PCR-enzyme immunoassay of rDNA in the diagnosis of candidemia and comparison with amplicon detection by agarose gel electrophoresis

Evaluation of Etest and MICRONAUT-AM Assay for Antifungal Susceptibility Testing of Candida auris: Underestimation of Fluconazole Resistance by MICRONAUT-AM and Overestimation of Amphotericin B Resistance by Etest

Multidrug-resistant Candida auris has recently caused major outbreaks in healthcare facilities. Rapid and accurate antifungal susceptibility testing (AST) of C. auris is crucial for proper management of invasive infections. The Commercial Sensititre Yeast One and Vitek 2 methods underestimate or overestimate the resistance of C. auris to fluconazole and amphotericin B (AMB). This study evaluated the AST results of C. auris against fluconazole and AMB by gradient-MIC-strip (Etest) and broth microdilution-based MICRONAUT-AM-EUCAST (MCN-AM) assays. Clinical C. auris isolates (n = 121) identified by phenotypic and molecular methods were tested. Essential agreement (EA, ±1 two-fold dilution) between the two methods and categorical agreement (CA) based on the Centers for Disease Control and Prevention's (CDC's) tentative resistance breakpoints were determined. Fluconazole resistance-associated mutations were detected by PCR-sequencing of ERG11. All isolates identified as C. auris belonged to South Asian clade I and contained the ERG11 Y132F or K143R mutation. The Etest-MCN-AM EA was poor (33%) for fluconazole and moderate (76%) for AMB. The CA for fluconazole was higher (94.2%, 7 discrepancies) than for AMB (91.7%, 10 discrepancies). Discrepancies were reduced when an MCN-AM upper-limit value of 4 µg/mL for fluconazole-susceptible C. auris and an Etest upper-limit value of 8 µg/mL for the wild type for AMB were used. Our data show that resistance to fluconazole was underestimated by MCN-AM, while resistance to AMB was overestimated by Etest when using the CDC's tentative resistance breakpoints of ≥32 µg/mL for fluconazole and ≥2 µg/mL for AMB. Method-specific resistance breakpoints should be devised for accurate AST of clinical C. auris isolates for proper patient management.

Increasing Trends of Reduced Susceptibility to Antifungal Drugs Among Clinical Candida glabrata Isolates in Kuwait

Among non-albicans Candida species, Candida glabrata is the leading cause of invasive infections in critically ill patients. It is intrinsically less susceptible to fluconazole/other azoles that limits therapeutic options. This study determined distribution of C. glabrata in clinical specimens and determined their susceptibility to fluconazole, caspofungin, and amphotericin B by E test. During 8-year period (2011-2018), 1,410 isolates were obtained from 1,410 patients including 600, 409, and 131 isolates from respiratory, urine, and bloodstream specimens, respectively. Proportion of C. glabrata isolates was nearly the same during the two 4-year periods. Demographic details were available from 731 patients and susceptibility data for 1,225 isolates. C. glabrata isolation from bloodstream, respiratory, and urine specimens was higher from elderly (>60 years) versus younger patients. More bloodstream and urine isolates were obtained from female patients, however, more respiratory isolates were recovered from male patients (p = <0.05). Resistance to all three drugs increased during 2015-2018 compared with 2011-2014 but was more pronounced for fluconazole (p = 0.001). More isolates with reduced susceptibility to fluconazole/amphotericin B were obtained from elderly patients versus younger subjects and urine versus respiratory samples (p = <0.05). Our data show increasing trends of reduced susceptibility to antifungals, particularly fluconazole, among clinical C. glabrata isolates in Kuwait. Most isolates with reduced susceptibility to fluconazole/amphotericin B were obtained from elderly patients and urine/respiratory samples with urinary tract appearing as the most favorable niche for antifungal drug resistance development. The study also highlights the need for continued surveillance and better antifungal drug stewardship to control resistance development in C. glabrata.

Candida auris in various hospitals across Kuwait and their susceptibility and molecular basis of resistance to antifungal drugs

BACKGROUND

Candida auris, a multidrug-resistant species, has the propensity of nosocomial transmission despite normal decontamination procedures. Here, we describe the isolation of C auris from patients in various hospitals in Kuwait during 2014-2018. Susceptibility to antifungal drugs and molecular basis of resistance to fluconazole, voriconazole and micafungin were also studied.

METHODS

Candida auris (n = 314) obtained from 126 patients in eight hospitals were studied. All isolates were identified by PCR amplification and/or PCR-sequencing of ribosomal DNA (rDNA). Antifungal susceptibility was determined by Etest. Molecular basis of resistance to fluconazole and micafungin was studied by PCR-sequencing of ERG11 and FKS1 genes, respectively.

FINDINGS

Bloodstream (n = 58), urine (n = 124), respiratory (n = 98) and other (n = 34) specimens yielded 314 C auris isolates. The proportion of bloodstream C auris among all yeast isolates was higher (42 of 307, 13.7%) in 2018 as compared to 2014-2017 (16 of 964, 1.7%) (P = .001). More bloodstream isolates (42 of 139) were cultured in 2018 than during 2014-2017 (16 of 175) (P = .001). Resistance to amphotericin B, fluconazole, voriconazole and micafungin was detected in 27.1%, 100%, 41.1% and 1.7% isolates, respectively. Fluconazole-resistant isolates contained either Y132F or K143R mutation in ERG11. Isolates with K143R mutation were additionally resistant to voriconazole. Micafungin-resistant isolates contained S639F mutation in hot spot 1 of FKS1.

CONCLUSIONS

Our study highlights spreading of C auris in major hospitals across Kuwait and its increasing role as a bloodstream pathogen in 2018. Cross-resistance to voriconazole was also seen in isolates with K143R mutation in ERG11, while micafungin-resistant isolates harboured S639F mutation in hot spot 1 of FKS1.

Lack of detection of Candida nivariensis and Candida bracarensis among 440 clinical Candida glabrata sensu lato isolates in Kuwait

Occurrence of Candida nivariensis and Candida bracarensis, two species phenotypically similar to Candida glabrata sensu stricto, in human clinical samples from different geographical settings remains unknown. This study developed a low-cost multiplex PCR (mPCR) and three species-specific singleplex PCR assays. Reference strains of common Candida species were used during development and the performance of mPCR and singleplex PCR assays was evaluated with 440 clinical C. glabrata sensu lato isolates. The internal transcribed spacer (ITS) region of rDNA was also sequenced from 85 selected isolates and rDNA sequence variations were used for determining genetic relatedness among the isolates by using MEGA X software. Species-specific amplicons for C. glabrata (~360 bp), C. nivariensis (~250 bp) and C. bracarensis (~180 bp) were obtained in mPCR while no amplicon was obtained from other Candida species. The three singleplex PCR assays also yielded expected results with reference strains of Candida species. The mPCR amplified ~360 bp amplicon from all 440 C. glabrata sensu lato isolates thus identifying all clinical isolates in Kuwait as C. glabrata sensu stricto. The results of mPCR were confirmed for all 440 isolates as they yielded an amplicon only in C. glabrata sensu stricto-specific singleplex PCR assay. The rDNA sequence data identified 28 ITS haplotypes among 85 isolates with 18 isolates belonging to unique haplotypes and 67 isolates belonging to 10 cluster haplotypes. In conclusion, we have developed a simple, low-cost mPCR assay for rapid differentiation of C. glabrata sensu stricto from C. nivariensis and C. bracarensis. Our data obtained from a large collection of clinical C. glabrata sensu lato isolates show that C. nivariensis and C. bracarensis are rare pathogens in Kuwait. Considerable genetic diversity among C. glabrata sensu stricto isolates was also indicated by rDNA sequence analyses.

Candida lusitaniae in Kuwait: Prevalence, antifungal susceptibility and role in neonatal fungemia

Objectives

Candida lusitaniae is an opportunistic yeast pathogen in certain high-risk patient populations/cohorts. The species exhibits an unusual antifungal susceptibility profile with tendency to acquire rapid resistance. Here, we describe prevalence of C. lusitaniae in clinical specimens in Kuwait, its antifungal susceptibility profile and role in neonatal fungemia.

Methods

Clinical C. lusitaniae isolates recovered from diverse specimens during 2011 to 2017 were retrospectively analyzed. All isolates were identified by germ tube test, growth on CHROMagar Candida and by Vitek 2 yeast identification system. A simple species-specific PCR assay was developed and results were confirmed by PCR-sequencing of ITS region of rDNA. Antifungal susceptibility was determined by Etest. Minimum inhibitory concentrations (MICs) were recorded after 24 h incubation at 35°C.

Results

Of 7068 yeast isolates, 134 (1.89%) were identified as C. lusitaniae including 25 (2.52%) among 990 bloodstream isolates. Species-specific PCR and PCR-sequencing of rDNA confirmed identification. Of 11 cases of neonatal candidemia, 9 occurred in NICU of Hospital A and are described here. Eight of 9 neonates received liposomal amphotericin B, which was followed by fluconazole in 7 and additionally by caspofungin in 2 cases as salvage therapy. Three of 8 (37.5%) patients died. No isolate exhibited reduced susceptibility to amphotericin B, fluconazole, voriconazole, caspopfungin, micafungin and anidulafungin. The MIC ± geometric mean values for amphotericin B, fluconazole, voriconazole, and caspofungin were as follows: 0.072 ± 0.037 μg/ml, 2.32 ± 0.49 μg/ml, 0.09 ± 0.01 μg/ml and 0.16 ± 0.08 μg/ml, respectively. Only two isolates exhibited reduced susceptibility to fluconazole.

Conclusions

This study describes the prevalence and antifungal susceptibility profile of clinical C. lusitaniae isolates in Kuwait. No isolate showed reduced susceptibility to amphotericin B. The study highlights the emerging role of C. lusitaniae as a healthcare-associated pathogen capable of causing fungemia in preterm neonates and causing significant mortality.

ERG6 and ERG2 Are Major Targets Conferring Reduced Susceptibility to Amphotericin B in Clinical Candida glabrata Isolates in Kuwait

Candida glabrata is intrinsically less susceptible to azoles, and resistance to echinocandins and reduced susceptibility (RS) to amphotericin B (AMB) have also been detected. The molecular mechanisms of RS to AMB were investigated in C. glabrata strains in Kuwait by sequence analyses of genes involved in ergosterol biosynthesis. A total of 1,646 C. glabrata isolates were tested by Etest, and results for 12 selected isolates were confirmed by reference broth microdilution. PCR sequencing of three genes (ERG2, ERG6, and ERG11) was performed for all isolates with RS to AMB (RS-AMB isolates) and 5 selected wild-type C. glabrata isolates by using gene-specific primers. The total cell sterol content was analyzed by gas chromatography-mass spectrometry. The phylogenetic relationship among the isolates was investigated by multilocus sequence typing. Wild-type isolates contained only synonymous mutations in ERG2, ERG6, or ERG11, and the total sterol content was similar to that of the reference strains. A nonsynonymous ERG6 mutation (AGA48AAA, R48K) was found in both RS-AMB and wild-type isolates. Four RS-AMB isolates contained novel nonsense mutations at Trp286, Tyr192, and Leu341, and 2 isolates contained a nonsynonymous mutation in ERG6 (V126F or C198F); and the sterol content of these isolates was consistent with ERG6 deficiency. Two other RS-AMB isolates contained a novel nonsynonymous ERG2 mutation (G119S or G122S), and their sterol content was consistent with ERG2 deficiency. Of 8 RS-AMB isolates, 1 fluconazole-resistant isolate also contained nonsynonymous Y141H plus L381M mutations, while 7 isolates contained only synonymous mutations in ERG11 All isolates with ERG6, ERG2, and ERG11 mutations were genotypically distinct strains. Our data show that ERG6 and ERG2 are major targets conferring RS-AMB in clinical C. glabrata isolates.

Increasing prevalence, molecular characterization and antifungal drug susceptibility of serial Candida auris isolates in Kuwait

Candida auris is an emerging yeast pathogen of global significance. Its multidrug-resistant nature and inadequacies of conventional identification systems pose diagnostic and therapeutic challenges. This study investigated occurrence of C. auris in clinical specimens in Kuwait and its susceptibility to antifungal agents. Clinical yeast strains isolated during 3.5-year period and forming pink-colored colonies on CHROMagar Candida were studied by wet mount examination for microscopic morphology and Vitek 2 yeast identification system. A simple species-specific PCR assay was developed for molecular identification and results were confirmed by PCR-sequencing of rDNA. Antifungal susceptibility testing of one isolate from each patient was determined by Etest. The 280 isolates forming pink-colored colonies on CHROMagar Candida, were identified by Vitek 2 as Candida haemulonii (n = 166), Candida utilis (n = 49), Candida kefyr (n = 45), Candida guilliermondii (n = 9), Candida famata (n = 6) and Candida conglobata (n = 5). Species-specific PCR and PCR-sequencing of rDNA identified 166 C. haemulonii isolates as C. auris (n = 158), C. haemulonii (n = 6) and Candida duobushaemulonii (n = 2). C. auris isolates originated from diverse clinical specimens from 56 patients. Of 56 C. auris isolates tested, all were resistant to fluconazole, 41/56 (73%) and 13/56 (23%) were additionally resistant to voriconazole and amphotericin B, respectively. Eleven (20%) isolates were resistant to fluconazole, voriconazole and amphotericin B. One isolate was resistant to caspofungin and micafungin. Increasing isolation of C. auris in recent years from diverse clinical specimens including bloodstream shows that C. auris is an emerging non-albicans Candida species in Kuwait causing a variety of infections. Inability of conventional identification methods to accurately identify this pathogen and multidrug-resistant nature of many strains calls for a greater understanding of its epidemiology, risk factors for acquiring C. auris infection and management strategies in high-risk patients. This is the first comprehensive study on the emergence of this multidrug-resistant yeast from Kuwait and the Middle East.

Rapid and Accurate Identification of Candida albicans and Candida dubliniensis by Real-Time PCR and Melting Curve Analysis

OBJECTIVE

Candida albicans and Candida dubliniensis are germ tube-positive pathogenic yeast species. Accurate identification of these two species is warranted since C. albicans is a highly pathogenic species while C. dubliniensis exhibits increased adherence to buccal epithelial cells, reduced susceptibility to azoles and resistance to flucytosine. We have developed a duplex real-time PCR assay for rapid detection and differentiation between clinical C. albicans and C. dubliniensis isolates.

MATERIALS AND METHODS

A duplex real-time PCR assay was developed by using two species-specific primer pairs and SYBR Green dye to differentiate C. albicans and C. dubliniensis isolates via melting curve analysis of real-time PCR amplicons. Amplification products were also analyzed by agarose gel electrophoresis to confirm real-time PCR results.

RESULTS

Melting temperatures (Tm) for reference strains of C. albicans and C. dubliniensis were 86.55 and 82.75°C, respectively. No amplicon was obtained with DNA from reference strains of 8 other common Candida spp. When real-time PCR was applied on 226 clinical isolates previously identified by the Vitek 2 system and/or PCR sequencing of rDNA, Tm values for C. albicans (n = 113) and C. dubliniensis (n = 98) were 86.68 ± 0.529 and 82.616 ± 0.535°C, respectively. The results were confirmed by agarose gel electrophoresis. No amplicon was obtained from 15 isolates belonging to 9 other Candida spp.

CONCLUSIONS

The real-time PCR assay described here does not require prior identification of clinical yeast isolates as C. albicans/C. dubliniensis by germ tube formation and accurately reports results within 2 h. Detection of amplicons by agarose gel electrophoresis is also suitable for resource-poor settings devoid of real-time PCR facilities.

Population structure and molecular genetic characterization of clinical Candida tropicalis isolates from a tertiary-care hospital in Kuwait reveal infections with unique strains

Candida tropicalis is a frequently isolated yeast species causing bloodstream, urinary tract and other infections particularly in patients admitted to intensive care units (ICUs) and those requiring prolonged urinary catheterization (UC) or receiving broad-spectrum antibiotics (BSA). This study investigated clinical characteristics and genetic relatedness among C. tropicalis strains isolated from patients at Al-Amiri Hospital in Kuwait. C. tropicalis strains (n = 63) isolated from blood, genito-urinary, respiratory (RT) and digestive (GIT) tracts and wound sites from 54 patients were used. All isolates were phenotypically identified and tested against six antifungal drugs by using Vitek 2 system. Molecular identification was performed by PCR amplification of rDNA. Fingerprinting was achieved by 6-loci-based multilocus sequence typing (MLST) and data were analyzed by BioNumerics software for phylogenetic relationships. Patients mean age was >65 years and >20% patients were hospitalized in ICUs. Most patients had underlying conditions that included UC, BSA, diabetes and RT/GIT abnormalities. Most candiduria cases had UC, ureteric stent or suprapubic catheters. All isolates were identified as C. tropicalis by Vitek 2 and by species-specific PCR. Sixty-two isolates were susceptible to all tested antifungal drugs. MLST identified 59 diploid sequence types (DSTs) including 54 newly-identified DSTs. C. tropicalis isolates from multiple sites of same patient usually belonged to different DSTs. Interestingly, 56 of 57 isolates from 48 patients belonged to unique genotypes. Only six isolates from six patients belonged to three DSTs (clusters), however, C. tropicalis strains in each cluster were isolated >3 months apart. Our data show diverse origins of C. tropicalis infections in Kuwait as most isolates were unique strains. There was no obvious correlation between cluster isolates with time of isolation and/or hospital ward of their origin. This study presents the first MLST analysis of C. tropicalis isolates from Middle East and may be useful for studying genetic relationships among global C. tropicalis strains.

Yeasts

Yeasts are unicellular organisms that reproduce mostly by budding and less often by fission. Most medically important yeasts originate from Ascomycota or Basidiomycota. Here, we review taxonomy, epidemiology, disease spectrum, antifungal drug susceptibility patterns of medically important yeast, laboratory diagnosis, and diagnostic strategies.

Population structure and molecular genetic characterization of 5-flucytosine-susceptible and -resistant clinical Candida dubliniensis isolates from Kuwait

Candida dubliniensis and Candida albicans are two closely related species. Although C. dubliniensis is less pathogenic, it has a higher propensity to develop resistance to fluconazole and some strains exhibit intrinsic resistance to 5-flucytosine (5-FC). All 5-FC-resistant isolates from Kuwait were previously shown to belong to one of seven internal transcribed spacer (ITS) region of rDNA-based haplotypes. This study performed fingerprinting of C. dubliniensis isolates by multilocus sequence typing (MLST) to determine population structure of 5-FC-resistant and -susceptible strains and compared the results with data from a global collection of isolates. Fifty-two C. dubliniensis isolates previously analyzed and 58 additional isolates mostly collected during 2010–2013 and characterized by phenotypic and molecular methods were used. ITS-based haplotypes were identified by haplotype-specific PCR and/or by PCR-DNA sequencing of rDNA. Population structure was determined by 8-loci-based MLST. E-test was used to determine susceptibility to 5-FC, fluconazole, voriconazole and amphotericin B. Five ITS haplotypes (ITSH) were detected among 110 C. dubliniensis isolates. The ITSH1 was most common (n = 80 isolates) followed by ITSH4 (n = 25 isolates). Two isolates each belonged to ITSH5 and ITSH8 while one isolate belonged to ITSH7. MLST identified 16 diploid sequence types (DSTs) including six new DSTs. DST11 (n = 52) and DST14 (n = 25) were dominant genotypes and were confined (together with DST21) to Middle-Eastern countries. Other DSTs (excluding some new DSTs) had a wider global distribution as they were identified from various other countries. Only ITSH4 isolates (n = 25) belonged to DST14, were resistant to 5-FC and contained S29L mutation in CdFCA1. ITSH5, ITSH7 and ITSH8 isolates belonged to different DSTs. Thus, clinical C. dubliniensis isolates in Kuwait exhibited limited genotypic heterogeneity and most isolates belonged to region-specific DSTs. All 5-FC-resistant C. dubliniensis isolates belonged to ITSH4 and MLST-based DST14 genotype. Placement of some isolates into additional ITS haplotypes is also supported by MLST data.

Epidemiology and Molecular Basis of Resistance to Fluconazole Among Clinical Candida parapsilosis Isolates in Kuwait

Fluconazole resistance among clinical Candida parapsilosis isolates is an emerging problem in many countries, including Kuwait. Resistance to fluconazole is mediated by amino acid substitutions in ERG11 and/or by overexpression of efflux pumps MDR1 and CDR1. Clinical C. parapsilosis sensu stricto isolates (n = 442) were tested for susceptibility to fluconazole by Etest, Vitek II, and broth microdilution methods. ERG11 was analyzed from fluconazole-resistant, fluconazole-susceptible dose-dependent, and selected fluconazole-susceptible isolates. Of 442 C. parapsilosis isolates, 425, 2, and 15 were identified as susceptible, susceptible dose-dependent, and resistant to fluconazole, respectively. PCR sequencing of ERG11 identified Y132F mutation in 5 of 11 fluconazole-resistant isolates available for analysis. This mutation was absent in 46 fluconazole-susceptible and 2 fluconazole-susceptible dose-dependent isolates. A multiplex allele-specific PCR was developed for detection of Y132F mutation in ERG11, and results correlated perfectly with PCR sequencing data for ERG11 codon 132 for all isolates analyzed. Detection of resistance in 15 and reduced susceptibility in 2 among 442 C. parapsilosis isolates highlights emerging resistance to fluconazole in Kuwait. The Y132F mutation in ERG11 was found in 5 of 11 (45%) fluconazole-resistant isolates only. Detection of fluconazole resistance in C. parapsilosis will help in proper management of patients infected with this species.

Molecular Fingerprinting Studies Do Not Support Intrahospital Transmission of Candida albicans among Candidemia Patients in Kuwait

Candida albicans, a constituent of normal microbial flora of human mucosal surfaces, is a major cause of candidemia in immunocompromised individuals and hospitalized patients with other debilitating diseases. Molecular fingerprinting studies have suggested nosocomial transmission of C. albicans based on the presence of clusters or endemic genotypes in some hospitals. However, intrahospital strain transmission or a common source of infection has not been firmly established. We performed multilocus sequence typing (MLST) on 102 C. albicans bloodstream isolates (representing 92% of all culture-confirmed candidemia patients over a 31-month period at seven major hospitals) to identify patient-to-patient transmission or infection from a common source in Kuwait, a small country in the Middle East where consanguineous marriages are common. Repeat bloodstream isolates from six patients and nine surveillance cultures from other anatomic sites from six patients were also analyzed. Fifty-five isolates belonged to unique genotypes. Forty-seven isolates from 47 patients formed 16 clusters, with each cluster containing 2–9 isolates. Multiple isolates from the same patient from bloodstream or other anatomical sites yielded identical genotypes. We identified four cases of potential patient-to-patient transmission or infection from a common source based on association analysis between patients' clinical/epidemiological data and the corresponding MLST genotypes of eight C. albicans isolates. However, further fingerprinting by whole genome-based amplified fragment length polymorphism (AFLP) analysis yielded 8 different genotypes, ruling out intrahospital transmission of infection. The findings suggest that related strains of C. albicans exist in the community and fingerprinting by MLST alone may complicate hospital infection control measures during outbreak investigations.

Persistent Candida conglobata bloodstream infection in a preterm neonate successfully treated by combination therapy with amphotericin B and caspofungin

Fungemia due to uncommon/rare Candida species is an emerging problem of global clinical significance. Here, we describe a case of Candida conglobata bloodstream infection in a preterm neonate. The diagnosis was established by repeated isolation of C. conglobata in blood cultures and by detection of rDNA of the fungus in serum samples. The identity of the isolate as C. conglobata was confirmed by sequencing of ITS region and D1/D2 domains of rDNA. Despite initial treatment with a liposomal amphotericin B (AmBisome) for 7 days, the blood culture remained positive. The neonate was successfully treated by combination therapy with caspofungin for 25 days. To the best of our knowledge, this is the first proven report unequivocally proving the etiologic role of C. conglobata in bloodstream infection.

Impact of short-term exposure of antifungal agents on hemolysin activity of oral Candida dubliniensis isolates from Kuwait and Sri Lanka

OBJECTIVE

Ability to produce hemolysin by Candida species is an important determinant of its pathogenicity. Candida dubliniensis is implicated in the causation of oral candidosis, which can be treated with polyene, echinocandin, and azole groups of antifungal agents as well as chlorhexidine. After oral application, however, the concentrations of these agents tend to decrease quickly to subtherapeutic levels due to the peculiarity of the oral environment. In this study, we have evaluated the effect of short-term exposure of sublethal concentrations of these drugs on hemolysin production by oral C. dubliniensis isolates obtained from two different geographical locale.

MATERIALS AND METHODS

Twenty C. dubliniensis oral isolates obtained from Kuwait and Sri Lanka were exposed to sublethal concentrations of nystatin, amphotericin B, caspofungin, ketoconazole, fluconazole, and chlorhexidine for 1 h. Thereafter, the drugs were removed by dilution and the hemolysin production determined by a previously described plate assay.

RESULTS

Hemolysin production of these isolates was significantly suppressed with a percentage reduction of 17.09, 16.45, 17.09, 11.39, 8.23 and 12.03 following exposure to nystatin, amphotericin B, caspofungin, ketoconazole, fluconazole, and chlorhexidine, respectively.

CONCLUSION

Brief exposure to sublethal concentrations of drugs with antifungal properties appears to reduce the pathogenic potential of C. dubliniensis isolates by suppressing hemolysin production.

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.

Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis

Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A rapid, low-cost mPCR assay for detection and differentiation of C. parapsilosis, C. orthopsilosis, C. metapsilosis and L. elongisporus has been developed.

In vitro postantifungal effect, adhesion traits and haemolysin production of Candida dubliniensis isolates following exposure to 5-fluorocytosine

The phenomenon of postantifungal effect (PAFE), which is the suppression of candidal growth following brief exposure to antifungal agents, is linked with candidal pathogenicity. Adhesion to buccal epithelial cells (BEC), germ tube (GT) formation and relative cell surface hydrophobicity (CSH) are all adhesion traits of candidal pathogenicity. Ability to produce haemolysin by Candida species is also a determinant of its pathogenicity. There is no information on either the PAFE or its impact on adhesion traits and haemolysin production of oral Candida dubliniensis isolates following exposure to 5-fluorocytosine (5-FC). Hence, the focus of this investigation was to research the in vitro PAFE, adhesion to BEC, GT formation, relative CSH and haemolysin production on 20 C. dubliniensis isolates following exposure to 5-FC. Following obtaining the minimum inhibitory concentration (MIC) of 5-FC, isolates of C. dubliniensis were exposed to sub-lethal concentrations (×3 MIC) of 5-FC for 1 h. After this brief exposure, the antimycotic was removed and PAFE, adhesion to BEC, GT formation, relative CSH and haemolysin production was determined by formerly described in vitro methods. MIC (μg/ml) of C. dubliniensis isolates to 5-FC ranged from 0.002 to 0.125. The mean PAFE (hours) elicited by 5-FC on C. dubliniensis isolates was approximately 1 h. Exposure to 5-FC suppressed the ability of C. dubliniensis isolates to adhere BEC, GT formation, relative CSH and haemolysin activity by a mean percentage reduction in 50.98%, 29.51%, 36.79% and 12.75% (P < 0.001 for all) respectively. Therefore, brief exposure of C. dubliniensis isolates to 5-FC appears to exert an antifungal effect by subduing its growth, adhesion traits as well as haemolysin production.

Molecular and nonmolecular diagnostic methods for invasive fungal infections

Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.

Candida fermentati as a cause of persistent fungemia in a preterm neonate successfully treated by combination therapy with amphotericin B and caspofungin

A case of persistent candidemia in a preterm neonate caused by Candida fermentati, identified by sequencing of the internally transcribed spacer region of ribosomal DNA (rDNA), is described. The neonate was treated for 30 days by combination therapy with amphotericin B (AmBisome) and caspofungin with a successful outcome, and no drug-related side effects were observed.

Development of a novel inhalational model of invasive pulmonary aspergillosis in rats and comparative evaluation of three biomarkers for its diagnosis

Aspergillus fumigatus, a thermotolerant fungus, is the main causative agent of invasive pulmonary aspergillosis (IPA) in immunocompromised patients that is associated with high mortality rates. Early diagnosis of IPA is crucial for mortality reduction and improved prognosis. An experimental inhalational model of IPA was developed in rats and the efficacy of three biomarkers, namely β-D-glucan (BDG), a panfungal marker, galactomannan (GM), a genus-specific marker, and A. fumigatus DNA, a species-specific marker was evaluated in serum and bronchoalveolar lavage (BAL) specimens at different time points postinfection for early diagnosis of IPA. BDG and GM were detected by using commercial Fungitell and Platelia Aspergillus EIA kits, respectively. A. fumigatus DNA was detected by developing a sensitive, single-step PCR assay. IPA was successfully developed in immunosuppressed rats and all animals until 5 days post-infection were positive for A. fumigatus by culture and KOH-calcofluor microscopy also showed A. fumigatus in 19 of 24 (79%) lung tissue samples. Fourteen of 30 (47%) and 27 of 30 (90%) serum and BAL specimens, respectively, were positive for all three biomarkers with 100% specificity (none of sera or BAL specimens of 12 control rats was positive for biomarkers). Our data show that BAL is a superior specimen than serum and combined detection of BDG, GM and A. fumigatus DNA provide a sensitive diagnosis of IPA in an experimental animal model. Moreover, combined detection of GM and DNA in BAL and detection of either GM or DNA in serum was also positive in 27 of 30 (90%) animals. For economic reasons and considering that the positive predictive value of BDG is low, the detection of GM and/or DNA in serum and BAL samples has the potential to serve as an integral component of the diagnostic-driven strategy in high-risk patients suspected for IPA.

Evaluation of chromogenic media and seminested PCR in the identification of Candida species

Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR) for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal’s medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn’t identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp.

Value of (1-3)-β-d-glucan, Candida mannan and Candida DNA detection in the diagnosis of candidaemia

This study determined the value of (1,3)-β-d-glucan (BDG), Candida mannan (MN) and Candida species-specific DNA as surrogates for diagnosis of candidaemia. Thirty-nine patients yielding Candida species in blood cultures were investigated for presence of BDG, MN and Candida species-specific DNA in serum samples. The Candida spp. bloodstream isolates included C. albicans (n = 16), C. tropicalis (n = 10), C. parapsilosis (n = 7), C. glabrata (n = 3) and C. dubliniensis (n = 3). Positivity of the three markers was as follows: Candida DNA for corresponding Candida species, 100%; BDG, 87%; MN, 59%. Despite varying sensitivities of these biomarkers, they provided a useful adjunct to the diagnosis of candidaemia.

Levels of (1→3)-β-D-glucan, Candida mannan and Candida DNA in serum samples of pediatric cancer patients colonized with Candida species

BACKGROUND

Surveillance cultures may be helpful in identifying patients at increased risk of developing invasive candidiasis. However, only scant information exists on the effect of Candida colonization on serum levels of diagnostic biomarkers. This prospective surveillance study determined the extent of Candida colonization among pediatric cancer patients and its possible impact on serum levels of (1-3)-β-D-glucan (BDG), Candida mannan and Candida DNA.

METHODS

A total of 1075 swabs originating from oropharynx (n = 294), nostrils (n = 600), rectum (n = 28), groin (n = 50), ear (n = 54), and axilla (n = 49) of 63 pediatric cancer patients were cultured for the isolation of Candida spp. Patients yielding Candida spp. from any sites were considered as colonized. Serum samples were collected from patients at the time of first surveillance culture for detection of BDG by Fungitell kit and Candida mannan by Platelia Candida Ag. Candida DNA was detected by using panfungal primers and identification was carried out by using species-specific primers and DNA sequencing.

RESULTS

Seventy-five (7.6%) swab cultures from 35 (55.5%) patients yielded Candida spp. These isolates included C. albicans (n = 62), C. dubliniensis (n = 8), C. glabrata and C. tropicalis (n = 2 each) and C. krusei (n = 1). Eleven patients were colonized at three or more sites. Eight of 36 serum samples from 6 colonized patients yielded BDG values higher than the currently recommended cut-off value of ≥80 pg/ml. However, none of the serum samples yielded Candida mannan levels ≥0.5 ng/ml and PCR test for Candida DNA was also negative in all the serum samples of colonized patients. During the study period, only two colonized patients subsequently developed candidemia due to C. tropicalis. Besides positive blood cultures, C. tropicalis DNA, BDG and Candida mannan were also detected in serum samples of both the patients.

CONCLUSIONS

The present study demonstrates that while mucosal colonization with Candida species in pediatric cancer patients is common, it does not give rise to diagnostically significant levels of Candida mannan or Candida DNA in serum specimens. However, BDG values may be higher than the cut-off value in some pediatric patients without clinical evidence of invasive Candida infection. The study suggests the utility of Candida mannan or Candida DNA in the diagnosis of invasive candidiasis, however, the BDG levels in pediatric cancer subjects should be interpreted with caution.

Echoviruses are a major cause of aseptic meningitis in infants and young children in Kuwait

Background

The etiologic agents of aseptic meningitis (AM) often include human enteroviruses. The role of enteroviruses causing AM in young children was investigated during a 3-year period in Kuwait.

Results

Enteroviral RNA was detected in cerebrospinal fluid (CSF) by reverse transcription-PCR and specific genotypes of enteroviruses were identified by direct DNA sequencing of VP4-VP2 region. Enteroviral RNA was detected in 92 of 387 (24%) suspected AM cases and the results were confirmed by hybridization of amplicons with an internal, enterovirus-specific probe. The CSF samples from 75 of 281 (27%) children < 2 years old but only from 3 of 38 (8%) 4-12 year-old children were positive for enteroviral RNA (p = 0.011). Majority of infections in children < 2 years old (49 of 75, 65%) were due to three echoviruses; echovirus type 9 (E9), E11 and E30. Only three other enteroviruses, namely coxsackievirus type B4, coxsackievirus type B5 and enterovirus 71 were detected among AM cases in Kuwait.

Conclusions

Our data show that three types of echoviruses (E9, E11 and E30) are associated with the majority of AM cases in Kuwait. To the best of our knowledge, this is the first report to characterize different enterovirus genotypes associated with AM in the Arabian Gulf region.

Rapid molecular differentiation and genotypic heterogeneity among Candida parapsilosis and Candida orthopsilosis strains isolated from clinical specimens in Kuwait

Recent molecular studies have led to the recognition of three distinct species within the Candida parapsilosis complex, namely Candida parapsilosis, Candida orthopsilosis and Candida metapsilosis. As currently available yeast identification systems fail to differentiate these species, there is a paucity of information on their occurrence in different geographical regions. This study describes a simple PCR-based protocol for rapid discrimination among C. parapsilosis, C. orthopsilosis and C. metapsilosis strains by using primers derived from unique sequences within the internally transcribed spacer 1 (ITS1)-5.8 rRNA-ITS2 region. Retrospective analysis of 114 C. parapsilosis-complex isolates recovered from clinical specimens in Kuwait identified 109 as C. parapsilosis, five as C. orthopsilosis and none as C. metapsilosis. The results were further validated by PCR-RFLP patterns of the secondary alcohol dehydrogenase gene fragment. DNA sequencing of the ITS region and the D1/D2 regions of the 28S rRNA gene confirmed the species-specific identification of all five C. orthopsilosis strains. The amplicon length of the intergenic spacer between the 28S and 5S rRNA genes (IGS1) was also species-specific, and PCR-RFLP analyses of the IGS1 region identified two distinct genotypes among the five C. orthopsilosis strains, which corresponded with the ITS region sequence data. The three bloodstream C. orthopsilosis strains were confined to a single genotype. Among 81 randomly selected C. parapsilosis strains, two genotypes were detected by IGS1 region analyses, indicating limited genotypic heterogeneity among C. parapsilosis sensu stricto strains. As far as is known, this is the first report on the identification of C. orthopsilosis from a bloodstream infection in the Arabian Gulf region.

Diagnostic value of DNA, (1-3)-β-d-glucan, and galactomannan detection in serum and bronchoalveolar lavage of mice experimentally infected with Aspergillus terreus

The aim of this study was to evaluate the diagnostic value of Aspergillus terreus-specific DNA, (1-3)-beta-d-glucan (BDG), and galactomannan (GM) in immunosuppressed mice infected intravenously with A. terreus conidia and sacrificed in groups of 12 each on days 1, 3, 5, 7, and 9. A. terreus-specific DNA, BDG, and GM in serum and bronchoalveolar lavage (BAL) were detected by nested polymerase chain reaction (nPCR), Fungitell kit (Associates of Cape Cod, E. Falmouth, MA), and Aspergillus Platelia kit (Bio-Rad, Marnes-laCoquette, France), respectively. Cultures of lung homogenate of all the animals yielded A. terreus. The BDG positivity, GM positivity, and nPCR positivity in serum specimens were 43%, 78%, and 73%, respectively. Combined detection enhanced the positivity to 95% for A. terreus DNA and GM, 83% for GM and BDG, and 95% for DNA, GM, and BDG. In BAL, the GM positivity and nPCR positivity were 80% and 81%, respectively, whereas combined detection increased the positivity to 98%. Detection of GM and DNA offers a sensitive and specific diagnostic option for invasive aspergillosis.

Biology of the pathogenic yeast Candida glabrata

The yeasts, being favorite eukaryotic microorganisms used in food industry and biotechnologies for production of biomass and various substances, are also used as model organisms in genetic manipulation, molecular and biological research. In this respect, Saccharomyces cerevisiae is the best-known species but current situation in medicine and industry requires the use of other species. Here we summarize the basic taxonomic, morphological, physiological, genetic, etc. information about the pathogenic yeast Candida glabrata that is evolutionarily very closely related to baker's yeast.

Novel lysine biosynthetic gene sequences (LYS1 and LYS5) used as PCR targets for the detection of the pathogenic Candida yeast

We report here a sensitive and specific polymerase chain reaction (PCR) detection assay for the pathogenic Candida yeast based on the novel LYS1 [encoding saccharopine dehydrogenase (SDH)] and LYS5 [encoding phosphopantetheinyl transferase (PPTase)] gene sequences of the fungal unique lysine biosynthetic pathway. Both LYS1 and LYS5 DNA-specific PCR primers SG1, SG2 and SG3, SG4, respectively, amplified predicted 483 and 648-bp fragments from Candida albicans genomic DNA but not from other selected fungal, bacterial, or human DNA. The 18S rDNA control primers exhibited positive amplifications in all PCR assays. The LYS1-and LYS5-specific primers strongly amplified C. albicans and Candida tropicalis target sequences; however, the LYS1 primers also weakly amplified fragments from Candida kefyr and Candida lusitaniae DNA. Both sets of primers amplified target sequences from less than 10 pg of serially diluted C. albicans DNA, and the LYS1 specific primers also detected DNA isolated from serially diluted 50 C. albicans cells. The PCR primers reported here are sufficiently sensitive and specific for the potential early detection of Candida infections with no possibility of false positive results from cross-contamination with bacterial or human DNA.

Evaluation of a newly developed down-flow immunoassay for detection of serum mannan antigens in patients with candidaemia

A down-flow immunoassay has been developed to detect serum mannan antigens, and the test was recently marketed as the Unimedi Candida monotest. Using 251 serum samples from 105 patients with candidaemia, a comparison of the Unimedi Candida monotest with the Cand-Tec latex agglutination test and 2 microplate enzyme immunoassay tests (Platelia Candida Ag test and Unimedi Candida) was conducted. One hundred and seventy-five febrile patients without clinical and microbiological evidence of fungal infections and pneumocytosis were examined as controls. The Cand-Tec test had a sensitivity of 38% and a specificity of 82%. The sensitivity and specificity of the Platelia Candida Ag test, the Unimedi Candida and the Unimedi Candida monotest were 53 and 92%, 69 and 89% and 82 and 96%, respectively. The sensitivity of the Unimedi Candida monotest was significantly (P<0.01) higher than that of the Plateria Candida Ag test for diagnosing candidaemia caused by Candida parapsilosis. The beta-D-glucan assay had a high sensitivity of 95%, with a specificity of 84%. Of 74 patients with candidaemia whose sera were available before or on positive blood culture sampling, 29 (39%), 38 (51%) and 48 (65%) patients had antigenemia detected using the Platelia Candida Ag test, the Unimedi Candida and the Unimedi Candida monotest, respectively. The Unimedi Candida monotest seems to be a promising tool for the early diagnosis of invasive candidiasis, because the test was sensitive, simple, rapid (approx. 1 h) and cost-effective.

Syscan3, a kit for detection of anti-Candida antibodies for diagnosis of invasive candidiasis

Sera from 76 immunocompetent and 293 immunocompromised subjects were assayed for anti-Candida antibodies. The sensitivity, specificity, positive predictive value, and negative predictive value for invasive candidiasis were 74%, 75%, 62%, and 84% in the immunocompetent group and 15%, 60%, 1.7%, and 93% in the immunocompromised group, respectively. Syscan3 has high negative predictive value.

Prevalence of Candida dubliniensis among germ tube-positive Candida isolates in a maternity hospital in Kuwait

In this study, 1644 germ tube-positive Candida isolates from a maternity hospital was prospectively examined for the prevalence of Candida dubliniensis. Candida species were isolated from different clinical specimens, but majority (>90%) of them came from high vaginal swabs and urine specimens. The phenotypic and molecular identification methods for C. dubliniensis included production of rough colonies and chlamydospores on simplified sunflower seed agar, determination of assimilation profile by Vitek 2 yeast identification system, specific amplification of rDNA of internally transcribed spacer (ITS)-2 region by semi-nested PCR and direct DNA sequencing of the ITS-1 and ITS-2 regions. Three germ tube-positive Candida isolates were identified as C. dubliniensis with an overall prevalence of 0.2%. Of these, two came from urine specimens and one from a vaginal swab. None of the C. dubliniensis isolates showed resistance against fluconazole, voriconazole and amphotericin B. The study reinforces the usefulness of sunflower seed agar in presumptive identification of C. dubliniensis and confirms the prevailing view that this species forms only a minor constituent of Candida species occurring in vagina or other anatomic sites of non-HIV/AIDS-infected individuals.

Phenotypic and molecular characterization of Candida dubliniensis isolates from clinical specimens in Kuwait

OBJECTIVE

This study was carried out to characterize Candida dubliniensis using phenotypic and molecular methods and to determine the occurrence of C. dubliniensis in clinical specimens in Kuwait.

MATERIALS AND METHODS

A total of 880 clinical specimens for isolation of fungi were processed according to standard procedures. Of these, 390 germ-tube-positive clinical isolates of Candida species were examined for rough colonies with hyphal fringes and chlamydospore production on simplified sunflower seed agar for their presumptive phenotypicidentification as C. dubliniensis. The identification of C. dubliniensis isolates was further confirmed by the Vitek 2 yeast identification system, semi-nested (sn) PCR amplification of high-copy rDNA and direct DNA sequencing of the internally transcribed spacer 2 (ITS2) region.

RESULTS

Of the 390 isolates of Candida species investigated, 12 were identified as C. dubliniensis, giving an overall occurrence of 3%. All the C. dubliniensis isolates formed rough colonies with hyphal fringes and abundant chlamydospores on sunflower seed agar, did not assimilate trehalose, lactate and alpha-methyl-D-glucoside, and were isolated from human immunodeficiency virus (HIV)-negative patients. Four C. dubliniensis isolates utilized D-xylose. The species-specific primer derived from the ITS2 sequence of C. dubliniensis and used together with the panfungal reverse primer in the reamplification step of the snPCR specifically amplified rDNA from reference and clinical C. dubliniensis isolates and not from C. albicans or other Candida species. The identity of two representative isolates was confirmed by DNA sequencing of the ITS2 region.

CONCLUSIONS

The identity of 12 C. dubliniensis isolates was first established by phenotypic characteristics and then by snPCR using species-specific primers derived from ITS2 sequences. The recovery of C. dubliniensis from HIV-negative patients from Kuwait reinforces the existing view that this novel yeast species has a worldwide distribution and its occurrence is not restricted to any particular immunocompromised population.