin / Boudet, Agathe / Stephan, Robin / Dunyach-Remy, Catherine / Zandotti, Christine / Lavigne, Jean-Philippe / Drancourt, Michel

Frontiers in microbiology

2023 Volume 13, Page(s) 1102130

Abstract: In southern France, cases of community-acquired meningitis syndrome (CAM) are typically clustered as outbreaks with determinants which remain unknown. This 61-month retrospective investigation in Nîmes and Marseille university hospital laboratories, ... ...

Abstract	In southern France, cases of community-acquired meningitis syndrome (CAM) are typically clustered as outbreaks with determinants which remain unknown. This 61-month retrospective investigation in Nîmes and Marseille university hospital laboratories, yielded 2,209/20,779 (10.63%) documented CAM cases caused by 62 different micro-organisms, represented by seasonal viral etiologies (78.8%), including Enterovirus,
Language	English
Publishing date	2023-01-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.1102130
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Article: Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR.

Boudet, Agathe / Stephan, Robin / Bravo, Sophie / Sasso, Milène / Lavigne, Jean-Philippe

Diagnostics (Basel, Switzerland)

2021 Volume 11, Issue 7

Abstract: Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR ...

Abstract	Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex
Language	English
Publishing date	2021-07-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics11071241
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Article ; Online: Evaluation of Two Methods for the Detection of Third Generation Cephalosporins Resistant Enterobacterales Directly From Positive Blood Cultures.

Durand, Clarisse / Boudet, Agathe / Lavigne, Jean-Philippe / Pantel, Alix

Frontiers in cellular and infection microbiology

2020 Volume 10, Page(s) 491

Abstract: Due to the importance of a rapid determination of patients infected by multidrug resistant bacteria, we evaluated two rapid diagnostic tests for the detection of third-generation cephalosporins (3GC)-resistant Enterobacterales directly from positive ... ...

Abstract	Due to the importance of a rapid determination of patients infected by multidrug resistant bacteria, we evaluated two rapid diagnostic tests for the detection of third-generation cephalosporins (3GC)-resistant Enterobacterales directly from positive blood cultures within 1 h: BL-RED
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Blood Culture ; Cephalosporins/pharmacology ; Drug Resistance, Multiple, Bacterial/drug effects ; Humans ; Microbial Sensitivity Tests ; beta-Lactamases
Chemical Substances	Anti-Bacterial Agents ; Cephalosporins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2020-09-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2020.00491
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Article ; Online: In-Host Emergence of Linezolid Resistance in a Complex Pattern of Toxic Shock Syndrome Toxin-1-Positive Methicillin-Resistant

Boudet, Agathe / Jay, Alexandre / Dunyach-Remy, Catherine / Chiron, Raphaël / Lavigne, Jean-Philippe / Marchandin, Hélène

Toxins

2021 Volume 13, Issue 5

Abstract: Methicillin- ... ...

Abstract	Methicillin-resistant
MeSH term(s)	Adolescent ; Child ; Cystic Fibrosis/complications ; Cystic Fibrosis/microbiology ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Female ; Genotyping Techniques ; Humans ; Linezolid/pharmacology ; Linezolid/therapeutic use ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Methicillin-Resistant Staphylococcus aureus/genetics ; Microbial Sensitivity Tests ; Multilocus Sequence Typing ; Shock, Septic/drug therapy ; Shock, Septic/microbiology ; Siblings ; Staphylococcal Infections/drug therapy ; Staphylococcal Infections/microbiology ; Whole Genome Sequencing
Chemical Substances	Linezolid (ISQ9I6J12J)
Language	English
Publishing date	2021-04-28
Publishing country	Switzerland
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518395-3
ISSN	2072-6651 ; 2072-6651
ISSN (online)	2072-6651
ISSN	2072-6651
DOI	10.3390/toxins13050317
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Article: Biofilm Formation in Methicillin-Resistant

Boudet, Agathe / Sorlin, Pauline / Pouget, Cassandra / Chiron, Raphaël / Lavigne, Jean-Philippe / Dunyach-Remy, Catherine / Marchandin, Hélène

Frontiers in microbiology

2021 Volume 12, Page(s) 750489

Abstract: Cystic fibrosis (CF) is a genetic disease with lung abnormalities making patients particularly predisposed to pulmonary infections. ...

Abstract	Cystic fibrosis (CF) is a genetic disease with lung abnormalities making patients particularly predisposed to pulmonary infections.
Language	English
Publishing date	2021-10-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.750489
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Article ; Online: Use of Deep Learning to Detect the Maternal Heart Rate and False Signals on Fetal Heart Rate Recordings.

Boudet, Samuel / Houzé de l'Aulnoit, Agathe / Peyrodie, Laurent / Demailly, Romain / Houzé de l'Aulnoit, Denis

Biosensors

2022 Volume 12, Issue 9

Abstract: We have developed deep learning models for automatic identification of the maternal heart rate (MHR) and, more generally, false signals (FSs) on fetal heart rate (FHR) recordings. The models can be used to preprocess FHR data prior to automated analysis ... ...

Abstract	We have developed deep learning models for automatic identification of the maternal heart rate (MHR) and, more generally, false signals (FSs) on fetal heart rate (FHR) recordings. The models can be used to preprocess FHR data prior to automated analysis or as a clinical alert system to assist the practitioner. Three models were developed and used to detect (i) FSs on the MHR channel (the FSMHR model), (ii) the MHR and FSs on the Doppler FHR sensor (the FSDop model), and (iii) FSs on the scalp ECG channel (the FSScalp model). The FSDop model was the most useful because FSs are far more frequent on the Doppler FHR channel. All three models were based on a multilayer, symmetric, GRU, and were trained on data recorded during the first and second stages of delivery. The FSMHR and FSDop models were also trained on antepartum recordings. The training dataset contained 1030 expert-annotated periods (mean duration: 36 min) from 635 recordings. In an initial evaluation of routine clinical practice, 30 fully annotated recordings for each sensor type (mean duration: 5 h for MHR and Doppler sensors, and 3 h for the scalp ECG sensor) were analyzed. The sensitivity, positive predictive value (PPV) and accuracy were respectively 62.20%, 87.1% and 99.90% for the FSMHR model, 93.1%, 95.6% and 99.68% for the FSDop model, and 44.6%, 87.2% and 99.93% for the FSScalp model. We built a second test dataset with a more solid ground truth by selecting 45 periods (lasting 20 min, on average) on which the Doppler FHR and scalp ECG signals were recorded simultaneously. Using scalp ECG data, the experts estimated the true FHR value more reliably and thus annotated the Doppler FHR channel more precisely. The models achieved a sensitivity of 53.3%, a PPV of 62.4%, and an accuracy of 97.29%. In comparison, two experts (blinded to the scalp ECG data) respectively achieved a sensitivity of 15.7%, a PPV of 74.3%, and an accuracy of 96.91% and a sensitivity of 60.7%, a PPV of 83.5% and an accuracy of 98.24%. Hence, the models performed at expert level (better than one expert and worse than the other), although a well-trained expert with good knowledge of FSs could probably do better in some cases. The models and datasets have been included in the Fetal Heart Rate Morphological Analysis open-source MATLAB toolbox and can be used freely for research purposes.
MeSH term(s)	Cardiotocography ; Deep Learning ; Electrocardiography ; Female ; Heart Rate/physiology ; Heart Rate, Fetal/physiology ; Humans ; Labor, Obstetric/physiology ; Pregnancy
Language	English
Publishing date	2022-08-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662125-3
ISSN	2079-6374 ; 2079-6374
ISSN (online)	2079-6374
ISSN	2079-6374
DOI	10.3390/bios12090691
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Article ; Online: Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR

Agathe Boudet / Robin Stephan / Sophie Bravo / Milène Sasso / Jean-Philippe Lavigne

Diagnostics, Vol 11, Iss 1241, p

2021 Volume 1241

Abstract	Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex ® , ID Solutions, Grabels, France) on 2207 nasopharyngeal samples that were positive for SARS-CoV-2. Using ID Solutions kit, 4.1% (92/2207) of samples were suspected to belonged to B.1.351 or P.1 variants. Next-generation sequencing that was performed on 67.4% (62/92) of these samples confirmed the presence of a B.1.351 variant in only 75.8% of the samples (47/62). Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. The thirteen with the UK variant presented one mutation in the S-gene , near the ΔH69/ΔV70 deletion (S71F or A67S), which impacted the detection of ΔH69/ΔV70 deletion. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3 ® PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. In conclusion, this study highlights the limitations of the screening strategy based on the detection of few mutations/deletions as well as it not being able to follow the virus evolution.
Keywords	SARS-CoV-2 ; RT-PCR ; screening method ; variants ; Medicine (General) ; R5-920
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In-Host Emergence of Linezolid Resistance in a Complex Pattern of Toxic Shock Syndrome Toxin-1-Positive Methicillin-Resistant Staphylococcus aureus Colonization in Siblings with Cystic Fibrosis

Agathe Boudet / Alexandre Jay / Catherine Dunyach-Remy / Raphaël Chiron / Jean-Philippe Lavigne / Hélène Marchandin

Toxins, Vol 13, Iss 317, p

2021 Volume 317

Abstract: Methicillin-resistant Staphylococcus aureus (MRSA) can cause chronic lung infections in patients with Cystic Fibrosis (CF). One option for managing them is the use of linezolid. We hereby report the in-host emergence of linezolid resistance (LR) in MRSA ... ...

Abstract	Methicillin-resistant Staphylococcus aureus (MRSA) can cause chronic lung infections in patients with Cystic Fibrosis (CF). One option for managing them is the use of linezolid. We hereby report the in-host emergence of linezolid resistance (LR) in MRSA in CF siblings via a population analysis. A collection of 171 MRSA strains from 68 samples were characterized by determining their linezolid Minimal Inhibitory Concentrations (MICs), analyzing the locus of staphylococcal protein A ( spa ) and whole genome sequencing. Courses of linezolid were retraced. Strains belonged to three spa types (t002, t045, t127) and two sequence types (ST1, ST5). Emergence of LR occurred under treatment, one year apart in both siblings, in the CC5-MRSA-I Geraldine clone harboring the toxic shock syndrome toxin-1-encoding gene. Resistance was related to a G2576T substitution present in a variable number of 23S rRNA gene copies. Susceptible and resistant strains were co-isolated within samples. Single Nucleotide Polymorphism-based analysis revealed complex colonizations by highly diversified, clonally related populations. LR remains rare in MRSA and there are very few longitudinal analyses documenting its emergence. Analyzing a large MRSA collection revealed new aspects of LR emergence: it emerges in specific subclonal lineages resulting from adaptive diversification of MRSA in the CF lung and this heterogeneity of intra-sample resistance may contribute to compromising antibiotic management.
Keywords	Staphylococcus aureus ; cystic fibrosis ; linezolid ; resistance ; emergence ; siblings ; Medicine ; R
Subject code	630
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Biofilm Formation by Staphylococcus aureus in the Specific Context of Cystic Fibrosis

Vincent Jean-Pierre / Agathe Boudet / Pauline Sorlin / Quentin Menetrey / Raphaël Chiron / Jean-Philippe Lavigne / Hélène Marchandin

International Journal of Molecular Sciences, Vol 24, Iss 1, p

2022 Volume 597

Abstract: Staphylococcus aureus is a major human pathogen whose characteristics support its success in various clinical settings including Cystic Fibrosis (CF). In CF, S. aureus is indeed the most commonly identified opportunistic pathogen in children and the ... ...

Abstract	Staphylococcus aureus is a major human pathogen whose characteristics support its success in various clinical settings including Cystic Fibrosis (CF). In CF, S. aureus is indeed the most commonly identified opportunistic pathogen in children and the overall population. S. aureus colonization/infection, either by methicillin-susceptible or methicillin-resistant strains, will become chronic in about one third of CF patients. The persistence of S. aureus in CF patients’ lungs, despite various eradication strategies, is favored by several traits in both host and pathogen. Among the latter, living in biofilm is a highly protective way to survive despite deleterious environmental conditions, and is a common characteristic shared by the main pathogens identified in CF. This is why CF has earned the status of a biofilm-associated disease for several years now. Biofilm formation by S. aureus , and the molecular mechanisms governing and regulating it, have been extensively studied but have received less attention in the specific context of CF lungs. Here, we review the current knowledge on S. aureus biofilm in this very context, i.e., the importance, study methods, molecular data published on mono- and multi-species biofilm and anti-biofilm strategies. This focus on studies including clinical isolates from CF patients shows that they are still under-represented in the literature compared with studies based on reference strains, and underlines the need for such studies. Indeed, CF clinical strains display specific characteristics that may not be extrapolated from results obtained on laboratory strains.
Keywords	Staphylococcus aureus ; biofilm ; cystic fibrosis ; multispecies biofilm ; anti-biofilm ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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