Multilocus Sequence Type Analysis Reveals both Clonality and Recombination in Populations of Candida glabrata Bloodstream Isolates from U.S. Surveillance Studies

Lott, Timothy J.; Frade, João P.; Lockhart, Shawn R.

doi:10.1128/ec.00002-10

Cited by 54 publications

(47 citation statements)

References 23 publications

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“…CgMT-J and CgMT-M yielded largely congruent results despite representing distinct chromosomes and coding versus noncoding loci. This congruence indicates that these single loci provide reliable phylogenetic information, and it confirms that C. glabrata is a predominantly clonal species in which sexual reproduction and horizontal gene transfer have contributed minimally to its evolution (30,33,43). On the other hand, this clonality means that strain resolution can be limiting; this is illustrated by large clusters such as N that include geographically diverse isolates (3 countries and at least 5 U.S. states).…”

Section: Resultssupporting

confidence: 48%

“…The most widely applied include (i) multilocus sequence typing (MLST), which analyzes 6 relatively conserved housekeeping loci for single nucleotide polymorphisms (SNPs) (29,30), (ii) pulsed-field gel electrophoresis (PFGE), which compares total DNA banding patterns with or without restriction enzyme digestion (14,23,31), (iii) multilocus variable-number tandem-repeat analysis (MLVA, also known as microsatellite analysis), which examines length variation in 6 to 9 PCR-amplified loci that contain polymorphic tandem repeats (32)(33)(34)(35), and (iv) random amplification of polymorphic DNA (RAPD), which compares banding patterns following PCR with a nonspecific primer (26,36). In general, these methods are comparable in their strain resolution, achieving diversity indexes of ca.…”

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confidence: 99%

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Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

et al. 2016

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The opportunistic yeast Candida glabrata is increasingly refractory to antifungal treatment or prophylaxis and relatedly is increasingly implicated in health care-associated infections. To elucidate the epidemiology of these infections, strain typing is required. Sequence-based typing provides multiple advantages over length-based methods, such as pulsed-field gel electrophoresis (PFGE); however, conventional multilocus sequence typing (targeting 6 conserved loci) and whole-genome sequencing are impractical for routine use. A commercial sequence-based typing service for C. glabrata that targets polymorphic tandem repeatcontaining loci has recently been developed. These CgMT-J and CgMT-M services were evaluated with 56 epidemiologically unrelated isolates, 4 to 7 fluconazole-susceptible or fluconazole-resistant isolates from each of 5 center A patients, 5 matched pairs of fluconazole-susceptible/resistant isolates from center B patients, and 7 isolates from a center C patient who responded to then failed caspofungin therapy. CgMT-J and CgMT-M generated congruent results, resolving isolates into 24 and 20 alleles, respectively. Isolates from all but one of the center A patients shared the same otherwise rare alleles, suggesting nosocomial transmission. Unexpectedly, Pdr1 sequencing showed that resistance arose independently in each patient. Similarly, most isolates from center B also clustered together; however, this may reflect a dominant clone since their alleles were shared by multiple unrelated isolates. Although distinguishable by their echinocandin susceptibilities, all isolates from the center C patient shared alleles, in agreement with the previously reported relatedness of these isolates based on PFGE. Finally, we show how phylogenetic clusters can be used to provide surrogate parents to analyze the mutational basis for antifungal resistance.

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Section: Resultssupporting

confidence: 48%

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confidence: 99%

Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

et al. 2016

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“…Indeed, we used the high concordance observed between clades, defined using the MLST method described by Dodgson et al (15,16), and CCs (Table 1). Interestingly, CC64, which was not associated with a given MLST clade, corresponds in a recent paper by Lott et al (33) to an MLST group clustering as many as 18.3% of the tested strains, supported by a 99% bootstrap value (100% in the Dodgson study), each with a synapomorphic NMT1 allele (NMT1-5). Conversely, we considered genotype RT60 to be included in a potential CC since the single strain we had exhibited allele 12 for the NMT1 locus (data not shown), characteristic of clade VII (15,31,33).…”

Section: Resultsmentioning

confidence: 88%

Multilocus Microsatellite Markers for Molecular Typing of Candida glabrata : Application to Analysis of Genetic Relationships between Bloodstream and Digestive System Isolates

et al. 2010

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Candida glabrata has emerged as the second most common etiologic agent, after Candida albicans, of superficial and invasive candidiasis in adults. Strain typing is essential for epidemiological investigation, but easy-to-use and reliable typing methods are still lacking. We report the use of a multilocus microsatellite typing method with a set of eight markers on a panel of 180 strains, including 136 blood isolates from hospitalized patients and 34 digestive tract isolates from nonhospitalized patients. A total of 44 different alleles were observed, generating 87 distinct genotypes. In addition to perfect reproducibility, typing ability, and stability, the method had a discriminatory power calculated at 0.97 when all 8 markers were associated, making it suitable for tracing strains. In addition, it is shown that digestive tract isolates differed from blood culture isolates by exhibiting a higher genotypic diversity associated with different allelic frequencies and preferentially did not group in clonal complexes (CCs). The demonstration of the occurrence of microevolution in digestive strains supports the idea that C. glabrata can be a persistent commensal of the human gut.

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“…Indeed, the dominating species was C. glabrata in swabs from both azole-and echinocandin-treated patients, despite the different initial species distributions in blood. This would not explain the prevalence of polyfungal oral swabs, however, and further studies are thus warranted to evaluate these hypotheses (10,30,35,36). One approximation for this study was to interpret the blood isolates as surrogate markers for baseline colonization and to compare this to subsequent oral colonization.…”

Section: Discussionmentioning

confidence: 99%

Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study

Jensen

Johansen

Søes

et al. 2016

Antimicrob Agents Chemother

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The prevalence of intrinsic and acquired resistance among colonizing Candida isolates from patients after candidemia was investigated systematically in a 1-year nationwide study. Patients were treated at the discretion of the treating physician. Oral swabs were obtained after treatment. Species distributions and MIC data were investigated for blood and posttreatment oral isolates from patients exposed to either azoles or echinocandins for <7 or >7 days. Species identification was confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS) sequencing, susceptibility was examined by EUCAST EDef 7.2 methodology, echinocandin resistance was examined by FKS sequencing, and genetic relatedness was examined by multilocus sequence typing (MLST). One hundred ninety-three episodes provided 205 blood and 220 oral isolates. MLST analysis demonstrated a genetic relationship for 90% of all paired blood and oral isolates. Patients exposed to azoles for >7 days (n ‫؍‬ 93) had a significantly larger proportion of species intrinsically less susceptible to azoles (particularly Candida glabrata) among oral isolates than among initial blood isolates (36.6% versus 12.9%; P < 0.001). A similar shift toward species less susceptible to echinocandins among 85 patients exposed to echinocandins for >7 days was not observed (4.8% of oral isolates versus 3.2% of blood isolates; P > 0.5). Acquired resistance in Candida albicans was rare (<5%). However, acquired resistance to fluconazole (29.4%; P < 0.05) and anidulafungin (21.6%; P < 0.05) was common in C. glabrata isolates from patients exposed to either azoles or echinocandins. Our findings suggest that the colonizing mucosal microbiota may be an unrecognized reservoir of resistant Candida species, especially C. glabrata, following treatment for candidemia. The resistance rates were high, raising concern in general for patients exposed to antifungal drugs.

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Multilocus Sequence Type Analysis Reveals both Clonality and Recombination in Populations of Candida glabrata Bloodstream Isolates from U.S. Surveillance Studies

Cited by 54 publications

References 23 publications

Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

Evaluation of Polymorphic Locus Sequence Typing for Candida glabrata Epidemiology

Multilocus Microsatellite Markers for Molecular Typing of Candida glabrata : Application to Analysis of Genetic Relationships between Bloodstream and Digestive System Isolates

Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study

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