Molecular Methods For Strain Typing of Candida Albicans Revew

Journal of Applied Microbiology ISSN 1364-5072
REVIEW ARTICLE
Molecular methods for strain typing of Candida albicans: a review

F. Saghrouni*, J. Ben Abdeljelil*, J. Boukadida and M. Ben Said
UR02SP13 Research Unit, Ministry of Public Health, Tunisia, Tunisia
Keywords Candida albicans, sequence polymorphisms, strain typing. Correspondence Jihene Ben Abdeljelil, Laboratoire de Parasitol^pital Farhat Hached 4000, ogie-Mycologie, Ho Sousse, Tunisie. E-mail: abdeljeliljihene@yahoo.fr *Both authors contributed to the work equally, and each should be considered rst author. 2013/1345: received 26 July 2012, revised 3 January 2013 and accepted 6 January 2013 doi:10.1111/jam.12132
Summary Candida albicans is one of the most medically important fungi because of its high frequency as a commensal and pathogenic microorganism causing supercial as well as invasive infections. Strain typing and delineation of the species are essential for understanding its biology, epidemiology and population structure. A wide range of molecular techniques have been used for this purpose including non-DNA-based methods (multi-locus enzyme electrophoresis), conventional DNA-based methods (electrophoretic karyotyping, random amplied polymorphic DNA, amplied fragment length polymorphism, restriction enzyme analysis with and without hybridization, rep-PCR) and DNA-based methods called exact typing methods because they generate unambiguous and highly reproducible typing data (including microsatellite length polymorphism and multi-locus sequence typing). In this review, the main molecular methods used for C. albicans strain typing are summarized, and their advantages and limitations are discussed with regard to their discriminatory power, reproducibility, cost and ease of performance. mating, reecting the plasticity of the genome (Chibana et al. 2000; Selmecki et al. 2010). Over the last three decades, C. albicans has become a medically important pathogen, responsible for supercial as well as deep infections. Most infections are opportunistic depending on the immune defence of the host and changes of the environment of the yeast in the organism (Hajjeh et al. 2004). Indeed, since the early 1980s, invasive candidiasis, mainly caused by C. albicans, has emerged as a prominent problem (Pfaller 1996; Pfaller and Diekema 2007), because of the increasing number of immunocompromised patients and the advances in medical intensive care. Consequently, C. albicans has become a frequent cause of nosocomial infections and represents a serious threat as invasive candidiasis is associated with high mortality rates that exceed 30% in many reports, despite availability of antifungal treatments, including novel azoles and echinocandins (Boucher et al. 2004; Pfaller and Diekema 2007; Horn et al. 2009). Although most Candida infections appear to originate from an endogenous source, nosocomial transmission is not uncommon and may occur either by cross-infection or by exposure to a common infecting source (Huang
1559
Introduction Candida albicans is a common commensal microorganism in humans and some warm blood animals. It colonizes mucosal surfaces of healthy subjects and is considered as a component of the normal ora of the digestive and genitourinary tracts (Kam and Xu 2002). The standard genome of C. albicans is diploid and composed of eight pairs of chromosome homologs, ranging in size from about 33 to 095 Mb (Chibana et al. 2000). Candida albicans has a predominantly clonal mode of reproduction (Pujol et al. 1993; Lockhart et al. 1995; Mata et al. 2000). It was the rst medically important pathogenic fungus for which the complete genome sequence was determined (Jones et al. 2004). The rst genome to be sequenced was that of the SC5314 clinical isolate that showed a high degree of heterozygosity, including more than 55 700 single-nucleotide polymorphisms (SNPs) in the 32-Mb diploid genome (Jones et al. 2004). Despite its diploidy and clonal reproduction, C. albicans is able to achieve a high rate of a genetic diversity in several ways, including recombination, chromosomal polymorphisms, gene replacement and cryptic
Journal of Applied Microbiology 114, 1559--1574 2013 The Society for Applied Microbiology
Molecular typing of Candida albicans
F. Saghrouni et al.
et al. 1998; Pfaller et al. 1998; Ben Abdeljelil et al. 2011). This underlines the need for implementing appropriate control measures, which obviously requires a high knowledge of the biology and the epidemiology of Candida species including C. albicans, that are recognized to be particularly complex. Indeed, the same healthy individual can harbour the same strain at different body locations, or carry unrelated strains at the same or different body sites (Kam and Xu 2002), strains can replace each other in recurrent infections (Odds et al. 2006), undergo microevolution (minor changes in genotype over a relatively small number of cell generations) (Lockhart et al. 1995; Shin et al. 2004; Bougnoux et al. 2006) and substrain shufing (changes in subpopulations within individuals over time) (Lockhart et al. 1995; Lott and Scarborough 2008), be transferred from one individual to another (Vazquez et al. 1993; Schmid et al. 1995; Ben Abdeljelil et al. 2011), specic strains may predominate in particular geographical areas and some strains may be endemic in some hospitals and can undergo microevolution in the hospital setting (Pfaller et al. 1998; Viviani et al. 2006). This highlights the need for efcient methods for typing and delineation of strains. The earliest methods used in the typing of C. albicans were based on phenotypic characteristics including serotyping, biotyping, morphotyping, resistance to various chemicals and toxins and antifungal susceptibility proles (Warnock 1984). However, phenotypic techniques have a very low degree of discrimination and reproducibility, which obviously constitutes a limitation for reliable epidemiological analysis. The advent of the molecular DNA-based techniques revolutionized the knowledge on the biology and epidemiology of C. albicans. Since then, various molecular approaches have been described that target various levels of polymorphism within a species (Odds and Jacobsen 2008). Herein, the main molecular techniques used so far in C. albicans strains typing are reviewed, including techniques that have been the subject of previous reviews but also the more recently described techniques in this eld. The review aims (i) to describe the principles of these molecular approaches, (ii) to highlight their strengths and their drawbacks and (iii) to discuss their input in different types of C. albicans molecular investigations. General Considerations Genotyping of C. albicans strains allows the following: (i) investigation of nosocomial candidiasis to identify outbreak-related strains, distinguish epidemic from endemic or sporadic strains and determine the origins of infection, the routes of acquisition and transmission of strains; (ii) assessing the diversity of isolates within a carrier and inves1560
tigation of the recurrent infections to recognize particularly virulent strains if any; (iii) monitoring of the emergence of drug-resistant strains; (iv) studying of the population structure, diversity and dynamics of the species. The choice of the method for strain typing is contingent upon the nature and the dened objectives of each molecular investigation. The performance of each typing technique should be assessed in terms of discriminatory power, reproducibility and ease of performance and interpretation. Discriminatory power refers to the ability of the technique to identify the same strain or highly related strains in independent isolates, to assess microevolution within the same strain, to group or cluster moderately related strains and to discriminate between unrelated strains (Clemons et al. 1997; Chen et al. 2005; Chowdhary et al. 2006). Interassay reproducibility is assessed by the repeat testing of the same strain that is expected to yield an identical result, and reproducibility between laboratories that allow comparison of data is essential for any standardization of the typing approach and the construction of general data bank for use by the international scientic community. Ease of performance and feasibility refers to the cost of specialized equipment and reagents, the facility to implement the technique in routine use, the technical complexity of the procedure and the ease of result interpretation. Moreover, data should be suitable for computerized analysis and storage, which is needed for the construction of databases (Schmid et al. 1990; Singh et al. 2006). Typing methods used for molecular characterization of C. albicans can be separated in two classes based on different approaches. The rst class includes non-DNA-based methods that assess the genetic intraspecies polymorphism indirectly by using comparisons of protein ngerprints [multi-locus enzyme electrophoresis (MLEE)]. The second class includes DNA-based techniques that directly analyse the polymorphism within various DNA markers and are separated into conventional typing methods and methods called exact DNA-based techniques because they generate unambiguous and highly reproducible typing data. The comparison of the performance characteristics of these methods is shown in Table 1. Non-DNA-Based Typing Methods Multi-locus enzyme electrophoresis MLEE characterizes enzymatic proteins and assesses their polymorphism by analysing their electrophoretic mobility on gels after specic enzyme staining procedures. The migration of an enzyme is inuenced by its molecular size and its net charge. Changes in the mobility of an enzyme protein reect a change in its amino acid
F. Saghrouni et al.
Table 1 Characteristics of the most widely used techniques for genotyping of Candida albicans Time required (days)
Discriminatory power Non-DNA-based techniques MLEE Good
Reproducibility
Ease of use
Ease of interpretation
Setup cost
Cost/ isolate
Comments
Good
Very difcult
Difcult
Low
Low
Several days
Protein-based method Time required depends on the number of enzymes to be assessed
Conventional DNA-based techniques EK Low Macrorestriction High REA with High Southern blotting RAPD Good AFLP High Rep- PCR Moderate Exact DNA-based techniques MLP Very high MLST Very high
Good Good High Low Good Good Very high Very high
Very difcult Very difcult Very difcult Very easy Difcult Easy Very easy Moderate
Very easy Easy Easy Easy Easy Very easy Very easy Very easy
High High High Moderate Moderate to high Moderate Very high Very high
Low Moderate Moderate Low Moderate Low Moderate Very high
4 4 2 1 2 1 1 2 Unambiguous data Unambiguous data Online databases
AFLP, amplied fragment length polymorphism; EK, electrophoretic karyotyping; MLEE, multi-locus enzyme electrophoresis; MLP, microsatellite length polymorphism; MLST, multilocus sequence typing; RAPD, random amplied polymorphic DNA; REA, restriction enzyme analysis.
sequence and, thus, by inference, the encoding DNA sequence. Therefore, if the enzyme banding patterns of two isolates differ, such differences are assumed to be DNA based and heritable. In addition, it is assumed that in diploid organisms, enzyme expression is co-dominant, that is, every allele at a locus is expressed, alleles being rarely missing. MLEE may provide valid measures of genetic distance because it assesses dened multilocus differences and information relevant to population genetic studies as well as to epidemiology (Pujol et al. 1993; Arnavielhe et al. 1997). MLEE is one of the earliest methods used for genetic and epidemiological studies of C. albicans and provided the rst insight into the populations structure of the species (Caugant and Sandven 1993; Pujol et al. 1993; Arnavielhe et al. 1997). It has been further used to ngerprint other Candida species (e.g. C. tropicalis, C. lusitaniae, C. haemulonii, C. parapsilosis and C. guillermondii) (Merz et al. 1992; Doebbeling et al. 1993; Lehmann et al. 1993; Lin et al. 1995; San Millan et al. 1997). MLEE is a reliable technique with a relatively high discriminatory power in the distinction between unrelated strains and shows good reproducibility (Arnavielhe et al. 2000; Boriollo et al. 2006). It outperforms many of the DNA-based methods and remains a useful tool for molecular investigation of natural populations of C. albicans (Santos et al. 2012).
The major drawback of the MLEE is that it assays the genome indirectly and evaluates variations accumulated very slowly in the species. On the other hand, MLEE does not detect all variations at the nucleotide level as nucleotide substitutions do not necessarily lead to a change in the amino acid composition of the enzyme. In addition, it may not be sensitive enough in measuring rapid microevolutionary changes and, thus, may not be an adequate method for revealing substrain shufing or microevolution in an infecting population over time. Indeed, when compared with other typing methods for their capacities to assess microevolution within a strain, MLEE showed a modest degree of resolution power (Boriollo et al. 2010). Finally, MLEE is time-consuming because it requires the combination of results from at least 10 enzymes to provide reliable typing data and detection of variability among isolates (Boriollo et al. 2006, 2010). Conventional DNA-Based Typing Methods Pulsed-eld gel electrophoresis Electrophoretic karyotyping The advent of pulsed-eld gel electrophoresis (PFGE) technique in 1984 revolutionized the study of the genome organization of eukaryotic organisms (Schwartz and Cantor 1984). In this technique and its variants
1561
F. Saghrouni et al.
[orthogonal-eld alternative gel electrophoresis (OFAGE), eld inversion gel electrophoresis (FIGE), contourclamped homogeneous electric eld (CHEF) or transverse alternate eld electrophoresis (TAFE)], intact DNA molecules migrate through an agarose gel matrix under the inuence of pulsed elds, which permit easy separation of DNA molecules of several megabases. As the size of C. albicans chromosomes range from around 1 to 4 Mb, this technique is ideal for the separation of chromosomesized DNA molecules, the analysis of the chromosomal banding patterns, known as electrophoretic karyotypes, and the detection of karyotypic variations within the species. Briey, cells are mixed with enzymes to remove the cell wall and then embedded in an agarose plug, which protects the large DNA molecules from shearing forces. Protease and detergent are added to remove membranes and digest proteins. The yeast chromosome-sized DNA fragments are separated according to size and then visualized by ethidium bromide staining. Assessment of differences in banding patterns can be performed visually or using computer-assisted methods (Sangeorzan et al. 1995). The earliest use of electrophoretic karyotyping (EK) demonstrated the extent of variation in the karyotypes of unrelated C. albicans isolates (Magee and Magee 1987; Lasker et al. 1989; Iwaguchi et al. 1990; Pittet et al. 1991; Sangeorzan et al. 1995). Indeed, despite the occurrence of a standard karyotype that consists of eight pairs of homologous chromosomes, variant karyotypes are very common among clinical isolates. Differences in the number of bands detected and their mobility patterns were presumed to be due to chromosome-length polymorphisms (different-sized chromosome homologs), reciprocal chromosome translocation or missing chromosomes (Bougnoux et al. 2007; Selmecki et al. 2010). EK has been extensively used to ngerprint C. albicans and other Candida species (e.g. C. lusitaniae, C. parapsilosis, C. tropicalis and C. glabrata) (Espinel-Ingroff et al. 1999; Trtkova and Raclavsky 2006). It has a moderate discriminatory power when used for typing unrelated C. albicans isolates and does not allow the discrimination between moderately related isolates nor the detection of microevolutionary changes in the same strain. However, EK shows good reproducibility, and the interpretation of the karyotypes is straightforward (Pittet et al. 1991; Sangeorzan et al. 1995). With respect to the technical aspects, the major limitations associated with EK relate to the initial cost of the specialized equipment and the prolonged turnaround time. A single experiment can involve electrophoretic separation times of several days, and the preparation of plugs is both tedious and time-consuming (Pittet et al. 1991; Sangeorzan et al. 1995).
1562
Currently, EK analysis is usually associated with other techniques, and it is shown to be the least discriminatory method when used for typing related isolates (Chen et al. 2005; Ben Abdeljelil et al. 2010, 2011). Nevertheless, the resolution power of EK analysis can be improved by the prior digestion of chromosome-length DNA with endonucleases before PFGE (Voss et al. 1995; Clemons et al. 1997; Shin et al. 2004; Ben Abdeljelil et al. 2012b). Chromosomal restriction fragment patterns In this method, the intact genomic DNA, embedded in the agarose plug, is separated by PFGE after digestion with a restriction enzyme with relatively few recognition sites. The restriction of the chromosome-length DNA with rare-cutting endonucleases, known as macrorestriction analysis, provides many variable large fragments, so that the patterns generated are complex enough to allow a quantitative measure of genetic relatedness between two isolates (Chu et al. 1993). SI and BssHII have been the most used endonucleases due to their higher resolving power (Voss et al. 1995; Poikonen et al. 2001; Shin et al. 2004; Ben Abdeljelil et al. 2012b). Macrorestriction analysis is a well-established method in C. albicans typing because of its stability and good reproducibility and its ability to differentiate between clinical isolates. It has been successfully used to investigate outbreaks and performed well when compared with other typing techniques (Krawczyk et al. 2009). In addition, it is a reliable tool for detecting microevolution among sequential isolates of C. albicans. By using restriction endonuclease analysis of genomic DNA by SI and BssHII, Shin et al. demonstrated that some C. albicans strains isolated from patients with catheterrelated candidemia undergo microevolution during catheter colonization and showed a good agreement between the macrorestriction analysis and the Southern hybridization with the C1 fragment of Ca3 as a probe, C1 ngerprinting being an excellent indicator of microevolutionary events. In the macrorestriction analysis, microevolution within a strain refers to minor changes with a one- or two-band difference in the patterns (Shin et al. 2004). Macrorestriction analysis raises the same technical difculties as the EK, but it has a higher resolving power. Restriction enzyme analysis Restriction enzyme analysis (REA) was widely used in the earliest epidemiological investigations of C. albicans infections (Matthews and Burnie 1989; Smith et al. 1989; Pfaller et al. 1990; Hunter 1991; Pearce and Howell 1991; Vazquez et al. 1991; Pfaller 1992; Robinson et al. 1993; Carlotti et al. 1994; Romano et al. 1994).
F. Saghrouni et al.
In this technique, total genomic DNA is puried and subsequently cleaved by a frequent cutting restriction endonuclease (e.g. EcoRI, MspI, BglII, HinF1 or HindIII) that produces a large number of short fragments resulting in a sequence-dependent restriction fragment length polymorphism (RFLP). The generated fragments are separated using common agarose gel electrophoresis and visualized after staining with ethidium bromide. Variation between strains is evidenced by different banding patterns. These variations occur as a result of changes or deletion of restriction site sequences or DNA deletions and insertions between the recognition sites (Smith et al. 1989; Carlotti et al. 1994). REA is straightforward, rapid and inexpensive. However, it may result in the generation of complex patterns with a large number of bands of unequal intensities, thereby making their objective interpretation and the differentiation of strains very difcult, whether visually or using computer-assisted methods. Unique sequences have a low degree of resolution as they are poorly stained by the ethidium bromide in contrast to repeated sequences that mainly correspond to rDNA and mitochondrial DNA sequences occurring in multiples copies in fungal genomes. Such repeated sequences are not polymorphic enough to assess genetic relatedness of moderately related isolates, whereas by convenience, comparison of REA patterns is often based on differences between the highly stained bands. The low discriminatory power together with difculties in the interpretation of patterns has been considered as the major limitations in REA analysis (Vazquez et al. 1991). To simplify the banding patterns obtained by restriction endonuclease digestion and to increase the discriminative power of REA analysis, generated fragments can be hybridized with species-specic radiolabelled or biotinylated DNA probes after transfer to nitrocellulose or nylon membranes (Southern blotting). Probes recognize repetitive sequences dispersed throughout the genome as a result of sequence homology. In contrast to ethidium bromide staining, hybridization probes allow the selective visualization of a limited number of fragments and generate proles that are easier to interpret but, at the same time, complex enough to provide an accurate and sensitive measure that reects the relatedness of isolates (Vazquez et al. 1991; Olive and Bean 1999). The most commonly used probes are the related (but nonidentical) 27A and Ca3 probes containing repetitive genomic sequences (Soll et al. 1987, 1989; Sadhu et al. 1991; Mercure et al. 1993). Ca3 is a moderately repetitive 11-kb gene fragment successfully used in many epidemiological studies. It contains an additional repetitive sequence, the B sequence, and generates a more complex hybridization pattern than the one generated by
27A probe (Anderson et al. 1993). Its effectiveness is due to the fact that it hybridizes to: (i) repetitive sequences dispersed throughout the genome, identifying interstrain variability at a variety of dispersed loci, (ii) some hypervariable sequences, revealing microevolution within a strain and (iii) additional less variable sequences. When used to probe Southern blots of EcoRI-digested DNA, Ca3 identies over 20 bands of various intensities that include invariable (monomorphic), moderately variable and hypervariable bands (Schmid et al. 1990). The Ca3 probe has been demonstrated to be highly effective in the analysis of C. albicans populations and has identied ve major clades (named I, II, III, SA and E) of closely related strain types (Schmid et al. 1995; Pujol et al. 1997, 2002; Blignaut et al. 2002; Soll and Pujol 2003). Clades exhibit different geographical specicities and phenotypic characteristics. Strains from SA and E predominate in South Africa and Europe, respectively. Strains from clade I have been reported from all investigated geographical areas. In vitro resistance of C. albicans to ucytosine was found to be nearly restricted to clade I isolates (Pujol et al. 2004). The complex Ca3 probe has been used in a large range of epidemiological studies involving signicant numbers of strains and was found to be highly effective in assessing microevolution within clonal populations over time, due primarily to the hypervariability of genomic sequences homologous to the C1 fragment of the probe (Soll et al. 1991; Anderson et al. 1993; Schmid et al. ppel et al. 1994; Lockhart et al. 1995, 1996). 1993; Schro The C1 region contains the repetitive DNA sequence (RPS element), which is present at different locations in the C. albicans genome (Iwaguchi et al. 1992; Lockhart et al. 1995). The microevolutionary changes identied by Ca3 are due to the insertion and deletion of the fulllength RPS elements at specic sites dispersed throughout the genome and thus can be detected after hybridization of genomic DNA with the C1 fragment of Ca3 (Lockhart et al. 1995; Pujol et al. 1999). Moreover, Ca3 hybridization has proven to be reproducible and amenable to computer-assisted analysis. Databases have been established for subsequent retrospective and comparative studppel et al. 1994; Lockhart ies (Schmid et al. 1990; Schro et al. 1996). Inherent drawbacks of Southern hybridization techniques include several laborious and time-consuming steps and the need to use DNA probes, which requires a transfer procedure to a solid support as well as adequate detection systems making implementation of the method in a medical laboratory analysis difcult. In addition, ngerprint data do not lend themselves to interlaboratory data exchange.
1563
F. Saghrouni et al.
Random amplied polymorphic DNA The random amplied polymorphic DNA (RAPD) technique is based on the amplication of genomic DNA with single short (typically 10 bp) primers of arbitrary sequence. Primers bind at random to the target DNA resulting in the amplication of fragments of unknown sequence. The amplication reaction is carried out under conditions of low stringency (typically 3540C, 25 mmol l1 MgCl2). Amplied products are separated on an agarose gel and stained with ethidium bromide. The interpretation of RAPD patterns is based on the number and the size of the amplied fragments. Overall, the RAPD assay generates relatively complex patterns that greatly vary among unrelated isolates. RAPD has been extensively used for typing of C. albicans, other Candida species (e.g. C. dubliniensis, C. parapsilosis, C. lusitaniae, C. tropicalis, C. glabrata and C. krusei) (Lehmann et al. 1992; Lott et al. 1993; Zeng et al. 1996; Coleman et al. 1997) and other fungi (e.g. Aspergillus fumigatus, Aspergillus avus, Cryptococcus neoformans and Blastomyces dermatitidis) (Bufngton et al. 1994; Yates et al. 1995; Anderson et al. 1996; Boekhout and van Belkum 1997) because it offers many advantages including simplicity, rapidity and cost-effectiveness and does not require any DNA sequence information (Lehmann et al. 1992). The discriminatory power of RAPD is moderate; nevertheless, if a greater level of discrimination is required, different primers can be used in independent runs and the data combined for the nal analysis (composite DNA type). This approach allows the discrimination between unrelated isolates, clustering of related isolates, identication of identical or highly related isolates and assessment of microevolution within the same strain. Indeed, Pujol et al. demonstrated a high concordance between RAPD analysis, MLEE and Southern blotting using the Ca3 probe. The Ca3 probe exhibited the greatest resolving power mainly in assessing microevolution within the strain (Pujol et al. 1997). Although the RAPD technique has been used successfully in several clinical studies, it raises the well-known problem of reproducibility and data comparison between laboratories. Indeed, banding patterns are easily affected by slight changes in the experimental conditions (Mg2+ concentration, primer-to-templateconcentration ratio, Taq polymerase concentration and source, the model of thermal cycler, thermal cycling parameters, etc.) (Meunier and Grimont 1993; Howell et al. 1996). Nevertheless, a good interassay reproducibility can be achieved under rigidly controlled conditions. The poor interlaboratory reproducibility of the technique remains insurmountable. For this reason, the RAPD method has been criticized by many investigators, but is still widely used in
1564
investigating C. albicans epidemiology at a local level, mainly because of its satisfactory discriminatory power in this setting, simplicity and accessibility under minimum molecular laboratory conditions and moderate investment (Lehmann et al. 1992; Steffan et al. 1997). Amplied fragment length polymorphism Amplied fragment length polymorphism (AFLP) was developed in the mid-1990s (Vos et al. 1995). Briey, it involves digestion of genomic DNA with two restriction enzymes (usually a frequent cutter and a rare cutter) followed by ligation of oligonucleotide adaptors to the sticky ends of the restriction fragments (Ball et al. 2004). Adaptors with site restriction sequences serve as target for primer annealing, and the ligated products are then amplied under high stringency conditions. The procedure allows the selection of a subset of the restriction fragments. Typically, 50100 amplied fragments are generated. To be visualized, these fragments need to be separated in highresolution electrophoresis systems (denaturing polyacrylamide gels). Fluorescent dye-labelled primers can be used allowing the detection of amplied fragments in gel-based or capillary DNA sequencers. This variant technique is referred to as uorescent amplied fragment length polymorphism (FAFLP) allowing the highest resolution of all fragments of different size (Kantardjiev et al. 2006; Levterova et al. 2010). AFLP usually involves two PCR steps. The rst one consists of the preselective amplication using unlabelled primers with a single selective nucleotide in the primer. The reaction product is then diluted to obtain the adequate template concentration for the second PCR amplication in which additional selective nucleotides are added in the primer to improve specicity. During this latter amplication, the labelled primers are used. AFLP is a highly resolutive typing technique. Like RAPD, AFLP is a universal and multilocus marker technique that can be applied to genomes of any source without requiring any prior sequence information. However, AFLP is more reproducible than RAPD as it uses specic primers, and amplication is achieved under high stringency conditions (Vos et al. 1995; Ball et al. 2004). Although AFLP has proved to be reliable and reproducible as a genotyping method, it has been rarely used for C. albicans typing mainly because it is multiple-step, fairly expensive and requires a relatively high level of expertise (Ball et al. 2004; Lopes et al. 2007; Levterova et al. 2010). Repetitive sequence-based PCR The repetitive sequence-based PCR (rep-PCR) method uses primers that target noncoding repetitive sequences
F. Saghrouni et al.
interspersed throughout the fungal genome (Stern et al. 1984; Versalovic et al. 1991). The amplied DNA fragments, when separated by conventional electrophoresis, constitute a genomic ngerprint that can be employed for strain typing (Versalovic and Lupski 2002). The development of a commercially available, semi-automated rep-PCR assay system, the DiversiLab System (Bacterial Barcodes, Inc., Houston, TX, USA), provided an easier standardization and higher reproducibility as compared to the manual, gel-based rep-PCR (Chau et al. 2004; Healy et al. 2005). The system allows for archiving of ngerprint patterns and creation of databases. Rep-PCR is easy to carry out and to implement in clinical laboratories at relatively low cost. Many studies using rep-PCR for genotyping of C. albicans (Chau et al. 2004; Chen et al. 2005; Abaci et al. 2011) and other members of the genus have been reported (Redkar et al. 1996; Healy et al. 2005). The discriminatory power of rep-PCR is moderate; however, it has been improved by combining rep-PCR and PFGE-based typing methods (Chen et al. 2005), but such approach makes the molecular investigation more difcult and increases its cost. Exact DNA-Based Typing Methods Most of the techniques described above have proven to be effective and reliable typing methods for the investigation of the C. albicans epidemiology at local level. These techniques are suitable for clinical studies in individual laboratory settings, but the exchange and comparison of data between laboratories are difcult, if not impossible. At present, only two techniques lend themselves well to this exchange because they generate unambiguous results with an excellent reproducibility. For this reason, these techniques are called exact DNA-based typing methods. They include microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST) (Klaassen 2009). Microsatellite length polymorphism MLP typing is a PCR-based system that exploits the high variability in the repeat number of microsatellite sequences, dened as tandemly repetitive stretches of two to six nucleotides. Microsatellite markers consist of a dened primer pair anking a specic microsatellite region in the genome. The PCR fragments amplied differ in length according to the number of repetitions of the microsatellite stretch. Microsatellites display a high polymorphism level and a mendelian codominant inheritance and thus can serve as excellent candidates for genetic analysis. For each isolate, MLP typing identies the presence of one (homozygous) or two (heterozygous)
different fragments, or alleles, at a given locus. As microsatellites are highly mutable sequences, one concern with MLP approach is that alleles may be identical not by inheritance but by mutation, resulting in homoplasy (Field et al. 1996; Ort et al. 1997). Fluorescently labelled primers are used to amplify specic loci, and the length of the alleles is measured by migration of the PCR products in a high-resolution gel electrophoresis achieved by an automatic sequencer (Botterel et al. 2001; Sampaio et al. 2005). The lengths of the alleles are numeric data and can be easily compared. MLP is easy to perform, rapid and is amenable for automation and high throughput. Overall, MLP is one of the most discriminative methods for C. albicans typing. However, its resolving power depends on the microsatellite marker used. Several polymorphic microsatellite loci (e.g. EF3, CDC3, HIS3, ERK1, 2NF1, CCN2, CPH2, EFG1, CAI and CAIII to CAVII) have been identied in the C. albicans genome, exhibiting an unequal discriminatory power ranging between 057 (for CAV) and 097 (for CAI) (Field et al. 1996; Bretagne et al. 1997; Lunel et al. 1998; Metzgar et al. 1998; Botterel et al. 2001; Sampaio et al. 2003, 2005). The selection of microsatellite marker to use should be based on its typing performance, mutation rate and discriminative power. Combining several markers located on different chromosomes in the same typing system allows more accurate characterization of C. albicans strains by MLP analysis. Multiplex PCR systems co-amplifying many microsatellite markers are possible when primers are labelled with different dyes allowing rapid and highly resolutive strains typing (Botterel et al. 2001; Sampaio et al. 2005). By combining the three CDC3, EF3 and HIS3 microsatellite polymorphic markers in a PCR multiplex system, Botterel et al. (2001) reported a discriminatory power of 097. A higher value, 0998, was obtained by Sampaio et al. (2005) with the multiplex system based on the CAI, CAIII and CAVI markers. Recently, high-resolution melting (HRM) technology was added to microsatellite marker typing of C. albicans strains and shown to increase the discriminatory power of MLP analysis (Costa et al. 2010; Ben Abdeljelil et al. 2012a). In contrast to conventional techniques where the number of specimens tested in the same run is limited by the constraints of conventional electrophoresis, MLP analysis proved to be very suitable for application in large-scale epidemiological studies as up to 96 samples can be analysed in a single run. (Bretagne et al. 1997; Dalle et al. 2000, 2003; Botterel et al. 2001; Sampaio et al. 2005; Eloy et al. 2006). Reproducibility of sequential tests is high (Botterel et al. 2001). However, interlaboratory exchange of microsatellite data can be difcult, because the use of different
1565
F. Saghrouni et al.
equipment and electrophoresis conditions can interfere with the allocation of a given length to a specic PCR product (Wenz et al. 1998; Garcia-Hermoso et al. 2010). To standardize microsatellite analysis for C. albicans and to assess interlaboratory reproducibly of results, GarciaHermoso et al. (2010), developed an allelic ladder including the most frequent alleles of the CDC3 microsatellite marker and tested it as an internal reference in six laboratories. Despite variations in size determination, alleles were correctly assigned, making data transportable between laboratories. However, the discriminatory power of CDC3 (077) is too low to be used as the sole locus in MLP typing of C. albicans strains (Botterel et al. 2001). Hence, further allelic ladders need to be designed for the other microsatellite markers, especially those exhibiting higher discriminatory power such as CAI (Sampaio et al. 2005). Unfortunately, with current technological limitations, the development of a global database for MLP analysis remains impossible. MLP is a robust technique and strongly recommended for epidemiological studies of C. albicans and other fungi such A. fumigatus and C. neoformans (Bart-Delabesse et al. 2001; Karaoglu et al. 2008). However, inherent drawbacks of MLP include the high cost of specialized equipment and the difculty of implementing the technique in routine use, especially in developing countries. To overcome this difculty, Li and Bai described singlestrand conformation polymorphisms (SSCP) of the microsatellite CAI and showed that SSCP analysis of this microsatellite marker is a powerful (discriminatory power of 0993) and cost-effective approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes (Li and Bai 2007). This technique was later used for accurate typing of vulvovaginitis C. albicans isolates (Fan et al. 2008; Liu et al. 2009). Multilocus sequence typing MLST is typically based on the analysis of nucleotide sequence polymorphisms within the sequences of internal fragments of six to eight independent genes (loci). Genes chosen for MLST analysis are generally those with housekeeping functions that are subject to stabilizing selection. In addition, selected loci must provide as much sequence diversity as possible to allow high levels of allelic discrimination (Bougnoux et al. 2002). MLST involves amplication of DNA fragments (400 500 bp) by PCR followed by DNA sequencing. For each housekeeping locus, different sequences are considered as distinct alleles. Each isolate is therefore characterized by a series of alleles at the different loci that correspond to the multilocus sequence type. Data generated by this DNA
1566
sequence analysis are unambiguous and can be stored and readily accessible in databases (Bougnoux et al. 2002; Tavanti et al. 2005a). In contrast to MLP, MLST proved to be highly reproducible between laboratories and thereby liable to standardization and portability (Tavanti et al. 2005a). It allows the exchange of genotyping data and the construction of international databases accessible via Internet. Online global databases for many microorganisms are currently available at www.mlst.net, including data from epidemiological studies carried out worldwide. This permits global epidemiological and population analysis. MLST methodology was rst developed and used for typing pathogenic bacteria and later some pathogenic fungi (e.g. Cryptococcus gatti, Fusarium solani and Batrachochytrium dendrobatidis) (Zhang et al. 2006; Bovers et al. 2007; Morgan et al. 2007). The technique was applied to C. albicans in the early 2000s. The rst protocol, based on the analysis of six loci and a second one, based on the analysis of eight loci, were developed by Bougnoux et al. in 2002 and Tavanti et al. in 2003, respectively. Later, an optimized protocol based on a set of seven loci was proposed as an international consensus unifying the MLST scheme for C. albicans (Bougnoux et al. 2003). Results from strain typing using this system are shared through public Internet-linked database (http://calbicans.mlst.net/.) where data have been accumulated from different geographical locations. This database provides an interesting source to evaluate the worldwide diversity of C. albicans and the relationships of isolates identied at various locations. It is worth mentioning that MLST is the only typing method that has a public database, not only for C. albicans but also for C. tropicalis, C. glabrata, C. dubliniensis and C. krusei. In contrast, C. parapsilosis shows too little sequence diversity to be typeable by MLST (Dodgson et al. 2003; Tavanti et al. 2005a,b,c; Jacobsen et al. 2007; McManus et al. 2007). Because C. albicans is diploid, nucleotide sequences generated by the MLST analysis are likely to show heterozygosity at polymorphic sites, and therefore, strains are unambiguously characterized by a diploid sequence type (DST) (Bougnoux et al. 2002). MLST analysis has been successfully applied to population genetics and molecular phylogeny studies of C. albicans (Tavanti et al. 2005a; Bougnoux et al. 2002, 2006; Chowdhary et al. 2006; Odds et al. 2006, 2007). In population genetic studies, MLST data have conrmed previous studies in the eld and, in some instances, rened our understanding of the epidemiology of C. albicans (Bougnoux et al. 2006; Chen et al. 2006; Odds et al. 2006). Population genetic analysis of C. albicans MLST data concerning isolates obtained from separate sources showed that the species could be divided into a large
F. Saghrouni et al.
number of clades and that clades differed in the proportions of isolates they included according to the geographical origin and the anatomical sources. However, the link between the geographical origin and the clade is not absolute probably because of movement and migration of human populations (Odds 2010). Clade I, found to be the most prevalent MLST cluster of related C. albicans strains, has been associated with resistance to ucytosine and terbinane. In addition, association between clade and the lengths of tandem repeats in some cell surface proteins, but not with virulence or type of infection, have been demonstrated (Odds 2010). Candida albicans population structure as determined by MLST typing showed a good correlation in the clustering obtained with Ca3 ngerprinting, with clades I, II, III and SA delimited by Ca3 probe (Robles et al. 2004; Tavanti et al. 2005a; Odds et al. 2007). However, clade E as identied by Ca3 ngerprinting has been separated by MLST analysis into various clades (Tavanti et al. 2005a; Odds et al. 2007). As data from more and more C. albicans isolates from different geographical sources are deposited in the database, data need to be regularly reviewed to provide a more robust reference basis for denition of MLST clades and to further characterize the genetic diversity of C. albicans. Many epidemiological studies on C. albicans using MLST have been reported. Viviani et al. (2006) used MLST analysis to investigate a suspected outbreak of C. albicans candidemia cases that occurred in the same hospital ward between 1987 and 1991 and showed that eight cases were caused by the same endemic strain, over a 4-year period. By comparing Ca3 Southern hybridization and MLST for their ability to discriminate between C. albicans isolates (n = 37) obtained from recurrent cases of oropharyngeal candidiasis in ten HIV-positive patients, Chowdhary et al. (2006) showed that MLST was at least as efcient as Ca3 Southern hybridization for dening genetic relatedness of sequentially isolated strains. Similarly, Robles et al. (2004) demonstrated that MLST was at least as effective as RAPD, MLEE and Ca3 Southern hybridization techniques. Chen et al. (2006) also demonstrated that MLST was superior in discriminating epidemiologically related strains than the restriction analysis of genomic DNA by BssHII (REAG-B). Additional reports suggest that MLST may have some limitations in discrimination of unrelated strains. Shin et al. performed MLST to investigate the genetic relatedness among C. albicans bloodstream isolates (n = 156) recovered from 10 Korean hospitals. The isolates generated 112 unique DSTs among which 17 DSTs were shared by 61 isolates (391%). In addition, authors carried out REAG-B to characterize isolates indistinguishable by MLST analysis. They showed that isolates with identical
DSTs, but which originated from different hospitals, had different REAG-B patterns (Shin et al. 2011). Similarly, Myoung et al. reported that, despite its high discriminatory power in distinguishing between epidemiologically related strains and detecting microevolution within the same strain, MLST may fail in distinguishing unrelated isolates. Indeed, the authors showed that some unrelated isolates were identical or similar according to the MLST analysis, but exhibited different REAG-B and C1 ngerprinting patterns. Thus, isolates with identical MLST types may need further genotypic characterization to assess clonal relationships (Myoung et al. 2011). Limitations of MLST in the characterization of unrelated strains may be explained by the fact that (i) the method analyses the sequences of only seven 300400bp loci, so that isolates with identical DSTs may differ substantially through large genomic rearrangements in regions that do not encompass the sequenced loci and (ii) the diploid nature of C. albicans can result in two strains yielding identical DSTs, even though they may differ in the organization of the heterozygous bases at the polymorphic sites (Bougnoux et al. 2002, 2003). An additional problem raised by the C. albicans MLST analysis is that three of the chromosomes of C. albicans (3, 5 and 7) are not represented in the consensus scheme. Lott and Scarborough developed SNP analysis by microarray to complement MLST typing and to extend the SNPs to all the yeast chromosomes. The array consists of multiple replicates of 79 SNPs, derived from 19 loci located on all eight chromosomes, including the seven genes (57 SNPs) that comprise the MLST consensus scheme. The remaining 22 SNPs are from 12 additional loci located on the remaining chromosomes (Lott and Scarborough 2008). Further studies are needed to assess the input of the system in the epidemiology and population genetic studies of C. albicans. According to Garcia-Hermoso et al. (2007), MLP and MLST are similarly efcient in typing and grouping C. albicans strains, indicating that MLST is a suitable technique for clustering analysis. However, it is important to state that for the typing of a single isolate by MLST analysis according to the consensus scheme, seven PCRs are needed, whereas MLP analysis requires only one multiplex PCR per isolate making MLP analysis faster, less tedious and expensive and more adapted for clinical studies than the MLST analysis. However, MLST analysis still remains more appropriate to investigate population structure of C. albicans than MLP-based approach. Conclusion Both conventional DNA-based methods and exact DNA-based methods have provided useful insights into the epidemiology and population structure of C. albicans.
1567
F. Saghrouni et al.
The major drawback of the conventional methods lies in their lack of standardization, reducing their potential for interlaboratory comparisons and therefore global population studies; but these methods are very suitable to investigate epidemiological trends at a local level. Exact DNA-based methods, including MLP and MLST, have emerged as very efcient typing tools. The main advantage of these methods is that generated data are unambiguous and highly reproducible and can be stored in databases offering an unprecedented degree of portability and accessibility to all interested users. Such techniques are much more appropriate for global epidemiology. At present, MLST is the only typing method that has a public database and represents the most powerful approach for phylogenetics of C. albicans, whereas MLP analysis needs further standardization. Both MLST and MLP are costly and require specialized equipment that represents an obstacle to their implementation in clinical mycology laboratories, especially those in developing countries with low income. The choice of the appropriate typing method depends on the purpose of the investigation. With the technical resources currently available, MLST remains the more suitable technique for C. albicans population genetic studies that aim to assess the population structure, diversity and dynamics of the species. However, in clinical studies (investigation of nosocomial candidiasis, recurrent infection, distinguishing epidemic from endemic or sporadic strains, and determination of the origins of infection, the routes of acquisition and transmission of strains), the selection of the technique depends on the local facilities. MLP analysis outperforms virtually all conventional DNAbased typing methods, but requires an expensive and specialized platform, which limits its implementation in developing countries where such platforms may be centrally managed and used by several investigators for a variety of molecular studies (bacterial, fungal or other) to reduce the cost of these studies and make the platform protable. In the absence of such platforms, other techniques may be recommended, such as SSCP analysis of the CAI polymorphic microsatellite marker, AFLP and PFGE after chromosomal restriction digest. Conict of Interests The authors declare that they have no conicts of interest. References
Abaci, O., Haliki-Uztan, A., Ozturk, B., Toksavul, S., Ulusoy, M. and Boyacioglu, H. (2011) Molecular typing of Candida albicans strains isolated from denture wearers by repetitive sequence-based PCR. Eur J Clin Microbiol Infect Dis 30, 141149.
Anderson, J., Srikantha, T., Morrow, T.B., Miyasaki, S.H., White, T.C., Agabian, N., Schmid, J. and Soll, D.R. (1993) Characterization and partial nucleotide sequence of the DNA ngerprinting probe Ca3 of Candida albicans. J Clin Microbiol 31, 14721480. Anderson, M.J., Gull, K. and Denning, D.W. (1996) Molecular typing by random amplication of polymorphic DNA and M13 southern hybridization of related paired isolates of Aspergillus fumigatus. J Clin Microbiol 34, 8793. Arnavielhe, S., Blancard, A., Malli e, M., Quilici, M. and Bastide, J.M. (1997) Multilocus enzyme electrophoresis analysis of Candida albicans isolates from three intensive care units. An epidemiological study. Mycoses 40, 159167. s, T., Blancard, A., Malli Arnavielhe, S., De Meeu e, M., Renaud, F. and Bastide, J.M. (2000) Multicentric genetic study of Candida albicans isolates from non-neutropenic patients using MLEE typing: population structure and mode of reproduction. Mycoses 43, 109117. Ball, L.M., Bes, M.A., Theelen, B., Boekhout, T., Egeler, R.M. and Kuijper, E.J. (2004) Signicance of amplied fragment length polymorphism in identication and epidemiological examination of Candida species colonization in children undergoing allogeneic stem cell transplantation. J Clin Microbiol 42, 16731679. Bart-Delabesse, E., Sarfati, J., Debeaupuis, J.P., van Leeuwen, W., van Belkum, A., Bretagne, S. and Latge, J.P. (2001) Comparison of restriction fragment length polymorphism, microsatellite length polymorphism, and random amplication of polymorphic DNA analyses for ngerprinting Aspergillus fumigatus isolates. J Clin Microbiol 39, 26832686. Ben Abdeljelil, J., Ben Saida, N., Saghrouni, F., Fathallah, A., Boukadida, J., Sboui, H. and Ben Said, M. (2010) Systemic neonatal candidosis: the karyotyping of Candida albicans strains isolated from neonates and health-workers. Mycoses 53, 7277. Ben Abdeljelil, J., Saghrouni, F., Emira, N., Valentin-Gomez, E., Chatti, N., Boukadida, J., Ben Sa d, M. and Del Castillo Agudo, L. (2011) Molecular typing of Candida albicans isolates from patients and health care workers in a neonatal intensive care unit. J Appl Microbiol 111, 12351249. Ben Abdeljelil, J., Saghrouni, F., Cabaret, O., Boukadida, J., Bretagne, S. and Ben Sa d, M. (2012a) a) Temporal similarity between Candida albicans genotypes in a Tunisian neonatal intensive care unit suggests several nosocomial cross-contamination episodes. DNA Cell Biol 31, 11611166. Ben Abdeljelil, J., Saghrouni, F., Khammari, I., Gheith, S., Fathallah, A., Ben Said, M. and Boukadida, J. (2012b) Investigation of a cluster of Candida albicans invasive candidiasis in a neonatal intensive care unit by PulsedField Gel Electrophoresis. Sci World J 2012, ID 138989, 7. Blignaut, E., Pujol, C., Lockhart, S., Joly, S. and Soll, D.R. (2002) Ca3 ngerprinting of Candida albicans isolates
1568
F. Saghrouni et al.
from human immunodeciency virus-positive and healthy individuals reveals new clade in South Africa. J Clin Microbiol 40, 826836. Boekhout, T. and van Belkum, A. (1997) Variability of karyotypes and RAPD types in genetically related strains of Cryptococcus neoformans. Curr Genet 32, 203208. ing, J.F. Boriollo, M.F., Rosa, E.A., Gonc alves, R.B. and Ho (2006) Parity among interpretation methods of MLEE patterns and disparity among clustering methods in epidemiological typing of Candida albicans. J Microbiol Methods 64, 346365. Boriollo, M.F., Dias, R.A., Fiorini, J.E., Oliveira, N.M., rio, D.M., de Souza, H.M., Figueira, A.V. and Spolido Pizzirani-Kleiner, A.A. (2010) Disparity between multilocus enzyme electrophoresis, microsatellite markers and pulsed-eld gel electrophoresis in epidemiological tracking of Candida albicans. J Microbiol Methods 82, 265281. Botterel, F., Desterke, C., Costa, C. and Bretagne, S. (2001) Analysis of microsatellite markers of Candida albicans used for rapid typing. J Clin Microbiol 39, 40764081. Boucher, H.W., Groll, A.H., Chiou, C.C. and Walsh, T.J. (2004) Newer systemic antifungal agents: pharmacokinetics, safety and efcacy. Drugs 64, 19972020. Bougnoux, M.E., Morand, S. and dEnfert, C. (2002) Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 40, 12901297. Bougnoux, M.E., Tavanti, A., Bouchier, C., Gow, N.A.R., Magnier, A., Davidson, A.D., Maiden, M.C.J., dEnfert, C. et al. (2003) Collaborative consensus for optimized multilocus sequence typing of Candida albicans. J Clin Microbiol 41, 52655266. Bougnoux, M.E., Diogo, D., Franc ois, N., Sendid, B., Veirmeire, S., Colombel, J.F., Bouchier, C., Van Kruiningen, H. et al. (2006) Multilocus sequence typing reveals intrafamilial transmission and microevolutions of Candida albicans isolates from the human digestive tract. J Clin Microbiol 44, 18101820. Bougnoux, M., Diogo, D., Pujol, C., Soll, D.R. and dEnfert, C. (2007) Molecular epidemiology and population dynamics in Candida albicans. In Candida Comparative and Functional Genomics ed. dEnfert, C. and Hube, B. pp. 5170. Wymondham, UK: Caister Academic Press. Bovers, M., Diaz, M.R., Hagen, F., Spanjaard, L., Duim, B., Visser, C.E., Hoogveld, H.L., Scharringa, J. et al. (2007) Identication of genotypically diverse Cryptococcus neoformans and Cryptococcus gattii isolates by Luminex xMAP technology. J Clin Microbiol 45, 18741883. Bretagne, S., Costa, J.M., Besmond, C., Carsique, R. and Calderone, R. (1997) Microsatellite polymorphism in the promoter sequence of the elongation factor 3 gene of Candida albicans as the basis for a typing system. J Clin Microbiol 35, 17771780.
Bufngton, J., Reporter, R., Lasker, B.A., McNeil, M.M., Lanson, J.M., Ross, L.A., Mascola, L. and Jarvis, W.R. (1994) Investigation of an epidemic of invasive aspergillosis: utility of molecular typing with the use of random amplied polymorphic DNA probes. Pediatr Infect Dis J 13, 386393. Carlotti, A., Zambardi, G., Couble, A., Lefranc ois, N., Martin, X. and Villard, J. (1994) Nosocomial infection with Candida albicans in a pancreatic transplant recipient investigated by means of restriction enzyme analysis. J Infect 29, 157164. Caugant, D.A. and Sandven, P. (1993) Epidemiological analysis of Candida albicans strains by multilocus enzyme electrophoresis. J Clin Microbiol 31, 215220. Chau, A.S., Mendrick, C.A., Sabatelli, F.J., Loebenberg, D. and McNicholas, P.M. (2004) Application of real-time quantitative PCR to molecular analysis of Candida albicans strains exhibiting reduced susceptibility to azoles. Antimicrob Agents Chemother 48, 21242131. Chen, K.W., Lo, H.J., Lin, Y.H. and Li, S.Y. (2005) Comparison of four molecular typing methods to assess genetic relatedness of Candida albicans clinical isolates in Taiwan. J Med Microbiol 54, 249258. Chen, K.W., Chen, Y.C., Lo, H.J., Odds, F.C., Wang, T.H., Lin, C.Y. and Li, S.Y. (2006) Multilocus sequence typing for analyses of clonality of Candida albicans strains in Taiwan. J Clin Microbiol 44, 21722178. Chibana, H., Beckerman, J.L. and Magee, P.T. (2000) Fineresolution physical mapping of genomic diversity in Candida albicans. Genome Res 10, 18651877. Chowdhary, A., Lee-Yang, W., Lasker, B.A., Brandt, M.E., Warnock, D.W. and Arthington-Skaggs, B.A. (2006) Comparison of multilocus sequence typing and Ca3 ngerprinting for molecular subtyping epidemiologicallyrelated clinical isolates of Candida albicans. Med Mycol 44, 405417. Chu, W.S., Magee, B.B. and Magee, P.T. (1993) Construction of an SI macrorestriction map of the Candida albicans genome. J Bacteriol 175, 66376651. Clemons, K.V., Feroze, F., Holmberg, K. and Stevens, D.A. (1997) Comparative analysis of genetic variability among Candida albicans isolates from different geographic locales by three genotypic methods. J Clin Microbiol 35, 13321336. Coleman, D., Sullivan, D., Harrington, B., Haynes, K., Henman, M., Shanley, D., Bennett, D., Moran, G. et al. (1997) Molecular and phenotypic analysis of Candida dubliniensis: a recently identied species linked with oral candidosis in HIV-infected and AIDS patients. Oral Dis 3, 96101. Costa, J.M., Garcia-Hermoso, D., Olivi, M., Cabaret, O., Farrugia, C., Lecellier, G., Dromer, F. and Bretagne, S. (2010) Genotyping of Candida albicans using length fragment and high-resolution melting analyses together with minisequencing of a polymorphic microsatellite locus. J Microbiol Methods 80, 306309.
1569
F. Saghrouni et al.
Dalle, F., Franco, N., Lopez, J., Vagner, O., Caillot, D., Chavanet, P., Cuisenier, B., Aho, S. et al. (2000) Comparative genotyping of Candida albicans bloodstream and nonbloodstream isolates at a polymorphic microsatellite locus. J Clin Microbiol 38, 45544559. Dalle, F., Dumont, L., Franco, N., Mesmacque, D., Caillot, D., Bonnin, P., Moiroux, C., Vagner, O. et al. (2003) Genotyping of Candida albicans oral strains from healthy individuals by polymorphic microsatellite locus analysis. Clin Microbiol 41, 22032205. Dodgson, A.R., Pujol, C., Denning, D.W., Soll, D.R. and Fox, A.J. (2003) Multilocus sequence typing of Candida glabrata reveals geographically enriched clades. J Clin Microbiol 41, 57095717. Doebbeling, B.N., Lehmann, P.F., Hollis, R.J., Wu, L.C., Widmer, A.F., Voss, A. and Pfaller, M.A. (1993) Comparison of pulsed-eld gel electrophoresis with isoenzyme proles as a typing system for Candida tropicalis. Clin Infect Dis 16, 377383. Eloy, O., Marque, S., Botterel, F., Stephan, F., Costa, J.M., Lasserre, V. and Bretagne, S. (2006) Uniform distribution of three Candida albicans microsatellite markers in two French ICU populations supports a lack of nosocomial cross-contamination. BMC Infect Dis 6, 162. Espinel-Ingroff, A., Vazquez, J.A., Boikov, D. and Pfaller, M.A. (1999) Evaluation of DNA-based typing procedures for strain categorization of Candida spp. Diagn Microbiol Infect Dis 33, 231239. Fan, S.R., Bai, F.Y., Liao, Q.P., Liu, Z.H., Li, J. and Liu, X.P. (2008) Genotype distribution of Candida albicans strains associated with different conditions of vulvovaginal candidiasis, as revealed by microsatellite typing. Sex Transm Infect 84, 103106. Field, D., Eggert, L., Metzgar, D., Rose, R. and Wills, C. (1996) Use of polymorphic short and clustered codingregion microsatellites to distinguish strains of Candida albicans. FEMS Immunol Med Microbiol 15, 7379. Garcia-Hermoso, D., Cabaret, O., Lecellier, G., DesnosOllivier, M., Hoinard, D., Raoux, D., Costa, J.M., Dromer, F. et al. (2007) Comparison of microsatellite length polymorphism and multilocus sequence typing for DNABased typing of Candida albicans. J Clin Microbiol 45, 39583963. Garcia-Hermoso, D., MacCallum, D.M., Lott, T.J., Sampaio, P., Serna, M.J., Grenouillet, F., Klaassen, C.H. and Bretagne, S. (2010) Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker. J Clin Microbiol 48, 25782581. Hajjeh, R.A.A., Sofair, A.N., Harrinson, L.H., Lyon, G.M., Arthingon-Skaggs, B.A., Mirza, S.A., Phelan, M., Morgan, J. et al. (2004) Incidence of bloodstream infections due to Candida species and in vitro susceptibilities of isolates collected from 1998 to 2000 in a population-based active surveillance program. J Clin Microbiol 42, 15191527.
Healy, M., Huong, J., Bittner, T., Lising, M., Frye, S., Raza, S., Schrock, R., Manry, J. et al. (2005) Microbial DNA typing by automated repetitive-sequence-based PCR. J Clin Microbiol 43, 199207. Horn, D.L., Neofytos, D., Anaissie, E.J., Fishman, J.A., Steinbach, W.J., Olyaei, A.J., Marr, K.A., Pfaller, M.A. et al. (2009) Epidemiology and outcomes of candidemia in 2009 patients: data from the prospective antifungal therapy alliance registry. Clin Infect Dis 48, 16951703. Howell, S.A., Anthony, R.M. and Power, E. (1996) Application of RAPD and restriction enzyme analysis to the study of oral carriage of Candida albicans. Lett Appl Microbiol 22, 125128. Huang, Y.C., Lin, T.Y., Peng, H.L., Wu, J.H., Chang, H.Y. and Leu, H.S. (1998) Outbreak of Candida albicans fungaemia in a neonatal intensive care unit. Scand J Infect Dis 30, 137142. Hunter, P.R. (1991) A critical review of typing methods for Candida albicans and their applications. Crit Rev Microbiol 17, 417434. Iwaguchi, S., Homma, M. and Tanaka, K. (1990) Variation in the electrophoretic karyotype analysed by the assignment of DNA probes in Candida albicans. J Gen Microbiol 136, 24332442. Iwaguchi, S., Homma, M., Chibana, H. and Tanaka, K. (1992) Isolation and characterization of a repeated sequence (RPS1) of Candida albicans. J Gen Microbiol 138, 18931900. Jacobsen, M.D., Gow, N.A., Maiden, M.C., Shaw, D.J. and Odds, F.C. (2007) Strain typing and determination of population structure of Candida krusei by multilocus sequence typing. J Clin Microbiol 45, 317323. Jones, T., Federspiel, N.A., Chibana, H., Dungan, J., Kalman, S., Magee, B.B., Newport, G., Thorstenson, Y.R. et al. (2004) The diploid genome sequence of Candida albicans. Proc Natl Acad Sci USA 101, 73297334. Kam, A.P. and Xu, J. (2002) Diversity of commensal yeasts within and among healthy hosts. Diagn Microbiol Infect Dis 43, 1928. Kantardjiev, T., Levterova, V., Brankova, N., Ivanov, I., Angelov, P. and Panaiotov, S. (2006) Role of uorescent amplied fragment length polymorphism analysis in taxonomy, identication and epidemiological examinations of yeast pathogens. Biotechnol Biotech Eq 20, 103106. Karaoglu, H., Lee, C.M., Carter, D. and Meyer, W. (2008) Development of polymorphic microsatellite markers for Cryptococcus neoformans. Mol Ecol Resour 8, 11361138. Klaassen, C.H. (2009) MLST versus microsatellites for typing Aspergillus fumigatus isolates. Med Mycol 47, 2733. Krawczyk, B., Leibner-Ciszak, J., Mielech, A., Nowak, M. and Kur, J. (2009) PCR melting prole (PCR MP)-a new tool for differentiation of Candida albicans strains. BMC Infect Dis 9, 177. Lasker, B.A., Carle, G.F., Kobayashi, G.S. and Medoff, G. (1989) Comparison of the separation of Candida albicans
1570
F. Saghrouni et al.
chromosome-sized DNA by pulsed-eld gel electrophoresis techniques. Nucleic Acids Res 17, 37833793. Lehmann, P.F., Lin, D. and Lasker, B.A. (1992) Genotypic identication and characterization of species and strains within the genus Candida by using random amplied polymorphic DNA. J Clin Microbiol 30, 32493254. Lehmann, P.F., Wu, L.C., Pruitt, W.R., Meyer, S.A. and Ahearn, D.G. (1993) Unrelatedness of groups of yeasts within the Candida haemulonii complex. J Clin Microbiol 31, 16831687. Levterova, V., Panaiotov, S., Brankova, N. and Tankova, K. (2010) Typing of genetic markers involved in stress response by uorescent cDNA-amplied fragment length polymorphism technique. Mol Biotechnol 45, 3438. Li, J. and Bai, F.Y. (2007) Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans. Med Mycol 45, 629635. Lin, D., Wu, L.C., Rinaldi, M.G. and Lehmann, P.F. (1995) Three distinct genotypes within Candida parapsilosis from clinical sources. J Clin Microbiol 33, 18151821. Liu, X.P., Fan, S.R., Bai, F.Y., Li, J. and Liao, Q.P. (2009) Antifungal susceptibility and genotypes of Candida albicans strains from patients with vulvovaginal candidiasis. Mycoses 52, 2428. Lockhart, S., Fritch, J.J., Meier, A.S., Schroppel, K., Srikantha, T., Galask, R. and Soll, D.R. (1995) Colonizing populations of Candida albicans are clonal in origin but undergo microevolution through C1 fragment reorganization as demonstrated by DNA ngerprinting and C1 sequencing. J Clin Microbiol 33, 15011509. Lockhart, S.R., Reed, B.D., Pierson, C.L. and Soll, D.R. (1996) Most frequent scenario for recurrent Candida vaginitis is strain maintenance with substrain shufing: demonstration by sequential DNA ngerprinting with probes Ca3, C1, and CARE2. J Clin Microbiol 34, 767777. Lopes, M.M., Silva, D., Freitas, G. and Tenreiro, R. (2007) Simultaneous identication and typing of Candida species by MSP-PCR and AFLP: study of clinical isolates from a Portuguese pediatric hospital Identication. J Med Myc 17, 157167. Lott, T.J. and Scarborough, R.T. (2008) Development of a MLST-biased SNP microarray for Candida albicans. Fungal Genet Biol 45, 803811. Lott, T.J., Keykendall, R.J., Welbel, S.F., Pramanik, A. and Lasker, B.A. (1993) Genomic heterogeneity in the yeast Candida parapsilosis. Curr Genet 23, 463467. Lunel, F.V., Licciardello, L., Stefani, S., Verbrugh, H.A., Melchers, W.J., Meis, J.F., Scherer, S. and van Belkum, A. (1998) Lack of consistent short sequence repeat polymorphisms in genetically homologous colonizing and invasive Candida albicans strains. J Bacteriol 180, 37713778. Magee, B.B. and Magee, P.T. (1987) Electrophoretic karyotypes and chromosome numbers in Candida species. J Gen Microbiol 133, 425430.
Mata, A.L., Rosa, R.T., Rosa, E.A.R., Goncalves, R.B. and Hoing, J.F. (2000) Clonal variability among oral Candida albicans assessed by allozyme electrophoresis analysis. Oral Microbiol Immunol 15, 350354. Matthews, R. and Burnie, J. (1989) Assessment of DNA ngerprinting for rapid identication of outbreaks of systemic candidiasis. Br Med J 298, 354357. McManus, B.A., Coleman, D.C., Moran, G., Pinjon, E., Diogo, D., Bougnoux, M.E., Boreck a-Melkusova, S., Bujd akova, H. et al. (2007) Multilocus sequence typing reveals that the population structure of Candida dubliniensis is signicantly less divergent than that of Candida albicans. J Clin Microbiol 46, 652664. Mercure, S., Poirier, S., Lemay, G., Auger, P., Montplaisir, S. and de Repentigny, L. (1993) Application of biotyping and DNA typing of Candida albicans to the epidemiology of recurrent vulvovaginal candidiasis. J Infect Dis 168, 502507. Merz, W.G., Khazan, U., Jabra-Rizk, M.A., Wu, L.C., Osterhout, G.J. and Lehmann, P.F. (1992) Strain delineation and epidemiology of Candida (Clavispora) lusitaniae. J Clin Microbiol 30, 449454. Metzgar, D., Field, D., Haubrich, R. and Wills, C. (1998) Sequence analysis of a compound coding-region microsatellite in Candida albicans resolves homoplasies and provides a high-resolution tool for genotyping. FEMS Immunol Med Microbiol 20, 103109. Meunier, J.R. and Grimont, P.A. (1993) Factors affecting reproducibility of random amplied polymorphic DNA ngerprinting. Res Microbiol 144, 373379. Morgan, J.A.T., Vredenburg, V.T., Rachowicz, L.J., Knapp, R.A., Stice, M.J., Tunstall, T., Bingham, R.E., Parker, J.M. et al. (2007) Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis. Proc Natl Acad Sci USA 104, 1384513850. Myoung, Y., Shin, J.H., Lee, J.S., Kim, S.H., Shin, M.G., Suh, S.P. and Ryang, D.W. (2011) Multilocus sequence typing for Candida albicans isolates from candidemic patients: comparison with Southern blot hybridization and pulsedeld gel electrophoresis analysis. Korean J Lab Med 31, 107114. Odds, F.C. (2010) Molecular phylogenetics and epidemiology of Candida albicans. Future Microbiol 5, 6779. Odds, F.C. and Jacobsen, M.D. (2008) Multilocus sequence typing of pathogenic Candida species. Eukaryot Cell 7, 10751084. Odds, F.C., Davidson, A.D., Jacobsen, M.D., Tavanti, A., Whyte, J.A., Kibbler, C.C., Ellis, D.H., Maiden, M.C. et al. (2006) Candida albicans strain maintenance, replacement, and microvariation demonstrated by multilocus sequence typing. J Clin Microbiol 44, 36473658. Odds, F.C., Bougnoux, M.E., Shaw, D.J., Bain, J.M., Davidson, A.D., Diogo, D., Jacobsen, M.D., Lecomte, M. et al. (2007) Molecular phylogenetics of Candida albicans. Eukaryot Cell 6, 10411452.
1571
F. Saghrouni et al.
Olive, D.M. and Bean, P. (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37, 16611669. Ort , G., Pearse, D.E. and Avise, J.C. (1997) Phylogenetic assessment of length variation at a microsatellite locus. Proc Natl Acad Sci 94, 1074510749. Pearce, M.A. and Howell, S.A. (1991) Restriction fragment length polymorphism analysis of azole-resistant and azolesusceptible Candida albicans strains. J Clin Microbiol 29, 13641367. Pfaller, M.A. (1992) The use of molecular techniques for epidemiologic typing of Candida species. Curr Top Med Mycol 4, 4363. Pfaller, M.A. (1996) Nosocomial candidiasis: emerging species, reservoirs, and modes of transmission. Clin Infect Dis 22, 8994. Pfaller, M.A. and Diekema, D.J. (2007) Epidemiology of invasive candidiasis: a persistent public health problem. Clin Microbiol Rev 20, 133163. Pfaller, M.A., Cabezudo, I., Hollis, R., Huston, B. and Wenzel, R.P. (1990) The use of biotyping and DNA ngerprinting in typing Candida albicans from hospitalized patients. Diagn Microbiol Infect Dis 13, 481489. Pfaller, M.A., Lockhart, S.R., Pujol, C.A., Swails-Wenger, J.A., Messer, S.A., Edmund, M.B., Jones, R.N., Wenzel, R.P. et al. (1998) Hospital specicity, vaginal specicity and uconazole-resistance of Candida albicans blood stream isolates. J Clin Microbiol 36, 15181529. Pittet, D., Monod, M., Filthuth, I., Frenk, E., Suter, P.M. and Auckenthaler, R. (1991) Contour-clamped homogeneous electric eld gel electrophoresis as a powerful epidemiologic tool in yeast infections. Am J Med 91, 256263. Poikonen, E., Vuopio-Varkila, J., Kaukoranta-Tolvanen, S.S., Sivonen, A., Siren, E. and Ruutu, P. (2001) Epidemiological typing of Candida albicans from bloodstream infections by restriction enzyme analysis. Scand J Infect Dis 33, 140144. Pujol, C., Reynes, J., Renaud, F., Raymond, M., Tibayrenc, M., Ayala, F.J., Janbon, F., Malli e, M. et al. (1993) The yeast Candida albicans has a clonal mode of reproduction in a population of infected human immunodeciency virus-positive patients. Proc Natl Acad Sci USA 90, 94569459. Pujol, C., Joly, S., Lockhart, S.R., Noel, S., Tibayrenc, M. and Soll, D.R. (1997) Parity among the randomly amplied polymorphic DNA method, multilocus enzymeelectrophoresis, and Southern blot hybridization with the moderately repetitive DNA probe Ca3 for ngerprinting Candida albicans. J Clin Microbiol 35, 23482358. Pujol, C., Joly, S., Nolan, B., Srikantha, T. and Soll, D.R. (1999) Microevolutionary changes in Candida albicans identied by the complex Ca3 ngerprinting probe involve insertions and deletions of the full-length repetitive
sequence RPS at specic genomic sites. Microbiology 145, 26352646. Pujol, C., Pfaller, M. and Soll, D.R. (2002) Ca3 ngerprinting of Candida albicans bloodstream isolates from the United States, Canada, South America, and Europe reveals a European clade. J Clin Microbiol 40, 27292740. Pujol, C., Pfaller, M.A. and Soll, D.R. (2004) Flucytosine resistance is restricted to a single genetic clade of Candida albicans. Antimicrob Agents Chemother 48, 262266. Redkar, R.J., Dub e, M.P., McCleskey, F.K., Rinaldi, M.G. and Del Vecchio, V.G. (1996) DNA Fingerprinting of Candida rugosa via Repetitive Sequence-Based PCR. J Clin Microbiol 34, 16771681. Robinson, J.L., Hartstein, A.I., Meuser, R.U., Morthland, V.H., Dragoon, M.E. and Wenman, W.M. (1993) Molecular epidemiology of Candida albicans colonization and fungemia in very low birth weight infants. Can J Infect Dis 4, 322327. Robles, J.C., Koreen, L., Park, S. and Perlin, D.S. (2004) Multilocus sequence typing is a reliable alternative method to DNA ngerprinting for discriminating among strains of Candida albicans. J Clin Microbiol 42, 24802488. Romano, F., Ribera, G. and Giuliano, M. (1994) A study of a hospital cluster of systemic candidosis using DNA typing methods. Epidemiol Infect 112, 393398. Sadhu, C., McEachern, M.J., Rustchenko-Bulgac, E.P., Schmid, J., Soll, D.R. and Hicks, J.B. (1991) Telomeric and dispersed repeat sequences in Candida yeasts and their use in strain identication. J Bacteriol 173, 842850. Sampaio, P., Gusm~ ao, L., Alves, C., Pina-Vaz, C., Amorim, A. and Pais, C. (2003) Highly polymorphic microsatellite for identication of Candida albicans strains. J Clin Microbiol 41, 552557. Sampaio, P., Gusm~ ao, L., Correia, A., Alves, C., Rodrigues, A.G., Pina-Vaz, C., Amorim, A. and Pais, C. (2005) New microsatellite multiplex PCR for Candida albicans strain typing reveals microevolutionary changes. J Clin Microbiol 43, 38693876. San Millan, R.M., Wu, L.C., Salkin, I.F. and Lehmann, P.F. (1997) Clinical isolates of Candida guilliermondii include Candida fermentati. Int J Syst Bacteriol 47, 385393. Sangeorzan, J.A., Zervos, M.J., Donabedian, S. and Kauffman, C.A. (1995) Validity of contour-clamped homogeneous electric eld electrophoresis as a typing system for Candida albicans. Mycoses 38, 2936. Santos, P.O., Melo, J.O., Ponzzes, C.M., Alves, J.A., de Melo, D.L., Botelho Nde, S., Yamada-Ogatta, S.F., Mann, R.S. et al. (2012) Multilocus enzyme electrophoresis analysis and exoenzymatic activity of Candida albicans strains isolated from women with vaginal candidiasis. Mycoses 55, 6472. Schmid, J., Voss, E. and Soll, D.R. (1990) Computer-assisted methods for assessing Candida albicans strain relatedness by Southern blot hybridization with repetitive sequence Ca3. J Clin Microbiol 28, 12361243.
1572
F. Saghrouni et al.
Schmid, J., Rotman, M., Reed, B., Pierson, C.L. and Soll, D.R. (1993) Genetic similarity of Candida albicans strains from vaginitis patients and their partners. J Clin Microbiol 31, 3946. Schmid, J., Tay, Y.P., Wan, L., Carr, M., Parr, D. and McKinney, W. (1995) Evidence for nosocomial transmission of Candida albicans obtained by Ca3 ngerprinting. J Clin Microbiol 33, 12231230. ppel, K., Rotman, M., Galask, R., Mac, K. and Soll, D.R. Schro (1994) Evolution and replacement of Candida albicans strains during recurrent vaginitis demonstrated by DNA ngerprinting. J Clin Microbiol 32, 26462654. Schwartz, D.C. and Cantor, C.R. (1984) Separation of yeast chromosome-sized DNAs by pulsed eld gradient gel electrophoresis. Cell 37, 6775. Selmecki, A., Forche, A. and Berman, J. (2010) Genomic plasticity of the human fungal pathogen Candida albicans. Eukaryot Cell 9, 9911008. Shin, J.H., Park, M.R., Song, J.W., Shin, D.H., Jung, S.I., Cho, D., Kee, S.J., Shin, M.G. et al. (2004) Microevolution of Candida albicans strains during catheter-related candidemia. J Clin Microbiol 42, 40254031. Shin, J.H., Bougnoux, M.E., dEnfert, C., Kim, S.H., Moon, C.J., Joo, M.Y., Lee, K., Kim, M.N. et al. (2011) Genetic diversity among Korean Candida albicans bloodstream isolates: assessment by multilocus sequence typing and restriction endonuclease analysis of genomic DNA by use of BssHII. J Clin Microbiol 49, 25722577. Singh, A., Goering, R.V., Simjee, S., Foley, S.L. and Zervos, M.J. (2006) Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev 19, 512 530. Smith, R.A., Hitchcock, C.A., Evans, E.G.V., Lacey, C.J.N. and Adams, D.J. (1989) The identication of Candida albicans strains by restriction fragment length polymorphism analysis of DNA. J Med Vet Mycol 27, 431434. Soll, D.R. and Pujol, C. (2003) Candida albicans clades. FEMS Immunol Med Mycol 1623, 17. Soll, D.R., Langtimm, C.J., McDowell, J., Hicks, J. and Galask, R. (1987) High-frequency switching in Candida strains isolated from vaginitis patients. J Clin Microbiol 25, 16111622. Soll, D.R., Galask, R., Isley, S., Rao, T.V.G., Stone, D., Hicks, J., Schmid, J., Mac, K. et al. (1989) Switching of Candida albicans during successive episodes of recurrent vaginitis. J Clin Microbiol 27, 681690. Soll, D.R., Galask, R., Schmid, J., Hanna, C., Mac, K. and Morrow, B. (1991) Genetic dissimilarity of commensal strains carried in different anatomical locations of the same healthy women. J Clin Microbiol 29, 17021710. Steffan, P., Vazquez, J.A., Boikov, D., Xu, C., Sobel, J.D. and Atkins, R.A. (1997) Identication of Candida species by randomly amplied polymorphic DNA ngerprinting of colony lysates. J Clin Microbiol 35, 20312039.
Stern, M.J., Ames, G.F., Smith, N.H., Robinson, E.C. and Higgins, C.F. (1984) Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell 37, 10151026. Tavanti, A., Davidson, A.D., Gow, N.A., Maiden, M.C. and Odds, F.C. (2005a) Candida orthopsilosis and Candida metapsilosis spp. nov. to replace Candida parapsilosis groups II and III. J Clin Microbiol 43, 284292. Tavanti, A., Davidson, A.D., Fordyce, M.J., Gow, N.A., Maiden, M.C. and Odds, F.C. (2005b) Population structure and properties of Candida albicans, as determined by multilocus sequence typing. J Clin Microbiol 43, 56015613. Tavanti, A., Davidson, A.D., Johnson, E.M., Maiden, M.C., Shaw, D.J., Gow, N.A. and Odds, F.C. (2005c) Multilocus sequence typing for differentiation of strains of Candida tropicalis. J Clin Microbiol 43, 55935600. Tavanti, A., Gow, N.A., Senesi, S., Maiden, M.C. and Odds, F.C. (2003) Optimization and validation of multilocus sequence typing for Candida albicans. J Clin Microbiol 41, 37653776. Trtkova, J. and Raclavsky, V. (2006) Molecular-genetic approaches to identication and typing of pathogenic Candida yeasts. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 150, 5161. Vazquez, J.A., Beckley, A., Sobel, J.D. and Zervos, M.J. (1991) Comparison of restriction enzyme analysis and pulsed-eld gradient gel electrophoresis as typing systems for Candida albicans. J Clin Microbiol 29, 962967. Vazquez, J.A., Sanchez, V., Dmuchowski, C., Dembry, L.M., Sobel, J.D. and Zervos, M.J. (1993) Nosocomial acquisition of Candida albicans: an epidemiologic study. J Infect Dis 168, 195201. Versalovic, J. and Lupski, J.R. (2002) Molecular detection and genotyping of pathogens: more accurate and rapid answers. Trends Microbiol 10, 1521. Versalovic, J., Koeuth, T. and Lupski, J.R. (1991) Distribution of repetitive DNA sequences in eubacteria and application to ngerprinting of bacterial genomes. Nucleic Acids Res 19, 68236831. Viviani, M.A., Cogliati, M., Esposto, M.C., Prigitano, A. and Tortorano, A.M. (2006) Four-year persistence of a single Candida albicans genotype causing bloodstream infections in a surgical ward proven by multilocus sequence typing. J Clin Microbiol 44, 218221. Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J. et al. (1995) AFLP: a new technique for DNA ngerprinting. Nucleic Acids Res 23, 44074414. Voss, A., Pfaller, M.A., Hollis, R.J., Rhine-Chalberg, J. and Doebbeling, B.N. (1995) Investigation of Candida albicans transmission in a surgical intensive care unit cluster by using genomic DNA typing methods. J Clin Microbiol 33, 576580.
1573
F. Saghrouni et al.
Warnock, D.W. (1984) Typing of Candida albicans. J Hosp Infect 5, 244252. Wenz, H., Robertson, J.M., Menchen, S., Oaks, F., Demorest, D.M., Scheibler, D., Rosenblum, B.B., Wike, C. et al. (1998) High-precision genotyping by denaturing capillary electrophoresis. Genome Res 8, 6980. Yates, S.K., Sander, D.M. and Keath, E.J. (1995) Genetic diversity in clinical isolates of the dimorphic fungus Blastomyces dermatitidis detected by a PCR-based random amplied polymorphic DNA assay. J Clin Microbiol 33, 21712175.
Zeng, S., Wu, L.C. and Lehmann, P.F. (1996) Random amplied polymorphic DNA analysis of culture collection strains of Candida species. J Med Vet Mycol 34, 293297. Zhang, N., ODonnell, K., Sutton, D.A., Nalim, A., Summerbell, R.C., Padhye, A.A. and Geiser, D.M. (2006) Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. J Clin Microbiol 44, 21862190.
1574

Molecular Methods For Strain Typing of Candida Albicans Revew

Transféré par

Informations du document

Description originale:

Titre original

Copyright

Formats disponibles

Partager ce document

Partager ou intégrer le document

Options de partage

Avez-vous trouvé ce document utile ?

Ce contenu est-il inapproprié ?

Droits d'auteur :

Formats disponibles

Molecular Methods For Strain Typing of Candida Albicans Revew

Transféré par

Droits d'auteur :

Formats disponibles

Journal of Applied Microbiology ISSN 1364-5072

Molecular methods for strain typing of Candida albicans: a review

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Discriminatory power Non-DNA-based techniques MLEE Good

Protein-based method Time required depends on the number of enzymes to be assessed

Low Moderate Moderate Low Moderate Low Moderate Very high

4 4 2 1 2 1 1 2 Unambiguous data Unambiguous data Online databases

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Molecular typing of Candida albicans

Vous aimerez peut-être aussi