Stéphane Ranque | Aix-Marseille Université (original) (raw)

Papers by Stéphane Ranque

Current Fungal Infection Reports, Sep 28, 2015

Typing is applied to highlight the genetic relationships between environmental and clinical funga... more Typing is applied to highlight the genetic relationships between environmental and clinical fungal isolates involved in colonization or infection. A variety of techniques can be used to type fungi, depending on the epidemiological question and the available equipment. The use of typing techniques during clinical fungal outbreak investigations demonstrated patient-to-patient propagation in dermatophytoses outbreaks, patient-to-health-care worker and health-care workerto-patient transmission in yeast infection outbreaks, airborne patient-to-patient transmission of the non-cultivable Pneumocystis jirovecii fungus involved in pneumonia outbreaks, and environmental sources of several mold outbreaks including aspergillosis or fusariosis keratitis. Typing was also useful to trace the source of invasive fungal disease outbreaks or epidemics, such as contaminated medical devices. More generally, typing provided important insights into fungal outbreak characteristics and helped to implement appropriate measures to control fungal infections, which are often severe, progress rapidly, and are difficult to diagnose and treat.

Clinical Microbiology and Infection, Jul 1, 2009

Polymerase chain reaction (PCR) assays have a very low theoretical detection threshold and are th... more Polymerase chain reaction (PCR) assays have a very low theoretical detection threshold and are therefore advocated for the diagnosis of fungaemia. However, their effectiveness in this respect remains to be assessed. This study compared real-time PCR (Can-G) and nested PCR assays with blood culture for the diagnosis of Candida spp. bloodstream infections. A total of 200 clinical blood samples obtained from 110 patients at risk for developing a systemic fungal infection, hospitalized in the University Hospital of Sfax (Tunisia), were submitted to testing by culture, nested PCR and real-time PCR. Blood culture was positive in 36 patients. When compared with culture, the Can-G assay (81% sensitivity, 96% specificity) performed better than the nested PCR assay (86% sensitivity, 54% specificity). The real-time PCR assay, which avoids both the contamination hazard with amplicons that may cause false-positive results and the use of time-consuming post-PCR steps, appears more suitable than the nested PCR assay for the laboratory diagnosis of Candida spp. bloodstream infections. In this study, real-time PCR did not enhance the diagnostic sensitivity for Candida spp. bloodstream infections compared with conventional blood culture; however, it may lead to earlier implementation of an adequately targeted antifungal treatment.

Medical Mycology, Nov 1, 2012

known to infl uence the outcome of IA are drug pharmacokinetics, site of infection, host factors,... more known to infl uence the outcome of IA are drug pharmacokinetics, site of infection, host factors, and the infecting fungus characteristics, including its susceptibility to the drug. In this setting, in vitro antifungal minimal inhibitory concentration (MIC) determination cannot reliably predict in vivo clinical outcome in a patient. In practice, while it may not always be possible to identify which patients will respond to therapy, in vitro susceptibility tests may be used to identify those who will have a decreased probability of responding. Lassl-Fl ö rl [2] recently reviewed the confl icting data, including those of experimental models of in vivo correlation of antifungal susceptibility testing results in Aspergillus spp. Three clinical studies found a tendency towards a correlation of amphotericin B (AMB) MIC with IA outcome. Only the fi rst one [3] was statistically signifi cant, the

Research Square (Research Square), Dec 9, 2021

A total of 77 strains of Malassezia were included in this study. Bio lm production and hydrolytic... more A total of 77 strains of Malassezia were included in this study. Bio lm production and hydrolytic enzymes were studied by using speci c solid media. Realtime Reverse Transcriptase qPCR method was applied to determine overexpression of genes encoding extracellular enzyme. All included Malassezia species produced bio lms. No statistical signi cant difference was observed between bio lm formation of the Malassezia species (P = 0.567). All Malassezia species produced lipase and 95% of M. globosa showed a strong enzymatic activity (Pz=0.55 ± 0.02). Statistical signi cant difference was observed between the mean keratinase indices of M. sloo ae and the others Malassezia species (P = 0.005). The overexpression of one or more genes was observed in 100% of strains isolated from patients with folliculitis, in 87.5% for pityriasis versicolor isolates and in 57.14% for the control group isolates. A statistical signi cant difference of the lipase gene expression (P = 0.072) was associated with the strains collected from patients with folliculitis vs group control. This investigation provides more information about the frequency of the production of the major enzymes considered to be virulence factors of Malassezia species. Interestingly, the overexpression of one or more genes was observed in strains isolated from patients with Malassezia disorder.

Veterinary Medicine and Science

BackgroundThe ubiquitous environmental fungus Aspergillus flavus is also a life‐threatening avian... more BackgroundThe ubiquitous environmental fungus Aspergillus flavus is also a life‐threatening avian pathogen.ObjectivesThis study aimed to assess the genetic diversity and population structure of A. flavus isolated from turkey lung biopsy or environmental samples collected in a poultry farm.MethodsA. flavus isolates were identified using both morphological and ITS sequence features. Multilocus microsatellite genotyping was performed by using a panel of six microsatellite markers. Population genetic indices were computed using FSTAT and STRUCTURE. A minimum‐spanning tree (MST) and UPGMA dendrogram were drawn using BioNumerics and NTSYS‐PC, respectively.ResultsThe 63 environmental (air, surfaces, eggshells and food) A. flavus isolates clustered in 36 genotypes (genotypic diversity = 0.57), and the 19 turkey lung biopsies isolates clustered in 17 genotypes (genotypic diversity = 0.89). The genetic structure of environmental and avian A. flavus populations were clearly differentiated, acc...

Emerging Infectious Diseases, Sep 1, 2020

S aprochaete clavata (previously Geotrichum clavatum) is a rare emerging pathogen, an ascomycetou... more S aprochaete clavata (previously Geotrichum clavatum) is a rare emerging pathogen, an ascomycetous yeast-producing arthroconidia that causes invasive fungal infections in immunocompromised patients. The species has mainly been reported in Europe, often associated with sporadic cases or small outbreaks (1,2). Unlike Magnusiomyces capitatus (3,4), which has been associated with dairy products, S. clavata has rarely been isolated from environmental samples (5,6). Patients most at risk for infections from Geotrichum spp. have hematologic diseases with severe neutropenia (7) and are undergoing chemotherapy, mainly with cytarabine (1) or caspofungin (8). They often have central venous catheters (9). In recent years, S. clavata fungemia outbreaks associated with high mortality rates in vulnerable patients with malignancies have been described throughout Europe, mainly in France (1), Italy (2,10), Czechia (11), and Spain (12). No source of contamination was identified in any of these outbreaks despite thorough investigation. During February 2016-December 2017, the Paoli-Calmettes Institute, a cancer center in Marseille, France, was faced with an outbreak of S. clavata infections involving 9 patients hospitalized in 3 different wards, suggesting a common source of contamination. We describe the findings of an outbreak investigation that recovered S. clavata in different environmental samples, including from a dishwasher in the central kitchen and another, available to patients and their families, in the stem-cell transplant ward. Whole-genome sequencing (WGS) confirmed that the environmental and clinical isolates from patients belonged to the same phylogenetic clade. Handwashing, avoiding direct skin contact, checking air quality, and sterilizing food are routine practice to prevent contamination in hematology wards; however, examining dishwashers for contamination and operability may not be done routinely. Our findings should prompt adding dishwasher inspections to guidelines for preventing infection. Materials and Methods Case Definition Criteria We defined S. clavata infection by obtaining ≥1 positive results for S. clavata blood culture from a usually sterile body site or from a bronchoalveolar lavage or tracheal aspirate of the respiratory tract. Infection was also confirmed by observing pleural fluid in a patient with pleural effusion or lung infection.

Clinical Microbiology and Infection, Dec 1, 2014

The clinical diagnosis of mould infections currently involves complex species identification base... more The clinical diagnosis of mould infections currently involves complex species identification based on morphological criteria, which is often prone to error. Employing an extensive mould species reference spectral library (up to 2832 reference spectra, corresponding to 708 strains from 347 species), we assessed the extent to which matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) enhanced the accuracy of species identification. MALDI-TOF MS data were validated against morphology-based and DNA sequence-based results with 262 clinical isolates collected over a 4-month period in 2013. The implementation of MALDI-TOF MS resulted in a dramatic improvement in mould identification at the species level (from 78.2% to 98.1%) and a marked reduction in the misidentification rate (from 9.8% to 1.2%). We then compared the mould identification results obtained before (i.e. 2011) and after (i.e. 2013) the implementation of MALDI-TOF MS in routine identification procedures, which showed an improvement from 64.57% to 100%. Reassessment of a set of isolates from 2011 with this procedure, including MALDI-TOF MS, yielded an increase in species diversity from 16 to 42 species. Finally, application of this procedure during a 16-month period (2012-2013) enabled the identification of 1094 of 1107 (98.8%) clinical mould isolates corresponding to 107 distinct species. MALDI-TOF MS-based mould species identification may soon challenge traditional techniques in the clinical laboratory, as patient prognosis is largely contingent on rapid and accurate diagnosis.

Scientific Reports, Feb 28, 2019

the opportunistic pathogen Mycobacterium ulcerans, which is responsible for Buruli ulcer, synthes... more the opportunistic pathogen Mycobacterium ulcerans, which is responsible for Buruli ulcer, synthesizes a series of plasmid-encoded macrolide exotoxins termed mycolactones. these toxins destabilize cell membranes and induce apoptosis-associated pleiotropic effects including tissue destruction, analgesic and anti-inflammatory effects. Despite its medical interest, M. ulcerans is primarily an environmental mycobacterium and the primary functions of mycolactones in the natural ecosystems are unknown. High throughput biochemical profiling findings suggested that M. ulcerans may interact with fungi. Here, we report that semi-purified and purified mycolactones significantly enhance spore germination of Scedosporium apiospermum, Fusarium equiseti and Mucor circinelloides; and that M. ulcerans mycolactones significantly attract colonies of M. circinelloides whereas no significant effect was observed on S. apiospermum and F. equiseti. these experimental results suggest that mycolactones exhibit a chemoattractant activity independent of their cytotoxicity. In natural ecosystems, M. ulcerans mycolactones may act as spore germination inducers and chemoattractants for some fungi, suggesting a novel role for this unique class of mycobacterial toxins in natural ecosystems. Mycolactones are a series of complex macrolide exotoxins whose plasmid-encoded synthesis is specific to the Mycobacterium marinum group of non-tuberculous mycobacteria 1. Mycolactones are hybrid polyketides comprising a conserved lactone core decorated with a variable fatty acid side chain. Six naturally occurring mycolactone types have been named mycolactones A/B, C, D, E, F and G 2. These mycolactones are produced by a group of closely related mycobacteria including M. marinum, Mycobacterium ulcerans and M. ulcerans subsp. shinshuense, Mycobacterium pseudoshottsii and Mycobacterium liflandii 3-8. In addition to its natural production, mycolactone A/B has also undergone total synthesis 1,9. In Buruli ulcer patients and animal models, mycolactones induce apoptosis in a large variety of cells including Schwann cells 10 by activating the pro-apoptotic regulator Bim 11. Accordingly, intradermic injection of mycolactones in laboratory animals or natural inoculation by still unknown vectors in human patients both cause extensive and disabling cutaneous and subcutaneous lesions referred to as Buruli ulcer in patients 2. Mycolactones further exhibit immunosuppressive effects by inhibiting the T cells Sec61 protein 12,13 and binding of mycolactone A/B to the neuronal angiotensin II type 2 receptors triggers potassium-dependent neuron hyperpolarization and analgesic effects 14. Each of these features has been observed in patients affected with Buruli ulcer 2. Buruli ulcer is a non-contagious mycobacteriosis, thus human infection is a dead-end in M. ulcerans life cycle 2. M. ulcerans reservoir is environmental in still poorly defined ecosystems near stagnant water. Its DNA has been detected in plants, moss, water bugs, mosquitoes, snails, fishes, amphibians and small mammals 2. Acquisition and conservation of complex mycolactone synthesis machinery contrasts with the global genome reduction that characterizes M. ulcerans evolution 15. The primary roles of mycolactones in the natural ecosystems remain unknown. In line with its aquatic environment, a previous high throughput biochemical profiling study revealed the potential for specific interactions between M. ulcerans and mollusks, bacterial consortia, algae and fungi 16. We hypothesized that mycolactones may play a role in these interactions and therefore tested possible interactions between mycolactones and environmental fungi. We found that mycolactones exhibit a chemoattractant and spore germination enhancer effect on three environmental fungi that we investigated.

Medical Mycology, 2009

For the last ten years, non-Aspergillus mold species have been increasingly involved in human inv... more For the last ten years, non-Aspergillus mold species have been increasingly involved in human invasive infections, probably as a consequence of more intense immunosuppression and prolonged patient survival, and of selective pressure since antifungal agents are currently used for prophylaxis or therapy. Scedosporium prolificans, one of these emerging fungi, has been isolated in a broad spectrum of clinical presentations in humans, including respiratory-tract colonization, superficial or locally invasive infections, and disseminated infections in immunocompromised patients. Here, we report the recent emergence of invasive infections due to S. prolificans in France, and describe four new cases diagnosed during the last six years. Only one disseminated scedosporiosis has been reported before this in France, in 1994. Three out of our four cases were breakthrough infections in immunocompromised patients receiving posaconazole or voriconazole therapy. The aims of the present review were thus to gain a better understanding of scedosporiosis epidemiology and clinical features, and to review recent advances in multimodal management of these infections, including surgery, recovery and/or enhancement of immunity, and antifungal combinations, especially voriconazole plus terbinafine.

Emerging Infectious Diseases, Apr 1, 2019

Journal of Antimicrobial Chemotherapy, 2020

Background Plasmodium falciparum resistance to most antimalarial compounds has emerged in Southea... more Background Plasmodium falciparum resistance to most antimalarial compounds has emerged in Southeast Asia and spread to Africa. In this context, the development of new antimalarial drugs is urgent. Objectives To determine the baseline in vitro activity of methylene blue (Proveblue®) on African isolates and to determine whether parasites have different phenotypes of susceptibility to methylene blue. Methods Ex vivo susceptibility to methylene blue was measured for 609 P. falciparum isolates of patients hospitalized in France for malaria imported from Africa. A Bayesian statistical analysis was designed to describe the distribution of median effective concentration (EC50) estimates. Results The EC50 ranged from 0.16 to 87.2 nM with a geometric mean of 7.17 nM (95% CI = 6.21–8.13). The 609 EC50 values were categorized into four components: A (mean = 2.5 nM; 95% CI = 2.28–2.72), B (mean = 7.44 nM; 95% CI = 7.07–7.81), C (mean = 16.29 nM; 95% CI = 15.40–17.18) and D (mean = 38.49 nM; 95% ...

Journal De Mycologie Medicale, Sep 1, 2015

Introduction L’identification au laboratoire des infections fongiques a levures doit etre rapide,... more Introduction L’identification au laboratoire des infections fongiques a levures doit etre rapide, fiable et capable de detecter des infections mixtes avec des especes montrant un profil de resistance aux antifongiques different. Ainsi, nous realisons en routine une recherche par culture sur milieu chromogene couplee a une identification des souches par spectrometrie de masse de type MALDI-TOF, soit un resultat preliminaire entre 36 et 48 h et un resultat definitif 4 jours apres reception du prelevement. Et si la spectrometrie de masse nous permettait, dans certains cas, de diminuer ce temps d’analyse, y compris en cas de culture mixte ? Materiel et methodes Nous avons construit une application WEB afin de permettre une identification rapide en ligne de spectres de masse issus de champignons et avons incremente ce systeme par diverses fonctionnalites dont une permet de verifier la purete des echantillons en identifiant des spectres composes de deux spectres d’especes differentes. Une re-analyse des resultats obtenus d’avril 2012 a avril 2013 dans notre laboratoire a montre que sur 5671 prelevements positifs de patients, 498 (8,78 %) etaient contamines par au moins deux especes de levures. Nous avons selectionne 225 spectres de masse qui correspondaient a la primo-culture d’une partie de ces 498 echantillons et nous les avons soumis a la fonctionnalite de recherche de melanges de notre application WEB. Resultats Pour 42 souches (18 %), nous avons pu mettre en evidence un melange. Dans 5 cas, une des especes identifiee dans le melange n’etait pas celle que nous avons retrouvee sur milieu chromogene (espece minoritaire qui a echappe a la remise en culture ?). Pour les 37 autres cas, l’application WEB a montre la presence, sur une colonie supposee isolee, d’un melange de spectres appartenant aux especes isolees plus tard sur milieu chromogene. Conclusion Ce travail nous laisse entrevoir les possibilites qu’il y aurait a mieux etudier mathematiquement les spectres, en particulier pour mettre en evidence des spectres mixtes, temoins de l’infection d’un patient par plusieurs especes fongiques differentes. Par ailleurs, le spectre de masse est une donnee numerique qui ne s’altere pas avec le temps et qui nous permet de realiser des analyses de qualite a posteriori. Que va-t-on decouvrir en faisant de la spectro-archeologie ?

Journal De Mycologie Medicale, Sep 1, 2014

BMC Public Health, Nov 21, 2006

Background: Spatial and temporal heterogeneities in the risk of malaria have led the WHO to recom... more Background: Spatial and temporal heterogeneities in the risk of malaria have led the WHO to recommend finescale stratification of the epidemiological situation, making it possible to set up actions and clinical or basic researches targeting high-risk zones. Before initiating such studies it is necessary to define local patterns of malaria transmission and infection (in time and in space) in order to facilitate selection of the appropriate study population and the intervention allocation. The aim of this study was to identify, spatially and temporally, high-risk zones of malaria, at the household level (resolution of 1 to 3 m). Methods: This study took place in a Malian village with hyperendemic seasonal transmission as part of Mali-Tulane Tropical Medicine Research Center (NIAID/NIH). The study design was a dynamic cohort (22 surveys, from June 1996 to June 2001) on about 1300 children (<12 years) distributed between 173 households localized by GPS. We used the computed parasitological data to analyzed levels of Plasmodium falciparum, P. malariae and P. ovale infection and P. falciparum gametocyte carriage by means of time series and Kulldorff's scan statistic for space-time cluster detection. Results: The time series analysis determined that malaria parasitemia (primarily P. falciparum) was persistently present throughout the population with the expected seasonal variability pattern and a downward temporal trend. We identified six high-risk clusters of P. falciparum infection, some of which persisted despite an overall tendency towards a decrease in risk. The first high-risk cluster of P. falciparum infection (rate ratio = 14.161) was detected from September 1996 to October 1996, in the north of the village. Conclusion: This study showed that, although infection proportions tended to decrease, high-risk zones persisted in the village particularly near temporal backwaters. Analysis of this heterogeneity at the household scale by GIS methods lead to target preventive actions more accurately on the high-risk zones identified. This mapping of malaria risk makes it possible to orient control programs, treating the high-risk zones identified as a matter of priority, and to improve the planning of intervention trials or research studies on malaria.

Annals of Occupational Hygiene, Oct 21, 2015

Many ailments can be linked to exposure to indoor airborne fungus. However, obtaining a precise m... more Many ailments can be linked to exposure to indoor airborne fungus. However, obtaining a precise measurement of airborne fungal levels is complicated partly due to indoor air fluctuations and non-standardized techniques. Electrostatic dust collector (EDC) sampling devices have been used to measure a wide range of airborne analytes, including endotoxins, allergens, β-glucans, and microbial DNA in various indoor environments. In contrast, viable mold contamination has only been assessed in highly contaminated environments such as farms and archive buildings. This study aimed to assess the use of EDCs, compared with repeated air-impactor measurements, to assess airborne viable fungal flora in moderately contaminated indoor environments. Indoor airborne fungal flora was cultured from EDCs and daily air-impaction samples collected in an office building and a daycare center. The quantitative fungal measurements obtained using a single EDC significantly correlated with the cumulative measurement of nine daily air impactions. Both methods enabled the assessment of fungal exposure, although a few differences were observed between the detected fungal species and the relative quantity of each species. EDCs were also used over a 32-month period to monitor indoor airborne fungal flora in a hospital office building, which enabled us to assess the impact of outdoor events (e.g. ground excavations) on the fungal flora levels on the indoor environment. In conclusion, EDC-based measurements provided a relatively accurate profile of the viable airborne flora present during a sampling period. In particular, EDCs provided a more representative assessment of fungal levels compared with single air-impactor sampling. The EDC technique is also simpler than performing repetitive air-impaction measures over the course of several consecutive days. EDC is a versatile tool for collecting airborne samples and was efficient for measuring mold levels in indoor environments.

Journal De Mycologie Medicale, Sep 1, 2012

Antimicrobial Agents and Chemotherapy, Nov 17, 2021

We determined the susceptibility of 182 Fusarium species isolates to five antifungal drugs (ampho... more We determined the susceptibility of 182 Fusarium species isolates to five antifungal drugs (amphotericin B, voriconazole, posaconazole, isavuconazole, and terbinafine) by the EUCAST method. Based on the latest taxonomic insights, isolates collected from 20 European centers were distributed into seven complexes and 27 species. The susceptibility was variable, depending on the species. Comparison with the gradient concentration strip method, which was used for 77 isolates, showed essential agreement values for voriconazole, posaconazole, isavuconazole, and amphotericin B of 17%, 91%, 83%, and 70%, respectively.

Journal of Fungi, Mar 25, 2021

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Medical Mycology, Oct 3, 2019

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) is ro... more Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) is routinely used in mycology laboratories to rapidly identify pathogenic yeasts. Various methods have been proposed to perform routine MS-based identification of clinically relevant species. In this study, we focused on Bruker technology and assessed the identification performance of three protocols: two pretreatment methods (rapid formic acid extraction directly performed on targets and full extraction using formic acid/acetonitrile in tubes) and a direct deposit protocol that omits the extraction step. We also examined identification performance using three target types (ground-steel, polished-steel, and biotargets) and two databases (Bruker and online MSI [biological-mass-spectrometry-identification application]) in a multicenter manner. Ten European centers participated in the study, in which a total of 1511 yeast isolates were analyzed. The 10 centers prospectively performed the three protocols on approximately 150 yeast isolates each, and the corresponding spectra were then assessed against two reference spectra databases (MSI and Bruker), with appropriate thresholds. Three centers evaluated the impact of the targets. Scores were compared between the various combinations, and identification accuracy was assessed. The protocol omitting the extraction step was inappropriate for yeast identification, while the full extraction method yielded far better results. Rapid formic acid extraction yielded variable results depending on the target, database and threshold. Selecting the optimal extraction method in combination with the appropriate target, database and threshold may enable simple and accurate identification of clinically relevant yeast samples. Concerning the widely used polished-steel targets, the full extraction method still ensured better scores and better identification rates.