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12. Are We Ready for Nosocomial Candida auris Infections? Rapid Identification and Antifungal Resistance Detection Using MALDI-TOF Mass Spectrometry May Be the Answer

Author

De Carolis, Elena, Marchionni, F., La Rosa, M., Meis, J. F., Chowdhary, A., Posteraro, Brunella, Sanguinetti, Maurizio, De Carolis E. (ORCID:0000-0003-4757-7256), Posteraro B. (ORCID:0000-0002-1663-7546), Sanguinetti M. (ORCID:0000-0002-9780-7059), De Carolis, Elena, Marchionni, F., La Rosa, M., Meis, J. F., Chowdhary, A., Posteraro, Brunella, Sanguinetti, Maurizio, De Carolis E. (ORCID:0000-0003-4757-7256), Posteraro B. (ORCID:0000-0002-1663-7546), and Sanguinetti M. (ORCID:0000-0002-9780-7059)

Abstract

The occurrence of multidrug-resistant Candida auris isolates and the increased mortality associated with invasive infections or outbreaks due to this Candida species have been reported in many healthcare settings. Therefore, accurate and rapid identification at the species level of clinical C. auris isolates as well as their timely differentiation as susceptible or resistant to antifungal drugs is mandatory. Aims of the present study were to implement the MALDI-TOF mass spectrometry (MS) Bruker Daltonics Biotyper® database with C. auris spectrum profiles and to develop a fast and reproducible MS assay for detecting anidulafungin (AFG) resistance in C. auris isolates. After creation of main C. auris spectra, a score-oriented dendrogram was generated from hierarchical cluster analysis, including spectra of isolates from C. auris and other Candida (C. glabrata, C. guilliermondii, C. haemulonii, C. lusitaniae, and C. parapsilosis) or non-Candida (Rhodotorula glutinis) species. Cluster analysis allowed to group and classify the isolates according to their species designation. Then, a three-hour incubation antifungal susceptibility testing (AFST) assay was developed. Spectra obtained at null, intermediate, or maximum AFG concentrations were used to create composite correlation index matrices for eighteen C. auris isolates included in the study. All six resistant C. auris isolates were detected as resistant whereas 11 of 12 susceptible C. auris isolates were detected as susceptible by the MS-AFST assay. In conclusion, our MS-based assay offers the possibility of rapidly diagnosing and appropriately treating patients with C. auris infection.

Published
2021

13. Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Author

Geiser, D. M., Al-Hatmi, A., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C, Bhattacharyya, M. K. K., Blomquist, C. L., Bowden, R., Brankovics, B., Guarro, J., Ward, T., Wickes, B., Everts, K. L., Wiederhold, N. P., Wingfield, M. J., Wood, A. K. M., Xu, J. R., Carrillo, J. D., Yang, X. B., Scauflaire, J., Yli-Matilla, T., Gugino, B., Yun, S. H., Zakaria, L., Zhang, H., Fernández-Pavía, S. P., Zhang, N., Zhang, S., Zhang, X., Chang, H. X., Kim, H., Chen, C. Y., Chen, W., Gutiérrez, S., Chilvers, M. I., Chulze, S. N., Coleman, J. J., Cuomo, C. A., da Silva, G. F., de Beer, Z. W., de Hoog, G. S., Kistler, H. C., Del Castillo-Múnera, J., Del Ponte, E., Dieguez-Uribeondo, Javier, Hammond-Kosack, K., Di Pietro, A., Edel-Hermann, V., Elmer, W. H., Foroud, N. A., Fourie, G., Frandsen, R. J. N., Nucci, M., Freeman, S., Munaut, F., Freitag, Michael, Frenkel, O., Harris, L. J., Fuller, K. K., Gagkaeva, T., Gardiner, D. M., Glenn, A. E., Gold, S., Kuldau, G. A., Gordon, T., Gregory, N. F., Gryzenhout, M., Homa, M., Hong, C. F., Hornok, L., Huang, J. W., Burgess, L. W., Ilkit, M., Nicholson, P., Kulik, T., Jacobs, A., Jacobs, K., Jiang, C., Jiménez-Gasco, M. Mar, Kang, S., Kasson, M. T., Kazan, K., Kennell, J. C., Kurzai, O., Laraba, I., Laurence, M. H., Lee, T. Y., Eskalen, A., Lee, Y. W., Schmale, D. III., Lee, Y. H., Leslie, J. F., Liew, E. C. Y., O'Donnell, K., Lofton, L. W., Logrieco, A., López-Berges, M. S., Luque, A. G., Tortorano, A. M., Lysøe, E., Ma, L. J., Short, D. P., Marra, R. E., Martin, Frank N., May, S. R., McCormick, S., Pasquali, M., McGee, C. T., Meis, J. F., Urban, M., Migheli, Q., Mohamed Nor, N. M. I., Monod, M., Šišic, A., Moretti, A., Mostert, D., Mulé, G., Pfenning, L. H., Prigitano, A., Proctor, R., Busman, M., Ranque, S., Brown, D. W., Rehner, S., Rep, M., Smith, J., Rodríguez-Alvarado, G., Rose, L. J., Roth, M. G., Ruiz-Roldán, C., Saleh, A. A., Vaillancourt, L. J., Salleh, B., Sang, H., Scandiani, M., Smyth, C. W., Son, H., Spahr, E., Stajich, Jason E., Epstein, L., Steenkamp, Emma, Bushley, K., Vallad, G. E., Steinberg, C., Subramaniam, R., Suga, H., Summerell, B. A., Susca, A., Swett, C. L., Toomajian, C., Torres-Cruz, T. J., van der Lee, T., Vanderpool, D., van Diepeningen, A. D., Vaughan, M., Munkvold, G. P., Venter, E., Esposto, M. C., Vermeulen, M., Verweij, P. E., Viljoen, A., Cano-Lira, J. F., Waalwijk, C., Wallace, E. C., Walther, G., Wang, J., Geiser, D. M., Al-Hatmi, A., Aoki, T., Arie, T., Balmas, V., Barnes, I., Bergstrom, G. C, Bhattacharyya, M. K. K., Blomquist, C. L., Bowden, R., Brankovics, B., Guarro, J., Ward, T., Wickes, B., Everts, K. L., Wiederhold, N. P., Wingfield, M. J., Wood, A. K. M., Xu, J. R., Carrillo, J. D., Yang, X. B., Scauflaire, J., Yli-Matilla, T., Gugino, B., Yun, S. H., Zakaria, L., Zhang, H., Fernández-Pavía, S. P., Zhang, N., Zhang, S., Zhang, X., Chang, H. X., Kim, H., Chen, C. Y., Chen, W., Gutiérrez, S., Chilvers, M. I., Chulze, S. N., Coleman, J. J., Cuomo, C. A., da Silva, G. F., de Beer, Z. W., de Hoog, G. S., Kistler, H. C., Del Castillo-Múnera, J., Del Ponte, E., Dieguez-Uribeondo, Javier, Hammond-Kosack, K., Di Pietro, A., Edel-Hermann, V., Elmer, W. H., Foroud, N. A., Fourie, G., Frandsen, R. J. N., Nucci, M., Freeman, S., Munaut, F., Freitag, Michael, Frenkel, O., Harris, L. J., Fuller, K. K., Gagkaeva, T., Gardiner, D. M., Glenn, A. E., Gold, S., Kuldau, G. A., Gordon, T., Gregory, N. F., Gryzenhout, M., Homa, M., Hong, C. F., Hornok, L., Huang, J. W., Burgess, L. W., Ilkit, M., Nicholson, P., Kulik, T., Jacobs, A., Jacobs, K., Jiang, C., Jiménez-Gasco, M. Mar, Kang, S., Kasson, M. T., Kazan, K., Kennell, J. C., Kurzai, O., Laraba, I., Laurence, M. H., Lee, T. Y., Eskalen, A., Lee, Y. W., Schmale, D. III., Lee, Y. H., Leslie, J. F., Liew, E. C. Y., O'Donnell, K., Lofton, L. W., Logrieco, A., López-Berges, M. S., Luque, A. G., Tortorano, A. M., Lysøe, E., Ma, L. J., Short, D. P., Marra, R. E., Martin, Frank N., May, S. R., McCormick, S., Pasquali, M., McGee, C. T., Meis, J. F., Urban, M., Migheli, Q., Mohamed Nor, N. M. I., Monod, M., Šišic, A., Moretti, A., Mostert, D., Mulé, G., Pfenning, L. H., Prigitano, A., Proctor, R., Busman, M., Ranque, S., Brown, D. W., Rehner, S., Rep, M., Smith, J., Rodríguez-Alvarado, G., Rose, L. J., Roth, M. G., Ruiz-Roldán, C., Saleh, A. A., Vaillancourt, L. J., Salleh, B., Sang, H., Scandiani, M., Smyth, C. W., Son, H., Spahr, E., Stajich, Jason E., Epstein, L., Steenkamp, Emma, Bushley, K., Vallad, G. E., Steinberg, C., Subramaniam, R., Suga, H., Summerell, B. A., Susca, A., Swett, C. L., Toomajian, C., Torres-Cruz, T. J., van der Lee, T., Vanderpool, D., van Diepeningen, A. D., Vaughan, M., Munkvold, G. P., Venter, E., Esposto, M. C., Vermeulen, M., Verweij, P. E., Viljoen, A., Cano-Lira, J. F., Waalwijk, C., Wallace, E. C., Walther, G., and Wang, J.

Abstract

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available

Published
2021

14. Genetic and phenotypic characterization of in-host developed azole-resistant aspergillus flavus isolates

Author

Buil, J. B., Houbraken, J., Reijers, M. H., Zoll, J., Sanguinetti, Maurizio, Meis, J. F., Verweij, P. E., Melchers, W. J. G., Sanguinetti M. (ORCID:0000-0002-9780-7059), Buil, J. B., Houbraken, J., Reijers, M. H., Zoll, J., Sanguinetti, Maurizio, Meis, J. F., Verweij, P. E., Melchers, W. J. G., and Sanguinetti M. (ORCID:0000-0002-9780-7059)

Abstract

Aspergillus flavus is a pathogenic fungal species that can cause pulmonary aspergillosis, and triazole compounds are used for the treatment of these infections. Prolonged exposure to azoles may select for compensatory mutations in the A. flavus genome, resulting in azole resistance. Here, we characterize a series of 11 isogenic A. flavus strains isolated from a patient with pulmonary as-pergillosis. Over a period of three months, the initially azole-susceptible strain developed itracona-zole and voriconazole resistance. Short tandem repeat analysis and whole-genome sequencing revealed the high genetic relatedness of all isolates, indicating an infection with one single isolate. In contrast, the isolates were macroscopically highly diverse, suggesting an adaptation to the environment due to (epi)genetic changes. The whole-genome sequencing of susceptible and azole-resistant strains showed a number of mutations that might be associated with azole resistance. The majority of resistant strains contain a Y119F mutation in the Cyp51A gene, which corresponds to the Y121F mutation found in A. fumigatus. One azole-resistant strain demonstrated a divergent set of muta-tions, including a V99A mutation in a major facilitator superfamily (MSF) multidrug transporter (AFLA 083950).

Published
2021

16. ESCMID and ECMM joint guidelines on diagnosis and management of hyalohyphomycosis: Fusarium spp., Scedosporium spp. and others

Author

Tortorano, A. M., Richardson, M., Roilides, E., van Diepeningen, A., Caira, M., Munoz, P., Johnson, E., Meletiadis, J., Pana, Z.-D., Lackner, M., Verweij, P., Freiberger, T., Cornely, O. A., Arikan-Akdagli, S., Dannaoui, E., Groll, A. H., Lagrou, K., Chakrabarti, A., Lanternier, F., Pagano, L., Skiada, A., Akova, M., Arendrup, M. C., Boekhout, T., Chowdhary, A., Cuenca-Estrella, M., Guinea, J., Guarro, J., de Hoog, S., Hope, W., Kathuria, S., Lortholary, O., Meis, J. F., Ullmann, A. J., Petrikkos, G., and Lass-Flörl, C.

Published
2014
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18. ESCMID† and ECMM‡ joint clinical guidelines for the diagnosis and management of mucormycosis 2013

Author

Cornely, O. A., Arikan-Akdagli, S., Dannaoui, E., Groll, A. H., Lagrou, K., Chakrabarti, A., Lanternier, F., Pagano, L., Skiada, A., Akova, M., Arendrup, M. C., Boekhout, T., Chowdhary, A., Cuenca-Estrella, M., Freiberger, T., Guinea, J., Guarro, J., de Hoog, S., Hope, W., Johnson, E., Kathuria, S., Lackner, M., Lass-Flörl, C., Lortholary, O., Meis, J. F., Meletiadis, J., Muñoz, P., Richardson, M., Roilides, E., Tortorano, A. M., Ullmann, A. J., van Diepeningen, A., Verweij, P., and Petrikkos, G.

Published
2014
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19. ESCMID and ECMM joint clinical guidelines for the diagnosis and management of systemic phaeohyphomycosis: diseases caused by black fungi

Author

Chowdhary, A., Meis, J. F., Guarro, J., de Hoog, G. S., Kathuria, S., Arendrup, M. C., Arikan-Akdagli, S., Akova, M., Boekhout, T., Caira, M., Guinea, J., Chakrabarti, A., Dannaoui, E., van Diepeningen, A., Freiberger, T., Groll, A. H., Hope, W. W., Johnson, E., Lackner, M., Lagrou, K., Lanternier, F., Lass-Flörl, C., Lortholary, O., Meletiadis, J., Muñoz, P., Pagano, L., Petrikkos, G., Richardson, M. D., Roilides, E., Skiada, A., Tortorano, A. M., Ullmann, A. J., Verweij, P. E., Cornely, O. A., Cuenca-Estrella, M., and Paul, M.

Published
2014
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23. Prevalence and Clonal Distribution of Azole-Resistant Candida parapsilosis Isolates Causing Bloodstream Infections in a Large Italian Hospital

Author

Martini, Cecilia, Torelli, Riccardo, de Groot, T., De Carolis, Elena, Morandotti, Grazia Angela, De Angelis, Giulia, Posteraro, Brunella, Meis, J. F., Sanguinetti, Maurizio, Martini C., Torelli R., De Carolis E. (ORCID:0000-0003-4757-7256), Morandotti G. A., De Angelis G. (ORCID:0000-0002-7087-7399), Posteraro B. (ORCID:0000-0002-1663-7546), Sanguinetti M. (ORCID:0000-0002-9780-7059), Martini, Cecilia, Torelli, Riccardo, de Groot, T., De Carolis, Elena, Morandotti, Grazia Angela, De Angelis, Giulia, Posteraro, Brunella, Meis, J. F., Sanguinetti, Maurizio, Martini C., Torelli R., De Carolis E. (ORCID:0000-0003-4757-7256), Morandotti G. A., De Angelis G. (ORCID:0000-0002-7087-7399), Posteraro B. (ORCID:0000-0002-1663-7546), and Sanguinetti M. (ORCID:0000-0002-9780-7059)

Abstract

The most prevalent cause of nosocomial bloodstream infection (BSI) among non-C. albicans Candida species, Candida parapsilosis, may not only be resistant to azole antifungal agents but also disseminate to vulnerable patients. In this survey of BSIs occurring at a large Italian hospital between May 2014 and May 2019, C. parapsilosis accounted for 28.5% (241/844) of all Candida isolates causing BSI episodes. The majority of episodes (151/844) occurred in medical wards. Across the 5 yearly periods, the rates of azole non-susceptibility were 11.8% (4/34), 17.8% (8/45), 28.6% (12/42), 32.8% (19/58), and 17.7% (11/62), respectively, using the Sensititre YeastOne® method. Among azole non-susceptible isolates (54/241; 22.4%), 49 were available for further investigation. Using the CLSI reference method, all 49 isolates were resistant to fluconazole and, except one (susceptible dose-dependent), to voriconazole. Forty (81.6%) isolates harbored the Erg11p Y132F substitution and nine (18.4%) isolates the Y132F in combination with the Erg11p R398I substitution. According to their genotypes, as defined using a microsatellite analysis based on six short tandem repeat markers, 87.7% of isolates (43/49) grouped in two major clusters (II and III), whereas 4.1% of isolates (2/49) belonged to a separate cluster (I). Interestingly, all the isolates from cluster II harbored the Y132F substitution, and those from cluster III harbored both Y132F and R398I substitutions. Of 56 non-Italian isolates included as controls, two Indian isolates with the Y132F substitution had a genotype clearly differing from that of the isolates from clusters II and I. In conclusion, these findings show the dominance of clonal Y132F isolates in our hospital and suggest detection of the Y132F substitution as helpful tool to prevent transmission among hospitalized patients at risk of BSI.

Published
2020

50. European expert opinion on the management of invasive candidiasis in adults

Author

Kullberg, B. J., Verweij, P. E., Akova, M., Arendrup, M. C., Bille, J., Calandra, T., Cuenca-Estrella, M., Herbrecht, R., Jacobs, F., Kalin, M., Kibbler, C. C., Lortholary, O., Martino, P., Meis, J. F., Muñoz, P., Odds, F. C., De Pauw, B. E., Rex, J. H., Roilides, E., Rogers, T. R., Ruhnke, M., Ullmann, A. J., Uzun, Ö., Vandewoude, K., Vincent, J.-L., and Donnelly, J. P.

Published
2011
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