This page has only limited features, please log in for full access.
In this paper, we describe the first complete genome sequence of Providencia vermicola species, a clinical multidrug-resistant strain harboring the New Delhi Metallo-β-lactamase-1 (NDM-1) gene, isolated at the Kinshasa University Teaching Hospital, in Democratic Republic of the Congo. Whole genome sequencing of an imipenem-resistant clinical Gram-negative P. vermicola P8538 isolate was performed using MiSeq and Gridion, and then complete genome analysis, plasmid search, resistome analysis, and comparative genomics were performed. Genome assembly resulted in a circular chromosome sequence of 4,280,811-bp and 40.80% GC and a circular plasmid (pPV8538_NDM-1) of 151,684-bp and 51.93%GC, which was identified in an Escherichia coli P8540 strain isolated in the same hospital. Interestingly, comparative genomic analysis revealed multiple sequences acquisition within the P. vermicola P8538 chromosome, including three complete prophages, a siderophore biosynthesis NRPS cluster, a Type VI secretion system (T6SS), a urease gene cluster, and a complete Type-I-F CRISPR-Cas3 system. Β-lactamase genes, including blaCMY-6 and blaNDM-1, were found on the recombinant plasmid pPV8538_NDM-1, in addition to other antibiotic resistance genes such as rmtC, aac6’-Ib3, aacA4, catA1, sul1, aac6’-Ib-cr, tetA, and tetB. Genome comparison with Providencia species revealed 82.95% of average nucleotide identity (ANI), with P. stuartii species exhibiting 90.79% of proteome similarity. We report the first complete genome of P. vermicola species and for the first time the presence of the blaNDM-1 gene in this species. This work highlights the need to improve surveillance and clinical practices in DR Congo in order to reduce or prevent the spread of such resistance.
David Lupande-Mwenebitu; Mariem Ben Khedher; Sami Khabthani; Lalaoui Rym; Marie-France Phoba; Larbi Zakaria Nabti; Octavie Lunguya-Metila; Alix Pantel; Jean-Philippe Lavigne; Jean-Marc Rolain; Seydina M. Diene. First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture. Microorganisms 2021, 9, 1751 .
AMA StyleDavid Lupande-Mwenebitu, Mariem Ben Khedher, Sami Khabthani, Lalaoui Rym, Marie-France Phoba, Larbi Zakaria Nabti, Octavie Lunguya-Metila, Alix Pantel, Jean-Philippe Lavigne, Jean-Marc Rolain, Seydina M. Diene. First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture. Microorganisms. 2021; 9 (8):1751.
Chicago/Turabian StyleDavid Lupande-Mwenebitu; Mariem Ben Khedher; Sami Khabthani; Lalaoui Rym; Marie-France Phoba; Larbi Zakaria Nabti; Octavie Lunguya-Metila; Alix Pantel; Jean-Philippe Lavigne; Jean-Marc Rolain; Seydina M. Diene. 2021. "First Genome Description of Providencia vermicola Isolate Bearing NDM-1 from Blood Culture." Microorganisms 9, no. 8: 1751.
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.
Agathe Boudet; Robin Stephan; Sophie Bravo; Milène Sasso; Jean-Philippe Lavigne. Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Diagnostics 2021, 11, 1241 .
AMA StyleAgathe Boudet, Robin Stephan, Sophie Bravo, Milène Sasso, Jean-Philippe Lavigne. Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Diagnostics. 2021; 11 (7):1241.
Chicago/Turabian StyleAgathe Boudet; Robin Stephan; Sophie Bravo; Milène Sasso; Jean-Philippe Lavigne. 2021. "Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR." Diagnostics 11, no. 7: 1241.
Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and the intestinal microbiota that has rarely been described in human infections. Besides its role in halitosis and oral infections, S. moorei is considered to be an opportunistic pathogen causing mainly bloodstream and surgical wound infections. We performed a retrospective study of 27 cases of infections involving S. moorei in two French university hospitals between 2006 and 2021 with the aim of increasing our knowledge of this unrecognized opportunistic pathogen. We also reviewed all the data available in the literature and in genetic and metagenomic sequence databases. In addition to previously reported infections, S. moorei had been isolated from various sites and involved in intra-abdominal, osteoarticular, and cerebral infections more rarely or not previously reported. Although mostly involved in polymicrobial infections, in seven cases, it was the only pathogen recovered. Not included in all mass spectrometry databases, its identification can require 16S rRNA gene sequencing. High susceptibility to antibiotics (apart from rifampicin, moxifloxacin, and clindamycin; 91.3%, 11.8%, and 4.3% of resistant strains, respectively) has been noted. Our global search strategy revealed S. moorei to be human-associated, widely distributed in the human microbiota, including the vaginal and skin microbiota, which may be other sources for infection in addition to the oral and gut microbiota.
Corentine Alauzet; Fabien Aujoulat; Alain Lozniewski; Safa Ben Brahim; Chloé Domenjod; Cécilia Enault; Jean-Philippe Lavigne; Hélène Marchandin. A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature. Microorganisms 2021, 9, 1229 .
AMA StyleCorentine Alauzet, Fabien Aujoulat, Alain Lozniewski, Safa Ben Brahim, Chloé Domenjod, Cécilia Enault, Jean-Philippe Lavigne, Hélène Marchandin. A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature. Microorganisms. 2021; 9 (6):1229.
Chicago/Turabian StyleCorentine Alauzet; Fabien Aujoulat; Alain Lozniewski; Safa Ben Brahim; Chloé Domenjod; Cécilia Enault; Jean-Philippe Lavigne; Hélène Marchandin. 2021. "A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature." Microorganisms 9, no. 6: 1229.
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.
Agathe Boudet; Alexandre Jay; Catherine Dunyach-Remy; Raphaël Chiron; Jean-Philippe Lavigne; Hélène Marchandin. 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. Toxins 2021, 13, 317 .
AMA StyleAgathe Boudet, Alexandre Jay, Catherine Dunyach-Remy, Raphaël Chiron, Jean-Philippe Lavigne, Hélène Marchandin. 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. Toxins. 2021; 13 (5):317.
Chicago/Turabian StyleAgathe Boudet; Alexandre Jay; Catherine Dunyach-Remy; Raphaël Chiron; Jean-Philippe Lavigne; Hélène Marchandin. 2021. "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." Toxins 13, no. 5: 317.
Background Diabetic foot infections (DFIs) represent a serious threat to public health because of their frequency and the severity of their consequences, i.e. osteomyelitis and amputation. The management of diabetic foot osteomyelitis (DFOM) requires prolonged antibiotic therapy. In Western countries, Gram-positive bacteria are the most commonly encountered pathogens. Objectives This study evaluated the in vitro activity of dalbavancin, a novel lipoglycopeptide with extended half-life, recently marketed in Europe for acute bacterial skin and skin structure infections, on a panel of Gram-positive bacteria responsible for DFOM. Methods Dalbavancin activity was evaluated against a panel of Gram-positive bacterial strains isolated from bone biopsies performed by a trained surgeon among patients with suspected DFOM. MICs were determined using MIC Test Strips (Liofilchem) and confirmed with the EUCAST broth microdilution method. Three other antimicrobial agents (vancomycin, teicoplanin and ceftobiprole) were used as comparators. Results Dalbavancin showed excellent activity against all Gram-positive bacterial strains tested, including one teicoplanin-resistant Staphylococcus epidermidis isolate. With MIC50 and MIC90 values of 0.047 and 0.094 mg/L, respectively, dalbavancin showed the most potent in vitro activity among antimicrobial agents tested. Conclusions With its efficacy, good tolerability and unique pharmacokinetic properties, dalbavancin appears to be a promising treatment for DFOM involving Gram-positive bacteria.
Alix Pantel; Oriane Nachar; Agathe Boudet; Paul Loubet; Sophie Schuldiner; Nicolas Cellier; Albert Sotto; Catherine Dunyach-Remy; Jean-Philippe Lavigne. In vitro activity of dalbavancin against Gram-positive bacteria isolated from diabetic foot osteomyelitis. Journal of Antimicrobial Chemotherapy 2021, 1 .
AMA StyleAlix Pantel, Oriane Nachar, Agathe Boudet, Paul Loubet, Sophie Schuldiner, Nicolas Cellier, Albert Sotto, Catherine Dunyach-Remy, Jean-Philippe Lavigne. In vitro activity of dalbavancin against Gram-positive bacteria isolated from diabetic foot osteomyelitis. Journal of Antimicrobial Chemotherapy. 2021; ():1.
Chicago/Turabian StyleAlix Pantel; Oriane Nachar; Agathe Boudet; Paul Loubet; Sophie Schuldiner; Nicolas Cellier; Albert Sotto; Catherine Dunyach-Remy; Jean-Philippe Lavigne. 2021. "In vitro activity of dalbavancin against Gram-positive bacteria isolated from diabetic foot osteomyelitis." Journal of Antimicrobial Chemotherapy , no. : 1.
Aim: We investigated the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in chicken meat in Western Algeria in 2017.Results: From February to July 2017, samples of chicken meat from three poultry farms in Western Algeria were screened for the presence of CPE. Strains were characterized with regard to antibiotic resistance, β-lactamase content, Plasmid-mediated quinolone resistance, sulfonamide resistance genes, clonality (repetitive sequence-based profiles and multilocus sequence typing) and virulence traits. Of 181 samples analyzed, 29 (16.0%) carbapenemase-producing Klebsiella pneumoniae were detected. Twenty-three OXA-48-producers (79.3%) and six (20.7%) New Delhi metallo (NDM)-1-producers were observed. Clonality analysis showed three distinct lineages and clonal expansions of the OXA-48-producing K. pneumoniae ST48 and the NDM-1-producing K. pneumoniae ST101. These isolates harbored fimH, ureA, mrkD, entB, uge, and wabG. Neither capsular serotype genes nor hypermucoviscous phenotype were detected. Plasmid analysis confirmed that all these isolates harbored the transferable IncL and IncFIIK plasmids.Conclusions: This study reports the spread of OXA-48 and NDM-1-producing K. pneumoniae ST48 and ST101 in chicken meat in Western Algeria and demonstrates that food represents a reservoir of the carbapenemases encoding genes.
Nadia Chaalal; Abdelaziz Touati; Sofiane Bakour; Mohamed Amine Aissa; Albert Sotto; Jean-Philippe Lavigne; Alix Pantel. Spread of OXA-48 and NDM-1-Producing Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria. Microbial Drug Resistance 2021, 27, 492 -500.
AMA StyleNadia Chaalal, Abdelaziz Touati, Sofiane Bakour, Mohamed Amine Aissa, Albert Sotto, Jean-Philippe Lavigne, Alix Pantel. Spread of OXA-48 and NDM-1-Producing Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria. Microbial Drug Resistance. 2021; 27 (4):492-500.
Chicago/Turabian StyleNadia Chaalal; Abdelaziz Touati; Sofiane Bakour; Mohamed Amine Aissa; Albert Sotto; Jean-Philippe Lavigne; Alix Pantel. 2021. "Spread of OXA-48 and NDM-1-Producing Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria." Microbial Drug Resistance 27, no. 4: 492-500.
Staphylococcus aureus is the most prevalent pathogen isolated from diabetic foot infections (DFIs). The purpose of this study was to evaluate its behavior in an in vitro model mimicking the conditions encountered in DFI. Four clinical S. aureus strains were cultivated for 16 weeks in a specific environment based on the wound-like medium biofilm model. The adaptation of isolates was evaluated as follows: by Caenorhabditis elegans model (to evaluate virulence); by quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) (to evaluate expression of the main virulence genes); and by Biofilm Ring test® (to assess the biofilm formation). After 16 weeks, the four S. aureus had adapted their metabolism, with the development of small colony variants and the loss of β-hemolysin expression. The in vivo nematode model suggested a decrease of virulence, confirmed by qRT-PCRs, showing a significant decrease of expression of the main staphylococcal virulence genes tested, notably the toxin-encoding genes. An increased expression of genes involved in adhesion and biofilm was noted. Our data based on an in vitro model confirm the impact of environment on the adaptation switch of S. aureus to prolonged stress environmental conditions. These results contribute to explore and characterize the virulence of S. aureus in chronic wounds.
Cassandra Pouget; Claude-Alexandre Gustave; Christelle Ngba-Essebe; Frédéric Laurent; Emmanuel Lemichez; Anne Tristan; Albert Sotto; Catherine Dunyach-Rémy; Jean-Philippe Lavigne. Adaptation of Staphylococcus aureus in a Medium Mimicking a Diabetic Foot Environment. Toxins 2021, 13, 230 .
AMA StyleCassandra Pouget, Claude-Alexandre Gustave, Christelle Ngba-Essebe, Frédéric Laurent, Emmanuel Lemichez, Anne Tristan, Albert Sotto, Catherine Dunyach-Rémy, Jean-Philippe Lavigne. Adaptation of Staphylococcus aureus in a Medium Mimicking a Diabetic Foot Environment. Toxins. 2021; 13 (3):230.
Chicago/Turabian StyleCassandra Pouget; Claude-Alexandre Gustave; Christelle Ngba-Essebe; Frédéric Laurent; Emmanuel Lemichez; Anne Tristan; Albert Sotto; Catherine Dunyach-Rémy; Jean-Philippe Lavigne. 2021. "Adaptation of Staphylococcus aureus in a Medium Mimicking a Diabetic Foot Environment." Toxins 13, no. 3: 230.
This study assessed the clonal diversity, the resistance profile and the virulence potential of Escherichia coli strains isolated from diabetic foot infection (DFI) and diabetic foot osteomyelitis (DFOM). A retrospective single-centre study was conducted on patients diagnosed with E. coli isolated from deep DFI and DFOM at Clinique du Pied Diabétique Gard-Occitanie (France) over a two-year period. Phylogenetic backgrounds, virulence factors (VFs) and antibiotic resistance profiles were determined. Whole-genome analysis of E. coli strains isolated from same patients at different periods were performed. From the two-years study period, 35 E. coli strains isolated from 33 patients were analysed; 73% were isolated from DFOM. The majority of the strains belonged to the virulent B2 and D phylogenetic groups (82%). These isolates exhibited a significant higher average of VFs number than strains belonging to other groups (p < 0.001). papG2 gene was significantly more detected in strains belonging to B2 phylogroup isolated from DFI compared to DFOM (p = 0.003). The most prevalent antibiotic resistance pattern was observed for ampicillin (82%), cotrimoxazole (45%), and ciprofloxacin (33%). The genome analysis of strains isolated at two periods in DFOM showed a decrease of the genome size, and this decrease was more important for the strain isolated at nine months (vs. four months). A shared mutation on the putative acyl-CoA dehydrogenase-encoding gene aidB was observed on both strains. E. coli isolates from DFOM were highly genetically diverse with different pathogenicity traits. Their adaptation in the bone structure could require genome reduction and some important modifications in the balance virulence/resistance of the bacteria.
Alexi Lienard; Michel Hosny; Joanne Jneid; Sophie Schuldiner; Nicolas Cellier; Albert Sotto; Bernard La Scola; Jean-Philippe Lavigne; Alix Pantel. Escherichia coli Isolated from Diabetic Foot Osteomyelitis: Clonal Diversity, Resistance Profile, Virulence Potential, and Genome Adaptation. Microorganisms 2021, 9, 380 .
AMA StyleAlexi Lienard, Michel Hosny, Joanne Jneid, Sophie Schuldiner, Nicolas Cellier, Albert Sotto, Bernard La Scola, Jean-Philippe Lavigne, Alix Pantel. Escherichia coli Isolated from Diabetic Foot Osteomyelitis: Clonal Diversity, Resistance Profile, Virulence Potential, and Genome Adaptation. Microorganisms. 2021; 9 (2):380.
Chicago/Turabian StyleAlexi Lienard; Michel Hosny; Joanne Jneid; Sophie Schuldiner; Nicolas Cellier; Albert Sotto; Bernard La Scola; Jean-Philippe Lavigne; Alix Pantel. 2021. "Escherichia coli Isolated from Diabetic Foot Osteomyelitis: Clonal Diversity, Resistance Profile, Virulence Potential, and Genome Adaptation." Microorganisms 9, no. 2: 380.
Aim: In Algeria, colistin is used as a metaphylactic treatment in the poultry industry for the treatment of Gram-negative gastrointestinal infections and also as a feed additive to promote animal growth. The aim of this study was to investigate the importance and genetic characteristics of colistin-resistant Enterobacterales from chicken meat in Western Algeria.Results: A total of 181 samples of chicken meat were collected from three poultry farms across three provinces in Western Algeria. The presence of colistin-resistant Enterobacterales isolates was screened on selective media. Resistance and virulence profiles were characterised by PCR and sequencing. The clonal relatedness of the different mcr positive isolates was studied using repetitive sequence-based PCR (Rep-PCR) and multilocus sequence typing. Transferability and characteristics of plasmids harboring mcr-1 positive gene were performed using conjugation, PCR-based replicon typing, and whole-genome sequencing. A total of 22 isolates with acquired colistin resistance were identified giving an overall prevalence of 12.2% (22/181): 17 Escherichia coli (predominantly ST224 [n = 4, 23.5%]) and 5 Klebsiella pneumoniae (ST17 [n = 2, 40%], ST646 [n = 2, 40%], and ST944 [n = 1, 20%]). mcr-1 gene was exclusively found in 11 E. coli (prevalence of 6.1% [11/181]) and was associated with IncFV (n = 7) and IncFIIK (n = 4) plasmids. All the isolates had a commensal origin (n = 11). One isolate harbored virulence profile, a high colistin resistance (minimum inhibitory concentration = 96 mg/L), with some new mutations in the chromosomic colistin-resistant genes and different pathogenicity islands typically identified in uropathogenic E. coli.Conclusions: This study reports the diffusion of mcr-1 producing Enterobacterales from chicken meat in Western Algeria. This represents a worrisome situation needing continuous monitoring.
Nadia Chaalal; Abdelaziz Touati; Alex Yahiaoui-Martinez; Mohamed Amine Aissa; Albert Sotto; Jean-Philippe Lavigne; Alix Pantel. Colistin-Resistant Enterobacterales Isolated from Chicken Meat in Western Algeria. Microbial Drug Resistance 2021, 1 .
AMA StyleNadia Chaalal, Abdelaziz Touati, Alex Yahiaoui-Martinez, Mohamed Amine Aissa, Albert Sotto, Jean-Philippe Lavigne, Alix Pantel. Colistin-Resistant Enterobacterales Isolated from Chicken Meat in Western Algeria. Microbial Drug Resistance. 2021; ():1.
Chicago/Turabian StyleNadia Chaalal; Abdelaziz Touati; Alex Yahiaoui-Martinez; Mohamed Amine Aissa; Albert Sotto; Jean-Philippe Lavigne; Alix Pantel. 2021. "Colistin-Resistant Enterobacterales Isolated from Chicken Meat in Western Algeria." Microbial Drug Resistance , no. : 1.
Click on the article title to read more.
Alexandre Chlilek; Saber‐Davide Barbar; Robin Stephan; Claudine Barbuat; Guillaume Cayla; Muhamed‐Kheir Taha; Jean‐Philippe Lavigne; Albert Sotto. First case of invasive meningococcal disease‐induced myopericarditis in a patient with human immunodeficiency virus infection. Internal Medicine Journal 2021, 51, 136 -137.
AMA StyleAlexandre Chlilek, Saber‐Davide Barbar, Robin Stephan, Claudine Barbuat, Guillaume Cayla, Muhamed‐Kheir Taha, Jean‐Philippe Lavigne, Albert Sotto. First case of invasive meningococcal disease‐induced myopericarditis in a patient with human immunodeficiency virus infection. Internal Medicine Journal. 2021; 51 (1):136-137.
Chicago/Turabian StyleAlexandre Chlilek; Saber‐Davide Barbar; Robin Stephan; Claudine Barbuat; Guillaume Cayla; Muhamed‐Kheir Taha; Jean‐Philippe Lavigne; Albert Sotto. 2021. "First case of invasive meningococcal disease‐induced myopericarditis in a patient with human immunodeficiency virus infection." Internal Medicine Journal 51, no. 1: 136-137.
The present study assessed the proportion of intensive care unit (ICU) patients who had a vancomycin serum concentration between 20 and 25 mg/L after 24–48 h of intravenous vancomycin administration. From 2016 to 2018, adult ICU patients with vancomycin continuous infusion (CI) for any indication were included. The primary outcome was the proportion of patients with a first-available vancomycin serum concentration between 20–25 mg/L at 24 h (D2) or 48 h (D3). Of 3894 admitted ICU patients, 179 were included. A median loading dose of 15.6 (interquartile range (IQR) = (12.5–20.8) mg/kg) was given in 151/179 patients (84%). The median daily doses of vancomycin infusion for D1 and D2 were 2000 [(IQR (1600–2000)) and 2000 (IQR (2000–2500)) mg/d], respectively. The median duration of treatment was 4 (2–7) days. At D2 or D3, the median value of first serum vancomycin concentration was 19.8 (IQR (16.0–25.1)) with serum vancomycin concentration between 20–25 mg/L reported in 43 patients (24%). Time spent in the ICU before vancomycin initiation was the only risk factor of non-therapeutic concentration at D2 or D3. Acute kidney injury occurred significantly more when vancomycin concentration was supra therapeutic at D2 or D3. At D28, 44 (26%) patients had died. These results emphasize the need of appropriate loading dose and regular monitoring to improve vancomycin efficacy and avoid renal toxicity.
Nicolas Perin; Claire Roger; Grégory Marin; Nicolas Molinari; Alexandre Evrard; Jean-Philippe Lavigne; Saber Barbar; Pierre Géraud Claret; Caroline Boutin; Laurent Muller; Jeffrey Lipman; Jean-Yves Lefrant; Samir Jaber; Jason A. Roberts. Vancomycin Serum Concentration after 48 h of Administration: A 3-Years Survey in an Intensive Care Unit. Antibiotics 2020, 9, 793 .
AMA StyleNicolas Perin, Claire Roger, Grégory Marin, Nicolas Molinari, Alexandre Evrard, Jean-Philippe Lavigne, Saber Barbar, Pierre Géraud Claret, Caroline Boutin, Laurent Muller, Jeffrey Lipman, Jean-Yves Lefrant, Samir Jaber, Jason A. Roberts. Vancomycin Serum Concentration after 48 h of Administration: A 3-Years Survey in an Intensive Care Unit. Antibiotics. 2020; 9 (11):793.
Chicago/Turabian StyleNicolas Perin; Claire Roger; Grégory Marin; Nicolas Molinari; Alexandre Evrard; Jean-Philippe Lavigne; Saber Barbar; Pierre Géraud Claret; Caroline Boutin; Laurent Muller; Jeffrey Lipman; Jean-Yves Lefrant; Samir Jaber; Jason A. Roberts. 2020. "Vancomycin Serum Concentration after 48 h of Administration: A 3-Years Survey in an Intensive Care Unit." Antibiotics 9, no. 11: 793.
Urinary tract infections (UTIs) are the most common bacterial infections around the world. Uropathogenic Escherichia coli (UPEC) is among the main pathogens isolated in UTIs. The rate of UPEC with high resistance towards antibiotics and multidrug-resistant bacteria have increased dramatically and conduct to the difficulty to treat UTIs. Due to the rarefaction of new antibiotics molecules, new alternative strategies must be evaluated. Since many years, propolis has demonstrated an interesting antibacterial activity against E. coli. Here, we evaluated its activity added to antibiotics on a panel of UPEC with different resistance mechanisms. Minimal inhibitory concentrations (MICs) and time–kill curves of fosfomycin, ceftriaxone, ertapenem and ofloxacin, with and without propolis, were determined. Significant diminution of the MICs was observed using ceftriaxone or ofloxacin + propolis. Propolis alone had a bacteriostatic activity with time-dependent effect against UPEC. The addition of this nutraceutical improved the effect of all the antibiotics evaluated (except fosfomycin) and showed a synergistic bactericidal effect (fractional inhibitory concentrations index ≤ 0.5 and a decrease ≥ 2 log CFU/mL for the combination of propolis plus antibiotics compared with the antibiotic alone). Propolis is able to restore in vitro antibiotic susceptibility when added to antibiotics against UPEC. This study showed that propolis could enhance the efficiency of antibiotics used in UTIs and could represent an alternative solution.
Jean-Philippe Lavigne; Jérémy Ranfaing; Catherine Dunyach-Rémy; Albert Sotto. Synergistic Effect of Propolis and Antibiotics on Uropathogenic Escherichia coli. Antibiotics 2020, 9, 739 .
AMA StyleJean-Philippe Lavigne, Jérémy Ranfaing, Catherine Dunyach-Rémy, Albert Sotto. Synergistic Effect of Propolis and Antibiotics on Uropathogenic Escherichia coli. Antibiotics. 2020; 9 (11):739.
Chicago/Turabian StyleJean-Philippe Lavigne; Jérémy Ranfaing; Catherine Dunyach-Rémy; Albert Sotto. 2020. "Synergistic Effect of Propolis and Antibiotics on Uropathogenic Escherichia coli." Antibiotics 9, no. 11: 739.
Foot infections are the main disabling complication in patients with diabetes mellitus. These infections can lead to lower-limb amputation, increasing mortality and decreasing the quality of life. Biofilm formation is an important pathophysiology step in diabetic foot ulcers (DFU)—it plays a main role in the disease progression and chronicity of the lesion, the development of antibiotic resistance, and makes wound healing difficult to treat. The main problem is the difficulty in distinguishing between infection and colonization in DFU. The bacteria present in DFU are organized into functionally equivalent pathogroups that allow for close interactions between the bacteria within the biofilm. Consequently, some bacterial species that alone would be considered non-pathogenic, or incapable of maintaining a chronic infection, could co-aggregate symbiotically in a pathogenic biofilm and act synergistically to cause a chronic infection. In this review, we discuss current knowledge on biofilm formation, its presence in DFU, how the diabetic environment affects biofilm formation and its regulation, and the clinical implications.
Cassandra Pouget; Catherine Dunyach-Remy; Alix Pantel; Sophie Schuldiner; Albert Sotto; Jean-Philippe Lavigne. Biofilms in Diabetic Foot Ulcers: Significance and Clinical Relevance. Microorganisms 2020, 8, 1580 .
AMA StyleCassandra Pouget, Catherine Dunyach-Remy, Alix Pantel, Sophie Schuldiner, Albert Sotto, Jean-Philippe Lavigne. Biofilms in Diabetic Foot Ulcers: Significance and Clinical Relevance. Microorganisms. 2020; 8 (10):1580.
Chicago/Turabian StyleCassandra Pouget; Catherine Dunyach-Remy; Alix Pantel; Sophie Schuldiner; Albert Sotto; Jean-Philippe Lavigne. 2020. "Biofilms in Diabetic Foot Ulcers: Significance and Clinical Relevance." Microorganisms 8, no. 10: 1580.
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-REDTM (electrochemical method) and β-LACTATM test (chromogenic method). A panel of 150 clinical strains characterized for their resistance profiles (e.g., penicillinases, extended-spectrum beta-lactamases (ESBLs), overproduction of cephalosporinase, carbapenemases, impermeability) was tested. Approximately 100 CFU of each isolate was spiked into sterile blood culture bottles and incubated in a BD BACTECTM FX automated system (Becton Dickinson, USA). Positive blood cultures were examined to parallel testing using the BL-REDTM and β-LACTATM tests and conventional susceptibility method (disc diffusion following EUCAST recommendations). For all phenotypes combined, the sensitivity, specificity, positive predictive value, and negative predictive value in the detection of 3GC resistance were, respectively (i) with BL-REDTM: 45.7, 100, 100, and 54.2% and (ii) with β-LACTATM test: 52.2, 100, 100, and 56.9%. The positivity of tests allows to adapt antibiotic treatment whereas the negative result requires other tests. Moreover, these tests detect most Ambler class A-producing Enterobacterales (KPC, ESBL, extended-spectrum OXY) with sensitivities and specificities of 87.5 and 99% for BL-REDTM, respectively and both 100% for β-LACTATM test (47/47 isolates). These two rapid tests failed to detect AmpC overexpressed (sensitivities of 2.7% for BL-REDTM and 0% for β-LACTATM test) and Ambler class B-producing Enterobacterales (sensitivities of 40% for both tests) notably strains without ESBLs associated (sensitivities of 0% for both tests). BL-REDTM and β-LACTATM tests are easy-to-use and mainly attractive when a positive result is obtained notably to detect most of the Ambler class A-producing Enterobacterales in <1 h after the positivity of the blood culture, allowing a rapid adaptation of the antibiotic therapy in patients.
Clarisse Durand; Agathe Boudet; Jean-Philippe Lavigne; Alix Pantel. Evaluation of Two Methods for the Detection of Third Generation Cephalosporins Resistant Enterobacterales Directly From Positive Blood Cultures. Frontiers in Cellular and Infection Microbiology 2020, 10, 1 .
AMA StyleClarisse Durand, Agathe Boudet, Jean-Philippe Lavigne, Alix Pantel. Evaluation of Two Methods for the Detection of Third Generation Cephalosporins Resistant Enterobacterales Directly From Positive Blood Cultures. Frontiers in Cellular and Infection Microbiology. 2020; 10 ():1.
Chicago/Turabian StyleClarisse Durand; Agathe Boudet; Jean-Philippe Lavigne; Alix Pantel. 2020. "Evaluation of Two Methods for the Detection of Third Generation Cephalosporins Resistant Enterobacterales Directly From Positive Blood Cultures." Frontiers in Cellular and Infection Microbiology 10, no. : 1.
Urinary tract infections (UTIs) mainly caused by Uropathogenic Escherichia coli (UPEC), are common bacterial infections. Many individuals suffer from chronically recurring UTIs, sometimes requiring long-term prophylactic antibiotic regimens. The global emergence of multi-drug resistant uropathogens in the last decade underlines the need for alternative non-antibiotic therapeutic and preventative strategies against UTIs. The research on non-antibiotic therapeutic options in UTIs has focused on the following phases of the pathogenesis: colonization, adherence of pathogens to uroepithelial cell receptors and invasion. In this review, we discuss vaccines, small compounds, nutraceuticals, immunomodulating agents, probiotics and bacteriophages, highlighting the challenges each of these approaches face. Most of these treatments show interesting but only preliminary results. Lactobacillus-containing products and cranberry products in conjunction with propolis have shown the most robust results to date and appear to be the most promising new alternative to currently used antibiotics. Larger efficacy clinical trials as well as studies on the interplay between non-antibiotic therapies, uropathogens and the host immune system are warranted.
Paul Loubet; Jérémy Ranfaing; Aurélien Dinh; Catherine Dunyach-Remy; Louis Bernard; Franck Bruyère; Jean-Philippe Lavigne; Albert Sotto. Alternative Therapeutic Options to Antibiotics for the Treatment of Urinary Tract Infections. Frontiers in Microbiology 2020, 11, 1509 .
AMA StylePaul Loubet, Jérémy Ranfaing, Aurélien Dinh, Catherine Dunyach-Remy, Louis Bernard, Franck Bruyère, Jean-Philippe Lavigne, Albert Sotto. Alternative Therapeutic Options to Antibiotics for the Treatment of Urinary Tract Infections. Frontiers in Microbiology. 2020; 11 ():1509.
Chicago/Turabian StylePaul Loubet; Jérémy Ranfaing; Aurélien Dinh; Catherine Dunyach-Remy; Louis Bernard; Franck Bruyère; Jean-Philippe Lavigne; Albert Sotto. 2020. "Alternative Therapeutic Options to Antibiotics for the Treatment of Urinary Tract Infections." Frontiers in Microbiology 11, no. : 1509.
Rapid but yet sensitive, specific and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostic that would not require specific reagents are worth to investigate not only for fighting the COVID-19 pandemic, but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. Simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.
Duarte Gouveia; Guylaine Miotello; Fabrice Gallais; Jean-Charles Gaillard; Stéphanie Debroas; Laurent Bellanger; Jean-Philippe Lavigne; Albert Sotto; Lucia Grenga; Olivier Pible; Jean Armengaud. Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window. 2020, 1 .
AMA StyleDuarte Gouveia, Guylaine Miotello, Fabrice Gallais, Jean-Charles Gaillard, Stéphanie Debroas, Laurent Bellanger, Jean-Philippe Lavigne, Albert Sotto, Lucia Grenga, Olivier Pible, Jean Armengaud. Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window. . 2020; ():1.
Chicago/Turabian StyleDuarte Gouveia; Guylaine Miotello; Fabrice Gallais; Jean-Charles Gaillard; Stéphanie Debroas; Laurent Bellanger; Jean-Philippe Lavigne; Albert Sotto; Lucia Grenga; Olivier Pible; Jean Armengaud. 2020. "Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window." , no. : 1.
J.P. Stahl; J.P. Bru; J.F. Gehanno; J.L. Herrmann; B. Castan; G. Deffontaines; A. Sotto; D. Lepelletier; P. Tattevin; N. Godefroy; E. Haddad; A. Mailles; J.P. Lavigne. Guidelines for the management of accidental exposure to Brucella in a country with no case of brucellosis in ruminant animals. Médecine et Maladies Infectieuses 2020, 50, 480 -485.
AMA StyleJ.P. Stahl, J.P. Bru, J.F. Gehanno, J.L. Herrmann, B. Castan, G. Deffontaines, A. Sotto, D. Lepelletier, P. Tattevin, N. Godefroy, E. Haddad, A. Mailles, J.P. Lavigne. Guidelines for the management of accidental exposure to Brucella in a country with no case of brucellosis in ruminant animals. Médecine et Maladies Infectieuses. 2020; 50 (6):480-485.
Chicago/Turabian StyleJ.P. Stahl; J.P. Bru; J.F. Gehanno; J.L. Herrmann; B. Castan; G. Deffontaines; A. Sotto; D. Lepelletier; P. Tattevin; N. Godefroy; E. Haddad; A. Mailles; J.P. Lavigne. 2020. "Guidelines for the management of accidental exposure to Brucella in a country with no case of brucellosis in ruminant animals." Médecine et Maladies Infectieuses 50, no. 6: 480-485.
The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing, and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (1), but the earliest vaccines were based on live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (2). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic. This article is protected by copyright. All rights reserved.
Jean Armengaud; Agnès Delaunay‐Moisan; Jean‐Yves Thuret; Eelco Van Anken; Diego Acosta‐Alvear; Tomás Aragón; Carolina Arias; Marc Blondel; Ineke Braakman; Jean‐François Collet; René Courcol; Antoine Danchin; Jean‐François Deleuze; Jean‐Philippe Lavigne Md; Sophie Lucas; Thomas Michiels; Edward R. B. Moore; Jonathon Nixon‐Abell; Ramon Rossello‐Mora; Zheng‐Li Shi; Antonio G. Siccardi; Roberto Sitia; Daniel Tillett; Kenneth N. Timmis; Michel B. Toledano Md; Peter Van Der Sluijs; Elisa Vicenzi. The importance of naturally attenuated SARS‐CoV ‐2 in the fight against COVID ‐19. Environmental Microbiology 2020, 22, 1997 -2000.
AMA StyleJean Armengaud, Agnès Delaunay‐Moisan, Jean‐Yves Thuret, Eelco Van Anken, Diego Acosta‐Alvear, Tomás Aragón, Carolina Arias, Marc Blondel, Ineke Braakman, Jean‐François Collet, René Courcol, Antoine Danchin, Jean‐François Deleuze, Jean‐Philippe Lavigne Md, Sophie Lucas, Thomas Michiels, Edward R. B. Moore, Jonathon Nixon‐Abell, Ramon Rossello‐Mora, Zheng‐Li Shi, Antonio G. Siccardi, Roberto Sitia, Daniel Tillett, Kenneth N. Timmis, Michel B. Toledano Md, Peter Van Der Sluijs, Elisa Vicenzi. The importance of naturally attenuated SARS‐CoV ‐2 in the fight against COVID ‐19. Environmental Microbiology. 2020; 22 (6):1997-2000.
Chicago/Turabian StyleJean Armengaud; Agnès Delaunay‐Moisan; Jean‐Yves Thuret; Eelco Van Anken; Diego Acosta‐Alvear; Tomás Aragón; Carolina Arias; Marc Blondel; Ineke Braakman; Jean‐François Collet; René Courcol; Antoine Danchin; Jean‐François Deleuze; Jean‐Philippe Lavigne Md; Sophie Lucas; Thomas Michiels; Edward R. B. Moore; Jonathon Nixon‐Abell; Ramon Rossello‐Mora; Zheng‐Li Shi; Antonio G. Siccardi; Roberto Sitia; Daniel Tillett; Kenneth N. Timmis; Michel B. Toledano Md; Peter Van Der Sluijs; Elisa Vicenzi. 2020. "The importance of naturally attenuated SARS‐CoV ‐2 in the fight against COVID ‐19." Environmental Microbiology 22, no. 6: 1997-2000.
This review assessed the molecular characterization of the methicillin-resistant Staphylococcus aureus (MRSA)-ST80 clone with an emphasis on its proportion of total MRSA strains isolated, PVL production, spa-typing, antibiotic resistance, and virulence. A systematic review of the literature was conducted on MRSA-ST80 clone published between 1 January 2000 and 31 August 2019. Citations were chosen for a review of the full text if we found evidence that MRSA-ST80 clone was reported in the study. For each isolate, the country of isolation, the sampling period, the source of isolation (the type of infection, nasal swabs, or extra-human), the total number of MRSA strains isolated, number of MRSA-ST80 strains, antibiotic resistance patterns, PVL production, virulence genes, and spa type were recorded. The data from 103 articles were abstracted into an Excel database. Analysis of the data showed that the overall proportion of MRSA-ST80 has been decreasing in many countries in recent years. The majority of MRSA-ST80 were PVL positive with spa-type t044. Only six reports of MRSA-ST80 in extra-human niches were found. This review summarizes the rise of MRSA-ST80 and the evidence that suggests that it could be in decline in many countries.
Assia Mairi; Abdelaziz Touati; Jean-Philippe Lavigne. Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review. Toxins 2020, 12, 119 .
AMA StyleAssia Mairi, Abdelaziz Touati, Jean-Philippe Lavigne. Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review. Toxins. 2020; 12 (2):119.
Chicago/Turabian StyleAssia Mairi; Abdelaziz Touati; Jean-Philippe Lavigne. 2020. "Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review." Toxins 12, no. 2: 119.
For the analysis of volatile bacterial compounds, solid phase microextraction (SPME) is currently the most widely used metabolite concentration technique. Recently, the potential of stir bar sorptive extraction (SBSE) for this use has been demonstrated. These two approaches were therefore used in combination with gas-chromatography coupled with mass-spectrometry (GC–MS) for the analysis of volatile and semi-volatile bacterial compounds produced by Staphylococcus aureus. In both cases, SPME and SBSE/headspace sorptive extraction (HSSE) enrichment was carried out in two coating phases. A whole analytical and statistical process was developed to differentiate the metabolites produced from the metabolites consumed. The results obtained with SBSE/HSSE and SPME were compared and showed the recovery of 90% of the compounds by SBSE/HSSE. In addition, we were able to detect the production of 12 volatile/semi-volatile compounds by S. aureus, six of which had never been reported before. The extraction by SBSE/HSSE showed higher concentration capacities and greater sensitivity than SPME concerning bacterial compounds, suggesting that this technique may therefore become the new preferred option for bacterial volatile and semi-volatile compound analysis.
Kevin Berrou; Catherine Dunyach-Remy; Jean-Philippe Lavigne; Benoit Roig; Axelle Cadiere. Comparison of Stir Bar Sorptive Extraction and Solid Phase Microextraction of Volatile and Semi-Volatile Metabolite Profile of Staphylococcus aureus. Molecules 2019, 25, 55 .
AMA StyleKevin Berrou, Catherine Dunyach-Remy, Jean-Philippe Lavigne, Benoit Roig, Axelle Cadiere. Comparison of Stir Bar Sorptive Extraction and Solid Phase Microextraction of Volatile and Semi-Volatile Metabolite Profile of Staphylococcus aureus. Molecules. 2019; 25 (1):55.
Chicago/Turabian StyleKevin Berrou; Catherine Dunyach-Remy; Jean-Philippe Lavigne; Benoit Roig; Axelle Cadiere. 2019. "Comparison of Stir Bar Sorptive Extraction and Solid Phase Microextraction of Volatile and Semi-Volatile Metabolite Profile of Staphylococcus aureus." Molecules 25, no. 1: 55.