ABSTRACT Though a confined or a broad population is exposed respectively to endemic or pandemic infections, in the same environment, some individuals resist the development of infections. The attributed reason is the inheritance of a set of immune system genes that can efficiently deal with the pathogens. In this study, we show how outbred mice differentially respond to Cryptococcus neoformans, a fungal pathogen, and the mechanism through which the surviving mice mount a protective immune defense. We identified that those mice developing antibodies specifically against Pep1p, an aspartic protease secreted by C. neoformans , had significantly improved survival. Vaccination (either prophylactic or therapeutic) with a recombinant Pep1p significantly increased the survival of the mice by decreasing the fungal load and stimulating a protective immune response. Passive immunization of C. neoformans- infected mice with monoclonal antibodies developed against Pep1p also improves the survival of the mice by increasing phagocytosis of C. neoformans and decreasing the multiplication of this fungus. Together, these data demonstrate the prophylactic and therapeutic potentials of the C. neoformans antigenic protein Pep1p or Pep1p-specific antibodies against this fungal infection. Also, this study suggests that the immunological interaction and thereby the responses developed against a pathogen guide the hosts to behave differentially against microbial pathogenicity. IMPORTANCE Vaccination and immunotherapies against fungal pathogens still remain a challenge. Here, we show using an in vivo model based on outbred mice that development of antibodies against Pep1p, an antigenic protein of the fungal pathogen Cryptococcus neoformans , confers resistance to this fungal infection. In support of this observation, prophylactic or therapeutic immunization of the mice with recombinant Pep1p could improve their survival when infected with a lethal dose of C. neoformans . Moreover, passive therapy with monoclonal anti-Pep1p antibodies also enhanced survival of the mice from C. neoformans infection. The associated antifungal mechanisms were mounting of a protective immune response and the development of fungal specific antibodies that decrease the fungal burden due to an increase in their phagocytosis and/or inhibit the fungal multiplication. Together, our study demonstrates (a) the mode of host–fungal interaction and the immune response developed thereby play a crucial role in developing resistance against C. neoformans ; (b) Pep1p, an aspartic protease as well as an antigenic protein secreted by C. neoformans , can be exploited for vaccination (both prophylactic and therapeutic) or immunotherapy to improve the host defense during this fungal infection.

La majorité des cas de cryptococcose en France surviennent actuellement chez des sujets séronégatifs pour le Virus de l'Immunodéficience Humain (VIH), mais les caractéristiques, les présentations, et la mortalité liée à ces infections n'ont jusqu'à présent pas été décrites. Pour tous les cas de cryptococcose chez des sujets VIH-négatifs identifiés entre 2005 et 2020, nous décrivons les principales caractéristiques démographiques, les présentations, les traitements entrepris, et la mortalité à 90 jours en fonction du facteur de risque sous-jacent et de la localisation de l'infection. Pour les sujets présentant une atteinte pulmonaire de cryptococcose, nous avons analysé les facteurs associés au fait d'avoir une localisation disséminée associée. Pour le sous-groupe de patients hospitalisés pour une cryptococcose neuroméningée et/ou disséminée, nous avons analysé les facteurs associés à la mortalité à 90 jours en utilisant un modèle de régression logistique. Entre 2005 et 2020, 632 cas de cryptococcose ont été identifiés chez des sujets séronégatifs pour le VIH. L'âge médian était de 61 ans, et 62% étaient des hommes. La majorité (61%) étaient dues à Cryptococcus neoformans sérotype A, et seuls 13 cas étaient dues à Cryptococcus gattii. Le taux de létalité à 90 jours était de 27.0% (IC95%: 23,3-31.0%). Parmi les 632 cas, 102 étaient transplantés d'organe solide (TOS) (20%, dont 71% étaient transplantés du rein), 202 avaient une néoplasie (32%, dont 81% avaient une hémopathie maligne, le plus souvent lymphoïde [68%]), 202 avaient un autre facteur de risque (32%, les plus fréquents étant une maladie auto-immune, une insuffisance hépatique ou rénale, ou une sarcoidose, et parmi lesquels 53% avaient reçu une corticothérapie systémique). Enfin, 99 (16%) n'avaient pas de facteur de risque identifié. La majorité des sujets (n= 401, 63%) avaient une cryptococcose neuroméningée et/ou disséminée. Celle-ci était associée à une létalité à 90 jours significativement plus élevée qu'en cas de localisation extra-neurologique isolée (34.2% vs. 14.7%, p<0.001). Les formes neuroméningées/disséminées était plus fréquentes chez les TOS (p<0.001), qui avaient également plus souvent un antigène cryptococcique (CrAg) sanguin positif, avec un titre >1:256 (p<0.001). La forme pulmonaire isolée était plus fréquente chez les patients avec 'autres facteurs' (p<0.001), et la forme cutanée isolée plus fréquente chez ceux sans facteur de risque (p<0.001). Les sujets ayant une néoplasie étaient plus âgés (p=0.0001), et avaient le taux de létalité à 90 jours le plus élevé (37.3%), comparés aux TOS (23.7%), ceux avec 'autres facteurs' (24.7%), et ceux sans facteur de risque identifié (13.9%) (p<0.001). Par ailleurs, 30% de sujets ayant une néoplasie et une forme neuroméningée n'ont pas reçu un traitement d'induction antifongique optimal associant de la flucytosine. 204 sujets avaient une localisation pulmonaire confirmée microbiologiquement. Les facteurs associés au fait d'avoir également une atteinte neurologique/disséminée associée étaient l'âge avancé (p=0.049), le sexe masculin (p=0.04), la greffe d'organe solide (p=0.047), et la positivité du CrAg sanguin (quel que soit le titre) (p<0.001). Sur 46 sujets avec une atteinte cutanée isolée, 31 (67%) avaient un facteur d'exposition professionnel identifié. Aucun n'était décédé à 3 mois. Parmi 401 sujets avec une atteinte neuroméningée et/ou disséminée, les facteurs associés à la mortalité à 90 jours en analyse univariée étaient l'âge avancé (3e tercile, odds ratio [OR]: 3.6 [1.9-6.8], p<0.001), la néoplasie (OR : 2.9 [1.1-7.5]), un titre de CrAg >1:256 dans le liquide cérébrospinal (OR: 7.8 [1.7-35], p=0.007), et le fait d'avoir reçu un traitement antifongique à base de flucytosine (OR: 0.54 [0.30-0.98], p=0.04). En analyse multivariée, seul l'âge avancé (aOR: 2.72 [1.31-5.65]) était indépendamment associé à un surrisque de mortalité. Les sujets VIH-négatifs représentent un groupe hétérogène de patients, avec des caractéristiques et présentations qui varient en fonction du facteur de risque sous-jacent et de la localisation de la maladie, ce qui implique une prise en charge individualisée. Aucun lien d'intérêt

Abstract S4.1 Treatment of rare mold infections in 2021: the role of new and old antifungals, September 22, 2022, 10:30 AM - 12:00 PM Background & Objectives The NRCMA oversees the surveillance of invasive fungal diseases in France. As part of our expertise, we perform antifungal susceptibility testing based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) methodology on all isolates. The antifungal profiles help us monitor the emergence of resistant isolates, determine the susceptibility pattern of wild-type strains to new antifungals, and in specific cases, determine the relationship between clinical failure and selection/emergence of a less susceptible isolate. We review the Minimum inhibitory concentrations (MIC) distribution of eight antifungals on clinical isolates of filamentous fungi identified at the NRCMA from 2003 to 2021. Methods Species identification was performed by a combination of morphological features and multilocus sequencing. Only strains that produced enough conidia or spores were tested. In vitro susceptibility testing was performed according to the EUCAST procedure. Eight antifungal agents were used: triazoles [itraconazole, voriconazole, posaconazole, isavuconazole (since 2015)], echinocandins (caspofungin, micafungin), amphothericin B, and terbinafine. The concentrations inhibiting 50% (MIC50) and 90% (MIC90) of the isolates were determined for species with at least 5 and 10 isolates, respectively. For Aspergillus fumigatus isolates exhibiting high azole MICs, we sequenced the cyp51A gene for mutation screening. Results MICs were obtained for 3343 pathogenic strains. We identified Aspergillus spp. including cryptic species (32%), Fusarium spp. (21%), Mucorales (18%), phaeohyphomycetes (10%), i.e., Alternaria spp., Curvularia spp., Fonsecaea, Exophiala, Phaeoacremonium, rare hyphomycetes (9%), i.e., Rasamsonia, Paecilomyces, Trichoderma, Scopulariopsis. Scedosporium spp. (7%) and emergent pathogens such as Nannizziopsis obscura (1%), dimorphic fungi (1%), or to a less extent basidiomycetous molds. Examples of MIC results are presented in Table 1. For the nine genera of the order Mucorales, amphotericin B (AmB) exhibited low MICs except for Cunninghamella species and Saksenaea vasiformis. Posaconazole had variable activity depending on the species (high MIC values were observed for Mucor species) while voriconazole and echinocandins had none. In section Fumigati, amphotericin B MIC values were high due to the intrinsic resistance of cryptic species Aspergillus lentulus and A. udagawae. Other cryptic species were identified such as A. hiratsukae isolates which exhibited low MICs to all antifungals. Members of Aspergillus section Nidulantes such as A. nidulans and A. quadrilineatus showed variable MICs to caspofungin and amphotericin B. Among melanized fungi, Alternaria infectoria and A. alternata species group displayed low MICs of all azoles with the exception of voriconazole. Four Exophiala species were analyzed and had similar azole MICs, E. spinifera being the species with the lowest values. Multi-drug resistant profiles were observed especially in species belonging to Microascales such as Lomentospora prolificans, Microascus cirrosus, and Scopulariopsis brevicaulis. Members of Fusarium species complexes had predictably high MIC values to all antifungals including isavuconazole. Only Fusarium dimerum species complex had low MICs to amphotericin B. Further distribution analysis is ongoing. These large datasets provide a baseline for monitoring the emergence of antifungal resistance in our country and supports the fact that MIC determination should be performed for rare/emergent species and also in case of infections due to cryptic species, which would benefit patient management.

The French National Reference Center for Invasive Mycoses and Antifungals leads an active and sustained nationwide surveillance program on probable and proven invasive fungal diseases (IFDs) to determine their epidemiology in France. Between 2012 and 2018, a total of 10,886 IFDs were recorded. The incidence increased slightly over time (2.16 to 2.36/10,000 hospitalization days, P = 0.0562) in relation with an increase of fungemia incidence (1.03 to 1.19/10,000, P = 0.0023), while that of other IFDs remained stable. The proportion of ≥65-year-old patients increased from 38.4% to 45.3% (P < 0.0001). Yeast fungemia (n = 5,444) was due mainly to Candida albicans (55.6%) with stable proportions of species over time. Echinocandins became the main drug prescribed (46.7% to 61.8%), but global mortality rate remained unchanged (36.3% at 1 month). Pneumocystis jirovecii pneumonia (n = 2,106) was diagnosed mostly in HIV-negative patients (80.7%) with a significantly higher mortality than in HIV-positive patients (21.9% versus 5.4% at 1 month, P < 0.0001). Invasive aspergillosis (n = 1,661) and mucormycosis (n = 314) were diagnosed mostly in hematology (>60% of the cases) with a global mortality rate of 42.5% and 59.3%, respectively, at 3 months and significant changes in diagnosis procedure over time. More concurrent infections were also diagnosed over time (from 5.4% to 9.4% for mold IFDs, P = 0.0115). In conclusion, we observed an aging of patients with IFD with a significant increase in incidence only for yeast fungemia, a trend toward more concurrent infections, which raises diagnostic and therapeutic issues. Overall, global survival associated with IFDs has not improved despite updated guidelines and new diagnostic tools. IMPORTANCE The epidemiology of invasive fungal diseases (IFDs) is hard to delineate given the difficulties in ascertaining the diagnosis that is often based on the confrontation of clinical and microbiological criteria. The present report underlines the interest of active surveillance involving mycologists and clinicians to describe the global incidence and that of the main IFDs. Globally, although the incidence of Pneumocystis pneumonia, invasive aspergillosis, and mucormycosis remained stable over the study period (2012 to 2018), that of yeast fungemia increased slightly. We also show here that IFDs seem to affect older people more frequently. The most worrisome observation is the lack of improvement in the global survival rate associated with IFDs despite the increasing use of more sensitive diagnostic tools, the availability of new antifungal drugs very active in clinical trials, and a still low/marginal rate of acquired in vitro resistance in France. Therefore, other tracks of improvement should be investigated actively.

Abstract Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives HIV-negative individuals make up an increasing proportion of cases of cryptococcosis in France, but the features of disease and outcomes in this population have yet to be characterized. We describe the presentations and outcomes according to host factors underlying cryptococcosis in HIV-negative individuals in France. Methods The French National Reference Centre for Invasive Mycoses and Antifungals has implemented nationwide surveillance of cryptococcosis since 1985 with the determination of the infecting serotype. We analyzed the characteristics of infection in HIV-negative patients diagnosed up to 2020. We also compared the demographic characteristics, presenting features, treatment regimen, and outcomes according to host factor and infecting serotype in patients diagnosed since 2005. Results The mean age of patients was 56.2 years, 60.8% were male, and 60.1% were born in Europe. Only 26 cases were due to Cryptococcus gattii, all others were caused by C. neoformans. Of the 1051 cases, 349 occurred in patients with malignancy (33.2%, including 268 patients with hematological malignancy, 69% of whom had lymphoid neoplasms), 205 occurred in solid-organ transplant (SOT) recipients (19.5%, including 147 kidney and 27 liver), and 298 occurred in patients with ‘other’ underlying factors (28.4%, including auto-immune disease (n = 86), end-stage liver or kidney disease (n = 47), sarcoidosis (n = 42), chronic pulmonary disease (n = 25), and diabetes mellitus (n = 16). A total of 19% of patients (n = 199) had no apparent underlying risk factor. Among 632 patients diagnosed since 2005, there were significant differences according to the four major categories of risk factors (malignancy, SOT, others, and none) in terms of age, diagnostic methods, proportion of patients with positive cryptococcal antigen (CrAg), antigen titers, disease localization, treatment regimens, and 90-day mortality. In the diagnostic workup, a lumbar puncture and blood culture were performed for 96% and 64.2% of patients, respectively, more frequently for immunocompromised patients than those with no underlying host factor (P = .09 and P <.001, respectively). SOT patients had more frequent central nervous system involvement (P <.001), and positive serum CrAg detection with antigen titers >1:512 (P <.001). Patients with malignancy were significantly older (P = .0001) with more frequent fungemia (P = .007). Isolated lung infections (P = .002) and isolated skin lesions (P <.001) were more frequent in patients with ‘other’ conditions and in those with no underlying factor, respectively. Immunocompromised patients were more likely to receive combination antifungals including flucytosine (66.7%, 45.4%, and 42.7% for SOT, malignancies, and ‘other’ conditions, respectively) compared with patients with no underlying factor (33.3%, P <.001). Overall, all cause 90-day mortality was 27.0% (95% CI: 23, 3-31.0%). Patients with malignancy had the highest 90-day mortality (37.3%, <0.001), compared with SOT recipients (23.7%), those with ‘other' conditions (24.7%), and those without underlying conditions (13.9%). Compared with patients with serotype D infections, those infected with serotype A were significantly younger (P = .004), more likely to be born in Africa (P <.001), to have isolated pulmonary disease (P <.005), and less likely to have isolated skin infections (P <.001). Conclusion HIV-seronegative patients with cryptococcosis are a heterogeneous group of patients encompassing different disease characteristics and outcomes. Management of cryptococcosis in HIV-negative patients should be tailored to underlying host factors, disease localization, and infecting serotype.

Since echinocandins are recommended as first line therapy for invasive candidiasis, detection of resistance, mainly due to alteration in FKS protein, is of main interest. EUCAST AFST recommends testing both MIC of anidulafungin and micafungin, and breakpoints (BPs) have been proposed to detect echinocandin-resistant isolates.

Invasive yeast infections represent a major global public health issue, and only few antifungal agents are available. Azoles are one of the classes of antifungals used for treatment of invasive candidiasis. The determination of antifungal susceptibility profiles using standardized methods is important to identify resistant isolates and to uncover the potential emergence of intrinsically resistant species.

Scedosporiosis/lomentosporiosis is a devastating emerging fungal infection. Our objective was to describe the clinical pattern and to analyze whether taxonomic grouping of the species involved was supported by differences in terms of clinical presentations or outcomes. We retrospectively studied cases of invasive scedosporiosis in France from 2005 through 2017 based on isolates characterized by polyphasic approach. We recorded 90 cases, mainly related to Scedosporium apiospermum (n = 48), S. boydii/S. ellipsoideum (n = 20), and Lomentospora prolificans (n = 14). One-third of infections were disseminated, with unexpectedly high rates of cerebral (41%) and cardiovascular (31%) involvement. In light of recent Scedosporium taxonomic revisions, we aimed to study the clinical significance of Scedosporium species identification and report for the first time contrasting clinical presentations between infections caused S. apiospermum, which were associated with malignancies and cutaneous involvement in disseminated infections, and infections caused by S. boydii, which were associated with solid organ transplantation, cerebral infections, fungemia, and early death. The clinical presentation of L. prolificans also differed from that of other species, involving more neutropenic patients, breakthrough infections, fungemia, and disseminated infections. Neutropenia, dissemination, and lack of antifungal prescription were all associated with 3-month mortality. Our data support the distinction between S. apiospermum and S. boydii and between L. prolificans and Scedosporium sp. Our results also underline the importance of the workup to assess dissemination, including cardiovascular system and brain. Lay Summary Scedosporiosis/lomentosporiosis is a devastating emerging fungal infection. Our objective was to describe the clinical pattern and to analyze whether taxonomic grouping of the species involved was supported by differences in terms of clinical presentations or outcomes.

The aim of this study was to evaluate diagnostic means, host factors, delay of occurrence, and outcome of patients with COVID-19 pneumonia and fungal coinfections in the intensive care unit (ICU). From 1 February to 31 May 2020, we anonymously recorded COVID-19-associated pulmonary aspergillosis (CAPA), fungemia (CA-fungemia), and pneumocystosis (CA-PCP) from 36 centers, including results on fungal biomarkers in respiratory specimens and serum. We collected data from 154 episodes of CAPA, 81 of CA-fungemia, 17 of CA-PCP, and 5 of other mold infections from 244 patients (male/female [M/F] ratio = 3.5; mean age, 64.7 +/- 10.8 years). CA-PCP occurred first after ICU admission (median, 1 day; interquartile range [IQR], 0 to 3 days), followed by CAPA (9 days; IQR, 5 to 13 days), and then CA-fungemia (16 days; IQR, 12 to 23 days) (P < 10(-4)). For CAPA, the presence of several mycological criteria was associated with death (P < 10(-4)). Serum galactomannan was rarely positive (,20%). The mortality rates were 76.7% (23/ 30) in patients with host factors for invasive fungal disease, 45.2% (14/31) in those with a preexisting pulmonary condition, and 36.6% (34/93) in the remaining patients (P = 0.001). Antimold treatment did not alter prognosis (P = 0.370). Candida albicans was responsible for 59.3% of CA-fungemias, with a global mortality of 45.7%. For CA-PCP, 58.8% of the episodes occurred in patients with known host factors of PCP, and the mortality rate was 29.5%. CAPA may be in part hospital acquired and could benefit from antifungal prescription at the first positive biomarker result. CA-fungemia appeared linked to ICU stay without COVID-19 specificity, while CA-PCP may not really be a concern in the ICU. Improved diagnostic strategy for fungal markers in ICU patients with COVID-19 should support these hypotheses. IMPORTANCE To diagnose fungal coinfections in patients with COVID-19 in the intensive care unit, it is necessary to implement the correct treatment and to prevent them if possible. For COVID-19-associated pulmonary aspergillosis (CAPA), respiratory specimens remain the best approach since serum biomarkers are rarely positive. Timing of occurrence suggests that CAPA could be hospital acquired. The associated mortality varies from 36.6% to 76.7% when no host factors or host factors of invasive fungal diseases are present, respectively. Fungemias occurred after 2 weeks in ICUs and are associated with a mortality rate of 45.7%. Candida albicans is the first yeast species recovered, with no specificity linked to COVID-19. Pneumocystosis was mainly found in patients with known immunodepression. The diagnosis occurred at the entry in ICUs and not afterwards, suggesting that if Pneumocystis jirovecii plays a role, it is upstream of the hospitalization in the ICU.

Replacement of fluconazole by echinocandins as the first-line therapy for yeast-related fungemia could have an impact on both the mortality rate and the epidemiology of yeast species responsible for candidemia. We analyzed the individual clinical and microbiological data collected through the active surveillance program on yeast fungemia (YEASTS program, 2004–2016, Paris area, France) within 14 University Hospitals. The cohort included 3,092 patients [male:female ratio: 1.56; median age 61.0 years (IQR: 23.8)]. The mean mortality rate within 30 days was 38.5% (1,103/2,868) and significantly higher in intensive care units (690/1,358, 50.8%) than outside (413/1,510, 27.4%, p < 0.0001) without significant change over time. The yeast species distribution [ Candida albicans ( n = 1,614, 48.0%), Candida glabrata ( n = 607, 18.1%), Candida parapsilosis ( n = 390, 11.6%), Candida tropicalis ( n = 299, 8.9%), Candida krusei ( n = 96, 2.9%), rare species ( n = 357, 10.6%)], minimal inhibitory concentration distribution, and the distribution between the patient populations (hematological malignancies, solid tumors, without malignancy) did not change either while the proportion of patients ≥60-years increased from 48.7% (91/187) in 2004 to 56.8% (133/234) in 2017 ( p = 0.0002). Fluconazole as first-line therapy dramatically decreased (64.4% in 2004 to 27.7% in 2017, p < 0.0001) with a corresponding increase in echinocandins (11.6% in 2004 to 57.8% in 2017, p < 0.0001). Survival rates did not differ according to the first antifungal therapy. The progressive replacement of fluconazole by echinocandins as the first-line antifungal therapy was not associated with change in global mortality, regardless of species involved and antifungal susceptibility profiles. Other factors remain to be uncovered to improve the prognosis of yeast fungemia.

Laboratory diagnosis of histoplasmosis is based on various methods, including microscopy, culture, antigen, and DNA detection of Histoplasma capsulatum var. capsulatum or Histoplasma capsulatum var. duboisii. To improve sensitivity of existing real-time quantitative PCR (qPCR) assays, we developed a new RT-qPCR assay that allows amplification of whole nucleic acids of Histoplasma spp. validated on suspected cases. The limit of detection was 20 copies, and the specificity against 114 fungal isolates/species was restricted to Histoplasma spp. Whole nucleic acids of 1319 prospectively collected consecutive samples from 907 patients suspected of having histoplasmosis were tested routinely between May 2015 and May 2019 in parallel with standard diagnostic procedures performed in parallel. Forty-four had proven histoplasmosis attributable to H. capsulatum var. capsulatum (n = 40) or H. capsulatum var. duboisii (n = 4) infections. The results of RT-qPCR were positive in 43 of 44 patients (97.7% sensitivity) in at least one specimen. Nine of 863 cases (99% specificity) were RT-qPCR positive and therefore classified as possible cases. RT-qPCR was positive in 13 of 30 (43.3%) blood samples tested in proven cases. A positive RT-qPCR result in blood was significantly associated with H. capsulatum var. capsulatum progressively disseminated histoplasmosis with a positive RT-qPCR result in 92.3% of the immunocompromised patients with disseminated disease. This new Histoplasma RT-qPCR assay enabling amplification of H. capsulatum var. capsulatum and H. capsulatum var. duboisii is highly sensitive and allows the diagnosis of histoplasmosis advantageously from blood and bronchoalveolar lavage fluid.

Background Trichosporonosis is a rare invasive infection in humans mainly due toTrichosporon asahii, and especially recovered from patients having haematological malignancy. Since 2012, IGS1 region sequencing is used as a genotyping method to distinguish isolates, with high frequency of one haplotype worldwide and a geographic specificity for some haplotypes. Objectives We compared the IGS1 genotyping method and whole genome sequencing (WGS) to study the relationship between clinical isolates involved in two grouped cases in France. Methods IGS1 sequencing and antifungal susceptibility testing were performed for 54 clinical isolates. Clinical data for 28 isolates included in surveillance programs were analysed. Whole genome was sequenced for 32 clinical isolates and the type strain. Results All isolates were intrinsically resistant to flucytosine, while voriconazole had the most potent in vitro activity. The majority of the isolates was recovered from patients with haematological malignancies (42.86%), with a high proportion of children (<15 yrs-old, 32.14%) and a high mortality rate at three months (46.15%). Based on the WGS analysis, isolates exhibiting IGS1 haplotype 1, 3 and 7 belonged to different clades. Five isolates recovered during the first grouped cases had the same IGS1 haplotype and shared 99% of SNPs similarity. For the second grouped cases, four isolates had 98.7% of SNPs similarity while the isolate recovered 4 years earlier was totally unlinked. Conclusions We confirmed the usefulness of IGS1 sequencing for grouped cases infection ofT. asahii. We underlined its limitation for the study of population structure and the utility of WGS analysis for the study of epidemiologically unrelated isolates.

Saprochaete clavata is a pathogenic yeast responsible for rare outbreaks involving immunocompromised patients, especially those with hematologic malignancies. During February 2016–December 2017, we diagnosed S. clavata infections in 9 patients (8 with fungemia), including 3 within 1 month, at a cancer center in Marseille, France. The patients (median age 58 years), 4 of 9 of whom had acute myeloid leukemia, were hospitalized in 3 different wards. Ten environmental samples, including from 2 dishwashers and 4 pitchers, grew S. clavata, but no contaminated food was discovered. The outbreak ended after contaminated utensils and appliances were discarded. Whole-genome sequencing analysis demonstrated that all clinical and environmental isolates belonged to the same phylogenetic clade, which was unrelated to clades from previous S. clavata outbreaks in France. We identified a dishwasher with a deficient heating system as the vector of contamination.

Summary Background Yarrowia lipolytica belongs to the normal human microbiota but is also found in substrates with high contents in lipids and used in biotechnological processes. It is sometimes reported as human pathogen and especially in catheter‐related candidaemia. Objectives Two apparently grouped cases of infections and/or contamination were reported involving 3 and 9 patients, respectively, in two hospitals. The goal of this study was to design a molecular tool to study the genetic diversity of Y lipolytica and confirm or not the common source of contamination during these grouped cases. Methods Given that there is no genotyping method, we used genomic markers assessed on environmental isolates to determine intra‐species relationship. We selected five highly polymorphic intergenic regions, totalling more than 3200 bp and sequenced them for clinical (n = 20) and environmental (n = 14) isolates. Antifungal susceptibility was determined by EUCAST broth microdilution method. Results Multiple alignment of the five sequences revealed divergence of 0%‐5.8% between isolates as compared to approximately 0.2%‐0.25% after alignment of whole genomes, suggesting their potential usefulness to establish genetic relatedness. The analysis showed the multiple origins of the isolates. It uncovered two grouped case of fungaemia involving 3 and 2 patients, respectively. It also revealed several unrelated sporadic cases despite their temporal relationship and one probable laboratory contamination by a common yet uncovered source, explaining several consecutive positive cultures without infection. All isolates had high minimal inhibitory concentration (MIC) for flucytosine, the majority (14/34) was susceptible to fluconazole, and all to the other antifungal agents tested. Conclusion This method could help elucidate cases related to the opportunistic pathogen Y lipolytica .

With new or emerging fungal infections, human and animal fungal pathogens are a growing threat worldwide. Current diagnostic tools are slow, non-specific at the species and subspecies levels, and require specific morphological expertise to accurately identify pathogens from pure cultures. DNA barcodes are easily amplified, universal, short species-specific DNA sequences, which enable rapid identification by comparison with a well-curated reference sequence collection. The primary fungal DNA barcode, ITS region, was introduced in 2012 and is now routinely used in diagnostic laboratories. However, the ITS region only accurately identifies around 75% of all medically relevant fungal species, which has prompted the development of a secondary barcode to increase the resolution power and suitability of DNA barcoding for fungal disease diagnostics. The translational elongation factor 1α (TEF1α) was selected in 2015 as a secondary fungal DNA barcode, but it has not been implemented into practice, due to the absence of a reference database. Here, we have established a quality-controlled reference database for the secondary barcode that together with the ISHAM-ITS database, forms the ISHAM barcode database, available online at http://its.mycologylab.org/ . We encourage the mycology community for active contributions.

Objectives: Isavuconazole is a recent extended-spectrum triazole with activity against yeasts. However, few data are available about the in vitro activity of rare yeast species. We report the MIC distribution of isavuconazole compared with fluconazole for a large collection of common or rare yeasts. Methods: Isavuconazole and fluconazole MICs were determined using the EUCAST method for 1457 clinical isolates, mainly recovered from invasive infections, belonging to 29 species. They were sent to the National Reference Centre for Invasive Mycoses & Antifungals between January 2015 and October 2017 and species identification was performed using a polyphasic approach (matrix-assisted laser desorption/ ionization time of flight analysis and a molecular method). Results: Isavuconazole had effective in vitro activity against Cryptococcus neoformans (MIC90 < 0.25 mg/L), the five most common Candida spp. (MIC90 <= 0.5 mg/L for Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei) and also against the majority of rare species, including Candida kefyr and Candida lusitaniae. A few isolates of C. albicans (0.7%, 3/404), C. glabrata (2.7%, 5/184), C. tropicalis (1.0%, 1/96) and C. parapsilosis (0.8%, 1/127) exhibited MIC >= 4 mg/L. All were also resistant to fluconazole according to the EUCAST breakpoints. Some isolates with isavuconazole MIC >= 4 mg/L were also observed among rarer species: Meyerozyma guilliermondii (8.7%, 2/23), Wickerhamomyces anomalus (10.0%, 1/10). Other rare species Saprochaete clavata, Magnusiomyces capitatus, and Rhodotorula mucilaginosa had high MIC50 (>= 1 mg/L) and MIC90 (>= 4 mg/L) and could be considered as resistant to isavuconazole. Conclusions: We confirmed the good in vitro activity of isavuconazole against common Candida, Cryptococcus species and the majority of the rare yeast species studied. (C) 2019 Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.

Cryptococcal antigen (CrAg) screening and targeted preemptive fluconazole in antiretroviral-naive human immunodeficiency virus-infected adults with CD4 cell counts < 100/mu L seems promising as a strategy to reduce the burden of cryptococcal meningitis (CM). We searched MEDLINE, EMBASE, and Web of Science and used random-effect meta-analysis to assess the prevalence of blood CrAg positivity (31 studies; 35 644 participants) and asymptomatic CM in CrAg-positive participants and the incidence of CM and the all-cause mortality rate in screened participants. The pooled prevalence of blood CrAg-positivity was 6% (95% confidence interval [CI], 5%-7%), and the prevalence of asymptomatic CM in CrAg-positive participants was 33% (95% CI, 21%-45%). The incidence of CM was 21.4% (95% CI, 11.6%-34.4%) without preemptive fluconazole and 5.7% (95% CI, 3.0%-9.7%) with preemptive fluconazole therapy initiated at 800 mg/d. In CrAg-positive participants, postscreening lumbar puncture before initiating preemptive fluconazole at 800 mg/d further reduced the incidence of CM to null and showed some survival benefits. However, the all-cause mortality rate remained significantly higher in CrAg-positive than in CrAg-negative participants (risk ratio, 2.2; 95% CI, 1.7-2.9; P<.001).

Following publication of the original article [1], we have been notified that one of the author names was listed incorrectly. Both incorrect and correct author names are presented below. The original publication has been corrected.