Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay.

Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available. Thus, we developed a real-time polymerase chain reaction (PCR) assay for testing environmental samples by modifying CocciDx, an assay validated for testing clinical specimens to facilitate coccidioidomycosis diagnosis. For this study, we collected soil samples from previously established locations of C. posadasii in Arizona and new locations in fall 2013 and spring 2014, and screened the extracted DNA with the new assay known as CocciEnv. To verify the presence of Coccidioides in soil using an alternate method, we employed next generation amplicon sequencing targeting the ITS2 region. Results show our modified assay, CocciEnv, is a rapid and robust method for detecting Coccidioides DNA in complex environmental samples. The ability to test a large number of soils for the presence of Coccidioides is a much-needed tool in the understanding of the ecology of the organism and epidemiology of the disease and will greatly improve our understanding of this human pathogen.

Transmission of methicillin-resistant Staphylococcus aureus infection through solid organ transplantation: confirmation via whole genome sequencing.

We describe two cases of donor-derived methicillin-resistant Staphylococcus aureus (MRSA) bacteremia that developed after transplantation of organs from a common donor who died from acute MRSA endocarditis. Both recipients developed recurrent MRSA infection despite appropriate antibiotic therapy, and required prolonged hospitalization and hospital readmission. Comparison of S. aureus whole genome sequence of DNA extracted from fixed donor tissue and recipients' isolates confirmed donor-derived transmission. Current guidelines emphasize the risk posed by donors with bacteremia from multidrug-resistant organisms. This investigation suggests that, particularly in the setting of donor endocarditis, even a standard course of prophylactic antibiotics may not be sufficient to prevent donor-derived infection.

Cottonwood hybridization affects tannin and nitrogen content of leaf litter and alters decomposition.

Cottonwoods are dominant riparian trees of the western United States and are known for their propensity to hybridize. We compared the decomposition of leaf litter from two species (Populus angustifolia and P. fremontii) and their hybrids. Three patterns were found. First, in one terrestrial and two aquatic experiments, decomposition varied twofold among tree types. Second, backcross hybrid leaves decomposed more slowly than those of either parent. Third, the variation in decomposition between F1 and backcross hybrids was as great as the variation between species. These results show significant differences in decomposition in a low-diversity system, where >80% of the leaf litter comes from just two species and their hybrids. Mechanistically, high concentrations of condensed tannins in leaves appear to inhibit decomposition (r 2=0.63). The initial condensed tannin concentration was high in narrowleaf leaves, low or undetectable in Fremont leaves, and intermediate in F1 hybrid leaves (additive inheritance). Backcross hybrids were high in condensed tannins and were not different from narrowleaf (dominant inheritance). Neither nitrogen (N) concentration nor the ratio of ash-free dry weight to N (a surrogate for carbon:nitrogen ratio) were significantly correlated with decomposition. The N content of leaf material at the end of each year's experiment was inversely correlated with rates of litter mass loss and varied 1.6- to 2.1-fold among tree classes. This result suggests that hybrids and their parental species are used differently by the microbial community.