Comparison between MALDI-TOF MS and MicroScan in the identification of emerging and multidrug resistant yeasts in a fourth-level hospital in Bogotá, Colombia

Ceballos-Garzón et al. BMC Microbiology https://doi.org/10.1186/s12866-019-1482-y (2019) 19:106 RESEARCH ARTICLE Open Access Comparison between MALDI-TOF MS and MicroScan in the identification of emerging and multidrug resistant yeasts in a fourthlevel hospital in Bogotá, Colombia Andrés Ceballos-Garzón1,4,5, Gloria Cortes2,4, Florent Morio5, Edna L. Zamora-Cruz1, Melva Y. Linares1,4, Beatriz E. Ariza2,4, Sandra L. Valderrama3,4, Javier R. Garzón3,4, Carlos A. Alvarez-Moreno4, Patrice Le Pape5 and Claudia M. Parra-Giraldo1,4* Abstract Background: The introduction of MALDI-TOF MS in the clinical microbiology laboratory has modified the approaches for the identification of fungi. Thanks to this tool, it is possible to identify cryptic species, which possess critical susceptibility patterns. Clinical strains were identified using the MicroScan and MALDI-TOF MS systems. Discrepant results from both methods were investigated using ITS rDNA barcoding. Finally, these isolates were also tested for in vitro susceptibility. Results: The percentage of agreement between both methods to 498 yeast isolates was of 93.6% (32 discrepant isolates). The concordance of ITS sequencing with MALDI-TOF MS was higher (99%) than that of MicroScan (94%). Several of these discordant yeasts displayed high MICs for antifungal agents. Conclusions: Our study highlights the need of the MS and molecular approaches such as MALDI-TOF MS and ITS rDNA barcoding for the correct identification of emerging or cryptic yeast species; besides, some of these could be multidrug resistant. This work was the first experience in the implementation of the MALDI-TOF MS technology in Colombia. We found the first uncommon yeasts including Candida auris and we could identify Trichosporon faecalis. Our work highlights a clear necessity of an accurate yeast identification as a much more pertinent technique than the susceptibility profiles, because the most unusual yeasts exhibit resistance profiles to the few available antifungals. Keywords: Comparison, MALDI-TOF MS, MicroScan, Unusual yeast, Yeast identification * Correspondence: Part of this study was presented at the 26th European Congress of Clinical Microbiology and Infectious Diseases, April 9–12, 2016, Amsterdam, the Netherlands (ECCMID 2016) as a poster session. Abstract #5556: Performance of MALDI-TOF MS for the identification of emerging yeasts of hospital patients, species distribution, in a third- level hospital in Bogotá, Colombia. 1 Departamento de Microbiología, Facultad de Ciencias, Unidad de Proteomica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Pontificia Universidad Javeriana, Bogotá, Colombia 4 Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Bogotá, Colombia Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Ceballos-Garzón et al. BMC Microbiology (2019) 19:106 Background In the last decades, the incidence of invasive fungal infections has progressively increased, especially in critically ill and immunocompromised patients [1, 2]. Yeast infections are mostly caused by Candida followed by Cryptococcus, and less frequently by Rhodotorula, Saccharomyces, Trichosporon and Pichia. These emerging species are also contributing to the epidemiological changes recorded in recent years, which significantly impact therapeutic regimens in patients as some yeasts can exhibit innate drug resistance [3–6]. Within the genus Candida, C. albicans is still the most common fungal pathogen worldwide. Despite being part of the mucocutaneous, gastrointestinal and genitourinary mycobiota in humans, C. albicans can be responsible for nearly 50% of candidaemia. In the 90’s the prevalence of candidaemia was between 64 and 48% but this percentage decreased to 38% during the period 2008–2011 due to increased prevalence of non C. albicans species [5, 7, 8]. For Cryptococcus, reports indicate a prevalence of 4%. Such a low percentage has not ever been described for emerging species [9–11]. The accurate identification of the fungal species that cause the infection is of paramount importance since the necessity to initiate the appropriate antifungal therapy. Furthermore, the time required for diagnosis/identification is also critical as any delay will affect the prognosis dramatically when dealing with invasive candidiasis as well as complicate a relevant stewardship [12, 13]. On South America mycological identification usually relies on phenotypic, biochemical, enzymatic and immunological approaches [14]. The MicroScan system is a rapid technology for microbial identification able to provide results after 4 h of inoculation [15]. Only available for yeast identification, this method relies on enzymatic reactions in a panel. The enzyme activities of each isolate are determined by colour changes in the chromogenic substrates (or a pH indicator). The biochemical reactions generate numerical profiles, which are then compared with a numerical database. In recent years, Mass Spectrometry (MS) using MALDI-TOF MS technology has been increasingly used as a tool for microbiological identification due to its high performance and less time required when compared with conventional methods [16]. Our aim was to compare the performance of MicroScan with that of MALDI-TOF MS for yeast identification. This study was conducted on a large collection of clinical isolates collected prospectively at the San Ignacio Hospital, Bogota, Colombia. Those isolates yielding discrepant results were further identified by the gold standard ITS and D1-D2 rDNA barcoding. Because of the few data on rare/emerging yeasts, susceptibility profiles were also determined. Page 2 of 10 Results Performance of MicroScan in comparison with Bruker MALDI-TOF MS With the MicroScan technology 497/498 (99.7%) strains were identified, belonging to 16 distinct species from 7 genera. When performing MALDI-TOF MS identification with the Bruker instrument 494 /498 (99%) strains were identified, belonging to 21 distinct species from 6 genera. The percentage of agreement between both methods was 93.5% (466 isolates) (Table 1). The remaining 32 isolates yielding discrepant results (n = 27) or being no-identified by one of the two methods were subjected to further investigations for molecular identification as the gold standard.th=tlb= Resolution of the discrepancies (...truncated)