Restriction fragment length polymorphism analysis of azole-resistant and azole-susceptible Candida albicans strains

Use of molecular methods in identification of Candida Species and evaluation of fluconazole resistance

The aim of this study was to evaluate the use of one of the molecular typing methods such as PCR (polymerase chain reaction) following by RFLP (restriction fragment length polymorphism) analysis in the identification of Candida species and then to differentiate the identified azole susceptible and resistant Candida albicans strains by using AP-PCR (arbitrarily primed-polymerase chain reaction). The identification of Candida species by PCR and RFLP analysis was based on the size and primary structural variation of rDNA intergenic spacer regions (ITS). Forty-four clinical Candida isolates comprising 5 species were included to the study. The amplification products were digested individually with 3 different restriction enzymes: HaeIII, DdeI, and BfaI. All the isolates tested yielded the expected band patterns by PCR and RFLP analysis. The results obtained from this study demonstrate that Candida species can be differentiated as C. albicans and non-C. albicans strains only by using HaeIII restriction enzyme and BfaI maintains the differentiation of these non-C. albicans species. After identification Candida species with RFLP analysis, C. albicans strains were included to the AP-PCR test. By using AP-PCR, fluconazole susceptible and resistant strains were differentiated. Nine fluconazole susceptible and 24 fluconazole resistant C. albicans were included to the study. Fluconazole resistant strains had more bands when evaluating with the agarose gel electrophoresis but there were no specific discriminatory band patterns to warrant the differentiation of the resistance. The identification of Candida species with the amplification of intergenic spacer region and RFLP analysis is a practical, short, and a reliable method when comparing to the conventional time-consuming Candida species identification methods. The fluconazole susceptibility testing with AP-PCR seems to be a promising method but further studies must be performed for more specific results.

Nosocomial Candida albicans acquisition in a geriatric unit: epidemiology and evidence for person-to-person transmission

This prospective study, which included 69 patients over a two-month period, was conducted to evaluate the incidence of community-acquired carriage and hospital-acquired yeasts in elderly patients hospitalized in a short stay care unit. Furthermore, possible person-to-person transmission was investigated by means of genotyping the Candida albicans isolates obtained from samples (throat swabs, urine and stools) systematically taken from the patients at different times during the hospitalization and from healthcare workers (throat swabs and handwashes) in the middle of the observation period. This study showed a high prevalence rate of 64% for community-acquired yeast carriage and a 40% incidence rate for hospital- acquired yeasts. Mycological analysis of the samples from the healthcare workers revealed eight of them to be colonized in the oral cavity. In addition, pulsed field gel electrophoresis and mitochondrial DNA analysis of the C. albicans isolates demonstrated person-to-person transmission. This study suggests that regular mycological sampling should be done as hospitalized elderly patients are frequently colonized by yeasts. Likewise, oropharyngeal swabs from healthcare workers may be helpful in this setting.

Genetic analysis of azole resistance in the Darlington strain of Candida albicans

High-level azole resistance in the Darlington strain of Candida albicans was investigated by gene replacement in C. albicans and expression in Saccharomyces cerevisiae. We sequenced the ERG11 gene, which encodes the sterol C(14)alpha-demethylase, from our copy of the Darlington strain. Both alleles contained the histidine for tyrosine substitution at position 132 (Y132H) reported in Darlington by others, but we also found a threonine-for-isoleucine substitution (I471T) not previously reported in the C. albicans ERG11. The encoded I471T change in amino acids conferred azole resistance when overexpressed alone and increased azole resistance when added to the Y132H amino acid sequence in an S. cerevisiae expression system. Replacement of one copy of ERG11 in an azole-susceptible strain of C. albicans with a single copy of the Darlington ERG11 resulted in expression of the integrated copy and a modest increase in azole resistance. The profound azole resistance of the Darlington strain is the result of multiple mutations.

Contribution of mutations in the cytochrome P450 14alpha-demethylase (Erg11p, Cyp51p) to azole resistance in Candida albicans

The cytochrome P450 14alpha-demethylase, encoded by the ERG11 (CYP51) gene, is the primary target for the azole class of antifungals. Changes in the azole affinity of this enzyme caused by amino acid substitutions have been reported as a resistance mechanism. Nine Candida albicans strains were used in this study. The ERG11 base sequence of seven isolates, of which only two were azole-sensitive, were determined. The ERG11 base sequences of the other two strains have been published previously. In these seven isolates, 12 different amino acid substitutions were identified, of which six have not been described previously (A149V, D153E, E165Y, S279F, V452A and G4655). In addition, 16 silent mutations were found. Two different biochemical assays, subcellular sterol biosynthesis and CO binding to reduced microsomal fractions, were used to evaluate the sensitivity of the cytochromes for fluconazole and itraconazole. Enzyme preparations from four isolates showed reduced itraconazole susceptibility, whereas more pronounced resistance to fluconazole was observed in five isolates. A three-dimensional model of C. albicans Cyp51p was used to position all 29 reported substitutions, 98 in total identified in 53 sequences. These 29 substitutions were not randomly distributed over the sequence but clustered in three regions from amino acids 105 to 165, from 266 to 287 and from 405 to 488, suggesting the existence of hotspot regions. Of the mutations found in the two N-terminal regions only Y132H was demonstrated to be of importance for azole resistance. In the C-terminal region three mutations are associated with resistance, suggesting that the non-characterized substitutions found in this region should be prioritized for further analysis.

DNA diagnosis of pulmonary infections: particular emphasis on Mycobacterium tuberculosis

The past two decades have brought significant changes to the clinical laboratory. Microbiologists now have highly sensitive, rapid and specific molecular methods of identifying infectious agents by the direct detection of DNA or RNA sequences unique to a particular organism. Advanced DNA technology such as nucleic-acid hybridization, PCR and DNA fingerprinting have been used in the direct detection of causative organisms in clinical specimens, with resultant benefits such as increased sensitivity and specificity of the diagnostic approach and reduction of turnaround time. This review outlines a brief description of the various DNA diagnostic tools used in the detection of pulmonary infections with emphasis on their applications in the diagnosis of Mycobacterium tuberculosis.

Contribution of molecular typing methods and antifungal susceptibility testing to the study of a candidemia cluster in a burn care unit

We investigated a cluster of cases of Candida septicemia diagnosed in four burn patients. Twenty clinical isolates of Candida albicans and two of Candida parapsilosis, plus eight isolates of C. albicans recovered from nurses' clothes, were analyzed by antifungal susceptibility testing and three genotyping methods (restriction fragment length polymorphism analysis with EcoRI and HinfI, arbitrarily primed PCR, and karyotyping). The high MICs of the azoles for all of the C. albicans isolates tested suggest either a natural resistance of the endogenous flora or the transmission of isolates with acquired resistance. The genotyping methods demonstrated the involvement of four different strains, cross-infections with one C. albicans strain and one C. parapsilosis strain, and identity between some of the strains from the patients and nurses. The origins of the strains remain unclear. Our results show that the use of a combination of at least two different methods such as those used in the present study is recommended for C. albicans typing.

Typing of Candida krusei clinical isolates by restriction endonuclease analysis and hybridization with CkF1,2 DNA probe

The use of restriction endonuclease analysis and Southern hybridization with our new CkF1,2 DNA probe, cold labeled with peroxidase, for the typing of Candida krusei isolates has been investigated. Fifty-five clinical samples isolated from forty-five patients hospitalized in eight centers, one environmental strain, and two reference strains were evaluated. Patterns were analyzed by a computer-assisted method and compared by numerical analysis. Clearer and less ambiguous patterns were obtained by restriction with endonuclease HinfI. It generated 9 to 14 (average, 11) well-separated fragments in the range of 6.5 to 2.0 kb. Both their numbers and sizes varied greatly among the strains studied. The CkF1,2 probe hybridized with one to seven fragments of HinfI patterns. A total of 48 distinct types were distinguished among the 58 strains studied. HinfI and CkF1,2 patterns showed similarities of less than 83 and 75% for unrelated strains and more than 91 and 100% for related strains, respectively. The methods showed 100% typeability, 98% reproducibility, and a discriminatory power of 1. C. krusei isolates from each patient were distinct, whether from one hospital or from different hospitals. Multiple isolates from the same patient were identical, both over time and at different anatomic sites. An endogenous origin is suggested for the colonizing and infecting isolates among the 45 patients. The CkF1,2 probe enhanced discrimination of the strains and provided a definitive comparison for strain identity. Genetic linkages between isolates were assessed at the subspecies level, and 12 clusters were delineated. A typing scheme is proposed for epidemiological studies of C. krusei.

Molecular epidemiology of Candida albicans colonization and fungemia in very low birthweight infants

OBJECTIVE

This study investigated the relationship between colonization and fungemia.

DESIGN

This was a prospective study involving surveillance cultures of the nares, base of umbilicus, point of entry of umbilical catheter and parenteral fluids. Blood cultures were done when sepsis was suspected. All Candida albicans isolates were typed using restriction enzyme analysis of DNA.

SETTING

Patients were from the neonatal intensive care unit of a tertiary care hospital.

POPULATION STUDIED

Twenty-nine very low birthweight infants.

MAIN RESULTS

Eleven babies were colonized with C albicans and five of these babies developed fungemia, including five of seven who were colonized at the point of entry of the umbilical catheter. Three different strains of C albicans caused fungemia. In four of the five patients, initial catheter entry site isolates were identical to the subsequent blood isolates. Occasionally, infants were colonized with more than one strain of C albicans.

CONCLUSIONS

Preceding colonization with C albicans and, in particular, colonization at the site of entry of umbilical vascular catheters are risk factors for subsequent development of C albicans fungemia. Fungemic and colonizing isolates are usually identical to one another by DNA typing.

Candida albicans genotyping in studies with patients with AIDS developing resistance to fluconazole

We characterized Candida albicans strains responsible for recurrent oropharyngeal candidosis (OPC) in four patients with AIDS who developed clinical and mycological resistance to fluconazole (FCZ). Karyotype and restriction fragment length polymorphism analyses were performed on the clonal populations to differentiate relapse from reinfection, and the results were assessed with those of serotype and FCZ MICs. Despite the polymorphism in chromosomal bands larger than 2.2 Mbp related to an intraclonal variation, karyotype analysis showed a single strain type attributable to each patient. On the other hand, EcoRI and HinfI restriction fragments revealed a polymorphism for one patient between the first sample and the subsequent ones, relevant to the acquisition of a new strain causing the following episodes of OPC. This result coincided with switching of the serotype and with the acquisition of a resistance to FCZ. For the other three patients, the similarity of the DNA electrophoretic patterns and the serotype of the samples suggested that recurrence can be due to the initial strain that generates FCZ resistance. Although useful for epidemiological studies, molecular typing methods seem to be inadequate to detect the acquisition of FCZ resistance.

Oligonucleotide fingerprinting of isolates of Candida species other than C. albicans and of atypical Candida species from human immunodeficiency virus-positive and AIDS patients

Oligonucleotide fingerprinting of genomic DNA from oral isolates of four different Candida species other than C. albicans and atypical chlamydospore-positive isolates from human immunodeficiency virus (HIV)-positive individuals and AIDS patients was investigated as a means for differentiating between isolates within individual species. Oligonucleotides composed of simple repetitive sequence motifs, including (GACA)4, (GATA)4, (GGAT)4, (GTG)5, and (GT)8, all yielded fingerprints suitable for strain segregation of 8 C. tropicalis isolates, 12 Torulopsis (Candida) glabrata isolates, 8 atypical Candida isolates, and, except for (GATA)4, 2 C. krusei probe in turn and so generate several distinct DNA fingerprints of the same DNA sample. However, none of the probes yielded fingerprints suitable for strain segregation with three C. parapsilosis isolates. The (GATA)4 probe was also used to detect restriction fragment length polymorphisms among a genetically closely related group of atypical Candida isolates on primary isolation from an additional HIV-infected patient. These chlamydospore-positive atypical Candida isolates were sucrose positive, were of C. albicans serotype A, hybridized weakly with the C. albicans-specific mid-repeat sequence probe 27A, and yielded fingerprint profiles by random polymorphic DNA analysis that were distinct from those derived from C. albicans isolates. The C. stellatoidea ex-type strain NCPF 3108 was indistinguishable from the atypical Candida isolates in all these tests and also yielded an identical carbohydrate and nitrogen source assimilation profile by using the ID 32C yeast identification system.

Colony morphotype on Sabouraud-triphenyltetrazolium agar: a simple and inexpensive method for Candida subspecies discrimination

A new method of Candida subspecies discrimination on Sabouraud-triphenyltetrazolium agar is reported. Five hundred sixty-two strains of Candida and Torulopsis glabrata, previously identified by conventional mycological methods, were studied. Each strain received a three-letter code and a number based on its colonial morphology. Sixteen morphotypes were found for Candida albicans, 6 were found for Candida parapsilosis, 4 were found for both Candida guilliermondii and Candida krusei, and 12 were found for Candida tropicalis. None of the 56 T. glabrata strains studied grew on this agar. A reproducibility of 95% was found for C. albicans. The simplicity and low cost could make this method useful for typing Candida spp.