A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC.

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

Microbiological characterization of Pneumocystis jirovecii pneumonia using quantitative PCR from nasopharyngeal specimens: a retrospective study in a Canadian province from 2019 to 2023.

Bronchoalveolar lavage is usually employed for molecular diagnosis of Pneumocystis jirovecii but requires a specialized procedure. By contrast, nasopharyngeal (NP) specimens are easily obtained. In this retrospective study of 35 patients with paired NP and bronchoscopy specimens, NP specimens had a 100% negative percent agreement (95% CI 80.5-100) but only 72.2% positive percent agreement (95% CI 46.5-90.3).

Quick versus Quantitative: Evaluation of Two Commercial Real-Time PCR Assays for the Detection of Pneumocystis jirovecii from Bronchoalveolar Lavage Fluids.

Two commercial real-time PCR assays for the detection of Pneumocystis jirovecii were compared, the quantitative RealStar P. jirovecii assay and the qualitative DiaSorin P. jirovecii assay, the latter of which can be used without nucleic acid extraction. Archived bronchoalveolar lavage (BAL) specimens (n = 66), previously tested by molecular methods, were tested by both assays, and the results were compared to the respective original result. The RealStar P. jirovecii assay demonstrated good positive percent agreement (PPA) (90% [95% confidence interval (CI), 72 to 97%]; 27/30) and negative percent agreement (NPA) (100% [95% CI, 88 to 100%]; 36/36) with the reference method. The DiaSorin P. jirovecii assay concordantly detected P. jirovecii in 19 of 24 positive BAL samples (PPA = 73% [95% CI, 52 to 88%]). All negative BAL samples gave concordant results (NPA = 100% [95% CI, 87 to 100%]; 34/34). Discordant results occurred mostly in samples with low fungal loads. In conclusion, the RealStar assay demonstrated good concordance with reference results, and the DiaSorin P. jirovecii assay performed well for negative BAL and positive BAL samples with P. jirovecii concentrations of greater than 260 copies/mL. IMPORTANCE Pneumonia, caused by the opportunistic fungus Pneumocystis jirovecii, poses a significant risk for immunocompromised individuals. Laboratory testing for P. jirovecii is progressively shifting toward the use of molecular tests such as real-time PCR; however, this is often performed at reference laboratories. Many frontline laboratories are looking into improving their service and reducing turnaround times for obtaining P. jirovecii results by bringing molecular P. jirovecii testing in-house. We evaluated and compared two commercial real-time PCR assays with different workflows for the detection of P. jirovecii from bronchoalveolar lavage specimens. The RealStar P. jirovecii assay requires nucleic acid extraction and provides a quantification of fungal load for positive samples. The DiaSorin P. jirovecii assay offers a simple workflow without nucleic extraction from patient samples and qualitative results. Results from this study provide valuable information on performance and workflow considerations for laboratories that wish to implement P. jirovecii molecular testing.

Energy poverty: an overlooked determinant of health and climate resilience in Canada.

OBJECTIVE: Despite Canada being an important energy producer, not all Canadians can access or afford adequate levels of energy services at home to meet their needs, maintain healthy indoor temperatures, and live a decent life-a situation known as energy poverty. Depending on the measure, 6-19% of Canadian households face energy poverty. Health risks associated with energy poverty are documented in countries with milder climates. This study explores, for the first time in the Canadian context, the association between energy poverty and health. METHODS: Cross-sectional data are from the 2018 Canadian Housing Survey. Analyses are conducted on a sample weighted to represent 14 million Canadian households. The associations between expenditure-based and self-reported measures of energy poverty and self-rated general and mental health were assessed using logistic regression models, adjusted for potential confounding variables. RESULTS: The odds of rating one's general (OR: 1.48; 95%CI: 1.29, 1.70) and mental (OR: 1.21; 1.04, 1.41) health as poor are significantly higher for Canadian adults in households with a high share of energy expenditure to income. The likelihood of poor general and mental health was significantly higher for those dissatisfied with the energy efficiency of their dwelling, and with their ability to maintain a comfortable temperature both in the winter and in the summer. CONCLUSION: Exposure to energy poverty is associated with significantly increased likelihood of poor general and mental health. Given the high proportion of Canadian households facing energy poverty, with demonstrated implications for population health, tackling energy poverty is essential for an equitable energy transition and for climate resilience.

RéSUMé: OBJECTIF: Bien que le Canada soit un important producteur d'énergie, entre 6 % et 19 % des ménages canadiens, selon la mesure retenue, sont en précarité énergétique, une situation qui survient lorsqu'un ménage n'a pas les moyens ou l'accès à des services énergétiques résidentiels adéquats pour maintenir une température ambiante confortable, répondre à ses besoins et vivre dans la dignité. Les risques socio-sanitaires associés à la précarité énergétique sont documentés dans des pays au climat tempéré. Cette étude explore, pour la première fois dans le contexte canadien, l'association entre la précarité énergétique et la santé. MéTHODES: Les données transversales proviennent de l'Enquête canadienne sur le logement de 2018. Les associations entre différentes mesures de précarité énergétique (mesures basées sur les dépenses des ménages et auto-rapportées) et la santé générale et mentale perçue sont estimées à l'aide de modèles de régression logistique ajustés pour des variables de confusion potentielles. Les analyses sont réalisées sur un échantillon pondéré pour représenter 14 millions de ménages. RéSULTATS: Les probabilités de déclarer une mauvaise santé générale (OR : 1,48; IC95% : 1,29-1,70) et mentale (OR : 1,21; 1,04-1,41) sont significativement plus élevées pour les adultes canadiens dont le ménage consacre une part importante de son revenu aux coûts énergétiques. Elles sont aussi significativement plus élevées pour ceux qui déclarent être insatisfaits avec l'efficacité énergétique de leur logement et de leur capacité à maintenir une température confortable en hiver et en été. CONCLUSION: Vivre en situation de précarité énergétique est associée à des probabilités accrues de déclarer une mauvaise santé générale et mentale chez les adultes canadiens. En raison de la proportion élevée de ménages canadiens confrontés à la précarité énergétique et des effets socio-sanitaires que cette situation engendre, lutter contre la précarité énergétique est essentiel pour une transition énergétique équitable et pour la résilience climatique.

Housing as a determinant of Inuit mental health: associations between improved housing measures and decline in psychological distress after rehousing in Nunavut and Nunavik.

INTERVENTION: In 2014-2015, more than 400 public housing units were constructed in Nunavut and Nunavik, two of the four Inuit regions in Canada. This provided the opportunity to assess the impact of improved housing conditions from a population health perspective in 12 Inuit communities where housing needs were the most severe. The aim of the research is to examine the associations between changes in housing conditions and changes in psychological distress pre-post rehousing. METHODS: A pre-post uncontrolled study was conducted in collaboration with Nunavut- and Nunavik-based organizations. Applicants at the top of public housing waitlists were recruited by local housing officers; participants completed questionnaires 1-6 months before rehousing, and 15-18 months after. Change in psychological distress was measured with the Kessler 6-item scale. Changes in three housing measures were examined: number of adults per household, number of children per household, and sense of home score. For each housing measure, a categorical variable stratified participants into three categories. The reference category included participants reporting significant change in the concerned housing measure; the two other categories included participants reporting little or no change. Associations were tested with linear multilevel regression models for change. RESULTS: A total of 102 Inuit adults completed the study. A reduction in the number of adults per household (living with 2 adults or less after rehousing) and an increase in sense of home were associated with significant decline in psychological distress pre-post rehousing (p < 0.001). CONCLUSION: Increased investments leading to such improvements in housing circumstances are promising ways to promote mental health in Inuit regions.

RéSUMé: INTERVENTION: En 2014-2015, plus de 400 logements sociaux ont été construits au Nunavut et au Nunavik, deux des quatre régions inuites du Canada, permettant ainsi d'évaluer l'impact de l'amélioration des conditions de logement sur la santé. Cette étude vise à examiner les associations entre les changements dans les conditions de logement et les changements dans la détresse psychologique avant et après le déménagement, dans 12 communautés inuites où les besoins en logement étaient les plus criants. MéTHODES: Une étude pré-post non contrôlée a été menée en collaboration avec des organisations du Nunavut et du Nunavik. Les participants figurant en tête des listes d'attente pour le logement social ont rempli les questionnaires de recherche 1-6 mois avant le déménagement et 15-18 mois après. Les changements de la détresse psychologique ont été mesurés à l'aide de l'échelle Kessler 6-item. Les changements des trois conditions de logement suivantes ont été examinés : le nombre d'adultes par ménage, le nombre d'enfants par ménage et le sentiment d'avoir un chez-soi. Pour chaque condition de logement, une variable catégorielle a été créée pour stratifier les participants ayant rapporté des changements (référence) et les participants n'ayant rapporté que peu ou pas de changement. Les associations ont été testées avec des modèles de régression linéaire multiniveaux. RéSULTATS: Un total de 102 adultes Inuit ont complété l'étude. Une réduction du nombre d'adultes par ménage (vivre avec 2 adultes ou moins après le déménagement) et une augmentation du sentiment d'avoir un chez-soi étaient associées à une baisse significative de la détresse psychologique (p < 0,001). CONCLUSION: Des investissements accrus menant à de telles améliorations des conditions de logement représentent une avenue prometteuse pour promouvoir la santé mentale dans les régions inuites.

The psychosocial dimension of housing in Nunavik: does social support vary with household crowding?

OBJECTIVES: Studies show that living in overcrowded households can contribute to the erosion of social support, which is an important factor in health and well-being. In this study, we examine the relationship between household crowding and social support for Inuit living in Nunavik (hereafter referred to as Nunavimmiut), a region where housing shortages are considered a serious public health problem. We assess whether overcrowding is associated with lower levels of perceived social support and whether this association varies by gender and age group. METHODS: Cross-sectional data are from Qanuilirpitaa? the 2017 Nunavik Health Survey (N = 1306; aged 16 years and older). A perceived social support index was derived from answers to questions related to three different components of social support: positive interaction, emotional support, and love and affection. Associations between overcrowding (more than one person per room) and perceived social support were assessed using weighted linear and logistic regressions, adjusted for several factors. Sex- and age-stratified analyses were also conducted. RESULTS: Nunavimmiut report significantly lower levels of social support when living in overcrowded households, independently of other covariates. Analyses stratified by sex and age further show that the detrimental association between overcrowding and perceived social support is higher and stronger for men and older adults (both men and women 55 years and older). CONCLUSION: Overcrowding is associated with lower levels of perceived social support, which is a key component of health for the general population and for Nunavimmiut. Future research should examine the factors creating stronger associations between overcrowding and lower social support for men and older adults.

RéSUMé: OBJECTIFS: Des études montrent que le fait de vivre dans un ménage surpeuplé peut contribuer à l'érosion du soutien social, qui est un facteur important de santé et de bien-être. Dans cette étude, nous examinons la relation entre le surpeuplement des ménages et le soutien social chez les Inuits du Nunavik, une région où la pénurie de logements est considérée comme un grave problème de santé publique. Nous évaluons si le surpeuplement est associé à des niveaux plus faibles de soutien social perçu chez les Inuits vivant au Nunavik (ci-après appelés Nunavimmiut), et si cette association varie selon le sexe et le groupe d'âge. MéTHODES: Les données transversales proviennent de Qanuilirpitaa? l'enquête sur la santé au Nunavik de 2017 (N = 1 306; âgés de 16 ans et plus). Un indice de soutien social perçu a été dérivé des réponses aux questions relatives à trois composantes différentes du soutien social : interaction positive, soutien émotionnel, et amour et affection. Les associations entre le surpeuplement résidentiel (plus d'une personne par pièce) et le soutien social perçu ont été évaluées à l'aide de régressions linéaires et logistiques pondérées, ajustées pour plusieurs facteurs. Des analyses stratifiées par sexe et par âge ont également été réalisées. RéSULTATS: Les Nunavimmiut déclarent des niveaux de soutien social significativement plus faibles lorsqu'ils vivent dans des ménages surpeuplés, indépendamment d'autres covariables. Les analyses stratifiées par sexe et par âge montrent en outre que l'association néfaste entre le surpeuplement et le soutien social perçu est plus élevée et plus forte chez les hommes et les adultes plus âgés (hommes et femmes de 55 ans et plus). CONCLUSION: Le surpeuplement résidentiel est associé à des niveaux inférieurs de soutien social perçu, lequel est une composante clé de la santé pour la population générale et pour les Nunavimmiut. Les recherches futures devraient examiner les facteurs en cause derrière l'association entre le surpeuplement résidentiel et l'affaiblissement du soutien social chez les hommes et les adultes plus âgés.

Multicenter Evaluation of Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) Spectroscopy-Based Method for Rapid Identification of Clinically Relevant Yeasts.

Fourier transform infrared (FTIR) spectroscopy has demonstrated applicability as a reagent-free whole-organism fingerprinting technique for both microbial identification and strain typing. For routine application of this technique in microbiology laboratories, acquisition of FTIR spectra in the attenuated total reflectance (ATR) mode simplifies the FTIR spectroscopy workflow, providing results within minutes after initial culture without prior sample preparation. In our previous central work, 99.7% correct species identification of clinically relevant yeasts was achieved by employing an ATR-FTIR-based method and spectral database developed by our group. In this study, ATR-FTIR spectrometers were placed in 6 clinical microbiology laboratories over a 16-month period and were used to collect spectra of routine yeast isolates for on-site identification to the species level. The identification results were compared to those obtained from conventional biochemical tests and/or matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Isolates producing discordant results were reanalyzed by routine identification methods, ATR-FTIR spectroscopy, and PCR gene sequencing of the D1/D2 and internal transcribed spacer (ITS) regions. Among the 573 routine clinical yeast isolates collected and identified by the ATR-FTIR-based method, 564 isolates (98.4%) were correctly identified at the species level, while the remaining isolates were inconclusive with no misidentifications. Due to the low prevalence of Candida auris in routine isolates, additional randomly selected C. auris (n = 24) isolates were obtained for evaluation and resulted in 100% correct identification. Overall, the data obtained in our multicenter evaluation study using multiple spectrometers and system operators indicate that ATR-FTIR spectroscopy is a reliable, cost-effective yeast identification technique that provides accurate and timely (∼3 min/sample) species identification promptly after the initial culture.

Four genomic clades of Candida auris identified in Canada, 2012-2019.

Candida auris is an emerging yeast that is associated with antifungal resistance and healthcare-associated outbreaks. From 2012 to 2019, there were 24 known cases of C. auris colonization or infection in Canada. Isolates were from axilla/groin (n = 6), ear (n = 5), blood (n = 4), toe (n = 2), and a variety of other sites (n = 7). Canadian isolates belonged to the four main genomic clades: Clade I (formerly called South Asian clade, n = 12), Clade II (East Asian, n = 3), Clade III (African, n = 4), and Clade IV (South American, n = 5). Isolates within each clade were clonal; however, whole genome sequencing may be helpful in identifying clusters within healthcare facilities. LAY SUMMARY: The fungal pathogen Candida auris has caused many hospital outbreaks and is often multidrug resistant. All four major strains of C. auris were identified in Canada from 2012 to 2019. Genomic epidemiology may be useful for identifying and reducing transmission of C. auris within hospitals.

Changing Patterns of Disease Severity in Blastomyces dermatitidis Infection, Quebec, Canada.

This retrospective multicenter cohort study assessed temporal changes in the severity and mortality rate of blastomycosis in Quebec, Canada, and identified risk factors for death in patients with blastomycosis in 1988-2016. The primary outcome was 90-day all-cause deaths. Among 185 patients, 122 (66%) needed hospitalization and 30 (16%) died. We noted increases in the proportion of severe cases, in age at diagnosis and in the proportion of diabetic and immunocompromised patients over time. Independent risk factors for death were age (adjusted odds ratio [aOR] 1.04, 95% CI 1.00-1.07), immunosuppression (aOR 4.2, 95% CI 1.5-11.6), and involvement of >2 lung lobes (aOR 5.3, 95% CI 1.9-14.3). There was no association between the Blastomyces genotype group and all-cause mortality. The proportion of severe cases of blastomycosis has increased in Quebec over the past 30 years, partially explained by the higher number of immunosuppressed patients.

Natural spring water gargle and direct RT-PCR for the diagnosis of COVID-19 (COVID-SPRING study).

BACKGROUND: Nasopharyngeal swab has long been considered the specimen of choice for the diagnosis of respiratory viral infections, including SARS-CoV-2 infection, but it suffers from several drawbacks: its discomfort limits screening acceptability, and it is vulnerable to shortages in both specialized materials and trained healthcare workers in the context of a pandemic. METHODS: We prospectively compared natural spring water gargle to combined oro-nasopharyngeal swab (ONPS) for the diagnosis of coronavirus disease 2019 (COVID-19) in paired clinical specimens (1005 ONPS and 1005 gargles) collected from 987 unique early symptomatic as well as asymptomatic individuals from the community. RESULTS: Using a direct RT-PCR method with the Allplex™ 2019-nCoV Assay (Seegene), the clinical sensitivity of the gargle was 95.3% (95% confidence interval [CI], 90.2 - 98.3%), similar to the sensitivity of the ONPS (93.8%; 95% CI, 88.2 - 97.3%), despite significantly lower viral RNA concentration in gargles, as reflected by higher cycle threshold values. No single specimen type detected all COVID-19 cases. SARS-CoV-2 RNA was stable in gargles at room temperature for at least 7 days. CONCLUSION: The simplicity of this sampling method coupled with the accessibility of spring water are clear advantages in a pandemic situation where testing frequency, turnaround time and shortage of consumables and trained staff are critical elements.

Corrigendum to 'Rhinitis due to Aspergillus pseudoviridinutans in an orange-winged Amazon parrot (Amazona amazonica)'[Med. Mycol. Case Rep. 30 (2020) 46-50].

[This corrects the article DOI: 10.1016/j.mmcr.2020.11.001.].

Long-lasting cluster of nosocomial pneumonia with a single Pneumocystis jirovecii genotype involving different organ allograft recipients.

Pneumocystis pneumonia (PCP) outbreaks may occur in solid organ transplant (SOT) patients. Transmissibility of Pneumocystis jirovecii among SOT and non-SOT patients has not been investigated. Ten SOT (ie, 4 heart, 4 kidney, 2 liver allograft recipients) and 11 non-SOT (ie, 7 HIV-infected, 3 hematologic malignancies, and 1 stem cell transplant) patients with PCP were admitted to London Health Sciences Center (LHSC) from October 2014 to August 2016. We investigated the course of illness and outcome of PCP in SOT and non-SOT patients. Post-transplant PCP was frequently an acute-onset disease (90% vs. 18.2%, p = .01) requiring ICU admission (70% vs. 20%, p = .03) and hemodialysis (60% vs. 0, p = .003). Mortality was more frequent in SOT patients (40% vs. 18.1%, p = .36). Multilocus sequence typing (MLST) demonstrated circulation of a single genotype of P. jirovecii among SOT patients. However, 8 different genotypes were detected from non-SOT patients. Reinstitution of prophylaxis successfully controlled post-transplant cluster until end of observation period in October 2019. No transmission was detected from non-SOT patients to SOT recipients. Detection of a single P. jirovecii genotype from all SOT recipients highlights the likelihood of nosocomial transmission. No source control method is recommended by current guidelines. Improvement of preventive strategies is required.

Prevalence and mechanisms of azole resistance in clinical isolates of Aspergillus section Fumigati species in a Canadian tertiary care centre, 2000 to 2013.

OBJECTIVES: Azole resistance among Aspergillus fumigatus isolates is a growing concern worldwide. Induction of mutations during azole therapy, environment-acquired mutations caused by azole fungicides and intrinsic resistance of cryptic Fumigati species all contribute to the burden of resistance. However, there is a lack of data in Canada on this emerging threat. METHODS: To gain insights into the magnitude and mechanisms of resistance, a 14 year collection of Aspergillus section Fumigati comprising 999 isolates from 807 patients at a Montreal hospital was screened for azole resistance, and resistance mechanisms were investigated with the combined use of genome sequencing, 3D modelling and phenotypic efflux pump assays. RESULTS: Overall azole resistance was low (4/807 patients; 0.5%). A single azole-resistant A. fumigatus sensu stricto strain, isolated from a patient with pulmonary aspergillosis, displayed efflux-pump-mediated resistance. Three patients were colonized or infected with azole-resistant cryptic Fumigati species (one Aspergillus thermomutatus, one Aspergillus lentulus and one Aspergillus turcosus). Evidence is presented that azole resistance is efflux-pump-mediated in the A. turcosus isolate, but not in the A. lentulus and A. thermomutatus isolates. CONCLUSIONS: Azole resistance is rare in our geographic area and currently driven by cryptic Fumigati species. Continued surveillance of emergence of resistance is warranted.

Relocating to a new or pre-existing social housing unit: significant health improvements for Inuit adults in Nunavik and Nunavut.

OBJECTIVES: In 2014-2015, over 400 social housing units were constructed in selected communities in Nunavik and Nunavut, two Inuit regions in northern Canada where housing shortages and poor quality housing are endemic and undermine population health. This paper presents results from a before-and-after study examining the effects of rehousing, i.e., relocating to a newly constructed or pre-existing social housing unit, on psychosocial health and asthma-related symptoms for Inuit adults. METHODS: Baseline data were collected 1-6 months before, and follow-up data 15-18 months after rehousing. Of the 289 participants at baseline, 186 were rehoused. Of the 169 participants eligible at follow-up, 102 completed the study. Self-reported health measures included psychological distress, perceived stress in daily life, perceived control over one's life, and asthma-related symptoms. Data are analyzed using multilevel models for longitudinal data. RESULTS: After adjusting for age, sex, and region of residence, participants reported significantly lower levels of psychological distress and perceived stress in daily life, and improved sense of control over their lives 15 to 18 months after rehousing. Participants were also significantly less likely to report asthma-related symptoms at follow-up. CONCLUSION: Significant positive health impacts are observed for adults who relocated to newly constructed or pre-existing social housing units. Increasing investments to redress the housing situation across Inuit Nunangat is required, not only to improve living conditions but also to improve the health and well-being of the population.

The infectious thyroid nodule: a case report of mucormycosis associated with ibrutinib therapy.

BACKGROUND: Acute invasive fungal infections of the head and neck secondary to tyrosine kinase inhibitors are rare and potentially life-threatening events. CASE PRESENTATION: We report a case of mucormycosis of the thyroid gland in a patient known for chronic lymphocytic leukemia receiving ibrutinib who presented with a rapidly growing thyroid nodule and dysphonia. An acute invasive fungal infection was identified on a core needle biopsy; mucormycosis was confirmed on culture. The patient was successfully treated with surgical debridement and long-term antifungal therapy. CONCLUSION: Patients on ibrutinib may be at risk of acute invasive fungal infections of the head and neck.

Identification of Candida auris by Use of the Updated Vitek 2 Yeast Identification System, Version 8.01: a Multilaboratory Evaluation Study.

Candida auris is an emerging multidrug-resistant yeast that has been systematically incorrectly identified by phenotypic methods in clinical microbiology laboratories. The Vitek 2 automated identification system (bioMérieux) recently included C. auris in its database (version 8.01). We evaluated the performance of the Vitek 2 YST ID card to identify C. auris and related species. A panel of 44 isolates of Candida species (C. auris, n = 35; Candida haemulonii, n = 5; Candida duobushaemulonii, n = 4) were tested by three different hospital-based microbiology laboratories. Among 35 isolates of C. auris, Vitek 2 yielded correct identification in an average of 52% of tested samples. Low-discrimination (LD) results with an inability to distinguish between C. auris, C. duobushaemulonii, and Candida famata were obtained in an average of 27% of samples. Incorrect identification results were obtained in an average of 21% of samples, the majority (91%) of which were reported as C. duobushaemulonii and the remaining 9% of which were reported as Candida lusitaniae/C. duobushaemulonii. The proportion of correct identification was not statistically different across different centers (P = 0.78). Stratification by genetic clades demonstrated that 100% (n = 8) of the strains of the South American clade were correctly identified compared to 7% (n = 10) and 0% (n = 4) from the African and East Asian clades, respectively. None of the non-auris Candida strains (n = 9) were incorrectly identified as C. auris Our results show that the Vitek 2 (version 8.01) yeast identification system has a limited ability to correctly identify C. auris These data suggest that an identification result for C. duobushaemulonii should warrant further testing to rule out C. auris The overall performance of the Vitek 2 seems to differ according to C. auris genetic clade, with the South American isolates yielding the most accurate results.

Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy.

Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.