Éditeur(s) : HAL CCSD
Résumé : International audience
This article describes a previously unreported mutation at position 210 (C210T) of the mitochondrial large subunit ribosomal RNA (mtLSUrRNA) gene of Pneumocystis jirovecii, which led to a false-negative result of a real-time polymerase chain reaction (PCR) assay. Since the aforementioned real-time PCR assay is widely used in France, a French multicenter study was conducted to estimate the mutation frequency and its potential impact on the routine diagnosis of Pneumocystis pneumonia (PCP). Through analysis of data obtained from eight centers, the mutation frequency was estimated at 0.28%. This low frequency should not call into question the routine use of this PCR assay. Nonetheless, the occurrence of the false-negative PCR result provides arguments for maintaining microscopic techniques combined to PCR assays to achieve PCP diagnosis.
Medical Mycology

hal-01477200
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477200
DOI : 10.1093/mmy/myw051
PUBMED : 27489302

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : National audience
La détection d’Aspergillus dans le liquide bronchiolo-alvéolaire (LBA) est un des critères du diagnostic probable ou prouvé de l’aspergillose invasive (AI). Parallèlement à l’examen mycologique (ED et/ou culture) et à la détection de l’antigène galactomannane (GM) identifiés comme critères EORTC/MSG du diagnostic d’AI probable (de Pauw 2008), la PCR sur prélèvements pulmonaires est devenue un argument majeur du diagnostic de routine. Plusieurs méthodes d’amplification ont été publiées et l’objectif de ce travail était d’évaluer les performances de 2 cibles d’amplification : le gène mitochondrial d’A. fumigatus (AFmito) et l’ARN ribosomal 28S. Entre 01/2012 et 10/2015, 324 LBA ont été prospectivement collectés et analysés sur le plan mycologique (ED et culture) et ont bénéficié d’une détermination du GM (EIA Platelia assay Biorad, seuil à 1,0 si mesure isolée dans le LBA, ou 0,8 si associée à une mesure dans le sérum > 0,5) et d’une PCR AFmito. Puis rétrospectivement, un test PCR 28S a été effectué sur les ADN extraits disponibles (312/324). Selon les critères EORTC/MSG modifiés de 2008, les patients testés étaient classés comme suit : 1 AI prouvée, 47 AI probables et 11 AI possibles. Les autres patients étaient considérés comme 11 colonisés, et 256 non infectés. Les sensibilités du GM dans le LBA, de la PCR 28S et de la PCR AFmito étaient de 58 %, 61 % et 50 %, respectivement. La sensibilité de l’examen mycologique (ED ± culture) était de 33 %. La spécificité du GM dans le LBA, des PCR 28S et AFmito PCR et de la culture étaient de 94 %, 97 %, 97 % et 98 %, respectivement. Les valeurs prédictives négatives étaient de 93 %, 95 %, 92 % et 89 %, respectivement. La concordance entre les 2 PCR était de 97 % (cœfficient kappa 0,84), alors qu’elle était de 88 % (kappa 0,40) entre la PCR 28S et le GM dans le LBA, et de 88 % (kappa 0,43) entre la PCR AFmito PCR et le GM dans le LBA. En conclusion, la PCR 28S a présenté la meilleure performance pour la détection moléculaire d’Aspergillus dans le LBA comparativement à la PCR AFmito. La combinaison de la PCR 28S et de la détection du GM dans le LBA permet d’atteindre une sensibilité de 80 % tout en conservant une excellente spécificité (91 %)
ISSN: 1156-5233

hal-01334068
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01334068
DOI : 10.1016/j.mycmed.2016.04.048

Éditeur(s) : HAL CCSD
Résumé : International audience
In vitro susceptibility of 933 Candida isolates, from 16 French hospitals, to micafungin was determined using the Etest in each center. All isolates were then sent to a single center for determination of MICs by the EUCAST reference method. Overall essential agreement between the two tests was 98.5% at ±2 log2 dilutions and 90.2% at ±1 log2 dilutions. Categorical agreement was 98.2%. The Etest is a valuable alternative to EUCAST for the routine determination of micafungin MICs in medical mycology laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Antimicrobial Agents and Chemotherapy

hal-01367142
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142/file/Multicenter%20comparison%20of%20the%20Etest.pdf
DOI : 10.1128/AAC.00630-16

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: In a malaria-endemic area the distribution of patients is neither constant in time nor homogeneous in space. The WHO recommends the stratification of malaria risk on a fine geographical scale. In the village of Cacao in French Guiana, the study of the spatial and temporal distribution of malaria cases, during an epidemic, allowed a better understanding of the environmental factors promoting malaria transmission. METHODS: A dynamic cohort of 839 persons living in 176 households (only people residing permanently in the village) was constituted between January 1st, 2002 and December 31st, 2007.The information about the number of inhabitants per household, the number of confirmed cases of Plasmodium vivax and house GPS coordinates were collected to search for spatial or temporal clustering using Kurlldorff's statistical method. RESULTS: Of the 839 persons living permanently in the village of Cacao, 359 persons presented at least one vivax malaria episode between 2002 and 2007. Five temporal clusters and four spatial clusters were identified during the study period. In all temporal clusters, April was included. Two spatial clusters were localized at the north of the village near the Comté River and two others localized close to orchards. CONCLUSION: The spatial heterogeneity of malaria in the village may have been influenced by environmental disturbances due to local agricultural policies: deforestation, cultures of fresh produce, or drainage of water for agriculture. This study allowed generating behavioural, entomological, or environmental hypotheses that could be useful to improve prevention campaigns.
ISSN: 1475-2875

inserm-00849010
http://www.hal.inserm.fr/inserm-00849010
http://www.hal.inserm.fr/inserm-00849010/document
http://www.hal.inserm.fr/inserm-00849010/file/2013_Basurko_-_Deforestation_agriculture_and_farm_jobs_a_good_recipe_for_Plasmodium_vivax_in_French_Guiana.pdf
DOI : 10.1186/1475-2875-12-90

Éditeur(s) : HAL CCSD
Résumé : International audience
Treatment failure and symptomatic relapse are major concerns in American tegumentary leishmaniasis (ATL). Such complications are seen frequently in L.guyanensis infections where patients respond variously to first-line anti-leishmanials and are more prone to develop chronic cutaneous leishmaniasis. The factors underlying this pathology, however, are unknown. Recently ,: we reported that a dsRNA virus (LRV1) nested within L.guyanensis parasites is able to exacerbate experimental murine leishmaniasis by inducing a hyper-inflammatory response. This report investigates the prevalence of LRV1 in human L.guyanensis infection and its effect on treatment efficacy as well as its correlation to symptomatic relapses after the first-line treatment. In our cohort of 75 patients diagnosed with primary-localised ATL, the prevalence of LRV1+ infection was elevated to 58%. All patients infected with LRV1-negative L.guyanensis were cured after one (22/31 i.e.71%) or two (31/31 i.e.100%) doses of pentamidine. Oppositely, 12 out of the 44 LRV1-positive patients presented with persistent infection and symptomatic relapse required extended therapy and the use of second-line drugs. Finally, LRV1 presence was associated with a significant increase in intra-lesional inflammatory markers. In conclusion, LRV1 status in L.guyanensis infection is significantly predictive (p=0.0009) of first-line treatment failure and symptomatic relapse, and could stand to guide therapeutic choices in ATL
Journal of Infectious Diseases

hal-01175528
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01175528
DOI : 10.1093/infdis/jiv355
PUBMED : 26123564

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Molecular diagnosis of congenital toxoplasmosis or disseminated toxoplasmosis is based mainly on PCR. The repeated DNA element rep529 has become the main DNA target used in most PCR methods, whether laboratory developed or commercial. In this multicenter study, we evaluated the Toxoplasma ELITe MGB (Elitech) commercial kit by comparison with three reference quantitative PCR assays (RAs) used routinely in three proficient laboratories of the French National Reference Center for Toxoplasmosis network, using Toxoplasma calibrated suspensions diluted to obtain a range of concentrations from 0.1 to 10,000 parasites/ml. These suspensions were extracted with either the DNA extraction kit (EXTRAblood; Elitech) recommended by the manufacturer or the QIAamp DNA minikit (Qiagen). The Toxoplasma ELITe MGB assay was also evaluated on a panel of 128 clinical samples, including 56 amniotic fluid samples, 55 placenta samples, and various other samples, of which 95 originated from patients with proven toxoplasmosis. The ELITe MGB assay amplified low-concentration replicates (<10 parasites/ml) of calibrated suspensions less frequently than the RAs of 2/3 laboratories. Additionally, the combination of EXTRAblood and Toxoplasma ELITe MGB yielded poorer sensitivity than the combination of QIAamp DNA minikit and ELITe MGB for low parasite concentrations (P < 0.001 for 1 parasite/ml). On clinical samples, the sensitivity and the specificity of the commercial assay were 89% and 100%, respectively. The sensitivity ranged from 79% (placenta samples) to 100% (amniotic fluid samples). Overall, this study shows that the Toxoplasma ELITe MGB assay is suitable for the diagnosis of toxoplasmosis from non-cell-rich or non-hemoglobin-rich samples and that the EXTRAblood kit is not optimal.
ISSN: 0095-1137

hal-01526432
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526432
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526432/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01526432/file/Evaluation%20of%20the%20Toxoplasma.pdf
DOI : 10.1128/JCM.02379-16

Éditeur(s) : HAL CCSD American Medical Association (AMA)
Résumé : International audience
IMPORTANCE Although frequently used in treating intensive care unit (ICU) patients with sepsis, empirical antifungal therapy, initiated for suspected fungal infection, has not been shown to improve outcome. OBJECTIVE To determine whether empirical micafungin reduces invasive fungal infection (IFI)-free survival at day 28. DESIGN, SETTING, AND PARTICIPANTS Multicenter double-blind placebo-controlled study of 260 nonneutropenic, nontransplanted, critically ill patients with ICU-acquired sepsis, multiple Candida colonization, multiple organ failure, exposed to broad-spectrum antibacterial agents, and enrolled between July 2012 and February 2015 in 19 French ICUs. INTERVENTIONS Empirical treatment with micafungin (100mg, once daily, for 14 days) (n = 131) vs placebo (n = 129). MAIN OUTCOMES AND MEASURES The primary end pointwas survival without proven IFI 28 days after randomization. Key secondary end points included new proven fungal infections, survival at day 28 and day 90, organ failure, serum (1-3)-beta-D-glucan level evolution, and incidence of ventilator-associated bacterial pneumonia. RESULTS Among 260 patients (mean age 63 years; 91 [35%] women), 251 (128, micafungin group; 123, placebo group) were included in the modified intent-to-treat analysis. Median values were 8 for Sequential Organ Failure Assessment (SOFA) score, 3 for number of Candida-colonized sites, and 99 pg/mL for level of (1-3)-beta-D-glucan. On day 28, there were 82 (68%) patients in the micafungin group vs 79 (60.2%) in the placebo group who were alive and IFI free (hazard ratio [HR], 1.35 [95% CI, 0.87-2.08]). Results were similar among patients with a (1-3)-beta-D-glucan level of greater than 80 pg/mL (n = 175; HR, 1.41 [95% CI, 0.85-2.33]). Day-28 IFI-free survival in patients with a high SOFA score (> 8) was not significantly different when compared between the micafungin vs placebo groups (HR, 1.69 [95% CI, 0.96-2.94]). Use of empirical micafungin decreased the rate of new invasive fungal infection in 4 of 128 patients (3%) in the micafungin group vs placebo (15/123 patients [12%]) (P =.008). CONCLUSIONS AND RELEVANCE Among nonneutropenic critically ill patients with ICU-acquired sepsis, Candida species colonization at multiple sites, and multiple organ failure, empirical treatment with micafungin, compared with placebo, did not increase fungal infection-free survival at day 28.
ISSN: 0098-7484

hal-01405822
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01405822
DOI : 10.1001/jama.2016.14655
PUBMED : 27706483

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Toxoplasmosis is a life-threatening infection in immunocompromised patients (ICPs). The definite diagnosis relies on parasite DNA detection, but the incidence and burden of disease are ill-known in HIV-negative patients. A three-year retrospective study was conducted in 15 reference laboratories from the network of the French National Reference Center for Toxoplasmosis, to record the frequency of Toxoplasma DNA detection in ICPs, to review the molecular methods used for diagnosis and the prevention measures implemented in transplant patients. During the study period, out of 31,640 PCR performed in ICPs, 610 were positive (323 patients). Blood (n=337), cerebrospinal fluid (n=101) and aqueous humor (n=100) samples were more frequently positive. Chemoprophylaxis schemes in transplant patients differed between centers. PCR follow-up of allogeneic hematopoietic stem-cell transplant (allo-HSCT) patients was implemented in 8/15 centers. Data from 180 patients (13 centers) were further analyzed regarding clinical setting and outcome. Only 68/180 (38%) patients were HIV+; the remaining 62% consisted in 72 HSCT, 14 solid-organ transplants, and 26 miscellaneous immunodeficiencies. Cerebral toxoplasmosis and disseminated toxoplasmosis were most frequently observed in HIV and transplant patients, respectively. Of 72 allo-HSCT patients with a positive PCR, 23 were asymptomatic; all were diagnosed in centers performing systematic blood PCR follow-up, and received specific treatment. Overall survival of allo-HSCT patients at two months was better in centers with PCR follow-up than in other centers (p<0.01). This study provides updated data on the frequency of toxoplasmosis in HIV-negative ICPs and suggests that regular PCR follow-up of allo-HSCT patients could guide pre-emptive treatment and improve outcome.
ISSN: 0095-1137

hal-01134189
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01134189
DOI : 10.1128/JCM.03282-14
PUBMED : 25762774

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Anti-Aspergillus IgG antibodies are important biomarkers for the diagnosis of chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA). We compared the performance of a new commercial EIA (Bordier Affinity Products) with those of the Bio-Rad and VirionSerion EIAs. This assay is novel in the association of two recombinant antigens with somatic and metabolic antigens of A. fumigatus. In a prospective multicentre study, 436 serum samples from 147 patients diagnosed with CPA (136 sera/104 patients) or ABPA (94 sera/43 patients) and from 205 controls (206 sera) were tested. We obtained sensitivities of 97%, 91.7%, and 86.1%, and specificities of 90.3%, 91.3%, and 81.5% for the Bordier, Bio-Rad and VirionSerion tests, respectively. The Bordier kit was more sensitive than the Bio-Rad kit (p < 0.01), which was itself more sensitive than the VirionSerion kit (p=0.04). The Bordier and Bio-Rad kits had similar specificities (p=0.8), both higher than that of the VirionSerion kit (p=0.02). The areas under the ROC curves confirmed the superiority of the Bordier kit over the Bio-Rad and the VirionSerion kits (0.977, 0.951 and 0.897, respectively; p < 0.01 for each comparison). In a subset analysis of 279 sera tested with the Bordier and Bio-Rad kits and an in-house immunoprecipitin assay (IPD), the Bordier kit had the highest sensitivity (97.7%), but the IPD tended to be more specific (71.2 and 84.7%, respectively; p=0.10).The use of recombinant, somatic and metabolic antigens in a single EIA improved the balance between sensitivity and specificity, resulting in an assay highly suitable for use in the diagnosis of chronic and allergic aspergillosis.
ISSN: 0095-1137

hal-01282328
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328/file/Prospective%20evaluation%20of%20a%20new%20Aspergillus.pdf
DOI : 10.1128/JCM.03261-15

Éditeur(s) : HAL CCSD Centers for Disease Control and Prevention
Résumé : International audience
To determine when risk for Buruli ulcer is highest, we examined seasonal patterns in a highly disease-endemic area of Cameroon during 2002-2012. Cases peaked in March, suggesting that risk is highest during the high rainy season. During and after this season, populations should increase protective behaviors, and case detection efforts should be intensified.
ISSN: 1080-6040

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01307147
https://hal-amu.archives-ouvertes.fr/hal-01307147
https://hal-amu.archives-ouvertes.fr/hal-01307147/document
https://hal-amu.archives-ouvertes.fr/hal-01307147/file/14-1336.pdf
DOI : 10.3201/eid2108.141336

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : National audience
The sources of exposure during diseases due to Aspergillus fungi in cystic fibrosis patients are still poorly explored. We assessed home fungal exposure in patients suffering from cystic fibrosis and analysed its impact on the presence of Aspergillus biological markers, the colonisation of airways, as well as the sensitization and Aspergillus serology. Between March 2012 and August 2012, 34 patients benefited from a visit performed by a home environment medical adviser including sampling for mycological analysis. The number of colonies of Aspergillus was not significantly different in the various sampling sites (P = 0.251), but the number of non-Aspergillus colonies was much higher in the kitchen (P = 0.0045). Subsequently, home fungal exposure was compared between the groups “absence of Aspergillus-related markers” and “presence of Aspergillus-related markers”. Home exposure to Aspergillus (P = 0.453) and non-Aspergillus (P = 0.972) flora was not significant between the 2 groups. Within this series of 34 patients that should be expanded, we note an absence of clear relationship between home exposure and the Aspergillus-linked markers in patients suffering from cystic fibrosis. This result should be taken into account regarding too restrictive hygiene advices provided to families, given the fact that fungal exposure can also results from activities performed away from home.
La source d’exposition au cours des pathologies aspergillaires du patient atteint de mucoviscidose reste encore peu explorée. Nous avons évalué l’exposition fongique domiciliaire chez des patients atteints de mucoviscidose, et analysé son impact sur la présence de marqueurs biologiques aspergillaires, colonisation des voies aériennes, ainsi que sensibilisation et sérologie anti-aspergillaire. Trente-quatre patients ont bénéficié d’une visite par un conseiller médical en environnement intérieur entre mars et août 2012, comprenant des prélèvements à visée mycologique. Le nombre de colonies aspergillaires ne différait pas significativement d’un site de prélèvement à l’autre (p = 0,251), mais le nombre de colonies non aspergillaires était significativement plus important dans la cuisine (p = 0,0045). L’exposition fongique domiciliaire a ensuite été comparée entre les groupes « marqueurs aspergillaires absents » et « marqueurs aspergillaires présents ». L’exposition domiciliaire à une flore aspergillaire (p = 0,453) et non aspergillaire (p = 0,972) ne différait pas significativement entre les 2 groupes. Sur cette série de 34 patients qui mérite d’être élargie, on note une absence de lien évident entre l’exposition domiciliaire et la pathologie aspergillaire. Ce résultat doit rendre prudent sur des conseils d’hygiène parfois très contraignants donnés aux familles, l’exposition fongique étant également importante dans le cadre des activités extra-domiciliaires.
ISSN: 1156-5233

hal-01158660
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01158660/file/Exposition%20domiciliaire%20aux%20moisissures%20postprint%20MYCMED-S-14-00173.pdf
DOI : 10.1016/j.mycmed.2015.03.005

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : National audience
Introduction L’objectif de cette étude est de disposer de données qualitatives et quantitatives sur la contamination de l’environnement intérieur hospitalier, microbiologique et chimique, afin d’évaluer l’exposition du personnel, des visiteurs et des patients et la variabilité spatio-temporelle de la contamination. Méthodes L’étude s’est déroulée dans différents lieux des CHU de Rennes et de Nancy : hall d’accueil, salle de soins infirmiers, salle de réveil post-opératoire, chambre d’un patient, unité de désinfection des endoscopes, laboratoire de parasitologie et salle de découpe de plâtres. Deux campagnes de prélèvement ont eu lieu en été 2014 et en hiver 2015. Les méthodes de prélèvement étaient nombreuses et complémentaires (Fig. 1). L’analyse des données a été réalisée sous IBM SPSS grâce au test de Mann-Whitney et le coefficient de corrélation de Pearson. Résultats Les concentrations d’aldéhydes, de composés organiques volatils (COV) et semi-volatils étaient faibles à très faibles dans les 2 établissements. Étaient détectables, mais sans différences globales entre les 2 établissements : la contamination fongique (m = 226 UFC/m3 ; p = 0,97) ou bactérienne (m = 352 UFC/m3 ; p = 0,14), les particules PM2,5 (m = 2,1 μg/m3 ; p = 0,97) et PM10 (m = 6,6 μg/m3 ; p = 0,84). Sur le plan saisonnier, la contamination fongique était plus importante en été pour les 2 établissements (p = 0,002). La contamination bactérienne ne varie pas significativement entre les locaux (p = 0,14) contrairement à la contamination fongique (p = 0,02) et particulaires PM2,5 (p = 0,01) ou PM10 (p = 0,01). Cette dernière est plus importante dans le hall (m = 879 UFC/m3), le laboratoire de parasitologie (m = 333 UFC/m3) et la salle de plâtre (m = 310 UFC/m3). Nous ne retrouvons pas de corrélation significative entre le nombre de personnes, le taux de CO2, l’humidité relative et le dénombrement bactérien ou fongique. Néanmoins nous retrouvons une relation forte entre la température du local et la contamination bactérienne (r = 0,7, p = 0,008) ou la contamination fongique (r = 0,56, p = 0,045) d’une part, et entre la contamination fongique et les PM10 (r = 0,52, p = 0,022) d’autre part. Conclusion Notre étude montre une très faible contamination par les aldéhydes, COV et sCOV comparativement à d’autres lieux publics. La forte variabilité spatio-temporelle de la contamination fongique et particulaire est liée à la saison, à l’activité et à la ventilation
ISSN: 1156-5233

hal-01334070
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01334070
DOI : 10.1016/j.mycmed.2016.04.026