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1. Pneumococcal Septic Arthritis among Adults, France, 2010–2018

Author

Farida Hamdad, Nadim El Bayeh, Gabriel Auger, Olivia Peuchant, Frédéric Wallet, Raymond Ruimy, Florence Reibel, Christian Martin, Marie-Cécile Ploy, Frédéric Robin, Chrislène Laurens, Philippe Lanotte, Marie Kempf, Jennifer Tetu, Hélène Revillet, Isabelle Patry, Philippe Cailloux, Mélissa Azouaou, Emmanuelle Varon, Pierre Duhaut, Alain Lozniewski, and Vincent Cattoir

Subjects
Streptococcus pneumoniae, joint infection, septic arthritis, adult, bacteria, France, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Streptococcus pneumoniae infection is considered an uncommon cause of arthritis in adults. To determine the clinical and microbiological characteristics of pneumococcal septic arthritis, we retrospectively studied a large series of cases among adult patients during the 2010–2018 conjugate vaccine era in France. We identified 110 patients (56 women, 54 men; mean age 65 years), and cases included 82 native joint infections and 28 prosthetic joint infections. Most commonly affected were the knee (50/110) and hip (25/110). Concomitant pneumococcal infections were found in 37.2% (38/102) and bacteremia in 57.3% (55/96) of patients, and underlying conditions were noted for 81.4% (83/102). Mortality rate was 9.4% (8/85). The proportion of strains not susceptible to penicillin was 29.1% (32/110). Of the 55 serotyped strains, 31 (56.4%) were covered by standard pneumococcal vaccines; however, several nonvaccine serotypes (mainly 23B, 24F, and 15A) had emerged, for which susceptibility to β-lactams was low.

Published
2025
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2. Ingestion of Bacillus cereus spores dampens the immune response to favor bacterial persistence

Author

Salma Hachfi, Alexandra Brun-Barale, Arnaud Fichant, Patrick Munro, Marie-Paule Nawrot-Esposito, Gregory Michel, Raymond Ruimy, Raphaël Rousset, Mathilde Bonis, Laurent Boyer, and Armel Gallet

Subjects
Science
Abstract

Abstract Strains of the Bacillus cereus (Bc) group are sporulating bacteria commonly associated with foodborne outbreaks. Spores are dormant cells highly resistant to extreme conditions. Nevertheless, the pathological processes associated with the ingestion of either vegetative cells or spores remain poorly understood. Here, we demonstrate that while ingestion of vegetative bacteria leads to their rapid elimination from the intestine of Drosophila melanogaster, a single ingestion of spores leads to the persistence of bacteria for at least 10 days. We show that spores do not germinate in the anterior part of the intestine which bears the innate immune defenses. Consequently, spores reach the posterior intestine where they germinate and activate both the Imd and Toll immune pathways. Unexpectedly, this leads to the induction of amidases, which are negative regulators of the immune response, but not to antimicrobial peptides. Thereby, the local germination of spores in the posterior intestine dampens the immune signaling that in turn fosters the persistence of Bc bacteria. This study provides evidence for how Bc spores hijack the intestinal immune defenses allowing the localized birth of vegetative bacteria responsible for the digestive symptoms associated with foodborne illness outbreaks.

Published
2024
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5. Acute Pyelonephritis with Bacteremia in an 89-Year-Old Woman Caused by Two Slow-Growing Bacteria: Aerococcus urinae and Actinotignum schaalii

Author

Laurène Lotte, Claire Durand, Alicia Chevalier, Alice Gaudart, Yousra Cheddadi, Raymond Ruimy, and Romain Lotte

Subjects
slow-growing bacteria, urinary culture, urinary tract infections, Biology (General), QH301-705.5
Abstract

Aerococcus urinae is an aerobic Gram-positive coccus that grows as tiny alpha-hemolytic colonies. Actinotignum schaalii is a slow-growing facultative anaerobic Gram-positive rod. These bacteria are part of the urogenital microbiota of healthy patients, but can also be involved in urinary tract infections (UTIs), particularly in elderly men and young children. Because A. urinae and A. schaalii are fastidious and are difficult to identify with phenotypic methods, they are underestimated causes of UTIs. Their growth is slow and requires a blood-enriched medium incubated under an anaerobic or 5% CO2 atmosphere for 48 h and from 24 to 48 h for A. schaalii and A. urinae, respectively. Furthermore, accurate identification is only possible using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or molecular-based methods. In rare cases, these bacteria can be responsible for invasive infections. We describe, here, an unusual case of bacteremic UTI caused by both A. schaalii and A. urinae in an 89-year-old woman. She presented with dyspnea, and bacteriuria was noted. This challenging clinical and microbiological diagnosis was made in our laboratory by Gram staining urine with a leucocyte count >50/μL and/or a bacterial count >14/μL urinary culture on a blood agar plate. After 10 days of antimicrobial treatment consisting of 2 g amoxicillin PO t.i.d., the patient was discharged with a complete clinical and biological recovery. A. schaalii and A. urinae are probably still underestimated causes of UTIs. Microbiologists could consider the presence of these two bacteria using appropriate culture and identification methods in cases where a positive direct examination of urine reveals small Gram-positive rods or cocci, where undocumented UTIs are present in elderly patients, but also where a urinary dipstick is negative for nitrites and is associated with leukocyturia.

Published
2023
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6. Major discrepancy between factual antibiotic resistance and consumption in South of France: analysis of 539,037 bacterial strains

Author

Ousmane Oumou Diallo, Sophie Alexandra Baron, Gregory Dubourg, Hervé Chaudet, Philippe Halfon, Sabine Camiade, Béatrice Comte, Stéphanie Joubert, Arnaud François, Philippe Seyral, François Parisot, Jean-Paul Casalta, Raymond Ruimy, Christophe Maruejouls, Jean-Christophe Achiardy, Sophie Burignat, Joseph Carvajal, Edouard Delaunay, Sandra Meyer, Pierre-Yves Levy, Patricia Roussellier, Patrick Brunet, Claude Bosi, Philippe Stolidi, Jean-Pierre Arzouni, Gisele Gay, Pierre Hance, Philippe Colson, Didier Raoult, and Jean-Marc Rolain

Subjects
Medicine, Science
Abstract

Abstract The burden of antibiotic resistance is currently estimated by mathematical modeling, without real count of resistance to key antibiotics. Here we report the real rate of resistance to key antibiotics in bacteria isolated from humans during a 5 years period in a large area in southeast in France. We conducted a retrospective study on antibiotic susceptibility of 539,107 clinical strains isolated from hospital and private laboratories in south of France area from January 2014 to January 2019. The resistance rate to key antibiotics as well as the proportion of bacteria classified as Difficult-to-Treat (DTR) were determined and compared with the Mann–Whitney U test, the χ2 test or the Fisher’s exact test. Among 539,037 isolates, we did not observe any significant increase or decrease in resistance to key antibiotics for 5 years, (oxacillin resistance in Staphylococcus aureus, carbapenem resistance in enterobacteria and Pseudomonas aeruginosa and 3rd generation cephalosporin resistance in Escherichia coli and Klebsiella pneumoniae). However, we observed a significant decrease in imipenem resistance for Acinetobacter baumannii from 2014 to 2018 (24.19–12.27%; p = 0.005) and a significant increase of ceftriaxone resistance in Klebsiella pneumoniae (9.9–24.03%; p = 0.001) and Enterobacter cloacae (24.05–42.05%; p = 0.004). Of these 539,037 isolates, 1604 (0.3%) had a DTR phenotype. Over a 5-year period, we did not observe a burden of AR in our region despite a high rate of antibiotic consumption in our country. These results highlight the need for implementation of real-time AR surveillance systems which use factual data.

Published
2020
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7. Nocardia takedensis: a newly recognized pathogen responsible for skin and soft tissue infections

Author

Romain Lotte, Alicia Chevalier, Sabine Dantas, Nicolas Degand, Alice Gaudart, Pierre-Simon Rörhlich, Laurent Boyer, Veronica Rodriguez-Nava, Pascal Del Giudice, and Raymond Ruimy

Subjects
Therapeutics. Pharmacology, RM1-950, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

Abstract Nocardia takedensis was first isolated in 2005, from soil in Japan. We report here two cases of lymphangitis in France (2012–2017) caused by N. takedensis both occurring after skin injury while gardening, which enabled its inoculation. The two patients were immunocompromised and successfully treated by an antimicrobial agent active on the isolated strain, trimethoprim-sulfamethoxazole and amoxicillin-clavulanic acid for patient one and patient two, respectively. Our study along with previous ones supports the idea of a newly recognized cutaneous opportunistic pathogen and reinforces the recommendation of using gloves during soil exposure for immunocompromised patients. Lastly, according to data found in the literature, we would recommend trimethoprim-sulfamethoxazole as an efficient empirical antibiotic therapy in case of cutaneous infection caused by N. takedensis.

Published
2020
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8. An unusual Staphylococcus saccharolyticus spondylodiscitis post kyphoplasty: a case report

Author

Marie-Charlotte Trojani, Brigitte Lamy, Raymond Ruimy, Nicolas Amoretti, Karine Risso, and Christian Roux

Subjects
Spondylodiscitis, Kyphoplasty, Healthcare-associated infection, Case report, Staphylococcus saccharolyticus, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Staphylococcus saccharolyticus is a rarely encountered coagulase-negative, which grows slowly and its strictly anaerobic staphylococcus from the skin. It is usually considered a contaminant, but some rare reports have described deep-seated infections. Virulence factors remain poorly known, although, genomic analysis highlights pathogenic potential. Case presentation We report a case of Staphylococcus saccharolyticus spondylodiscitis that followed kyphoplasty, a procedure associated with a low rate but possible severe infectious complication (0.46%), and have reviewed the literature. This case specifically stresses the risk of healthcare-associated S. saccharolyticus infection in high-risk patients (those with a history of alcoholism and heavy smoking). Conclusion S. saccharolyticus infection is difficult to diagnose due to microbiological characteristics of this bacterium; it requires timely treatment, and improved infection control procedure should be encouraged for high-risk patients.

Published
2020
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9. Drosophila melanogaster Systemic Infection Model to Study Altered Virulence during Polymicrobial Infection by Aeromonas

Author

Alexandre Robert, Emilie Talagrand-Reboul, Maria-Jose Figueras, Raymond Ruimy, Laurent Boyer, and Brigitte Lamy

Subjects
polymicrobial infection, Drosophila melanogaster, infection model, opportunistic pathogen, Aeromonas, microbial interference, Medicine
Abstract

Background: Polymicrobial infections are complex infections associated with worse outcomes compared to monomicrobial infections. We need simple, fast, and cost-effective animal models to assess their still poorly known pathogenesis. Methods: We developed a Drosophila melanogaster polymicrobial infection model for opportunistic pathogens and assessed its capacity to discriminate the effects of bacterial mixtures taken from cases of human polymicrobial infections by Aeromonas strains. A systemic infection was obtained by needle pricking the dorsal thorax of the flies, and the fly survival was monitored over time. Different lineages of the flies were infected by a single strain or paired strains (strain ratio 1:1). Results: Individual strains killed more than 80% of the flies in 20 h. The course of infection could be altered with a microbial mix. The model could distinguish between the diverse effects (synergistic, antagonistic, and no difference) that resulted in a milder, more severe, or similar infection, depending on the paired strain considered. We then investigated the determinants of the effects. The effects were maintained in deficient fly lineages for the main signaling pathways (Toll deficient and IMD deficient), which suggests an active microbe/microbe/host interaction. Conclusion: These results indicate that the D. melanogaster systemic infection model is consistent with the study of polymicrobial infection.

Published
2023
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10. Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infectionResearch in context

Author

Ghiles Grine, Romain Lotte, David Chirio, Alicia Chevalier, Didier Raoult, Michel Drancourt, and Raymond Ruimy

Subjects
Medicine, Medicine (General), R5-920
Abstract

Background: Urinary tract infections are known to be caused by bacteria, but the potential implications of archaea have never been studied in this context. Methods: In two different university hospital centres we used specific laboratory methods for the detection and culture of archaeal methanogens in 383 urine specimens prospectively collected for diagnosing urinary tract infection (UTI). Findings: Methanobrevibacter smithii was detected by quantitative PCR and sequencing in 34 (9%) of the specimens collected from 34 patients. Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Enterococcus faecium and mixed cultures were detected along with M. smithii in eighteen, six, three, one and six urine samples, respectively. Interestingly, using our specific culture method for methanogens, we also isolated M. smithii in 31 (91%) of the 34 PCR positive urine samples. Genotyping the 31 isolates using multispacer sequence typing revealed three different genotypes which have been previously reported in intestinal microbiota. Antibiotic susceptibility testing found the 31 isolates to be in vitro susceptible to metronidazole (MIC: 1 mg/L) but resistant to fosfomycin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanate and ofloxacin, commonly used to treat bacterial UTI. Finally, 19 (54%) of the 34 patients in whose urine samples M. smithii was detected were diagnosed with UTIs, including cystitis, pyelonephritis and prostatitis. Interpretation: Our results show that M. smithii is part of the urinary microbiota of some individuals and could play a role in community-acquired UTI in association with enteric bacteria. Fund: This study was supported by IHU Méditerranée Infection, Marseille, France.

Published
2019
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11. Evaluation of an Antibiotic Susceptibility Testing Method on Enterobacterales-Positive Blood Cultures in Less Than 8 h Using the Rapid Mueller-Hinton Diffusion Method in Conjunction with the SIRscan 2000 Automatic Reading Device

Author

Mathilde Payen, Alice Gaudart, Kevin Legueult, James Kasprzak, Audrey Emery, Grégoire Mutambayi, Christian Pradier, Frédéric Robin, Romain Lotte, and Raymond Ruimy

Subjects
antibiotic susceptibility testing, rapid AST, bacteremia, Biology (General), QH301-705.5
Abstract

Enterobacterales bloodstream infections are life-threatening and require rapid, targeted antibiotherapy based on antibiotic susceptibility testing (AST). A new method using Muller-Hinton Rapid-SIR (MHR-SIR) agar (i2a, Montpellier, France) allows complete direct AST (dAST) to be read from positive blood culture bottles (BCBs) for all Enterobacterales species after 6–8 h of incubation. We evaluated (i) the performance of dAST from positive BCBs on MHR-SIR agar using two different inoculum protocols; (ii) the categorical agreement between dAST results obtained with MHR-SIR agar vs. those obtained with Muller-Hinton (MH) agar; and (iii) the ability of the MHR-SIR medium to detect β-lactam resistant Enterobacterales. Finally, we estimated the saved turnaround time (TAT) with MHR-SIR compared with MH agar in our 24/7 laboratory. Our results showed that the most suitable inoculation protocol for dAST on MHR-SIR agar was 1 drop of BCB/5 mL H2O. For monomicrobial Enterobacterales BCBs, dAST performed on MHR-SIR medium showed 99.3% categorical agreement with AST on MH agar. Furthermore, MHR-SIR agar allows early detection of β-lactam resistance mechanisms, including AmpC hyperproduction, extended-spectrum β-lactamase, and carbapenemase. Finally, TAT reduction in our 24/7 laboratory was 16 h, enabling a significantly faster provision of antibiotic advice.

Published
2022
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12. Spontaneous Bacterial Peritonitis: The Incremental Value of a Fast and Direct Bacterial Identification from Ascitic Fluids Inoculated in Blood Culture Bottles by MALDI-TOF MS for a Better Management of Patients

Author

Romain Lotte, Audrey Courdurié, Alice Gaudart, Audrey Emery, Alicia Chevalier, Albert Tran, Mathilde Payen, and Raymond Ruimy

Subjects
direct identification of bacteria, MALDI-TOF, ascites, Biology (General), QH301-705.5
Abstract

Spontaneous bacterial peritonitis (SBP) is a severe infection that requires fast and accurate antibiotic therapy to improve the patient outcome. Direct bacterial identification using MALDI-TOF mass spectrometry from ascitic fluid inoculated in blood culture bottles (BCBs) could therefore improve patients’ management. We evaluated the impact of the implementation of this method for the treatment of patients. Our identification protocol was performed on 136 positive BCBs collected from 61 patients between December 2018 and December 2020. The therapeutic impact of our protocol was evaluated using a before (2015–2016) and after (2019–2020) case–control study in two populations of 41 patients diagnosed with SBP and treated with antibiotics. The decrease in time to first identification and the optimization of antibiotic therapy following communication of the identification result were evaluated. Our protocol allowed us to identify 78% of bacteria in ascitic fluids. The transmission of the direct identification allowed the introduction or adaption of the antibiotic therapy early in 37% of SBP, with a mean decrease in time to first antibiotic change of 17 h. Our direct identification protocol for positive inoculated ascitic fluids is fast, reliable and inexpensive. Its routine integration into a microbiology laboratory allows the early introduction of appropriate antibiotic therapy and improves the management of patients with SBP.

Published
2022
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13. Clindamycin Efficacy for Cutibacterium acnes Shoulder Device-Related Infections

Author

Audrey Courdurié, Romain Lotte, Raymond Ruimy, Vincent Cauhape, Michel Carles, Marc-Olivier Gauci, Pascal Boileau, and Johan Courjon

Subjects
Cutibacterium acnes, shoulder implant, clindamycin, Therapeutics. Pharmacology, RM1-950
Abstract

Clindamycin is an antibiotic with high bioavailability and appropriate bone diffusion, often proposed as an alternative in guidelines for C. acnes prosthetic joint infections. We aimed to evaluate the efficacy of clindamycin in the treatment of C. acnes shoulder implant joint infections (SIJI). Methods: A retrospective analysis was conducted at the University Hospital of Nice (France) between 2010 and 2019. We included patients with one shoulder implant surgical procedure and at least one C. acnes positive sample. We selected the C. acnes SIJI according to French and international recommendations. The primary endpoint was favorable outcome of C. acnes SIJI treatment after at least 1-year follow-up in the clindamycin group compared to another therapeutic group. Results: Forty-eight SIJI were identified and 33 were treated with clindamycin, among which 25 were treated with monotherapy. The median duration of clindamycin antibiotherapy was 6 weeks. The average follow-up was 45 months; one patient was lost to follow-up. Twenty-seven patients out of 33 (82%) were cured with clindamycin, compared to 9/12 (75%) with other antibiotics. The rate of favorable outcomes increased to 27/31 (87%) with clindamycin and to 9/10 (90%) for other antibiotics when no septic revision strategies were excluded (P = 1.00). Conclusions: The therapeutic strategy based on one- or two-stage revision associated with 6 weeks of clindamycin seems to be effective.

Published
2022
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14. Patients with community-acquired bacteremia of unknown origin: clinical characteristics and usefulness of microbiological results for therapeutic issues: a single-center cohort study

Author

Johan Courjon, Elisa Demonchy, Nicolas Degand, Karine Risso, Raymond Ruimy, and Pierre-Marie Roger

Subjects
Bacteremia, Empirical antibiotic treatment, Severe sepsis, Bacteremia of unknown origin, Antimicrobial resistance, Primary bacteremia, Therapeutics. Pharmacology, RM1-950, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

Abstract Bacteremia of unknown origin (BUO) are associated with increased mortality compared to those with identified sources. Microbiological data of those patients could help to characterize an appropriate empirical antibiotic treatment before bloodcultures results are available during sepsis of unknown origin. Based on the dashboard of our ward that prospectively records several parameters from each hospitalization, we report 101 community-acquired BUO selected among 1989 bacteremic patients from July 2005 to April 2016, BUO being defined by the absence of clinical and paraclinical infectious focus and no other microbiological samples retrieving the bacteria isolated from blood cultures. The in-hospital mortality rate was 9%. We retrospectively tested two antibiotic associations: amoxicillin–clavulanic acid + gentamicin (AMC/GM) and 3rd generation cephalosporin + gentamicin (3GC/GM) considered as active if the causative bacteria was susceptible to at least one of the two drugs. The mean age was 71 years with 67% of male, 31 (31%) were immunocompromised and 52 (51%) had severe sepsis. Eleven patients had polymicrobial infections. The leading bacterial species involved were Escherichia coli 25/115 (22%), group D Streptococci 12/115 (10%), viridans Streptococci 12/115 (10%) and Staphylococcus aureus 11/115 (9%). AMC/GM displayed a higher rate of effectiveness compared to 3GC/GM: 100/101 (99%) vs 94/101 (93%) (p = 0.04): one Enterococcus faecium strain impaired the first association, Bacteroides spp. and Enterococcus spp. the second. In case of community-acquired sepsis of unknown origin, AMC + GM should be considered.

Published
2017
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15. Virulence Analysis of Bacillus cereus Isolated after Death of Preterm Neonates, Nice, France, 2013

Author

Romain Lotte, Anne-Laure Hérissé, Yasmina Berrouane, Laurène Lotte, Florence Casagrande, Luce Landraud, Sabine Herbin, Nalini Ramarao, Laurent Boyer, and Raymond Ruimy

Subjects
Bacillus cereus, emerging pathogen, virulence, bacteria, environmental pathogen, neonates, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

After the deaths of 2 preterm neonates with Bacillus cereus systemic infection in the same intensive care unit, we investigated the pathogenic potential of this bacterium. Genetic and virulence analysis indicated the neonates were infected with 2 different strains with a virulence potential similar to environmental strains, indicating likely patient immune response failure.

Published
2017
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16. Seawater drowning-associated pneumonia: a 10-year descriptive cohort in intensive care unit

Author

Alexandre Robert, Pierre-Éric Danin, Hervé Quintard, Nicolas Degand, Nihal Martis, Denis Doyen, Céline Pulcini, Raymond Ruimy, Carole Ichai, Gilles Bernardin, and Jean Dellamonica

Subjects
Drowning, Seawater, Pneumonia, Antibiotic, Resistance, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Abstract Background Pneumonia is one of the major complications of drowning, but the optimal empirical antibiotic treatment is not clearly defined. Multidrug-resistant (MDR) bacteria and fungi have been identified in a recent series of freshwater drowning-associated pneumonia. However, microbial data in seawater drowning are scarce. The objective of the study is to describe the microorganisms isolated in early respiratory specimens obtained from seawater drowning-associated pneumonia and to provide their antibiotic susceptibility pattern. Methods All patients admitted for seawater drowning between 2003 and 2013 to two intensive care units, from the region in France with the highest drowning rate, were retrospectively included. Demographics, antimicrobial therapy and microbiological data from respiratory samples collected within the first 48 h after admittance were analyzed. Results Seventy-four drowned patients were included, of which 36 (49%) were diagnosed by the clinician as having early pneumonia. Concerning the overall population, the median simplified acute physiology score (version 2) was 45 (30–65), and the mortality was 26%. Twenty-four respiratory samples from different patients were obtained within the first 48 h. Sixteen were positive. The main microorganisms found were Enterobacteriaceae (Enterobacter spp., Klebsiella spp. and Escherichia coli) and Gram-positive aerobic cocci (Streptococcus pneumonia and Staphylococcus aureus) with a low rate of antimicrobial resistance. No MDR bacteria or fungi were identified. However, among the positive respiratory samples collected, 5/16 (31%) grew bacteria with natural resistance to amoxicillin–clavulanate, the first-line antibiotic commonly used in our cohort. Resistance was only found among Gram-negative bacteria and from respiratory samples of patients with a higher drowning grade at admission (p = 0.01). Conclusions This 10-year descriptive study, the largest cohort to date, provides early respiratory samples from seawater drowning patients. The microorganisms retrieved were either mostly part of the human oro-pharyngeal flora or Enterobacteriaceae and displayed low rates of antimicrobial resistance. Respiratory samples should nonetheless be collected at admittance to the ICU to avoid inappropriate treatment. Empiric use of cephalosporin could be restricted to severe patients or if Gram-negative bacilli are found after direct examination.

Published
2017
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17. Extensive Comparative Genomic Analysis of Enterococcus faecalis and Enterococcus faecium Reveals a Direct Association between the Absence of CRISPR–Cas Systems, the Presence of Anti-Endonuclease (ardA) and the Acquisition of Vancomycin Resistance in E. faecium

Author

Kodjovi D. Mlaga, Vincent Garcia, Philippe Colson, Raymond Ruimy, Jean-Marc Rolain, and Seydina M. Diene

Subjects
comparative genomics, E. faecalis, E. faecium, CRISPR–Cas, vancomycin resistance, recombinations, Biology (General), QH301-705.5
Abstract

Here, we performed a comparative genomic analysis of all available genomes of E. faecalis (n = 1591) and E. faecium (n = 1981) and investigated the association between the presence or absence of CRISPR-Cas systems, endonuclease/anti-endonuclease systems and the acquisition of antimicrobial resistance, especially vancomycin resistance genes. Most of the analysed Enterococci were isolated from humans and less than 14% of them were from foods and animals. We analysed and detected CRISPR–Cas systems in 75.36% of E. faecalis genomes and only 4.89% of E. faecium genomes with a significant difference (p-value < 10−5). We found a negative correlation between the number of CRISPR–Cas systems and genome size (r = −0.397, p-value < 10−5) and a positive correlation between the genome %GC content and the number of CRISPR–Cas systems (r = 0.215, p-value < 10−5). Our findings showed that the presence of the anti-endonuclease ardA gene may explain the decrease in the number of CRISPR–Cas systems in E. faecium, known to deactivate the endonucleases’ protective activities and enable the E. faecium genome to be versatile in acquiring mobile genetic elements, including carriers of antimicrobial resistance genes, especially vanB. Most importantly, we observed that there was a direct association between the absence of CRISPR–Cas, the presence of the anti-CRISPR ardA gene and the acquisition of vancomycin resistance genes.

Published
2021
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18. Bacillus cereus, a serious cause of nosocomial infections: Epidemiologic and genetic survey.

Author

Benjamin Glasset, Sabine Herbin, Sophie A Granier, Laurent Cavalié, Emilie Lafeuille, Cyprien Guérin, Raymond Ruimy, Florence Casagrande-Magne, Marion Levast, Nathalie Chautemps, Jean-Winoc Decousser, Laure Belotti, Isabelle Pelloux, Jerôme Robert, Anne Brisabois, and Nalini Ramarao

Subjects
Medicine, Science
Abstract

Bacillus cereus is the 2nd most frequent bacterial agent responsible for food-borne outbreaks in France and the 3rd in Europe. In addition, local and systemic infections have been reported, mainly describing individual cases or single hospital setting. The real incidence of such infection is unknown and information on genetic and phenotypic characteristics of the incriminated strains is generally scarce. We performed an extensive study of B. cereus strains isolated from patients and hospital environments from nine hospitals during a 5-year study, giving an overview of the consequences, sources and pathogenic patterns of B. cereus clinical infections. We demonstrated the occurrence of several hospital-cross-contaminations. Identical B. cereus strains were recovered from different patients and hospital environments for up to 2 years. We also clearly revealed the occurrence of inter hospital contaminations by the same strain. These cases represent the first documented events of nosocomial epidemy by B. cereus responsible for intra and inter hospitals contaminations. Indeed, contamination of different patients with the same strain of B. cereus was so far never shown. In addition, we propose a scheme for the characterization of B. cereus based on biochemical properties and genetic identification and highlight that main genetic signatures may carry a high pathogenic potential. Moreover, the characterization of antibiotic resistance shows an acquired resistance phenotype for rifampicin. This may provide indication to adjust the antibiotic treatment and care of patients.

Published
2018
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19. Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

Author

David M. Aanensen, Edward J. Feil, Matthew T. G. Holden, Janina Dordel, Corin A. Yeats, Artemij Fedosejev, Richard Goater, Santiago Castillo-Ramírez, Jukka Corander, Caroline Colijn, Monika A. Chlebowicz, Leo Schouls, Max Heck, Gerlinde Pluister, Raymond Ruimy, Gunnar Kahlmeter, Jenny Åhman, Erika Matuschek, Alexander W. Friedrich, Julian Parkhill, Stephen D. Bentley, Brian G. Spratt, and Hajo Grundmann

Subjects
Microbiology, QR1-502
Abstract

ABSTRACT The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools. IMPORTANCE The spread of antibiotic-resistant bacteria is a public health emergency of global concern, threatening medical intervention at every level of health care delivery. Several recent studies have demonstrated the promise of routine whole-genome sequencing (WGS) of bacterial pathogens for epidemiological surveillance, outbreak detection, and infection control. However, as this technology becomes more widely adopted, the key challenges of generating representative national and international data sets and the development of bioinformatic tools to manage and interpret the data become increasingly pertinent. This study provides a road map for the integration of WGS data into routine pathogen surveillance. We emphasize the importance of large-scale routine surveys to provide the population context for more targeted or localized investigation and the development of open-access bioinformatic tools to provide the means to combine and compare independently generated data with publicly available data sets.

Published
2016
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20. Clonal Comparison of Staphylococcus aureus Isolates from Healthy Pig Farmers, Human Controls, and Pigs

Author

Laurence Armand-Lefevre, Raymond Ruimy, and Antoine Andremont

Subjects
S. aureus, Pig farmers, MLST, Phylogenetic distribution, France, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

Pig farming is a risk factor for increased nasal Staphylococcus aureus colonization. Using sequence typing and phylogenetic comparisons, we showed that overcolonization of farmers was caused by a few bacterial strains that were not present in nonfarmers but often caused swine infections. This finding suggests a high rate of strain exchange between pigs and farmers.

Published
2005
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21. Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates.

Author

Sandra Moore, Berthe Miwanda, Adodo Yao Sadji, Hélène Thefenne, Fakhri Jeddi, Stanislas Rebaudet, Hilde de Boeck, Bawimodom Bidjada, Jean-Jacques Depina, Didier Bompangue, Aaron Aruna Abedi, Lamine Koivogui, Sakoba Keita, Eric Garnotel, Pierre-Denis Plisnier, Raymond Ruimy, Nicholas Thomson, Jean-Jacques Muyembe, and Renaud Piarroux

Subjects
Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract

BackgroundSince cholera appeared in Africa during the 1970s, cases have been reported on the continent every year. In Sub-Saharan Africa, cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa.Methodology/principal findingsIn this study, we applied MLVA (Multi-Locus Variable Number Tandem Repeat Analysis) typing of 337 Vibrio cholerae isolates from recent cholera epidemics in the Democratic Republic of the Congo (DRC), Zambia, Guinea and Togo. We aimed to assess the relationship between outbreaks. Applying this method, we identified 89 unique MLVA haplotypes across our isolate collection. MLVA typing revealed the short-term divergence and microevolution of these Vibrio cholerae populations to provide insight into the dynamics of cholera outbreaks in each country. Our analyses also revealed strong geographical clustering. Isolates from the African Great Lakes Region (DRC and Zambia) formed a closely related group, while West African isolates (Togo and Guinea) constituted a separate cluster. At a country-level scale our analyses revealed several distinct MLVA groups, most notably DRC 2011/2012, DRC 2009, Zambia 2012 and Guinea 2012. We also found that certain MLVA types collected in the DRC persisted in the country for several years, occasionally giving rise to expansive epidemics. Finally, we found that the six environmental isolates in our panel were unrelated to the epidemic isolates.Conclusions/significanceTo effectively combat the disease, it is critical to understand the mechanisms of cholera emergence and diffusion in a region-specific manner. Overall, these findings demonstrate the relationship between distinct epidemics in West Africa and the African Great Lakes Region. This study also highlights the importance of monitoring and analyzing Vibrio cholerae isolates.

Published
2015
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22. Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock

Author

Lance B. Price, Marc Stegger, Henrik Hasman, Maliha Aziz, Jesper Larsen, Paal Skytt Andersen, Talima Pearson, Andrew E. Waters, Jeffrey T. Foster, James Schupp, John Gillece, Elizabeth Driebe, Cindy M. Liu, Burkhard Springer, Irena Zdovc, Antonio Battisti, Alessia Franco, Jacek Żmudzki, Stefan Schwarz, Patrick Butaye, Eric Jouy, Constanca Pomba, M. Concepción Porrero, Raymond Ruimy, Tara C. Smith, D. Ashley Robinson, J. Scott Weese, Carmen Sofia Arriola, Fangyou Yu, Frederic Laurent, Paul Keim, Robert Skov, and Frank M. Aarestrup

Subjects
Microbiology, QR1-502
Published
2013
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23. Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock

Author

Lance B. Price, Marc Stegger, Henrik Hasman, Maliha Aziz, Jesper Larsen, Paal Skytt Andersen, Talima Pearson, Andrew E. Waters, Jeffrey T. Foster, James Schupp, John Gillece, Elizabeth Driebe, Cindy M. Liu, Burkhard Springer, Irena Zdovc, Antonio Battisti, Alessia Franco, Jacek Żmudzki, Stefan Schwarz, Patrick Butaye, Eric Jouy, Constanca Pomba, M. Concepción Porrero, Raymond Ruimy, Tara C. Smith, D. Ashley Robinson, J. Scott Weese, Carmen Sofia Arriola, Fangyou Yu, Frederic Laurent, Paul Keim, Robert Skov, and Frank M. Aarestrup

Subjects
Microbiology, QR1-502
Abstract

ABSTRACT Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n = 89), including MRSA and methicillin-susceptible S. aureus (MSSA) from animals and humans spanning 19 countries and four continents. We identified 4,238 single nucleotide polymorphisms (SNPs) among the 89 core genomes. Minimal homoplasy (consistency index = 0.9591) was detected among parsimony-informative SNPs, allowing for the generation of a highly accurate phylogenetic reconstruction of the CC398 clonal lineage. Phylogenetic analyses revealed that MSSA from humans formed the most ancestral clades. The most derived lineages were composed predominantly of livestock-associated MRSA possessing three different staphylococcal cassette chromosome mec element (SCCmec) types (IV, V, and VII-like) including nine subtypes. The human-associated isolates from the basal clades carried phages encoding human innate immune modulators that were largely missing among the livestock-associated isolates. Our results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA. The lineage appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance. Further analyses are required to estimate the number of independent genetic events leading to the methicillin-resistant sublineages, but the diversity of SCCmec subtypes is suggestive of strong and diverse antimicrobial selection associated with food animal production. IMPORTANCE Modern food animal production is characterized by densely concentrated animals and routine antibiotic use, which may facilitate the emergence of novel antibiotic-resistant zoonotic pathogens. Our findings strongly support the idea that livestock-associated MRSA CC398 originated as MSSA in humans. The jump of CC398 from humans to livestock was accompanied by the loss of phage-carried human virulence genes, which likely attenuated its zoonotic potential, but it was also accompanied by the acquisition of tetracycline and methicillin resistance. Our findings exemplify a bidirectional zoonotic exchange and underscore the potential public health risks of widespread antibiotic use in food animal production.

Published
2012
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24. Porphyromonas gingivalis participates in pathogenesis of human abdominal aortic aneurysm by neutrophil activation. Proof of concept in rats.

Author

Sandrine Delbosc, Jean-Marc Alsac, Clement Journe, Liliane Louedec, Yves Castier, Martine Bonnaure-Mallet, Raymond Ruimy, Patrick Rossignol, Philippe Bouchard, Jean-Baptiste Michel, and Olivier Meilhac

Subjects
Medicine, Science
Abstract

BACKGROUND: Abdominal Aortic Aneurysms (AAAs) represent a particular form of atherothrombosis where neutrophil proteolytic activity plays a major role. We postulated that neutrophil recruitment and activation participating in AAA growth may originate in part from repeated episodes of periodontal bacteremia. METHODS AND FINDINGS: Our results show that neutrophil activation in human AAA was associated with Neutrophil Extracellular Trap (NET) formation in the IntraLuminal Thrombus, leading to the release of cell-free DNA. Human AAA samples were shown to contain bacterial DNA with high frequency (11/16), and in particular that of Porphyromonas gingivalis (Pg), the most prevalent pathogen involved in chronic periodontitis, a common form of periodontal disease. Both DNA reflecting the presence of NETs and antibodies to Pg were found to be increased in plasma of patients with AAA. Using a rat model of AAA, we demonstrated that repeated injection of Pg fostered aneurysm development, associated with pathological characteristics similar to those observed in humans, such as the persistence of a neutrophil-rich luminal thrombus, not observed in saline-injected rats in which a healing process was observed. CONCLUSIONS: Thus, the control of periodontal disease may represent a therapeutic target to limit human AAA progression.

Published
2011
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25. Ingestion ofBacillus cereusspores dampens the immune response to favor bacterial persistence

Author

Salma Hachfi, Alexandra Brun-Barale, Patrick Munro, Marie-Paule Nawrot-Esposito, Gregory Michel, Arnaud Fichant, Mathilde Bonis, Raymond Ruimy, Laurent Boyer, and Armel Gallet

Abstract

SUMMARYSpores are considered as dormant entities highly resistant to extreme conditions. Among them,Bacillus cereusspores are commonly associated with foodborne outbreaks. Nevertheless, the pathological processes associated with spore ingestion and germination remain poorly understood. Here, we show that while ingestion of vegetative bacteria leads to their elimination from the midgut and small intestines ofDrosophilaand mice, respectively, a single ingestion of spores leads to the persistence of bacteria for at least 10 days. UsingDrosophilagenetics, we demonstrate that spores escape the innate immune response of the anterior midgut. Once in the posterior midgut, spores germinate, and the vegetative cells dampen the immune signaling through the induction of amidases which are negative regulators of the immune response. This study provides evidence for howB. cereusspores hijack the intestinal immune defenses allowing the localized birth of vegetative bacteria responsible for the digestive symptoms associated with foodborne illness outbreaks.

Published
2023
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26. Real-world evaluation of ceftolozane/tazobactam therapy and clinical outcomes in France

Author

D. Boutoille, Carole Mackosso, Brune Akrich, Anna Amode, Bernard Castan, Joy Mootien, Raymond Ruimy, Fabrice Ruiz, Anne Berthelot, Lucie Mathis, Jean-François Timsit, and Laurie Levy-Bachelot

Subjects
Adult, Male, Tazobactam, medicine.medical_specialty, medicine.drug_class, Antibiotics, Internal medicine, Humans, Medicine, Pseudomonas Infections, Prospective Studies, Medical prescription, Risk factor, Prospective cohort study, business.industry, Middle Aged, medicine.disease, Cephalosporins, Pneumonia, Infectious Diseases, Concomitant, Pseudomonas aeruginosa, Ceftolozane, business, medicine.drug
Abstract

Objectives To describe the real-world clinical use of ceftolozane/tazobactam (C/T) and associated outcomes in France. Patients and methods Multicenter, prospective cohort study conducted in 22 hospitals. All adult patients who received at least one dose of C/T were asked to participate (2018-2019). Patients were treated according to standard hospital practice and followed up until C/T stop. Results At the time of the analysis, 84 patients were evaluated. The median age was 64.8 years, and 67.9% (57/84) of patients were males. Fifty-seven patients (57/82, 69.5%) had one or more risk factors for multidrug-resistant (MDR) infections (missing MDR risk factor data for two patients). Most patients were critically ill and had several comorbidities. A majority (59/84, 70.2%) of patients had nosocomial infections. Half of all patients (n = 42) had a diagnosis of pneumonia, of which 69% (29/42) were hospital acquired. Overall, 90.5% (76/84) of patients had MDR bacteria. Pseudomonas aeruginosa was the most frequently isolated bacterium (71/80, 88.8%), including 93% (80/86) of C/T-susceptible strains. C/T was prescribed as the first-line treatment to 29.8% (25/84) of patients. A concomitant antibiotic treatment was prescribed to 48.8% (41/84) of patients, of whom 65.9% (27/41) were prescribed concomitant antibiotics at the same time as C/T initiation. Empirical C/T prescription was microbiologically appropriate in 11/16 patients after susceptibility testing. Most patients (44/72, 61.1%) were cured and four (4/72, 5.6%) deaths were reported. Conclusions The results showed that C/T was most frequently prescribed for documented cases of P. aeruginosa infections. Most outcomes were positive, including among pneumonia patients.

Published
2021
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28. 24/7 workflow for bloodstream infection diagnostics in microbiology laboratories: the first step to improve clinical management

Author

David Chirio, Elisa Demonchy, Marion Le Marechal, Alice Gaudart, Romain Lotte, Michel Carles, and Raymond Ruimy

Subjects
Sepsis, Biochemistry (medical), Clinical Biochemistry, Humans, Bacteremia, General Medicine, Laboratories, Workflow, Retrospective Studies, Anti-Bacterial Agents
Abstract

Objectives We aimed to evaluate the impact of an uninterrupted workflow regarding blood cultures on turnaround time and antibiotic prescription. Methods Monomicrobial episodes of bacteremia were retrospectively evaluated before and after a continuous 24/7 workflow was implemented in our clinical microbiology laboratory (pre- and post-intervention periods; PREIP and POSTIP). Primary outcome was the time from specimen collection to the first change in antibiotic therapy. Secondary outcomes included the time from specimen collection to effective antibiotic therapy and to antibiotic susceptibility testing results (or turnaround time), as well as hospital length of stay and all-cause mortality at 30 days. Results A total of 548 episodes of bacteremia were included in the final analysis. There was no difference in PREIP and POSTIP regarding patient characteristics and causative bacteria. In POSTIP, the mean time to the first change in antibiotic therapy was reduced by 10.4 h (p Conclusions Around the clock processing of blood cultures allows for a reduction in turnaround time, which in turn reduces the delay until effective antibiotic therapy prescription.

Published
2022

29. Massive analysis of 64,628 bacterial genomes to decipher water reservoir and origin of mobile colistin resistance genes: is there another role for these enzymes?

Author

Didier Raoult, Toilhata Riziki, Sophie Alexandra Baron, Seydina M. Diene, Mariem Ben Khedher, Jean-Marc Rolain, Raymond Ruimy, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - Faculté de pharmacie (AMU PHARM), Aix Marseille Université (AMU), and Centre Hospitalier Universitaire de Nice (CHU Nice)

Subjects
0301 basic medicine, 030106 microbiology, Antimicrobial peptides, lcsh:Medicine, Microbial communities, Bacterial genome size, medicine.disease_cause, Microbiology, Article, Bacteriophage, 03 medical and health sciences, Bacterial Proteins, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Bacterial, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:Science, Gene, Escherichia coli, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, chemistry.chemical_classification, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, biology, Bacteria, Whole Genome Sequencing, Animal Sources, Colistin, lcsh:R, Water, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, 030104 developmental biology, Enzyme, chemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Molecular evolution, lcsh:Q, Genome, Bacterial, hormones, hormone substitutes, and hormone antagonists
Abstract

Since 2015, new worrying colistin resistance mechanism, mediated by mcr-1 gene has been reported worldwide along with eight newly described variants but their source(s) and reservoir(s) remain largely unexplored. Here, we conducted a massive bioinformatic analysis of bacterial genomes to investigate the reservoir and origin of mcr variants. We identified 13’658 MCR-1 homologous sequences in 494 bacterial genera. Moreover, analysis of 64’628 bacterial genomes (60 bacterial genera and 1’047 species) allows identifying a total of 6’651 significant positive hits (coverage >90% and similarity >50%) with the nine MCR variants from 39 bacterial genera and more than 1’050 species. A high number of MCR-1 was identified in Escherichia coli (n = 862). Interestingly, while almost all variants were identified in bacteria from different sources (i.e. human, animal, and environment), the last variant, MCR-9, was exclusively detected in bacteria from human. Although these variants could be identified in bacteria from human and animal sources, we found plenty MCR variants in unsuspected bacteria from environmental origin, especially from water sources. The ubiquitous presence of mcr variants in bacteria from water likely suggests another role in the biosphere of these enzymes as an unknown defense system against natural antimicrobial peptides and/or bacteriophage predation.

Published
2020
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30. Carbapenem heteroresistance of KPC-producing Klebsiella pneumoniae results from tolerance, persistence and resistance

Author

Adriana Chiarelli, Nicolas Cabanel, Isabelle Rosinski-Chupin, Thomas Obadia, Raymond Ruimy, Thierry Naas, Rémy A. Bonnin, and Philippe Glaser

Abstract

Carbapenemase-producing Klebsiella pneumoniae (CPKp) have disseminated globally and represent a major threat in hospitals with few therapeutic options and high mortality rates. Isolates producing the carbapenemase KPC (KPC-Kp) might be classified as susceptible according to clinical breakpoints by antibiotic susceptibility testing (AST), allowing the use of imipenem or meropenem for treatment of infections. However, some KPC-Kp show heteroresistance (HR) to carbapenems, with colonies growing in the inhibition halo of agar-based AST. HR KPC-Kp have been associated with a higher risk of treatment failure. Here, we characterized the diversity of mechanisms behind HR to imipenem of these isolates. By analyzing a diverse collection of CPKp, we showed that HR is frequent among KPC-Kp. By monitoring single HR colony appearance using the ScanLag setup, we discriminated surviving cells in two subpopulations leading to a Gaussian-like distribution of early-appearing colonies, with a delayed emergence compared to colonies arising in the absence of antibiotics, and a long tail of late-appearing colonies. A subset of colonies showed a reduced growth rate. Characterization of surviving populations by AST and whole-genome sequencing of 333 colonies revealed a majority of parental genotypes and a broad landscape of genetic alterations in 28% of the colonies, including gene loss, DNA amplification and point mutations. This unveils the complexity of imipenem HR among KPC-Kp isolates, which involves tolerant and persistent cells, but also resistant bacteria. These observations contribute to a better understanding of reasons behind carbapenem treatment failure of KPC-Kp isolates.IMPORTANCEThe ability of a bacterium to defeat antibiotics not only depends upon resistance, but also on tolerance and persistence, which allow a bacterial population to temporarily survive high drug doses. Carbapenems are antibiotics of last resort and Klebsiella pneumoniae isolates producing the carbapenemase KPC are a threat to hospitals, although they might remain susceptible to carbapenems. However, seemingly homogeneous populations of KPC-K. pneumoniae isolates frequently show varying degrees of susceptibility to carbapenem, i.e., a phenomenon called heteroresistance. We characterized bacteria surviving a high dose of imipenem, progressively degraded by the released carbapenemase, by monitoring the growth of the resulting colonies using the ScanLag system, their genome sequence and carbapenem susceptibility. We show that the observed phenotypic diversity combines tolerance, persistence and resistance making the treatment with high doses of carbapenems frequently inefficient.

Published
2022
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31. Bacillus cereus Invasive Infections in Preterm Neonates: an Up-to-Date Review of the Literature

Author

Romain Lotte, Alicia Chevalier, Laurent Boyer, and Raymond Ruimy

Subjects
Microbiology (medical), General Immunology and Microbiology, Epidemiology, fungi, Infant, Newborn, Public Health, Environmental and Occupational Health, Review, Foodborne Diseases, Infectious Diseases, Bacillus cereus, Bacillus anthracis, Humans, Gram-Positive Bacterial Infections, Infant, Premature, Phylogeny
Abstract

Bacillus cereus group species are widespread, Gram-positive, spore-forming environmental bacteria. B. cereus sensu stricto is one of the major causes of food poisoning worldwide. In high-risk individuals, such as preterm neonates, B. cereus infections can cause fatal infections. It is important to note that the phenotypic identification methods commonly used in clinical microbiology laboratories make no distinction between B. cereus sensu stricto and the other members of the group (Bacillus anthracis excluded). As a result, all the invasive infections attributed to B. cereus are not necessarily due to B. cereus sensu stricto but likely to other closely related species of the B. cereus group. Next-generation sequencing (NGS) should be used to characterize the whole genome of the strains belonging to the B. cereus group. This could confirm whether the strains involved in previously reported B. cereus invasive infections preferentially belong to formerly known or emerging individual species. Moreover, infections related to B. cereus group species have probably been overlooked, since their isolation in human bacteriological samples has for a long time been regarded as an environmental contaminant of the cultures. Recent studies have questioned the emergence or reemergence of B. cereus invasive infections in preterm infants. This review reports our current understanding of B. cereus infections in neonates, including taxonomical updates, microbiological characteristics, bacterial identification, clinical features, host-pathogen interactions, environmental sources of contamination, and antimicrobial resistance.

Published
2022
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32. Clindamycin Efficacy for

Author

Audrey, Courdurié, Romain, Lotte, Raymond, Ruimy, Vincent, Cauhape, Michel, Carles, Marc-Olivier, Gauci, Pascal, Boileau, and Johan, Courjon

Abstract

Clindamycin is an antibiotic with high bioavailability and appropriate bone diffusion, often proposed as an alternative in guidelines forA retrospective analysis was conducted at the University Hospital of Nice (France) between 2010 and 2019. We included patients with one shoulder implant surgical procedure and at least oneForty-eight SIJI were identified and 33 were treated with clindamycin, among which 25 were treated with monotherapy. The median duration of clindamycin antibiotherapy was 6 weeks. The average follow-up was 45 months; one patient was lost to follow-up. Twenty-seven patients out of 33 (82%) were cured with clindamycin, compared to 9/12 (75%) with other antibiotics. The rate of favorable outcomes increased to 27/31 (87%) with clindamycin and to 9/10 (90%) for other antibiotics when no septic revision strategies were excluded (The therapeutic strategy based on one- or two-stage revision associated with 6 weeks of clindamycin seems to be effective.

Published
2022

33. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies

Author

Jean-Marc Rolain, Mariem Ben khedher, Kais Ghedira, Olivier Croce, Raymond Ruimy, Centre Hospitalier Universitaire de Nice (CHU Nice), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre méditerranéen de médecine moléculaire (C3M), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), This research was funded by the French government through the CNRS and the UCAJEDI Investments in the Future project managed by the National Research Agency (ANR), with the reference number ANR-15-IDEX-01., ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Ben Hassine, AbdelHakim, and Idex UCA JEDI - - UCA JEDI2015 - ANR-15-IDEX-0001 - IDEX - VALID

Subjects
QH301-705.5, [SDV]Life Sciences [q-bio], whole-genome sequencing (WGS), Catalysis, Inorganic Chemistry, transcriptomics, genomics, Animals, Humans, Physical and Theoretical Chemistry, Biology (General), Molecular Biology, QD1-999, Spectroscopy, Molecular Epidemiology, metagenomics, metatranscriptomics, Bacteria, Whole Genome Sequencing, Organic Chemistry, Computational Biology, High-Throughput Nucleotide Sequencing, General Medicine, Computer Science Applications, bacterial genomes, [SDV] Life Sciences [q-bio], Chemistry, long-read sequencing, next-generation sequencing, Genome, Bacterial
Abstract

International audience; Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.

Published
2022
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34. Complete Circular Genome Sequences of Three Bacillus cereus Group Strains Isolated from Positive Blood Cultures from Preterm and Immunocompromised Infants Hospitalized in France

Author

Laurent Boyer, Florence Fenollar, Armel Gallet, Alicia Chevalier, Mariem Ben Khedher, Olivier Croce, Grégory Dubourg, Florence Casagrande, Fredrik Nindo, Jean-Marc Rolain, Romain Lotte, Raymond Ruimy, Stéphane Bonacorsi, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Aix Marseille Université (AMU), Hôpital Archet 2 [Nice] (CHU), Centre méditerranéen de médecine moléculaire (C3M), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Hôpital Robert Debré, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Université Côte d'Azur (UCA), Institut Sophia Agrobiotech (ISA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Fondation Mediterranee Infection, Marseille, France, ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Gallet, Armel, and Idex UCA JEDI - - UCA JEDI2015 - ANR-15-IDEX-0001 - IDEX - VALID

Subjects
0303 health sciences, 030306 microbiology, Genome Sequences, Bacillus cereus, Biology, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genome, 3. Good health, Microbiology, 03 medical and health sciences, Immunology and Microbiology (miscellaneous), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Intensive care, Minion, Genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Nanopore sequencing, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Biology, 030304 developmental biology
Abstract

We report here the complete genome sequences of three Bacillus cereus group strains isolated from blood cultures from premature and immunocompromised infants hospitalized in intensive care units in three French hospitals. These complete genome sequences were obtained from a combination of Illumina HiSeq X Ten short reads and Oxford Nanopore MinION long reads.

Published
2021
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35. Time to blood culture positivity: An independent predictor of infective endocarditis and mortality in patients with Staphylococcus aureus bacteraemia

Author

V. Le Moing, Sandrine Barbas, Elodie Curlier, Hélène Jean-Pierre, Willem Vanwamel, Damien Fournier, Isabelle Patry, Eric Bellissant, Jacques Reynes, Sandrine Gohier-Treuvelot, François Alla, Catherine Chirouze, Fabienne Le Gac, Catherine Neuwirth, Philippe Géraud, François Goehringer, Christine Selton-Suty, Bruno Hoen, Virginie Sussmuth, Christine Delonca, Nathalie Keil, Catherine Sportouch, Thanh Doco-Lecompte, S. Tubiana, F. Vandenesch, Laetitia Minary, S. Desage, Catherine Leport, Hepher Malela, Cécile Descottes-Genon, Lionel Piroth, Christian Michelet, Pascale Rausch, Matthieu Revest, Bernard Iung, Jerome Etienne, Albert Sotto, Vincent Le Moing, J.-P. Lavigne, Catherine Cornu, Fernando Rivadeneira, Elise Thebault, Nathalie Bedos, Pierre-Yves Donnio, Lucie Vettoretti, Michèle Bes, S. Siméon, Jean-Christophe Eicher, Catherine Lechiche, X. Duval, François Vandenesch, Marie Célard, Pascal Chavanet, Sarah Tubiana, Raymond Ruimy, M.-L. Erpelding, Thierry May, André Pechinot, Nejla Aissa, Emila Ilic Habensus, François Delahaye, C.-A. Gustave, Lorraine Letranchant, Taissia Lelekov-Boissard, C. Chirouze, Anne Tristan, Audrey Coma, Jean-Philippe Lavigne, Xavier Duval, Pierre Tattevin, Alex van Belkum, Pierre Braquet, Marie-Line Erpelding, Pascale Longuet, Malika Hadid, Marie-Christine Greusard, Florence Galtier, Anne Verchère, P. Tattevin, Service des maladies infectieuses et réanimation médicale [Rennes] = Infectious Disease and Intensive Care [Rennes], CHU Pontchaillou [Rennes], Maladies Infectieuses [CHU de Montpellier], Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), CIC1425 Bichat [AP-HP Hôpital Bichat - Claude Bernard] (INSERM), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Bactériologie [CHRU Besançon], Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Virulence bactérienne et maladies infectieuses (VBMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Service de Microbiologie [CHU Caremeau, Nîmes], Hôpital Universitaire Carémeau [Nîmes] (CHU Nîmes), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Centre d'investigation clinique [Nancy] (CIC), Université de Lorraine (UL)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de référence des Staphylocoques [HCL, Lyon] (Institut des Agents Infectieux), Hospices Civils de Lyon (HCL), Laboratoire de Bactériologie [HCL, Lyon] (Institut des Agents Infectieux), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), ARN régulateurs bactériens et médecine (BRM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), VIRSTA/AEPEI Study Group. Chirouze C, Curlier E, Descottes-Genon C, Hoen B, Patry I, Vettoretti L, Chavanet P, Eicher JC, Gohier-Treuvelot S, Greusard MC, Neuwirth C, Péchinot A, Piroth L, Célard M, Cornu C, Delahaye F, Hadid M, Rausch P, Coma A, Galtier F, Géraud P, Jean-Pierre H, Le Moing V, Sportouch C, Reynes J, Aissa N, Doco-Lecompte T, Goehringer F, Keil N, Letranchant L, Malela H, May T, Selton-Suty C, Bedos N, Lavigne JP, Lechiche C, Sotto A, Duval X, Habensus EI, Iung B, Leport C, Longuet P, Ruimy R, Bellissant E, Donnio PY, Le Gac F, Michelet C, Revest M, Tattevin P, Thebault E, Alla F, Braquet P, Erpelding ML, Minary L, Tubiana S, Bès M, Etienne J, Lelekov-Boissard T, Tristan A, Vandenesch F, Van Belkum A, Rivadeneira F, Vanwamel W, Barbas S, Delonca C, Sussmuth V, Verchère A., Service des maladies infectieuses et réanimation médicale, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon), CHU Caremeau, Nîmes, CIC-Nancy, Institut Lorrain du Coeur et des Vaisseaux Louis Mathieu [Nancy]-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), CIC Hôpital Bichat, Institut National de la Santé et de la Recherche Médicale (INSERM)-UFR de Médecine-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Modèles et méthodes de l'évaluation thérapeutique des maladies chroniques (U738 / UMR_S738), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), service de maladies infectieuses CHU J Minjoz Besancon, Hôpital Jean Minjoz, Centre National de référence des Staphylocoques, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL), Service des Maladies Infectieuses et Tropicales [Point-à-Pitre, Guadeloupe], CHU Pointe-à-Pitre/Abymes [Guadeloupe], Centre d'Investigation Clinique Antilles-Guyane (CIC - Antilles Guyane), Université des Antilles et de la Guyane (UAG)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de Fort de France-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Service de Cardiologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Biologie Laboratoire de Bacteriologie, Laboratoire de Microbiologie Médicale et Moléculaire, Université de Bourgogne (UB), Département d'infectiologie (CHU de Dijon), Evaluation et modélisation des effets thérapeutiques, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), REseau national d'Investigation clinique en VACcinologie (REIVAC), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP]-Hôtel-Dieu-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de Gestion des Essais de Produits de Santé (CeNGEPS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Département Maladies Infectieuses et Tropicales, Hôpital Universitaire, Montpellier, France, Service de Bactériologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service des Maladies Infectieuses et Tropicales [CHRU Nancy], Service de Cardiologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nîmes (CHRU Nîmes), Laboratoire universitaire d'antibiologie, Université Montpellier 1 (UM1), CIC - CHU Bichat, Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Bichat - Claude Bernard, Centre d'Investigation Clinique [Rennes] (CIC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Hôpital Pontchaillou-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiologie : Risques Infectieux, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-Faculté de Chirurgie Dentaire de Rennes-Faculté d'Odontologie-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Service des maladies infectieuses, Maladies chroniques, santé perçue, et processus d'adaptation (APEMAC), Université de Lorraine (UL), CHU Montpellier, Service d'Epidémiologie et Evaluations Cliniques [CHRU Nancy] (Pôle S2R), Centre National de Reference des Staphylocoques, Université de Lyon, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Laboratoire Chrono-environnement (UMR 6249) (LCE), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Jonchère, Laurent

Subjects
Male, Methicillin-Resistant Staphylococcus aureus, 0301 basic medicine, Microbiology (medical), Staphylococcus aureus, bacteraemia, medicine.medical_specialty, Time Factors, Multivariate analysis, 030106 microbiology, Bacteremia, Independent predictor, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Interquartile range, hemic and lymphatic diseases, Internal medicine, medicine, Humans, Blood culture, Prospective Studies, 030212 general & internal medicine, time to blood culture positivity, Prospective cohort study, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Aged, medicine.diagnostic_test, infective endocarditis, business.industry, Endocarditis, Bacterial, General Medicine, Middle Aged, Staphylococcal Infections, respiratory system, medicine.disease, mortality, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Quartile, Blood Culture, Infective endocarditis, Female, business, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; Objectives - Time to blood culture positivity (TTP), a routinely available parameter in automated blood culture systems, may be a proxy for infectious burden in patients with bloodstream infections. We aimed to study the association between TTP and infective endocarditis (IE), or death, in patients with Staphylococcus aureus bacteraemia. Methods - VIRSTA is a multicenter prospective cohort study that included all adult patients with S. aureus bacteraemia in eight university hospitals in France (2009-2011). We analyzed data from four centers which collected data on TTP. Regression models were used to study the association between TTP and definite IE (Duke-Li criteria), and 30 day-mortality. Results - We included 587 patients with S. aureus bacteraemia: mean age was 65.3±16.3 years, 420/587 patients (71.6%) were male, 121/587 (20.6%) died, and 42/587 (7.2%) had definite IE. Median TTP of first positive blood culture was 13.7 h (interquartile range, 9.9-18). On multivariate analysis, 30-day mortality was associated with TTP≤13.7 h (74/295 (25.1%) vs 47/292 (16.1%), P=0.02), as well as old age, McCabe score, methicillin resistance, stroke, pneumonia, and C-Reactive Protein. TTP was also independently associated with IE, but with a U-shape curve: IE was more common in the first (TTP18 h, 8/146, 5.5%) quartiles of TTP, P=0.002. Conclusions - TTP provides reliable information in patients with S. aureus bacteraemia, on the risk of IE, and prognosis, with short TTP being an independent predictor of death. This data readily available at no cost may be used to identify patients who require specific attention.

Published
2019
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36. Genomic analysis of CTX-M-115 and OXA-23/-72 co-producing Acinetobacter baumannii, and their potential to spread resistance genes by natural transformation

Author

Jean-Baptiste Vuillemenot, Maxime Bour, Racha Beyrouthy, Richard Bonnet, Maria-Halima Laaberki, Xavier Charpentier, Raymond Ruimy, Patrick Plésiat, Anaïs Potron, Centre National de Référence de la Résistance aux Antibiotiques (CNR), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Centre National de Référence de la Résistance aux Antibiotiques [CHU Clermont-Ferrand] (CNR), CHU Clermont-Ferrand, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), and Sante publique France agency

Subjects
Pharmacology, Microbiology (medical), Acinetobacter baumannii, Genomics, Microbial Sensitivity Tests, beta-Lactamases, Anti-Bacterial Agents, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Aminoglycosides, Bacterial Proteins, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Humans, Pharmacology (medical), Acinetobacter Infections, Multilocus Sequence Typing
Abstract

Objectives To characterize Acinetobacter baumannii strains co-producing the ESBL CTX-M-115 and carbapenem-hydrolysing class D β-lactamases (CHDLs), and to assess the potential diffusion of their resistance genes by horizontal transfer. Methods Nineteen CTX-M-115/CHDL-positive A. baumannii were collected between 2015 and 2019 from patients hospitalized in France. Their whole-genome sequences were determined on Illumina and Oxford Nanopore platforms and were compared through core-genome MLST (cgMLST) and SNP analyses. Transferability of resistance genes was investigated by natural transformation assays. Results Eighteen strains were found to harbour CHDL OXA-72, and another one CHDL OXA-23, in addition to CTX-M-115, narrow-spectrum β-lactamases and aminoglycoside resistance determinants including ArmA. cgMLST typing, as well as Oxford Scheme ST and K locus typing, confirmed that 17 out of the 18 CTX-M-115/OXA-72 isolates belonged to new subclades within clonal complex 78 (CC78). The chromosomal region carrying the blaCTX-M-115 gene appeared to vary greatly both in gene content and in length (from 20 to 79 kb) among the strains, likely because of IS26-mediated DNA rearrangements. The blaOXA-72 gene was localized on closely related plasmids showing structural variations that occurred between pdif sites. Transfer of all the β-lactamase genes, as well as aminoglycoside resistance determinants to a drug-susceptible A. baumannii recipient, was easily obtained in vitro by natural transformation. Conclusions This work highlights the propensity of CC78 isolates to collect multiple antibiotic resistance genes, to rearrange and to pass them to other A. baumannii strains via natural transformation. This process, along with mobile genetic elements, likely contributes to the considerable genomic plasticity of clinical strains, and to the diversity of molecular mechanisms sustaining their multidrug resistance.

Published
2021
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37. Case Report: A New Mycobacterium ulcerans Genotype Causing Buruli Ulcer in Côte d’Ivoire

Author

Michel Drancourt, Yoan Di Filippo, Nassim Hammoudi, Jamal Saad, Philippe Bahadoran, Alice Gaudart, Raymond Ruimy, Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Bactériologie [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice)-Hôpital Archet 2 [Nice] (CHU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre Hospitalier Universitaire de Nice (CHU Nice), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and ANR-17-CE35-0006,PRIME,PRédire la niche écologique de souches Infectieuses de pathogènes humains comme un facteur déterminant dans l'éMErgence des maladies infectieuses(2017)

Subjects
Buruli ulcer, 030231 tropical medicine, Cote d ivoire, 03 medical and health sciences, Opportunistic pathogen, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Genotype, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, skin and connective tissue diseases, Whole genome sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Articles, biology.organism_classification, medicine.disease, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Infectious Diseases, Mycobacterium ulcerans, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Parasitology, Rural population
Abstract

Mycobacterium ulcerans, the opportunistic pathogen causing Buruli ulcer, is reported to affect rural populations in 36 tropical countries. We report one case of Buruli ulcer in a peri-urban area in Côte d’Ivoire, confirmed by whole genome sequencing which indicated a M. ulcerans genotype previously unreported in Côte d’Ivoire.

Published
2021
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38. Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice

Author

Alexandre Gallerand, Arnaud Jacquel, Pedro Henrique Viana Saavedra, Cedric Torre, Paul Chaintreuil, Sandrine Marchetti, Alissa Majoor, Mohamed Lamkanfi, Raymond Ruimy, Céline Loubatier, Amaury Rey, Anne Doye, Laurent Boyer, Benedicte F. Py, Grégory Michel, Johan Courjon, Rodolphe Guinamard, Patrick Munro, Dorota Czerucka, Orane Visvikis, Océane Dufies, Els Verhoeyen, Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice (CHU Nice), Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre Scientifique de Monaco (CSM), Laboratoire International Associé Réponse des Organismes et Populations face au Stress Environnemental - Université Côte d’Azur - Centre Scientifique de Monaco (LIA ROPSE), Université Côte d’Azur - Centre Scientifique de Monaco, Université Nice Sophia Antipolis (1965 - 2019) (UNS), Universiteit Gent = Ghent University (UGENT), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE15-0001,AVI,Identification de l'inflammasome impliqué dans l'Immunité Anti-Virulence: Impact sur notre façon de combattre la bactériémie(2017), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Guinamard, Rodolphe

Subjects
Microbiology (medical), Inflammasomes, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Immunology, Bacterial Toxins, Bacteremia, GTPase, Applied Microbiology and Biotechnology, Microbiology, Article, 03 medical and health sciences, Mice, PAK1, NLR Family, Pyrin Domain-Containing 3 Protein, Genetics, medicine, Escherichia coli, Animals, Phosphorylation, p21-activated kinases, Escherichia coli Infections, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, integumentary system, 030306 microbiology, Chemistry, Kinase, Escherichia coli Proteins, Pyroptosis, Pattern recognition receptor, Inflammasome, Cell Biology, Bacterial Load, Immunity, Innate, 3. Good health, Cell biology, rac GTP-Binding Proteins, [SDV] Life Sciences [q-bio], Cytokine, p21-Activated Kinases, medicine.drug, Signal Transduction
Abstract

Inflammasomes are signalling platforms that are assembled in response to infection or sterile inflammation by cytosolic pattern recognition receptors. The consequent inflammasome-triggered caspase-1 activation is critical for the host defence against pathogens. During infection, NLRP3, which is a pattern recognition receptor that is also known as cryopyrin, triggers the assembly of the inflammasome-activating caspase-1 through the recruitment of ASC and Nek7. The activation of the NLRP3 inflammasome is tightly controlled both transcriptionally and post-translationally. Despite the importance of the NLRP3 inflammasome regulation in autoinflammatory and infectious diseases, little is known about the mechanism controlling the activation of NLRP3 and the upstream signalling that regulates the NLRP3 inflammasome assembly. We have previously shown that the Rho-GTPase-activating toxin from Escherichia coli cytotoxic necrotizing factor-1 (CNF1) activates caspase-1, but the upstream mechanism is unclear. Here, we provide evidence of the role of the NLRP3 inflammasome in sensing the activity of bacterial toxins and virulence factors that activate host Rho GTPases. We demonstrate that this activation relies on the monitoring of the toxin’s activity on the Rho GTPase Rac2. We also show that the NLRP3 inflammasome is activated by a signalling cascade that involves the p21-activated kinases 1 and 2 (Pak1/2) and the Pak1-mediated phosphorylation of Thr 659 of NLRP3, which is necessary for the NLRP3–Nek7 interaction, inflammasome activation and IL-1β cytokine maturation. Furthermore, inhibition of the Pak–NLRP3 axis decreases the bacterial clearance of CNF1-expressing UTI89 E. coli during bacteraemia in mice. Taken together, our results establish that Pak1 and Pak2 are critical regulators of the NLRP3 inflammasome and reveal the role of the Pak–NLRP3 signalling axis in vivo during bacteraemia in mice. Here, the authors present the upstream pathway that controls the activation of the NLRP3 inflammasome during bacteraemia. The CNF1 toxin from Escherichia coli activates the Rho GTPase Rac2 and its activity is sensed by NLRP3, which is activated by a signalling cascade involving p21-activated kinases 1 and 2.

Published
2021
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39. A Population Pharmacokinetic Analysis of Continuous Infusion of Cloxacillin during Staphylococcus aureus Bone and Joint Infections

Author

François Jehl, Christophe Trojani, David Chirio, Jean-Luc Raynier, Mikaël Chelli, Johan Courjon, Sylvain Goutelle, Pierre-Marie Roger, Thibaud Lavrut, Elisa Demonchy, Antoine Grillon, Raymond Ruimy, Laura Cabane, Margaux Garzaro, Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë, and Université de Strasbourg (UNISTRA)

Subjects
Pharmacology, 0303 health sciences, education.field_of_study, 030306 microbiology, business.industry, Population, Liter, [SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences, 030226 pharmacology & pharmacy, Crossover study, 3. Good health, Penicillin, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, Cloxacillin, Pharmacokinetics, Pharmacodynamics, Anesthesia, medicine, Pharmacology (medical), Dosing, education, business, medicine.drug
Abstract

Intravenous administration of antibiotics is recommended during the early phase of methicillin-susceptible S. aureus (MSSA) bone and joint infection (BJI). We sought to compare the plasma concentrations of cloxacillin administered alternately by continuous and intermittent infusion (CI and ItI) in patients with MSSA BJI. In this prospective crossover trial, patients were randomly assigned to receive either 3 days of CI (two 75-mg/kg 12-h cloxacillin infusions per day) and then 3 days of ItI (four 37.5-mg/kg 1-h cloxacillin infusions per day) or vice versa. The drug concentration measurement was performed on day 3 of each type of administration at 1, 6, and 11 h and at 1, 2, 3, 4, and 6 h after the beginning of CI and ItI, respectively. We used the nonparametric algorithm NPAG to estimate population pharmacokinetic (PK) parameters. The final model was used to perform pharmacokinetic/pharmacodynamic (PK/PD) simulations and calculate the probabilities of target attainment (PTA) for several ItI and CI dosing regimens. We considered two PK/PD targets of time spent above the MIC for free cloxacillin concentrations (fT>MIC): 50 and 100%. Eighty-four concentrations from 11 patients were analyzed. A two-compartment model adequately described the data. ItI with q6h regimens and short 1-h infusions of 2,000 or 3,000 mg were associated with low PTA, even for the low target (50% fT>MIC) while 3-h infusions and continuous infusions (6 to 12 g/day) were associated with a PTA of >90% for an MIC up to 0.5 mg/liter. These results support the use of prolonged or continuous infusion of cloxacillin in patients with BJI.

Published
2020
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40. A Population Pharmacokinetic Analysis of Continuous Infusion of Cloxacillin during

Author

Johan, Courjon, Margaux, Garzaro, Pierre-Marie, Roger, Raymond, Ruimy, Thibaud, Lavrut, Mikaël, Chelli, Jean-Luc, Raynier, David, Chirio, Elisa, Demonchy, Laura, Cabane, François, Jehl, Christophe, Trojani, Antoine, Grillon, and Sylvain, Goutelle

Subjects
Staphylococcus aureus, Humans, Microbial Sensitivity Tests, Prospective Studies, Clinical Therapeutics, Infusions, Intravenous, Cloxacillin, Anti-Bacterial Agents
Abstract

Intravenous administration of antibiotics is recommended during the early phase of methicillin-susceptible S. aureus (MSSA) bone and joint infection (BJI). We sought to compare the plasma concentrations of cloxacillin administered alternately by continuous and intermittent infusion (CI and ItI) in patients with MSSA BJI. In this prospective crossover trial, patients were randomly assigned to receive either 3 days of CI (two 75-mg/kg 12-h cloxacillin infusions per day) and then 3 days of ItI (four 37.5-mg/kg 1-h cloxacillin infusions per day) or vice versa. The drug concentration measurement was performed on day 3 of each type of administration at 1, 6, and 11 h and at 1, 2, 3, 4, and 6 h after the beginning of CI and ItI, respectively. We used the nonparametric algorithm NPAG to estimate population pharmacokinetic (PK) parameters. The final model was used to perform pharmacokinetic/pharmacodynamic (PK/PD) simulations and calculate the probabilities of target attainment (PTA) for several ItI and CI dosing regimens. We considered two PK/PD targets of time spent above the MIC for free cloxacillin concentrations (fT(>MIC)): 50 and 100%. Eighty-four concentrations from 11 patients were analyzed. A two-compartment model adequately described the data. ItI with q6h regimens and short 1-h infusions of 2,000 or 3,000 mg were associated with low PTA, even for the low target (50% fT(>MIC)) while 3-h infusions and continuous infusions (6 to 12 g/day) were associated with a PTA of >90% for an MIC up to 0.5 mg/liter. These results support the use of prolonged or continuous infusion of cloxacillin in patients with BJI.

Published
2020

41. Staphylococcus capitis isolated from bloodstream infections: a nationwide 3-month survey in 38 neonatal intensive care units

Author

Sylvie Joron, Stéphane Marret, Fabrice Lapeyre, Jérôme Larche, Jacqueline Grando, David Leyssene, Jean Nakhleh, Clarisse Dupin, Tania Foucan, Stéphanie Bordes-Couecou, Géraldine Abadie, Franck Labbe, Marie Kempf, Manuel Petitfrere, Audrey Robine, Marie Decalonne, Chantal Chaplain, Philippe Jouvencel, Florent Goube, Benjamin Cotte, Laurent Villeneuve, Adeline Lacazette, Raoul Baron, Jean-Marc Jellimann, Anne-Sophie Trentesaux, Nathalie Chautemps, Laurent Mereghetti, Olivier Dauwalder, Nicolas Fortineau, Christine Roques Ceschin, Rafik Ben Ammar, Sandra Bourdon, Alain Gravet, Audrey Glanard, Olivier Belmonte, Jacques Gilquin, Arnaud Florentin, Souad Slimani, Annick Lefebvre, Jérôme Guinard, Edith Malpote, Céline Chatelet, Isabelle Bauvin, Alain Lozniewski, Anaëlle Muggeo, Geneviève Héry-Arnaud, Stéphane Le Vu, Isabelle Ligi, Anne Le Pourhiennec, Christian Cattoen, Olivier Join-Lambert, Bruno Pozetto, Carole De Chillaz, Amine Siali, Pascale Martres, Michel Drancourt, Claire Lesteven, Sandra C. dos Santos, Nadège Bourgeois-Nicolaos, Aude Davy, Claude Olive, Rémi Gimenes, Laure Gibert, Raymond Ruimy, Virginie Morange, Antoine Bouissou, Julien Mourdie, Emmanuelle Bille, Marie-Noëlle Noulard, Vincent Cattoir, Martine Delorme, Dominique Trivier, Luc Desfrere, Hugues Patural, Patrick Barthelemy, Nadia Idri, Florence Lemann, Franck-Olivier Mallaval, Sophie Ketterer-Martinon, Christian Vandenbussche, Pierre Frange, Sylvie Ledru, Mouna Khecharem, Pierre Lureau, Sophie Boyer, Philippe Berthelot, Salma Ben Hadj Yahia, Clément Legeay, Emilie Benabid, Guillaume Menard, Marion Levast-Raffin, Céline Coroller-Bec, Claire Huart, Maryvonne Demasure, Pascal Bolot, Yasmina Berrouane, Hélène Cormier, Pascale Minery, Pascale Penn, Peggy Larroude, Evelyne Werner, Géraldine Gascoin, Virginie Forget, Nathalie van der Mee-Marquet, Stéphanie Soive, Karine Gambarotto, Vanina Ambrogi, Aurore Claudinon, Serge Klosowski, Brigitte Riviere, Véronique Merle, Laura Menvielle, Véronique Faraut-Derouin, Saïd Aberrane, Alain Beuchee, Nolwenn Le Sache, Hôpital Bretonneau, CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre hospitalier Félix-Guyon [Saint-Denis, La Réunion], Centre Hospitalier René Dubos [Pontoise], Centre Hospitalier Intercommunal de Créteil (CHIC), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Hôpital de la Conception [CHU - APHM] (LA CONCEPTION), Centre hospitalier de Pau, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier de Calais, Centre Hospitalier Universitaire de Nice (CHU Nice), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), CHU Pontchaillou [Rennes], Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier de Saint-Denis [Ile-de-France], Centre Hospitalier de la Côte Basque (CHCB), Groupe Hospitalier du Havre, Hôpital Charles Nicolle [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU), Centre hospitalier [Valenciennes, Nord], Centre Hospitalier Universitaire [Rennes], GHT de l'Artois, Centre Hospitalier Victor Dupouy, Centre Hospitalier Métropole Savoie [Chambéry], Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Centre Hospitalier Le Mans (CH Le Mans), Clinique du Val d'Ouest, CHU Necker - Enfants Malades [AP-HP], Hospices Civils de Lyon (HCL), Centre hospitalier Saint-Brieuc, Centre Hospitalier Georges Renon [Niort] (CH Georges Renon Niort), Centre Hospitalier Régional d'Orléans (CHRO), Hôpital Louis Mourier - AP-HP [Colombes], Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), CHU de Saint-Brieuc, Interactions Gènes-Risques environnementaux et Effets sur la Santé (INGRES), Université de Lorraine (UL), Unité de Recherche Environnement Physique de la plante Horticole (EPHOR), Université d'Angers (UA)-AGROCAMPUS OUEST, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CHU Pointe-à-Pitre/Abymes [Guadeloupe], Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Hôpital Hôtel-Dieu [Paris], Hôpital Delafontaine, Centre Hospitalier de Mulhouse, site du Hasenrain (Mulhouse), Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Service de réanimation néonatale [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Pathogénie des infections systémiques (UMR_S 570), Centre Régional de PharmacoVigilance Nord-Pas-de-Calais [CHU Lille] (CRPV), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Faculté de Médecine Henri Warembourg - Université de Lille, Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), CHU de la Martinique [Fort de France], Groupe Hospitalier du Havre Hôpital Jacques Monod (MONTIVILLIERS) (GHH), Polyclinique Médipôle Saint-Roch [Cabestany], Centre Hospitalier Universitaire de Reims (CHU Reims), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Université d'Auvergne - Clermont-Ferrand I (UdA), Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Service de microbiologie [CHU Nancy], Service psychiatrique de l'enfant et de l'adolescent [CHU Hôpital Robert Debré], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré, Service de bactériologie-virologie [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Hôpital Bretonneau, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Registre EPIMAD, Normandie Université (NU)-Normandie Université (NU)-CHU Amiens-Picardie-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Groupe Hospitalier Artois-Ternois Centre Hospitalier d’Arras, Système Nerveux Autonome - Epidémiologie, Physiologie, Ingénierie, Santé (SNA - EPIS), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Jean Monnet - Saint-Étienne (UJM), ELSAN Polyclinique Majorelle, Centre Hospitalier Intercommunal Castres-Mazamet (CHIC-CM), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Centre Hospitalier Universitaire de Martinique [Fort-de-France, Martinique], Centre Hospitalier de Lens, Institut de Veille Sanitaire (INVS), Hôpital Trousseau, Jonchère, Laurent, Centre Hospitalier Universitaire de Saint-Etienne (CHU de Saint-Etienne), Le CHCB, Centre Hospitalier de la Côte Basque, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Système Nerveux Autonome - Epidémiologie, Physiologie, Ingénierie, Santé (SNA-EPIS), Université Jean Monnet - Saint-Étienne (UJM)-Centre Hospitalier Universitaire de Saint-Etienne, CHU Saint-Etienne, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université Lille 2 - Faculté de Médecine, Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-CHU Amiens-Picardie, Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Jean Monnet [Saint-Étienne] (UJM)-Centre Hospitalier Universitaire de Saint-Etienne, CHU Toulouse [Toulouse], Centre Hospitalier Universitaire Félix-Guyon [Saint-Denis, La Réunion, France], Centre Hospitalier Universitaire de Toulouse, Department of Microbiology Brest, Department of Microbiology, Brest, CHU CLAMART, Centre Hospitalier Universitaire de Nice (CHU de Nice), Centre Hospitalier Côte Basque, Bayonne, CHU Le Havre, Laboratory of microbiology and infection control, Assistance publique-Hôpitaux de Paris, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Universitaire Charles Nicolle, Partenaires INRAE, CHU de la Réunion, Saint-Denis, France., CHU Lens, CHU Argenteuil, Centre Hospitalier Métropole Savoie-Site de Chambéry, La Clinique du Val d'Ouest, Hôpitaux Est Hôpital Louis Pradel - Hospices Civils de Lyon, Centre Hospitalier Régional d'Orléans (CHR), Hopital Louis Mourier - AP-HP [Colombes], Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Service de virologie, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes], Hôpital Antoine Béclère, Assistance Publique - Hôpitaux de Paris (AP-HP), Service de Bactériologie-Virologie, Hôpital Bretonneau-Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre d'infectiologie Necker-Pasteur [CHU Necker], Service de chirurgie infantile, CHU Felix Guyon, Saint Denis de La Réunion, Hôtel-Dieu, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu, Unité d'Hygiène Hospitalière, hospices civils de Lyon, Hôpital du Hasenrain, Mulhouse, CHU Valenciennes, Université Henri Poincaré - Nancy 1 (UHP), Hôpital de Bayonne [Bayonne], CHU Kremlin-Bicétre, Anofel Cryptosporidium National Network, Polyclinique de St Roch, CHU Pau, Unité de prévention et de lutte contre les infections nosocomiales [CHU Angers], PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Division of Neonatology, La Conception Hospital, Assistance Publique-Hôpitaux de Marseille and Faculté de Médecine, Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie clinique et environnementale [Pointe-à-Pitre, Guadeloupe, France], Centre Hospitalier Universitaire de Rennes (CHU Rennes), Hôpital privé de l'Estuaire [Le Havre], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Hôpital d'Arras, CHU Le MAns, Polyclinique Majorelle, Laboratoire de Microbiologie, Centre Hospitalier Intercommunal Castres-Mazamet, Laboratoire de bactériologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Laboratoire de Recherche Opérationnelle et Mathématiques de la Décision - LAROMAD (Alger, Algérie), Centre Hospitalier d’Arras, Unité de Méthodologie en Recherche Clinique, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)

Subjects
Male, 0301 basic medicine, Pediatrics, Clone (cell biology), NRCS-A clone, 030501 epidemiology, Staphylococcus capitis, Medical microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Multiple, Bacterial, Medicine, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Brief Report, Gestational age, General Medicine, Staphylococcal Infections, Anti-Bacterial Agents, 3. Good health, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Nationwide active surveillance, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Vancomycin, Female, France, 0305 other medical science, Infant, Premature, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, medicine.drug, Microbiology (medical), medicine.medical_specialty, Bloodstream catheter-related infection, Birth weight, Preterm babies, 030106 microbiology, Late onset, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Intensive Care Units, Neonatal, Sepsis, Intensive care, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, business.industry, Neonatal Intensive Care Unit (NICU), Infant, Newborn, Neonates, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Catheter-Related Infections, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, business
Abstract

To increase the knowledge about S. capitis in the neonatal setting, we conducted a nationwide 3-month survey in 38 neonatal intensive care units (NICUs) covering 56.6% of French NICU beds. We demonstrated 14.2% of S. capitis BSI (S.capBSI) among nosocomial BSIs. S.capBSI incidence rate was 0.59 per 1000 patient-days. A total of 55.0% of the S.capBSIs were late onset catheter-related BSIs. The S. capitis strains infected preterm babies (median gestational age 26 weeks, median birth weight 855 g). They were resistant to methicillin and aminoglycosides and belonged to the NRCS-A clone. Evolution was favorable in all but one case, following vancomycin treatment.

Published
2020
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42. Fatal pulmonary infection related to Nocardiopsis dassonvillei in a patient with chronic obstructive pulmonary disease

Author

Raymond Ruimy, R. Scussel, J. Gillon, Romain Lotte, M. Chassang, D. Boudoumi, Université Côte d'Azur (UCA), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
16S rDNA sequencing, 0301 basic medicine, [SDV]Life Sciences [q-bio], 030106 microbiology, Pulmonary disease, Pulmonary infection, Human pathogen, Microbiology, Chronic obstructive, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Emerging pathogen, Medicine, lcsh:RC109-216, pulmonary disease, business.industry, Nocardiopsis dassonvillei, Nocardiopsis species, New Resistant Microbes in Human, 3. Good health, 030104 developmental biology, Infectious Diseases, business
Abstract

Nocardiopsis species are aerobic, gram-positive, non-acid fast rods isolated from soil, waters, and animals. They are opportunistic human pathogens, but very few cases have been published so far. We report the first case of fatal pulmonary infection related to Nocardiopsis dassonvillei in an immunocompetent patient with chronic obstructive pulmonary disease.

Published
2020
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43. Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese

Author

Pierre-Edouard Fournier, Bruno Senghor, Didier Raoult, Raymond Ruimy, Saber Khelaifia, Hubert Bassene, Catherine Robert, Cheikh Sokhna, Jean-Christophe Lagier, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
DNA, Bacterial, Male, 0301 basic medicine, 030106 microbiology, Oceanobacillus senegalensis, Biology, Halophilic bacteria, Human gut, Microbiology, law.invention, West africa, Feces, 03 medical and health sciences, law, RNA, Ribosomal, 16S, Humans, Child, Bacillaceae, Molecular Biology, Phylogeny, ComputingMilieux_MISCELLANEOUS, Oceanobacillus senegalensis genome, 2. Zero hunger, Base Composition, Culturomics, Taxonogenomic, Oceanobacillus timonensis, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, C content, Senegal, Halophile, Bacterial Typing Techniques, 030104 developmental biology, Gram staining, Female, Bacteria
Abstract

Oceanobacillus timonensis Marseille-P3532(T) (CSUR P3532, CCUG 70981) and Oceanobacillus senegalensis Marseille-P3587(T) (CSUR P3587, CCUG 70613), are the type strains of O. timonensis sp. nov. and O. senegalensis sp. nov., respectively. They are moderately halophilic, aerobic, motile and Gram-stain positive bacteria. The strains P3532(T) and P3587(T) were isolated from stools with 3.8% and 2.1% sodium chloride (NaCl) of healthy 10 year old female and male 7-year-old children, respectively and living respectively at Dielmo and N'diop two villages in Senegal (West Africa). This study aimed to describe the genome and phenotypic characteristics of O. timonensis Marseille-P3532(T) and O. senegalensis Marseille-P3587(T). The genomes are 4,485,335bp long for O. timonensis and 4,300,331 bp for O. senegalensis with 38.78% and 36.92% G+C content, respectively. They contain 4306 and 3979 protein-coding and 87 and 273 RNAs genes, respectively.

Published
2018
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44. Description of the First Case of Catheter-Related Bloodstream Infection Due To Pantoea eucrina in a Cancer Patient

Author

Dominique Neri, Nicolas Weiss, Romain Lotte, Raymond Ruimy, Matteo Vassallo, Audrey Sindt, and Laurene Lotte

Subjects
0301 basic medicine, medicine.medical_specialty, Abdominal pain, biology, medicine.drug_class, business.industry, 030106 microbiology, Antibiotics, Pantoea eucrina, Cancer, Gut flora, biology.organism_classification, medicine.disease, 03 medical and health sciences, Catheter, 030104 developmental biology, Internal medicine, Bacteremia, Bloodstream infection, medicine, medicine.symptom, business
Abstract

We describe here the first case of catheter-related bloodstream infection due to Pantoea eucrina in a 23-year-old female patient with colon adenocarcinoma and congenital hypogammaglobulinemia. In May 2018, she was admitted for fever and abdominal pain. Blood cultures withdrawn from peripheral inserted central catheter and periphery revealed the presence of Pantoea eucrina, with differential time of positivity in favor of catheter-related bloodstream infection. Catheter was removed and antibiotic started, with rapid recovery. Species of genus Pantoea are mainly environmental strains and plant pathogens, rarely responsible for human infection. Patient’s comorbid conditions and gut microbiota imbalance could have been responsible for such bacteremia. Identification of Pantoea eucrina was performed using the MALDI-TOF technique. Infections due to Pantoea eucrina were probably until recently underestimated, as older methods such as Phoenix frequently lead to false identification.

Published
2018
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45. Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result

Author

B. Lamy, Grégory Dubourg, Raymond Ruimy, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Pathogènes Hydriques Santé Environnement (PHySE ), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Université Nice Sophia Antipolis (... - 2019) (UNS)

Subjects
0301 basic medicine, Microbiology (medical), Susceptibility testing, medicine.medical_specialty, 030106 microbiology, Bacteremia, Microbial Sensitivity Tests, Time-to-Treatment, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Bloodstream infection, Ionization time of flight, medicine, Humans, Blood culture, Intensive care medicine, Bacteriological Techniques, Bacteria, medicine.diagnostic_test, business.industry, Time to result, General Medicine, 3. Good health, Clinical microbiology, Phenotype, Infectious Diseases, Workflow, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Identification (biology), business
Abstract

Background Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection. Aims We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing. Sources A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source. Content Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered. Implications The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.

Published
2018
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46. It takes two to tango: two Aeromonas isolates combine virulence and multidrug resistance in flap infection following leech therapy

Author

Alexandre Robert, Lucie Laval, B. Lamy, Laurent Boyer, Olivier Barraud, David Morquin, and Raymond Ruimy

Subjects
0301 basic medicine, Microbiology (medical), animal structures, biology, 030106 microbiology, Leech, Virulence, General Medicine, Drug resistance, biochemical phenomena, metabolism, and nutrition, Integron, biology.organism_classification, Microbiology, Multiple drug resistance, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, Aeromonas, biology.protein, Leech Therapy, 030212 general & internal medicine, Aeromonas veronii
Abstract

Most leech infections are caused by an obligate bacterial symbiont of the crop of leeches, Aeromonas sp. Here, we describe a flap infection following leech therapy mediated by two Aeromonas veronii isolates that presented complementary and synergistic features in terms of virulence and antimicrobial drug resistance. One strain was multidrug resistant and harboured an ESBL-encoding blaVEB-1 gene embedded within a class 1 integron. This is the first report that a bacterial mixture including an ESBL Aeromonas may have worsened the course of a flap infection following leech therapy.

Published
2020
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47. An unusual Staphylococcus saccharolyticus spondylodiscitis post vertebroplasty, a case report

Author

Marie Charlotte Trojani, brigitte Lamy, Raymond Ruimy, nicolas Amoretti, Karine Risso, and christian roux

Abstract

Background: Staphylococcus saccharolyticus is a rarely encountered coagulase-negative slowly grower and strictly anaerobic staphylococcus from the skin. It is usually considered as a contaminant, but some rare reports describe deep-seated infections. Virulence factors remain poorly known although genomic analysis highlight pathogenic potential.Case presentation: we report a case of Staphylococcus saccharolyticus spondylodiscitis that followed kyphoplasty, a procedure associated with a low rate of sometimes severe infectious complication (0.46%) and we reviewed the literature. This case specifically stresses the risk of S. saccharolyticus health-care associated infection in patients of poor condition.Conclusion: infection to S. saccharolyticus is difficult to diagnose due to microbiological characteristics of this bacterium, requires timely treatment and improved infection control procedure should be encouraged for patients with poor condition.

Published
2020
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49. Thickened Drinks and Oral Nutritional Supplements as Potential Reservoirs of Oral Microorganisms: Microbial Assays In Vitro

Author

Nadine Molinari, Isabelle Prêcheur, Aïmen Bouhlel, Raymond Ruimy, and Caroline Jung

Subjects
Polypharmacy, Preservative, 030504 nursing, 030214 geriatrics, biology, business.industry, Health Policy, media_common.quotation_subject, Microorganism, Gerontological nursing, biology.organism_classification, Oral hygiene, Corpus albicans, 03 medical and health sciences, 0302 clinical medicine, Hygiene, Medicine, Food science, Geriatrics and Gerontology, 0305 other medical science, business, Candida albicans, Gerontology, General Nursing, media_common
Abstract

Oral hygiene is difficult to achieve for frail older adults. Aging, chronic diseases, polypharmacy, mouth-washes, and crushed drugs can contribute to uncontrolled proliferation and microbial deposits in the mouth. Looking for avoidable risk factors, in vitro microbial survival or proliferation in thickened drinks and oral nutritional supplements (ONS) was investigated. The safest thickened drinks were ready-to-use products containing preservatives. Escherichia coli , Staphylococcus aureus, and Candida albicans proliferated in dairy ONS at room temperature. C. albicans also proliferated in juices. Oral anerobic bacteria were recovered from part eaten ONS. Thickened drinks and ONS could contribute to microbial proliferation, especially with patients who have swallowing alterations or cognitive troubles, who may keep these solutions longer than necessary in their mouth. These products can also constitute microbial reservoirs in the environment of frail older adults. It is important for health care workers and family members to respect hand hygiene and refrigeration procedures. [ Research in Gerontological Nursing, 13 (4), 203–209.]

Published
2019

50. ‘Nissabacter archeti’ gen. nov., sp. nov., a new member of Enterobacteriaceae family, isolated from human sample at Archet 2 Hospital, Nice, France

Author

K. D. Mlaga, Romain Lotte, Jean-Marc Rolain, H. Montaudié, Raymond Ruimy, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice (CHU Nice), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, pustule, Enterobacteria, Nissabacter archeti, 030106 microbiology, New Species, Nice, Biology, biology.organism_classification, Microbiology, Enterobacteriaceae, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Taxonomy (biology), human infection, lcsh:RC109-216, computer, scalp, computer.programming_language
Abstract

We propose the main characteristics of a new bacterium species named Nissabacter archeti strain 2134 (CSURP3445 = LT631518), isolated from pustule scalp of a 29-year-old man at hospital Archet 2, Nice, south of France.

Published
2017
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