Browsing by Author "Jiang, Ying"
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Item Fungal empyema thoracis in cancer patients(Elsevier, 2016) Nigo, Masayuki; Vial, Macarena; Munita, José; Jiang, Ying; Tarrand, Jeffrey; Jimenez, Carlos; Kontoyiannis, DimitriosOBJECTIVES: Fungal empyema thoracis (FET) is a rare life-threatening infection. We sought to describe the clinical characteristics of FET in a large academic cancer center. METHODS: We conducted a retrospective chart review of all cancer patients who had a fungal isolate from the pleural fluid culture between 1/2005 and 8/2013. RESULTS: A total of 106 fungal isolates were identified in 97 patients. Yeasts accounted for 62% of the isolates whereas 38% were identified as molds. The most frequent pathogens were Candida spp. (58%) and Aspergillus spp. (12%). All patients with Aspergillus and 83% with Candida met criteria for proven fungal disease. Compared to the Aspergillus group, Candida FET was associated with recent abdominal or thoracic surgical procedures (44% vs. 0%, p = 0.01). Overall, 6-week mortality was high, with no significant differences between Candida and Aspergillus (31% vs. 45%, respectively [p = 0.48]). Only 1 out of 11 patients with uncommon molds died at 6 weeks, despite only 2 of them received appropriate antifungal therapy. CONCLUSIONS: Development of FET carries a high mortality in cancer patients. A history of a recent surgical procedure is a risk factor for FET due to Candida. Isolation of uncommon molds is likely to represent a contamination of the pleural fluid.Item Whole genome sequencing accurately identifies resistance to extended spectrum β-lactams for major gram-negative bacterial pathogens(Oxford University Press, 2017) Shelburne, Samuel; Kim, Jiwoong; Munita, José; Sahasrabhojane, Pranoti; Shields, Ryan; Press, Ellen G; Li, Xiqi; Arias, Cesar; Cantarel, Brandi; Jiang, Ying; Kim, Min; Aitken, Samuel L.; Greenberg, DavidBACKGROUND: There is marked interest in using DNA based methods to detect antimicrobial resistance (AMR) with targeted polymerase chain reaction (PCR) approaches increasingly being incorporated into clinical care. Whole genome sequencing (WGS) could offer significant advantages over targeted PCR for AMR detection, particularly for species where mutations are major drivers of AMR. METHODS: Illumina MiSeq WGS and broth microdilution (BMD) assays were performed on 90 bloodstream isolates of the four most common gram-negative bacteria causing bloodstream infections in neutropenic patients. The WGS data, including both gene presence/absence and detection of mutations in an array of AMR relevant genes, were used to predict resistance to four β-lactams commonly used in the empiric treatment of neutropenic fever. The genotypic predictions were then compared to phenotypic resistance as determined by BMD and by commercial methods during routine patient care. RESULTS: Out of 133 putative instances of resistance to the β-lactams of interest identified by WGS, only 87 (65%) would have been detected by a typical PCR based approach. The sensitivity, specificity, positive and negative predictive values for WGS in predicting AMR were 0.87, 0.98, 0.97, and 0.91 respectively. Using broth microdilution as the gold standard, our genotypic resistance prediction approach had a significantly higher positive predictive value compared to minimum inhibitory concentrations generated by commercial methods (0.97 vs. 0.92, P = 0.025). CONCLUSIONS: These data demonstrate the potential feasibility of using WGS to guide antibiotic treatment decisions for patients with life-threatening infections for an array of medically important pathogens.