The present study was undertaken as part of a long-term prospective surveillance to determine species distribution and drug resistance profiles in hospital-associated Candida
bloodstream infections (8
). Isolates studied were all incident bloodstream isolates collected from residents of each surveillance area. From a total of 230 isolates, representing the sequencing of ~7.7 × 105
base pairs, we observed only two new mutations, both nonsynonymous polymorphisms. We described six additional isolates as new STs resulting from new combinations of existing alleles.
A number of interesting observations have resulted from this analysis. For these selected U.S. isolates, the uncovering of new polymorphisms (by definition, new alleles) may be increasingly proportional to the number of isolates examined, suggesting a finite number of alleles in the population. The definition of an allele as a discrete set of polymorphisms as described by Dodgson et al. (4
) is strongly supported, with little evidence of homoplasy in the creation of allelic combinations. There is evidence from our analysis for recombination in this species. Because alleles and STs are shared among all populations in this study, this implies that recombination has, or is, occurring among our defined populations. Earlier studies have suggested that such recombination is sexual (meiotic) recombination (3
). As in earlier work (4
), our data supports the concept that these six unlinked loci are representative of the genome as a whole and reflect the underlying mechanisms creating diversity and differentiation in this species.
We have also provided evidence that there is a clonal component to the population, such as the increasing proportion of ST16 in Atlanta and the overall abundance both temporally and geographically of ST16, ST19, and ST3. The temporal stability of some STs suggests that at least some isolates with identical STs may be related by descent. More specifically, the isolates in the major STs may be clonally related. Both the IA
and linkage association analyses support this concept, even when populations were clone corrected. Our findings are in agreement with other published work (4
) and are supported by the knowledge that these MLST loci are physically unlinked (18
). Additionally, we have reanalyzed IA
and rBarD for a subpopulation of 20 isolates containing groups I, IV, V, VI, and VII. As seen in , this large middle group of STs are lacking in bootstrap support for the branch nodes. The IA
and rBarD values for the clone-corrected subpopulation were found to be 0.598 and 0.135, respectively. Although still below the level of statistical significance for recombination (P
< 0.02), these values are less than those for the the combined population as a whole (). We interpret this as suggesting that some subpopulations may be recombining at low, but variable, rates.
From a population standpoint, we have observed slight differences in the overall abundance of individual STs among geographic groups, primarily among minor STs, although frequency shifts in the major STs were also found. This is consistent with other observations which have shown FST
values between cities and countries to be generally smaller than those between continents (3
). Our data showing that the C. glabrata
population in three large U.S. cities consists of a relatively small number of major STs are consistent with the previous study of U.S. isolates, in which the same and other major STs were observed (4
). For example, STs 3 and 10 have been shown to be major STs worldwide (4
). Some of the major STs in other collections do not appear in ours, while one of the major STs observed in this study, ST16, appears to be restricted to the United States (4
). In addition, we observed a large temporal increase in the frequency of ST16 in Atlanta. Taken collectively, this suggests that STs may vary, or drift, between major and minor types over distance and time. The abundance of a particular ST in a geographic locale may be a reflection of the adaptation of a specific ST to a geographic niche, while the general drift in the temporal and geographic populations may reflect the ability of isolates of C. glabrata
to adapt to new environments.
The low FST
and genetic distance values among the populations are, in part, a reflection of the relative abundance in each population of the three major STs, ST19, ST16, and ST3, which account for an average of 50% of the isolates across all populations. The amount of diversity within a population ranged from one unique ST for every 2.4 isolates in Atlanta from 1992 to 1993 to one unique ST for every 4.8 patients in Baltimore in 2008. Two other studies of ST diversity of C. glabrata
isolates have been recently published. Odds and coworkers (12
) identified 27 STs from 50 patients in a 1-year study of Candida
isolates from Scotland, for a ratio of one unique ST for every 1.9 isolates. Lin and coworkers (11
) identified 15 STs from 37 patients in a single hospital in Taiwan over 2 years, for a ratio of one unique ST for every 2.5 isolates. Ratios from both of these previous studies indicate a higher degree of diversity in these populations in terms of STs than we have found. However, ST is not indicative of overall allelic diversity within a population. Because neither dendrograms nor individual STs were provided in either of the previous studies, it is not possible to tell whether the ST diversity is a reflection of overall diversity or whether it reflects a diverse population of closely related isolates. The populations observed in the other studies were also not bound by the constraints of case patient residency in a defined geographic boundary.
There is an intriguing correlation between genetic distance measures and incidence rates in the Atlanta and Baltimore populations. When the two Baltimore populations were compared temporally, they were shown to be highly similar genetically. The incidence rate of C. glabrata
in Baltimore from 1998 to 2000 was 6.6/100,000 (8
). Preliminary analysis showed that this rate dropped only slightly in 2008 to 6.3/100,000 (2
). In contrast, the largest amount of genetic diversity was seen between the two Atlanta populations when they were compared temporally. The incidence rate of C. glabrata
in Atlanta from 1992 to 1993 was only 0.96/100,000 (10
). Preliminary analysis showed that in 2008 the incidence rate in Atlanta was 3.9/100,000 (2
). It is interesting to note that the large change in the C. glabrata
population structure in Atlanta also correlated with an increased incidence rate. While there are multiple factors that contribute to an increased incidence rate, it is reasonable to speculate that changes in the population structure of the organism, perhaps to better fill an available niche, played a contributing role. Knowledge of the population genetic structure of the various C. glabrata
populations within the ongoing candidemia surveillance will contribute significantly to our further analysis of incidence rates, patient outcomes, and antifungal resistance within these populations. Research to better understand these relationships is ongoing.