Epidemiology of candidemia in Qatar, the Middle East: performance of MALDI-TOF MS for the identification of Candida species, species distribution, outcome, and susceptibility pattern

The Antimicrobial Resistance of Candida: A 5-Year Retrospective Analysis at a Tertiary Hospital in Jordan

Candida infections are a global health concern, increasingly complicated by rising antimicrobial resistance (AMR). This study analyzed the prevalence and AMR patterns of circulating Candida species in Amman, Jordan, using electronic records from a tertiary teaching hospital's microbiology lab (from 2017 to 2022). Complete records of Candida isolates (n = 2673) were assessed by sample type, species, and AMR. Among positive blood samples, C. albicans accounted for the majority (38.7%), followed by C. tropicalis (19.0%), C. parapsilosis (18.3%), Nakaseomyces glabratus (14.6%), and Pichia kudriavzevii (9.5%). Non-albicans species demonstrated higher resistance to Caspofungin, notably P. kudriavzevii (23.1%), N. glabratus (30.0%), and C. parapsilosis (32.0%), compared to C. albicans (1.9%). In high vaginal swabs, C. albicans was most prevalent (63.7%), with N. glabratus also notable (28.6%); Fluconazole resistance in C. albicans remained low (2.0%). Across all pooled isolates, AMR was similar between inpatients and outpatients, except for Micafungin, where inpatient resistance was significantly higher. In conclusion, non-albicans species predominated in blood infections and demonstrated pronounced AMR. Micafungin resistance was notably higher among inpatients. Variations in Candida species and AMR by sample type suggest that aggregating samples in registry studies may obscure critical patterns.

Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections

Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.

Molecular epidemiology of clinical filamentous fungi in Qatar beyond Aspergillus and Fusarium with notes on the rare species

Due to an increasing number of patients at risk (i.e., those with a highly compromised immune system and/or receiving aggressive chemotherapy treatment), invasive fungal infections (IFI) are increasingly being reported and associated with high mortality rates. Aspergillus spp., particularly A. fumigatus, is the major cause of IFI caused by filamentous fungi around the world followed by Fusarium spp., however, other fungi are emerging as human pathogens. The aim of this study was to explore the epidemiology and prevalence of the non-Aspergillus and non-Fusarium filamentous fungi in human clinical samples over an 11-year period in Qatar using molecular techniques. We recovered 53 filamentous fungal isolates from patients with various clinical conditions. Most patients were males (75.5%), 9.4% were immunocompromised, 20.7% had IFI, and 11.3% died within 30 days of diagnosis. The fungal isolates were recovered from a variety of clinical samples, including the nasal cavity, wounds, respiratory samples, body fluids, eye, ear, tissue, abscess, and blood specimens. Among the fungi isolated, 49% were dematiaceous fungi, followed by Mucorales (30%), with the latter group Mucorales being the major cause of IFI (5/11, 45.5%). The current study highlights the epidemiology and spectrum of filamentous fungal genera, other than Aspergillus and Fusarium, recovered from human clinical samples in Qatar, excluding superficial infections, which can aid in the surveillance of uncommon and emerging mycoses.

Mass spectrometry in research laboratories and clinical diagnostic: a new era in medical mycology

Diagnosis by clinical mycology laboratory plays a critical role in patient care by providing definitive knowledge of the cause of infection and antimicrobial susceptibility data to physicians. Rapid diagnostic methods are likely to improve patient. Aggressive resuscitation bundles, adequate source control, and appropriate antibiotic therapy are cornerstones for success in the treatment of patients. Routine methods for identifying clinical specimen fungal pathogen are based on the cultivation on different media with the subsequent examination of its phenotypic characteristics comprising a combination of microscopic and colony morphologies. As some fungi cannot be readily identified using these methods, molecular diagnostic methods may be required. These methods are fast, but it can cost a lot. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs. It can be considered an alternative for conventional biochemical and molecular identification systems in a microbiological laboratory. The reliability and accuracy of this method have been scrutinized in many surveys and have been compared with several methods including sequencing and molecular methods. According to these findings, the reliability and accuracy of this method are very high and can be trusted. With all the benefits of this technique, the libraries of MALDI-TOF MS need to be strengthened to enhance its performance. This review provides an overview of the most recent research literature that has investigated the applications and usage of MT-MS to the identification of microorganisms, mycotoxins, antifungal susceptibility examination, and mycobiome research.

Clinical characteristics and outcome of candidemia: Experience from a tertiary referral center in Saudi Arabia

Background:

Candida bloodstream infections cause significant excess morbidity and mortality in the health-care setting. There is limited evidence regarding Candida species causing invasive infections in Saudi Arabia.

Objective:

To identify Candida species causing bloodstream infection and determine the clinical outcome and factors associated with mortality in a tertiary center in Saudi Arabia.

Materials and Methods:

This retrospective study included all cases of positive blood culture for Candida in patients admitted to King Abdulaziz Medical City, a tertiary care center in Riyadh, Saudi Arabia, between January 1, 2013 and June 30, 2019.

Results:

A total of 532 patients with candidemia were identified (male: 55.4%; mean age: 54 ± 26.2 years). The most common Candida species isolated was Candida albicans (26.7%), followed by Candida glabrata (22.7%), Candida parapsilosis (22.2%), and Candida tropicalis (18.4%). Non-albicans candidemia was more common in patients with diabetes (76.7%; P = 0.0560), neutropenia (89.8%; P = 0.0062), recent exposure to fluconazole (85.7%; P = 0.0394), and active chemotherapy (83.1%; P = 0.0128). In non-albicans, susceptibility to fluconazole varied from 95.9% with C. tropicalis to 41.5% with C. parapsilosis; nonetheless, all species were highly susceptible to echinocandins. The overall 30- and 90-day mortality rates were 39.9% and 56.4%, respectively. The mortality rate was nonsignificantly higher with non-albicans species at 30 days (41.2% vs. 35.9%; P = 0.2634) and 90 days (58.2% vs. 51.4%; P = 0.1620).

Conclusion:

This study found a changing pattern in the Candida species causing bloodstream infections and an epidemiological shift toward more non-albicans Candida species in Saudi Arabia.

Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy

Candida glabrata is the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinical C. glabrata isolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The current C. glabrata MLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-quality C. glabrata reference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify the C. glabrata MLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination of TRP1 (a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification in C. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing of C. glabrata in clinical and research settings.

Species Distribution, Antifungal Susceptibility, and Molecular Epidemiology of Candida Species Causing Candidemia in a Tertiary Care Hospital in Bangkok, Thailand

Candida species represent a common cause of bloodstream infection (BSI). Given the emergence of non-albicans Candida (NAC) associated with treatment failure, investigations into the species distribution, fungal susceptibility profile, and molecular epidemiology of pathogens are necessary to optimize the treatment of candidemia and explore the transmission of drug resistance for control management. This study evaluated the prevalence, antifungal susceptibility, and molecular characteristics of Candida species causing BSI in a tertiary-level hospital in Bangkok, Thailand. In total, 54 Candida isolates were recovered from 49 patients with candidemia. C. tropicalis was the most prevalent species (33.3%), followed by C. albicans (29.6%). Most Candida species were susceptible to various antifungal agents, excluding C. glabrata and C. tropicalis, which had increased rates of non-susceptibility to azoles. Most C. glabrata isolates were non-susceptible to echinocandins, especially caspofungin. The population structure of C. albicans was highly diverse, with clade 17 predominance. GoeBURST analysis of C. tropicalis revealed associations between genotype and fluconazole resistance in a particular clonal complex. The population structure of C. glabrata appeared to have a low level of genetic diversity in MLST loci. Collectively, these data might provide a fundamental database contributing to the development of novel antifungal agents and diagnostic tests.

Catastrophic Candida prosthetic valve endocarditis and COVID-19 comorbidity: A rare case

BACKGROUND AND PURPOSE

Coronavirus disease 2019 (COVID-19) and Candida prostatic valve endocarditis present various clinical manifestations which may overlap; hence, discrimination between them is extremely difficult.

CASE REPORT

The case was a 66-year-old man with a past medical history of mitral and aortic valves replacement one year before COVID-19 co-infection. He was admitted with fever (for 7 days), shortness of breath, cough, seizure, lethargy, headache, and 85% oxygen saturation. Transesophageal echocardiography revealed multiple large-sized, highly mobile masses on both sides of the mechanical mitral valve highly suggestive of vegetation. Chest computed tomography scanning showed simulating scattered COVID-19 peripheral ground-glass opacities confirmed by reverse-transcription polymerase chain reaction. The set of blood cultures yielded yeast colonies that were identified as Candida tropicalis. The patient died of septic shock shortly after receiving antifungal therapy.

CONCLUSION

This case emphasized the importance of early diagnosis and implementation of antifungal treatment, particularly in patients with prosthetic cardiac valves, to reduce their unfavorable outcomes in COVID-19 patients.

Green Approach to Overcome the Resistance Pattern of Candida spp. Using Biosynthesized Silver Nanoparticles Fabricated by Penicillium chrysogenum F9

Candida species are the most common causative agents responsible for the majority of morbidity as well as mortality rates due to invasive fungal infections worldwide. In this study, a green approach was developed to control the pathogenic Candida spp. isolated from clinical samples, and prior data collections, ethics approval was obtained. Sixty candida isolates were obtained from the different device-associated infections and identified as Candida albicans, Candida tropicalis, Candida krusei, Candida parapsilosis, and Candida glabrata with prevalence rates 41.6, 38.3, 8.3, 6.6, and 5%, respectively. On the other hand, silver nanoparticles (Ag-NPs) were extra-cellular synthesized by biomass filtrate of previously identified Penicillium chrysogenum strain F9. The physico-chemical characterizations of biosynthesized Ag-NPs were assessed by using UV-Vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD) patterns, transmission electron microscope (TEM), dynamic light scattering (DIS), and zeta potential (ζ) analysis. Data revealed successful synthesis of crystallographic spherical Ag-NPs with average size 18 to 60 nm at maximum absorption peak 415 nm. FT-IR analysis confirmed the presence of functional groups related to reduction, capping, and stabilizing Ag-NPs. The DLS analysis showed that NPs were homogenous and stable with poly-dispersity index (PDI) and ζ value 0.008 and - 21 mV, respectively. Susceptibility pattern analysis revealed that sixty Candida isolates (100%) were susceptible to Ag-NPs as compared to 25 isolates (41.6%), and 30 isolates (50%) were susceptible to fluconazole and amphotericin B, respectively. Interestingly, 30 Candida isolates (50%) were resistant to amphotericin B, which are more than those recorded for fluconazole (17 isolates with percent 28.3%), while 18 candida isolates (30%) were susceptible dose-dependent to fluconazole. The recorded minimum inhibitory concentration _50/90 (MIC_50/90) was 62.5/125, 16/64, and 1/4 for Ag-NPs, fluconazole, and amphotericin B, respectively. However, green synthesized Ag-NPs can be used to overcome the resistance pattern of Candida spp., and recommended as an anti-candida agent.

Predominance of Candida Glabrata among Non-albicans Candida Species in a 16-Year Study of Candidemia at a Tertiary Care Center in Lebanon

Background: Candidemia is associated with a high mortality rate, and its incidence is increasing worldwide with a rise in non-albicans candidemia (NAC). Epidemiologic data from Arab countries are scarce and there are no data from Lebanon; Methods: This is a single-center retrospective chart review of patients with candidemia in a tertiary care center in Lebanon from 2004 to 2019. We extracted data on patient characteristics, isolated Candida species antifungal susceptibility, management and outcomes; Results: We included 170 cases of candidemia. NAC was more common than albicans candidemia (64.7% vs. 35.3%). C. glabrata was the most common non-albicans species (37 isolates) followed by C. tropicalis (14). Recent use of antifungals was a risk factor for NAC (OR = 2.8, p = 0.01), while the presence of a central venous catheter was protective (OR = 0.41, p = 0.02). Fluconazole resistance was 12.5% in C. albicans and 21.5% in non-albicans spp. Mortality at 30 days was 55.5%, with no difference between NAC and albicans candidemia. It was higher in older and critically ill patients but lower in patients whose central venous catheter was removed after detecting fungemia; Conclusions: Candidemia is associated with high mortality in Lebanon, with a predominance of NAC and high prevalence of C. glabrata.

Drug-Resistant Fungi: An Emerging Challenge Threatening Our Limited Antifungal Armamentarium

The high clinical mortality and economic burden posed by invasive fungal infections (IFIs), along with significant agricultural crop loss caused by various fungal species, has resulted in the widespread use of antifungal agents. Selective drug pressure, fungal attributes, and host- and drug-related factors have counteracted the efficacy of the limited systemic antifungal drugs and changed the epidemiological landscape of IFIs. Species belonging to Candida, Aspergillus, Cryptococcus, and Pneumocystis are among the fungal pathogens showing notable rates of antifungal resistance. Drug-resistant fungi from the environment are increasingly identified in clinical settings. Furthermore, we have a limited understanding of drug class-specific resistance mechanisms in emerging Candida species. The establishment of antifungal stewardship programs in both clinical and agricultural fields and the inclusion of species identification, antifungal susceptibility testing, and therapeutic drug monitoring practices in the clinic can minimize the emergence of drug-resistant fungi. New antifungal drugs featuring promising therapeutic profiles have great promise to treat drug-resistant fungi in the clinical setting. Mitigating antifungal tolerance, a prelude to the emergence of resistance, also requires the development of effective and fungal-specific adjuvants to be used in combination with systemic antifungals.

Human Fungal Infections in Kuwait-Burden and Diagnostic Gaps

Fungal infections are an increasingly important public health issue, yet accurate statistics on fungal burden worldwide and in Kuwait are scarce. Here we estimate the incidence and prevalence of fungal infections in Kuwait. Population statistics from 2018 collected by the Public Authority for Civil Information were used, as well as data from the Ministry of Health. A literature search for Kuwait data on mycotic diseases and population at risk (chronic obstructive pulmonary disease, HIV infection/AIDS, cancer, and transplant patients) was conducted. The population in 2018 was estimated at 4,226,920 million people: 1,303,246 million Kuwaitis and 2,923,674 million expatriates. We determined the annual burden of serious fungal infections number (per 100,000) from high to low based on earlier reported fungal rates for populations at risk: recurrent Candida vaginitis 54,842 (2595); severe asthma with fungal sensitisation 10,411 (246); allergic bronchopulmonary aspergillosis, 7887 (187); chronic pulmonary aspergillosis 995 (21.3); invasive aspergillosis 704 (16.7); fungal keratitis 654 (15.5); candidaemia 288 (6.8); Candida peritonitis 63 (3.5) and oesophageal candidiasis in HIV 33 (0.8). Besides identifying rising new risk groups and expanding reports on antifungal resistance, surveillance programs and further epidemiological studies are needed to achieve more precise assessments of fungal disease epidemiology and correlated morbidity and mortality.

Accuracy of matrix-assisted LASER desorption ionization-time of flight mass spectrometry for identification of Candida

Background: Candida is a fungus that causes various types of candidemia, which is the fourth major infectious disease of the blood system. MALDI-TOF-MS is a simple and rapid detection instrument. The aim of the present study was to verify the accuracy of MALDI-TOF-MS in detecting Candida.

Method: A pooled analysis of articles on MALDI-TOF-MS for diagnosis of candidemia was performed. The quality of original research was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines. Stata 12.0 software was used to merge the correct identification rates of Candida and Candida subspecies and obtain pooled sensitivity and specificity of the diagnostic methods. Heterogeneity was found in the subgroup analysis of the included articles. Hence, we explored the factors causing the heterogeneity and its impact on the overall situation. Sensitivity analysis was used to examine the effect of Candida level on total response. Egger’s test was used to evaluate the publication bias of the included articles.

Results: A total of 16 articles in Pubmed, 79 articles in Embase, 1 article in Cochrane Library, 30 articles in Web of Science and 3 from other sources were identified, of which 10 articles were included based on the inclusion and exclusion criteria. The overall identification accuracy was 100%.

Conclusion: The accuracy of MALDI-TOF-MS for the identification of Candida was 100%. Further research is necessary to determine whether MALDI-TOF-MS can be used as a clinical diagnostic standard for the identification of Candida.

Update on invasive fungal infections in the Middle Eastern and North African region

In the recent years, the epidemiology of invasive fungal infections (IFIs) has changed worldwide. This is remarkably noticed with the significant increase in high-risk populations. Although surveillance of such infections is essential, data in the Middle Eastern and North African (MENA) region remain scarce. In this paper, we reviewed the existing data on the epidemiology of different IFIs in the MENA region. Epidemiological surveillance is crucial to guide optimal healthcare practices. This study can help to guide appropriate interventions and to implement antimicrobial stewardship and infection prevention and control programs in countries.

Assessment of antifungal resistance and associated molecular mechanism in Candida albicans isolates from different cohorts of patients in North Indian state of Haryana

The present study examines the trend in distribution of Candida species and their antifungal resistance patterns in hospitals across Haryana, a North Indian state with poorly addressed epidemiology of fungal infections. In our collection of 228 Candida isolates, Candida albicans dominated in both high vaginal swab (HVS) and urine samples while Candida glabrata and Candida tropicalis were the second-highest non-albicans Candida species (NAC), respectively. Of note, in blood samples, C. tropicalis and C. albicans were present in equal numbers. All 228 isolates were subjected to antifungal susceptibility tests, whereby 51% of C. albicans recovered from HVS samples displayed fluconazole resistance. To understand its mechanistic basis, expression profiling of efflux pump genes CDR1, CDR2, MDR1 and azole drug target, ERG11 was performed in 20 randomly selected resistant isolates, wherein many isolates elicited higher expression. Further, ERG11 gene sequencing suggested that most of the isolates harbored mutations, which are not reported with azole resistance. However, one isolate, RPCA9 (MIC 64 μg/mL) harbored triple mutation (Y132C, F145L, A114V), wherein Y132 and F145 sites were previously implicated in azole resistance. Interestingly, one isolate, (RPCA61) having MIC > 128 μg/mL harbored a novel mutation, G129R. Of note, HVS isolates RPCA 21, RPCA 22, and RPCA 44 (MICs 64 to > 128 μg/mL) did not show any change in alteration in ERG11 or overexpression of efflux pump genes. Together, this study presents a first report of Candida infections in selected hospitals of Haryana State.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

The epidemiology of Candida species in the Middle East and North Africa

In recent decades, the epidemiology of invasive candidiasis (IC) has progressively changed worldwide. This notably includes emergence of several Candida species. Although some surveillance programs provided global trends in IC epidemiology, data from countries from the Middle East and North Africa (MENA) remain scarce. In this manuscript, we reviewed the existing available data on the epidemiology of Candida species associated with IC, particularly candidemia, in MENA region regarding species distribution. As witnessed worldwide, an evident shift of Candidaalbicans towards non-albicansCandida (NAC) has been observed in the MENA region. The worrying emergence of multi-drug resistant Candida species in MENA calls for a better understanding of their epidemiology. This represents an essential prerequisite for the implementation of effective infection control strategies and surveillance systems to prevent IC among high-risk patients.

Epidemiology and burden of invasive fungal infections in the countries of the Arab League

The burden of invasive fungal infections is alarming worldwide. The aim of this paper is to review the published literature and evaluate the knowledge gap pertaining to studies on invasive fungal infections in the countries of the Arab League. Few countries from this region have published reports. The most commonly studied invasive fungal infections is invasive candidiasis. Candida albicans remains overall the most common causative pathogen (33.8-60%), however, non-albicans Candida species are increasing. Antifungal susceptibility testing is non-standardized across the published studies. Data on aspergillosis and other fungal infections is scarce. This sheds light on the need for standardized surveillance in the region encompassing more countries of the Arab League to guide diagnostic approach and empiric therapy.

Changing trends in epidemiology and antifungal susceptibility patterns of six bloodstream Candida species isolates over a 12-year period in Kuwait

Changing trends in incidence and antifungal susceptibility patterns of six Candida species causing candidemia in Kuwait between 2006–2017 are reported. A total of 2075 isolates obtained from 1448 patients were analyzed. Identity of Candida species isolates was determined by phenotypic methods and confirmed by PCR amplification/PCR-sequencing of rDNA and/or MALDI-TOF MS. Antifungal susceptibility was determined by Etest. C. albicans accounted for 539 (37.22%) cases followed by C. parapsilosis (n = 502, 34.67%), C. tropicalis (n = 210, 14.5%), C. glabrata (n = 148, 10.22%), C. krusei (n = 27, 1.81%) and C. dubliniensis (n = 22, 1.5%). The comparative percent distribution of Candida species causing candidemia between 2006–2011 and 2012–2017 was as follows: C. albicans 41.8% and 33.1%, C. parapsilosis complex 32.01% and 37.04%, C. tropicalis 13.59% and 15.31%, and C. glabrata 8.77% and 11.51%, C. krusei 2.0% and 1.7%, and C. dubliniensis 1.75 and 1.3%, respectively. Three of 371 C. albicans isolates during 2006–2011 and five of 363 during 2012–2017 were resistant to fluconazole. Among C. parapsilosis isolates, one of 310 during 2006–2011 and 21 of 446 during 2012–2017 were resistant to this drug. Furthermore, at an epidemiologic cutoff value (ECV) of ≤0.5 μg/ml, 70.1% C. albicans isolates were wild-type for fluconazole during 2006–2011 as compared to 58.1% during 2012–2017. Likewise, at an ECV of ≤2 μg/ml, 98.0% of C. parapsilosis isolates were wild-type during 2006–2011 as compared to 93.4% during 2012–2017. Clonal spread of fluconazole-resistant C. parapsilosis in one major hospital was documented. An 8.8% shift in favor of non-albicans Candida species with concomitant increase in MICs between the two periods preludes emergence of fluconazole-resistant candidemia cases in Kuwait.

Epidemiologic characteristics of adult candidemic patients in a secondary hospital in Kuwait: A retrospective study

Candida blood steam infection is a life-threatening disease that seems to be under estimated. Understanding epidemiology of such disease is crucial for improved diagnosis, optimized treatment, and better outcome. Through this retrospective study, we aimed to determine the incidence of candidemia in a secondary care hospital, and to describe the epidemiology and outcome of candidemia among adult patients. The incidence of candidemia for all age groups was 0.24, 0.16 and 0.15 cases/1000 patient-days in 2014, 2015 and 2016 respectively. Among adult patients, 82 cases were identified. The patients had the following clinical characteristics with varying proportions: old age, diabetes, antibiotic exposure, use of vascular catheter, abdominal surgery, ICU hospitalization, haemodialysis, and total parenteral nutrition. All-cause 30-day mortality was 54% and ICU hospitalization was a recognized risk factor for death. The leading causative agents were Candida albicans (32%), and Candida parapsilosis (32%), followed by Candida tropicalis (20%), Candida glabrata (13%) and one each by Candida dubliniensis, Candida famata, and Candida auris. Almost all tested isolates were susceptible to caspofungin and amphotericin B. With regard to fluconazole, C. glabrata showed variable susceptibility. Other species were susceptible except one isolate, each of C. parapsilosis and C. auris. The study highlights the growing importance of non-C. albicans Candida species in the etiology of candidemia. Emergence of C. auris is a warning sign and needs to be closely monitored.

Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting

No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species.

Identification of nine cryptic species of Candida albicans, C. glabrata, and C. parapsilosis complexes using one-step multiplex PCR

Background

Candida albicans, Candida glabrata, and Candida parapsilosis are three prevalent causes of candidiasis, worldwide. These species are considered as nine medically important complex species. Limited knowledge about these newly recognized species prompted us to develop a one-step, multiplex PCR to detect and identify them in clinical settings.

Methods

Primers targeting Hyphal Wall Protein I gene for the C. albicans, C. dubliniensis, C. africana, Intergenic Spacer for the C. glabrata, C. nivariensis, C. bracarensis, and Intein and ITS rDNA for the C. parapsilosis, C. orthopsilosis, and C. metapsilosis were designed. Using 168 CBS reference strains and 280 clinical isolates, the specificity and reproducibility of the developed assay were evaluated.

Results

Our developed assay successfully identified and distinguished all the nine species. No cross-reaction with closely- and distantly-related yeast species, Aspergillus species and human DNA was observed, resulting in 100% specificity. The ambiguous results obtained by MALDI-TOF for C. albicans and C. africana were corrected by our 9-plex PCR assay. This assay identified all the cryptic complex species from two test sets from Iran and China, correctly.

Conclusions

Our developed multiplex assay is accurate, specific, cost/time-saving, and works without the tedious DNA extraction steps. It could be integrated into routine clinical laboratories and as a reliable identification tool and has the potential to be implemented into epidemiological studies to broaden the limited knowledge of cryptic species complexes.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3381-5) contains supplementary material, which is available to authorized users.

Emerging Candida species isolated from renal transplant recipients: Species distribution and susceptibility profiles

Candidiasis is a major challenge among renal transplant recipients (RTRs) worldwide and is associated with high morbidity and mortality rates. Fluconazole is the most commonly used agent for Candida infections. However, frequent relapse and treatment failure are still reported among patients affected with this infection. In the present study, Candida species obtained from RTRs were characterized based on conventional and molecular assays. Furthermore, the antifungal susceptibility profiles of these species were determined. This study was conducted on a total of 126 RTRs within 2012-2016. The patients were categorized according to the referenced diagnostic criteria. The identification of Candida species was accomplished based on conventional examination, assimilation profile test, and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The minimum inhibitory concentrations (MICs) of amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, and caspofungin were determined based on the guidelines of Clinical and Laboratory Standards Institute. The patients with Candida infection were diagnosed with urinary tract candidiasis (n = 17), peritonitis (n = 8), intra-abdominal candidiasis (n = 6), candidemia (n = 4), hepatosplenic candidiasis (n = 3), and Candida pneumonia (n = 3). A total of 41 Candida isolates, including C. albicans (n = 18), C. famata (n = 8), C. kefyr (n = 4), C. tropicalis (n = 4), C. parapsilosis (n = 3), C. glabrata (n = 2), and C. lusitaniae (n = 2), were isolated from 32.5% (41/126) renal transplant recipients. Fluconazole-resistance was observed in seven isolates, entailing C. albicans (n = 6) and C. tropicalis (n = 1). Fluconazole MIC for C. lusitaniae isolates was above the epidemiologic cut-off value (4-16 μg/ml). Furthermore, MIC range values of fluconazole against C. famata and C. kefyr were obtained as 4-32 μg/ml and 4-8 μg/ml, respectively. Posaconazole exhibited potent activity against Candida isolates, followed by caspofungin. The identification of Candida species, together with susceptibility testing, provides important data about the geographic trends of the fluconazole-resistance profiles of Candida species. It is necessary to maintain a consistent method for the implementation of early diagnosis and adoption of treatment regimen.

Molecular Analysis of Resistance and Detection of Non-Wild-Type Strains Using Etest Epidemiological Cutoff Values for Amphotericin B and Echinocandins for Bloodstream Candida Infections from a Tertiary Hospital in Qatar

A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiary hospital in Qatar were evaluated. Out of all Candida infections, 53% were diagnosed in patients admitted to the intensive care units. Steady increases in non-albicans Candida species were reported from 2009 to 2014 (30.2% for Candida albicans versus 69.8% for the other Candida species). Etest antifungal susceptibility testing was performed on all recovered clinical isolates to determine echinocandin (micafungin and anidulafungin) and amphotericin B susceptibilities and assess non-wild-type (non-WT) strains (strains for which MICs were above the epidemiological cutoff values). DNA sequence analysis was performed on all isolates to assess the presence of FKS mutations, which confer echinocandin resistance in Candida species. A total of 3.9% of isolates (12/301) among strains of C. albicans and C. orthopsilosis contained FKS hot spot mutations, including heterozygous mutations in FKS1 For C. tropicalis, the Etest appeared to overestimate strains non-WT for micafungin, anidulafungin, and amphotericin B, as 14%, 11%, and 35% of strains, respectively, had values above the epidemiological cutoff value. However, no FKS mutations were identified in this species. For all other species, micafungin best reported the echinocandin non-WT strains relative to the FKS genotype, as anidulafungin tended to overestimate non-wild-type strains. Besides C. tropicalis, few strains were classified as non-WT for amphotericin B.

Comparison of the incidence, clinical features and outcomes of invasive candidiasis in children and neonates

Background

Invasive candidiasis differs greatly between children and neonates. We aimed to investigate the different therapeutic approaches and their effects on treatment outcomes of these two groups.

Methods

Episodes of neonatal invasive candidiasis were compared with non-neonatal pediatric episodes during a 12-year cohort study. Clinical isolates were documented by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and DNA sequencing, and antifungal susceptibility testing was performed.

Results

A total of 342 episodes of invasive candidiasis (113 neonatal and 229 non-neonatal pediatric episodes) in 281 pediatric patients (96 neonates and 185 children) were identified. Candida albicans was the most common pathogen causing invasive candidiasis in neonates and children (47.8% vs. 44.1%). The antifungal susceptibility profiles were not significantly different between neonates and children. More neonates received amphotericin B as therapy, whereas more children received fluconazole or caspofungin. Compared with children, neonates had a significantly longer duration of fungemia, higher rates of septic shock (34.5% vs. 21.8%; P = 0.013), sepsis-attributable mortality (28.3% vs. 17.5%; P = 0.024) and in-hospital mortality (42.7% vs. 25.4%; P = 0.004) than children. Independent risk factors for treatment failure of invasive candidiasis were septic shock (odds ration [OR] 16.01; 95% confidence interval [CI] 7.64–33.56; P <  0.001), delayed removal of intravenous catheter (OR 6.78; 95% CI 2.80–17.41; P <  0.001), renal failure (OR 5.38; 95% CI 1.99–14.57; P = 0.001), and breakthrough invasive candidiasis (OR 2.99; 95% CI 1.04–8.67; P = 0.043).

Conclusions

Neonatal invasive candidiasis has worse outcomes than non-neonatal pediatric candidiasis. Neonatologists and pediatricians must consider age-specific differences when developing treatment and prevention guidelines, or when interpreting studies of other age groups.

Diversity of culturable yeasts associated with zoanthids from Brazilian reef and its relation with anthropogenic disturbance

Some of the main threats to coral reefs come from human actions on marine environment, such as tourism, overfishing and pollution from urban development. While several studies have demonstrated an association between bacteria and corals, demonstrating how these communities react to different anthropogenic stressors, yeast communities associated with corals have received far less attention from researchers. The aim of this work was therefore to describe cultivable yeasts associated with three coral species and to evaluate the influence of sewage discharge on yeasts community. We obtained 130 isolates, mostly belonging to phylum Ascomycota and many of them had previously been isolated from human samples or are considered pathogens. The mycobiota was more similar among corals collected from the same reef, indicating that the composition of reef yeast community is more influenced by environmental conditions than host species. We suggest further studies to elucidate which factors are most influential on the composition of the coral-associated yeast community.

Candida bloodstream infections in Serbia: First multicentre report of a national prospective observational survey in intensive care units

Candida bloodstream infections (BSI) are a significant cause of mortality in intensive care units (ICU), hereof the prospective 12-months (2014-2015) hospital- and laboratory-based survey was performed at the Serbian National Reference Medical Mycology Laboratory (NRMML). Candida identification was done by a matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and a susceptibility test, according to the Clinical and Laboratory Standards Institute methodology. Among nine centres (265 beds; 10 820 patient admissions), four neonatal/paediatric (NICU/PICUs) and five adult centres (ICUs) participated, representing 89 beds and 3446 patient admissions, 166 beds and 7347 patient admissions respectively. The NRMML received 43 isolates, 17 from NICU/PICUs and 26 from adult ICUs. C. albicans dominated highly in NICU/PICUs (~71%), whereas C. albicans and C. parapsilosis were equally distributed within adults (46%, each), both accounting for ~90% of received isolates. The resistance to itraconazole and flucytosine were 25% and 2.4% respectively. In addition, the 2 C. albicans were azole cross-resistant (4.6%). The overall incidence of CandidaBSI was ~3.97 cases/1000 patient admissions (4.93 in NICU/PICU and 3.53 in adult ICU). The 30-day mortality was ~37%, most associated with C. tropicalis and C. glabrataBSI. Data from this national survey may contribute to improving the Balkan and Mediterranean region epidemiology of CandidaBSI within ICUs.

Prevalence, virulence factors and antifungal susceptibility of Candida spp. isolated from bloodstream infections in a tertiary care hospital in Brazil

Candida spp. are responsible for 80% of all systemic fungal infections and are associated with high mortality rates. This study characterised 79 bloodstream isolates of C. albicans, C. glabrata, C. orthopsilosis, C. parapsilosis and C. tropicalis from patients in a Brazilian hospital. The susceptibility to amphotericin B, caspofungin, fluconazole and voriconazole was determined; virulence factor production was assessed based on haemolysin, phospholipase and proteinase activities, and the patients' clinical characteristics were analysed. C. albicans was the predominant species (44%), followed by C. glabrata (19%), C. tropicalis (19%), C. parapsilosis (14%) and C. orthopsilosis (4%). The candidemia incidence was 1.52 per 1000 admissions, and the crude mortality rate was 52%. One C. albicans isolate was resistant to fluconazole and voriconazole. Moreover, 20.2%, 2.5% and 3.8% of the isolates exhibited dose-dependent susceptibility to fluconazole, voriconazole and caspofungin, respectively. In conclusion, although the C. glabrata incidence was higher than that usually described in Brazil, its increase was previously observed in studies conducted worldwide. Furthermore, the azole resistance of the C. albicans isolate could be due to previous exposure to these antifungals. These results highlight the importance of epidemiological studies and will facilitate an improved understanding of candidemia in the studied hospital.

Epidemiological and mycological characteristics of candidemia in Iran: A systematic review and meta-analysis

To date, there has been no comprehensive review of the epidemiology, risk factors, species distribution, and outcomes of candidemia in Iran. This study aimed to perform a systematic review and meta-analysis of all reported candidemia cases in Iran until December 2015. The review process occurred in three steps, namely a literature search, data extraction and statistical analyses. After a comprehensive literature search, we identified 55 cases. The mean age of patients was 46.80±24.30 years (range 1-81 years). The main risk factors for candidemia were surgery and burns (23.6%), followed by malignancies (20%), use of broad-spectrum antibiotics (18.2%), and diabetes (7.3%). Candida parapsilosis (n=17, 30.8%) was the leading agent, followed by Candida albicans (n=15, 27.3%), Candida glabrata (n=10, 18.2%), and Candida tropicalis (n=8, 14.5%). The frequencies of candidemia cases due to C. glabrata, C. parapsilosis, and C. albicans were significantly higher among patients aged>60, 21-40, and 41-60 years, respectively. Comparison of risk factors for candidemia by multiple logistic regression showed that one of the most important risk factors was surgery (OR: 4.245; 95% CI: 1.141-15.789; P=0.031). The outcome was recorded in only 19 cases and 13 of those patients (68.4%) expired. This study confirms that knowledge of the local epidemiology is important when conducting surveillance studies to prevent and control candidemia and will be of interest for antifungal stewardship.

Burden of fungal infections in Qatar

Few estimates of fungal disease frequency have been attempted in the Middle East. We have estimated the burden of fungal infections in Qatar. The aim of the study was to compute and determine the burden of serious fungal infections, in an attempt to estimate fungal disease frequency, which has not previously been attempted in this country. Disease statistics were collected from the Microbiology laboratory database and from 2011 WHO statistics. The data are expressed per 100,000 populations. The reported cases of candidaemia rose to 288 with an estimated rate of 15.4/100,000. A real increase in the burden of candidaemia was found over that previously reported (12.9/100,000) for the years 2004-2009. Candida peritonitis was estimated in 8.02 cases/100,000 population. Recurrent (≥4 year(-1) ) vaginal infections affect at least 32,782 women with a rate of 3506/100,000 inhabitants. Severe asthma with fungal sensitisation affected 1486 people, allergic bronchopulmonary aspergillosis 1126 people and chronic pulmonary aspergillosis 176 people. Rhinosinusitis, mucormycosis and Fusarium infection occurred at rates of 2.31, 1.23, 1.86 cases/100,000 respectively. The estimated rate of invasive aspergillosis was very low (0.6/100,000). Low rates of Cryptococcus meningitis and Pneumocystis pneumonia are attributable to low HIV infection rates. In conclusion, fungal infections are increasingly reported, especially candidaemia. Surveillance and guidelines are needed to optimise care and management of common fungal infections. In addition, a fungal registry system needs development for surveillance.

Identification and antifungal susceptibility of Candida species isolated from bloodstream infections in Konya, Turkey

Background

In this study, our aim was to identify Candida species isolated from bloodstream infections and to determine their susceptibilities to various antifungal agents to demonstrate the local resistance profiles and to guide empirical treatment for clinicians.

Methods

Two hundred Candida isolates (95 Candida albicans, 105 non-albicans Candida strains) were included in the study. Candida species were identified by conventional, biochemical and molecular methods. Antifungal susceptibility tests for amphotericin B, fluconazole, voriconazole, posaconazole, caspofungin and anidulafungin were performed with broth microdilution method according to the Clinical and Laboratory Standards Institute M27-A3 document.

Results

Of the 200 Candida strains, the most prevalent species were C. albicans (47.5 %), Candida glabrata (18.0 %) and Candida parapsilosis complex (14.0 %). All Candida species except for three (1.5 %) Candida kefyr strains were susceptible to amphotericin B. Only one (2.8 %) C. glabrata was resistant to fluconazole (MIC ≥ 64 μg/ml), and the others (97.2 %) exhibited dose-dependent susceptibility. All species, but C. glabrata strains, were susceptible to fluconazole. Resistance to voriconazole, posaconazole, caspofungin and anidulafungin was not detected in any strain.

Conclusion

Candida albicans were susceptible to all antifungal drugs. Three C. kefyr strains were resistant to amphotericin B. Only one C. glabrata was resistant to fluconazole. All the strains were susceptible to voriconazole, posaconazole, caspofungin and anidulafungin. In vitro antifungal susceptibility tests should be performed to select of appropriate and effective antifungal therapy, and monitor the development of resistance.

Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies

The Candida parapsilosis species complex comprises a group of emerging human pathogens of varying virulence. This complex was recently subdivided into three different species: C. parapsilosis sensu stricto, C. metapsilosis, and C. orthopsilosis. Within the latter, at least two clearly distinct subspecies seem to be present among clinical isolates (Type 1 and Type 2). To gain insight into the genomic differences between these subspecies, we undertook the sequencing of a clinical isolate classified as Type 1 and compared it with the available sequence of a Type 2 clinical strain. Unexpectedly, the analysis of the newly sequenced strain revealed a highly heterozygous genome, which we show to be the consequence of a hybridization event between both identified subspecies. This implicitly suggests that C. orthopsilosis is able to mate, a so-far unanswered question. The resulting hybrid shows a chimeric genome that maintains a similar gene dosage from both parental lineages and displays ongoing loss of heterozygosity. Several of the differences found between the gene content in both strains relate to virulent-related families, with the hybrid strain presenting a higher copy number of genes coding for efflux pumps or secreted lipases. Remarkably, two clinical strains isolated from distant geographical locations (Texas and Singapore) are descendants of the same hybrid line, raising the intriguing possibility of a relationship between the hybridization event and the global spread of a virulent clone.

In Vitro Activities of Six Antifungal Drugs Against Candida glabrata Isolates: An Emerging Pathogen

Background

Candida glabrata is a pathogenic yeast with several unique biological features and associated with an increased incidence rate of candidiasis. It exhibits a great degree of variation in its pathogenicity and antifungal susceptibility.

Objectives

The aim of the present study was to evaluate the in vitro antifungal susceptibilities of the following six antifungal drugs against clinical C. glabrata strains: amphotericin B (AmB), ketoconazole (KTZ), fluconazole (FCZ), itraconazole (ITZ), voriconazole (VCZ), and caspofungin (CASP).

Materials and Methods

Forty clinical C. glabrata strains were investigated using DNA sequencing. The in vitro antifungal susceptibility was determined as described in clinical laboratory standard institute (CLSI) documents (M27-A3 and M27-S4).

Results

The sequence analysis of the isolate confirmed as C. glabrata and deposited on NCBI GenBank under the accession number no. KT763084-KT763123. The geometric mean MICs against all the tested strains were as follows, in increasing order: CASP (0.17 g/mL), VCZ (0.67 g/mL), AmB (1.1 g/mL), ITZ (1.82 g/mL), KTZ (1.85 g/mL), and FCZ (6.7 g/mL). The resistance rates of the isolates to CASP, FCZ, ITZ, VZ, KTZ, and AmB were 5%, 10%, 72.5%, 37.5%, 47.5%, and 27.5%, respectively.

Conclusions

These findings confirm that CASP, compared to the other antifungals, is the potent agent for treating candidiasis caused by C. glabrata. However, the clinical efficacy of these novel antifungals remains to be determined.

Community acquired fungemia caused by Candida pulcherrima: diagnostic contribution of MALDI-TOF mass spectrometry

BACKGROUND

Community-onset candidemia constitute a distinct clinical entity the incidence of which is increasing. Contribution of non-albicans Candida species is rising.

CASE PRESENTATION

We describe here the first reported case of community acquired fungemia due to Candida pulcherrima. Identification to the species level was performed by MALDI-TOF mass spectrometry. Treatment with fluconazole was successful.

CONCLUSION

This case confirms the pathogenic role of C. pulcherrima and the contribution of MALDI-TOF mass spectrometry for identification of rare Candida species.

Molecular Identification and Echinocandin Susceptibility of Candida parapsilosis Complex Bloodstream Isolates in Italy, 2007-2014

The Candida parapsilosis group encompasses three species: C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Here, we describe the incidence and echinocandin susceptibility profile of bloodstream isolates of these three species collected from patients admitted to an Italian university hospital from 2007 to 2014. Molecular identification of cryptic species of the C. parapsilosis complex was performed using polymerase chain reaction amplification of the gene encoding secondary alcohol dehydrogenase, followed by digestion with the restriction enzyme BanI. Minimum inhibitory concentrations were determined using the broth microdilution method according to European Committee for Antimicrobial Susceptibility Testing (EUCAST EDef 7.2) and Clinical Laboratory Standards Institute (CLSI M27-A3) guidelines, and the results were compared with those obtained using the E-test and Sensititre methods. Of the 163 C. parapsilosis complex isolates, 136 (83.4%) were identified as C. parapsilosis, and 27 (16.6%) as C. orthopsilosis. The species-specific incidences were 2.9/10,000 admissions for C. parapsilosis and 0.6/10,000 admissions for C. orthopsilosis. No resistance to echinocandins was detected with any of the methods. The percent essential agreement (EA) between the EUCAST and E-test/Sensititre methods for anidulafungin, caspofungin, and micafungin susceptibility was, respectively, as follows: C. parapsilosis, 95.6/97.8, 98.5/88.2, and 93.4/96.3; C. orthopsilosis, 92.6/92.6, 96.3/77.8, and 63.0/66.7. The EA between the CLSI and E-test/Sensititre methods was, respectively, as follows: C. parapsilosis, 99.3/100, 98.5/89.0, and 96.3/98.5; C. orthopsilosis, 96.3/92.6, 100/81.5, and 92.6/88.9. Only minor discrepancies, ranging from 16.9% (C. parapsilosis) to 11.1% (C. orthopsilosis), were observed between the CLSI and E-test/Sensititre methods. In conclusion, this epidemiologic study shows a typical C. parapsilosis complex species distribution, no echinocandin resistance, and it reinforces the relevance of using commercially available microbiological methods to assess antifungal susceptibility. These data improve our knowledge of the national distribution of species of the psilosis group, as there are very few studies of these species in Italy.

First isolation of Candida metapsilosis in Kuwait, an emerging global opportunistic pathogen

Invasive infections due to uncommon and rare yeast species are increasing worldwide in prevalence and are associated with high mortality rates. Here, we describe the first isolation and characterization of Candida metapsilosis cultured from the blood sample of a 10-year-old Saudi girl, who suffered from a neurodegenerative disorder, in Kuwait. The yeast isolate was identified by sequencing of ITS region and D1/D2 domains of rDNA. The report extends the geographic distribution of C. metapsilosis to the Middle East and highlights the emerging role of uncommon yeast species causing infections in susceptible hosts.

Activity of Isavuconazole and Other Azoles against Candida Clinical Isolates and Yeast Model Systems with Known Azole Resistance Mechanisms

Isavuconazole is a novel, broad-spectrum, antifungal azole. In order to evaluate its interactions with known azole resistance mechanisms, isavuconazole susceptibility among different yeast models and clinical isolates expressing characterized azole resistance mechanisms was tested and compared to those of fluconazole, itraconazole, posaconazole, and voriconazole. Saccharomyces cerevisiae expressing the Candida albicans and C. glabrata ATP binding cassette (ABC) transporters (CDR1, CDR2, and CgCDR1), major facilitator (MDR1), and lanosterol 14-α-sterol-demethylase (ERG11) alleles with mutations were used. In addition, pairs of C. albicans and C. glabrata strains from matched clinical isolates with known azole resistance mechanisms were investigated. The expression of ABC transporters increased all azole MICs, suggesting that all azoles tested were substrates of ABC transporters. The expression of MDR1 did not increase posaconazole, itraconazole, and isavuconazole MICs. Relative increases of azole MICs (from 4- to 32-fold) were observed for fluconazole, voriconazole, and isavuconazole when at least two mutations were present in the same ERG11 allele. Upon MIC testing of azoles with clinical C. albicans and C. glabrata isolates with known resistance mechanisms, the MIC90s of C. albicans for fluconazole, voriconazole, itraconazole, posaconazole, and isavuconazole were 128, 2, 1, 0.5, and 2 μg/ml, respectively, while in C. glabrata they were 128, 2, 4, 4, and 16 μg/ml, respectively. In conclusion, the effects of azole resistance mechanisms on isavuconazole did not differ significantly from those of other azoles. Resistance mechanisms in yeasts involving ABC transporters and ERG11 decreased the activity of isavuconazole, while MDR1 had limited effect.

Characterising atypical Candida albicans clinical isolates from six third-level hospitals in Bogotá, Colombia

BACKGROUND

Candida species are the most frequently found fungal pathogens causing nosocomial disease in a hospital setting. Such species must be correctly identified to ensure that appropriate control measures are taken and that suitable treatment is given for each species. Candida albicans is causing most fungal disease burden worldwide; the challenge lies in differentiating it from emerging atypical, minor and related species such as Candida dubliniensis and Candida africana. The purpose of this study was to compare identification based on MALDI-TOF MS to standard identification systems using a set of nosocomial isolates.

METHODS

Eleven nosocomial samples were collected from 6 third-level hospitals in Bogotá, Colombia. All the samples were identified by combining MALDI-TOF MS with morphological characters, carbohydrate assimilation and molecular markers (D1/D2 and HWP1).

RESULTS

The present work describes the first collection of atypical Colombian Candida clinical isolates; these were identified as Candida albicans/Candida africana by their MALDI-TOF MS profile. Phenotypical characteristics showed that they were unable to produce chlamydospores, assimilate trehalose, glucosamine, N- acetyl-glucosamine and barely grew at 42 °C, as would be expected for Candida africana. The molecular identification of the D1/D2 region of large subunit ribosomal RNA and HWP1 hyphal cell wall protein 1 sequences from these isolates was consistent with those for Candida albicans. The mass spectra obtained by MALDI-TOF MS were analysed by multi-dimensional scaling (MDS) and cluster analysis, differences being revealed between Candida albicans, Candida africana, Candida dubliniensis reference spectra and two clinical isolate groups which clustered according to the clinical setting, one of them being clearly related to C. albicans.

CONCLUSION

This study highlights the importance of using MALDI-TOF MS in combination with morphology, substrate assimilation and molecular markers for characterising Candida albicans-related and atypical C. albicans species, thereby overcoming conventional identification methods. This is the first report of hospital-obtained isolates of this type in Colombia; the approach followed might be useful for gathering knowledge regarding local epidemiology which could, in turn, have an impact on clinical management. The findings highlight the complexity of distinguishing between typical and atypical Candida albicans isolates in hospitals.

Epidemiological and mycological characteristics of candidemia in patients with hematological malignancies attending a tertiary-care center in India

BACKGROUND AND OBJECTIVES

We undertook the present study to ascertain the contributing risk factors and explore the epidemiological and mycological characteristics of opportunistic candidemia among patients with hematological malignancies.

DESIGN AND SETTINGS

Observational cross-sectional study in a tertiary care center.

PATIENTS AND METHODS

Consecutive patients with hematological malignancies reporting to the collaborating medical and pediatric units with a febrile episode were recruited and screened for candidemia by blood culture. Recovered Candida isolates were speciated and antifungal susceptibility testing was performed as per Clinical and Laboratory Standards Institute guideline (CLSI) guidelines M44-A. Further analysis was done for potential risk factors and compared between culture positive and negative patients.

RESULTS

Of 150 patients recruited, the majority (n=27) were between 51 and 60 years and the male to female ratio was 1.63:1. Fifteen patients (10%) were culture positive. The culture positivity was significantly higher in acute lymphocytic leukemia (ALL) than in non-ALL patients (p=0.03). There was significant association of candidaemia with leucopenia, chemotherapeutic drugs, corticosteroids and presence of indwelling devices. Duration of disease (p=0.032) and duration of hospitalization (p=0.003) were significantly prolonged in culture positive patients. C. tropicalis was the commonest isolate (46.67%), with non- Candida albicans outnumbering C. albicans in all categories of hematological malignancies (2.75:1). All isolates of C. albicans were uniformly sensitive to all the azoles, but only 50% were sensitive to amphotericin B and none to nystatin and flucytosine.

CONCLUSIONS

This observational study identifies ALL and chronic lymphocytic leukemia (CLL) as the forms of hematological malignancy predominantly associated with candidemia; specifies risk factors and chemotherapeutic agents predisposing patients towards its occurrence; reports a preponderance of C. tropicalis among the causative agents and finds voriconazole to be the most effective antifungal agent against the recovered isolates. This information could assist in tailoring prophylactic and therapeutic antifungal practices for this infection, according to local epidemiological and mycological characteristics.

Isavuconazole

Objective: To review the pharmacology, chemistry, in vitro susceptibility, pharmacokinetics, clinical efficacy, safety, tolerability, dosage, and administration of isavuconazole, a triazole antifungal agent. Data Sources: Studies and reviews were identified through an English language MEDLINE search (1978 to March 2015) and from http://www.clinicaltrials.gov , Food and Drug Administration (FDA) briefing documents, program abstracts from international symposia, and the manufacturer’s Web site. Study Selection and Data Extraction: All published and unpublished trials, abstracts, in vitro and preclinical studies, and FDA briefing documents were reviewed. Data Synthesis: Isavuconazole has activity against a number of clinically important yeasts and molds, including Candida spp, Aspergillus spp, Cryptococcus neoformans, and Trichosporon spp and variable activity against the Mucorales. Isavuconazole, available for both oral and intravenous administration, is characterized by slow elimination allowing once-daily dosing, extensive tissue distribution, and high (>99%) protein binding. The most commonly reported adverse events, which are mild and limited in nature, include nausea, diarrhea, and elevated liver function tests. Its drug interaction potential appears to be similar to other azole antifungals but less than those observed with voriconazole. Comparative trials are under way or have been recently completed for the treatment of candidemia, invasive candidiasis and aspergillosis, and rare mold infections. Conclusions: Isavuconazole has a broad spectrum of activity and favorable pharmacokinetic properties, providing an advantage over other currently available broad-spectrum azole antifungals and a clinically useful alternative to voriconazole for the treatment of invasive aspergillosis. It may also prove useful for the treatment of candidemia and invasive mold infections; however, these indications await the results of clinical trials.

Species distribution and susceptibility profile to fluconazole, voriconazole and MXP-4509 of 551 clinical yeast isolates from a Romanian multi-centre study

This is the first multi-centre study regarding yeast infections in Romania. The aim was to determine the aetiological spectrum and susceptibility pattern to fluconazole, voriconazole and the novel compound MXP-4509. The 551 isolates were identified using routine laboratory methods, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and DNA sequence analysis. Susceptibility testing was performed using the European Committee for Antimicrobial Susceptibility Testing (EUCAST) method and breakpoints. The yeasts originated from superficial infections (SUP, 51.5 %), bloodstream infections (BSI, 31.6 %) and deep-seated infections (DEEP, 16.9 %), from patients of all ages. Nine genera and 30 species were identified. The 20 Candida species accounted for 94.6 % of all isolates. C. albicans was the overall leading pathogen (50.5 %). Lodderomyces elongisporus is reported for the first time as a fungaemia cause in Europe. C. glabrata and Saccharomyces cerevisiae, as well as the non-Candida spp. and non-albicans Candida spp. groups, showed decreased fluconazole susceptibility (<75 %). The overall fluconazole resistance was 10.2 %. C. krusei accounted for 27 of the 56 fluconazole-resistant isolates. The overall voriconazole resistance was 2.5 % and was due mainly to C. glabrata and C. tropicalis isolates. Fluconazole resistance rates for the three categories of infection were similar to the overall value; voriconazole resistance rates differed: 4 % for BSI, 3.2 % for DEEP and 1.4 % for SUP. The antifungal activity of MXP-4509 was superior to voriconazole against C. glabrata and many fluconazole-resistant isolates. There was a large percentage of non-albicans Candida isolates. A large part of the high fluconazole resistance was not acquired but intrinsic, resulting from the high percentage of C. krusei.

Candidaemia observed at a university hospital in Milan (northern Italy) and review of published studies from 2010 to 2014

BACKGROUND

Candida species represent the fourth leading cause of nosocomial bloodstream infections (BSI) worldwide. However, candidaemia rates and species involved vary geographically.

OBJECTIVES

To evaluate the epidemiological pattern, risk factors for mortality and antifungal therapy of Candida BSI over a 5-year period (2008-2012) in a university hospital in northern Italy together with a review of the recent literature concerning candidaemia.

METHODS

A retrospective cohort study cross-linked with microbiology database was performed.

RESULTS

A total of 89 Candida BSI were identified in 42 males (47 %) and 47 females (52.8 %). The median age was 69 years (interquartile range 55-78) with 61.8 % of patients being older than 65 years. Considering all hospitalized patients, the overall incidence rate of candidaemia increased significantly from 2008 to 2012 (from 0.4 to 1.68 episodes per 10,000 patient/days) (p = 0.0001) with a mean linear increase in 5 new cases per year. Candida albicans was the predominant species isolated (64 %) followed by C. glabrata (19.1 %). The latter species was observed with significantly higher frequency in Internal Medicine and Intensive Care Units (ICU). In-hospital crude mortality was 41.6 %.

CONCLUSIONS

Candidaemia is an increasing BSI in our university hospital, in accordance with that observed in northern Italy, and it is still associated with high in-hospital crude mortality.

Interlaboratory comparison of sample preparation methods, database expansions, and cutoff values for identification of yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry using a yeast test panel

An interlaboratory study using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) to determine the identification of clinically important yeasts (n = 35) was performed at 11 clinical centers, one company, and one reference center using the Bruker Daltonics MALDI Biotyper system. The optimal cutoff for the MALDI-TOF MS score was investigated using receiver operating characteristic (ROC) curve analyses. The percentages of correct identifications were compared for different sample preparation methods and different databases. Logistic regression analysis was performed to analyze the association between the number of spectra in the database and the percentage of strains that were correctly identified. A total of 5,460 MALDI-TOF MS results were obtained. Using all results, the area under the ROC curve was 0.95 (95% confidence interval [CI], 0.94 to 0.96). With a sensitivity of 0.84 and a specificity of 0.97, a cutoff value of 1.7 was considered optimal. The overall percentage of correct identifications (formic acid-ethanol extraction method, score ≥ 1.7) was 61.5% when the commercial Bruker Daltonics database (BDAL) was used, and it increased to 86.8% by using an extended BDAL supplemented with a Centraalbureau voor Schimmelcultures (CBS)-KNAW Fungal Biodiversity Centre in-house database (BDAL+CBS in-house). A greater number of main spectra (MSP) in the database was associated with a higher percentage of correct identifications (odds ratio [OR], 1.10; 95% CI, 1.05 to 1.15; P < 0.01). The results from the direct transfer method ranged from 0% to 82.9% correct identifications, with the results of the top four centers ranging from 71.4% to 82.9% correct identifications. This study supports the use of a cutoff value of 1.7 for the identification of yeasts using MALDI-TOF MS. The inclusion of enough isolates of the same species in the database can enhance the proportion of correctly identified strains. Further optimization of the preparation methods, especially of the direct transfer method, may contribute to improved diagnosis of yeast-related infections.