The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

Objective: Tamoxifen (TAM) lowers breast cancer recurrence by 40-50% with evidence of individual variability in responsiveness. A ≥10% decrease in mammography-determined breast density (BD) after 12–18 months of TAM use has been associated with clinical benefit. Early determination of changes in BD may offer a strategy to tailor hormone therapy in non-responders; for responders, it may encourage adherence. Fat-water decomposition MRI (FWD-MRI) is an accurate and fast (< 5 minutes) method for measuring BD without ionizing radiation or contrast agent. Here, we examined whether change in FWD-MRI-derived BD predicts decrease in BD at earlier time points than observable with a 12-month measure of BD. Methods: The study population included a subset of 44 pre- and post-menopausal women receiving TAM for treatment of early-stage breast cancer or prevention who were enrolled in a randomized, placebo-controlled trial of diindolylmethane. Eligibility for this analysis included participants with FWD-MRI scans at baseline, 6 and 12 months. Median time on TAM at baseline was 13 months (IQR, 5–26 months). All MRI images were acquired on a 1.5T GE Signa NV-CV/i scanner. Automated breast segmentation was performed using MATLAB software and validated against manual ROI drawings. MRI-based BD was calculated as the ratio of breast voxels with <80% apparent fat fraction (Fra80) over the entire breast, a measure previously shown by our group to be highly correlated with mammography-derived BD. For 40 participants, the unaffected, contralateral breast was analyzed. For 4 patients with two unaffected breasts, BD data from the left breast were analyzed. Change in BD was conservatively defined as > 2 times the test-retest variability of Fra80 (0.032). McNemar's test was used to test the association between change from baseline to 6 months and change from baseline to 12 months. Results and Discussion: At 12 months, 15 (34%) participants had a decrease in BD, whereas 29 (66%) remained unchanged or increased. Of these 29, 28 also had no decrease at 6 months (specificity = 97%), and 9 of the 15 women who showed a decrease at 12 months had a decrease at 6 months (sensitivity = 60%; McNemar's test, P = 0.06). Conversely, for those women with a measured decrease in BD from baseline to 6 months, 9 of 10 had a measured decrease at 12 months. A study limitation is inclusion of participants on TAM for varying duration as the greatest change in BD likely would have occurred earlier. Ongoing efforts will focus on FWD-MRI for measures of change in BD in patients initiating TAM. Conclusion: Use of the specified cut point would fail to detect a decrease in BD at 12 months in 40% of women. However, a decrease in BD from baseline to 6 months was highly associated with decrease from baseline to 12 months and in some women may be useful as an early biomarker of effect. Ongoing effort is needed to determine the impact of factors such as baseline BD, menopausal status, and time on TAM in misclassification of BD change using the 6-month measure. Acknowledgement: NIH grants CA149417, CA161534.Objective: Tamoxifen (TAM) lowers breast cancer recurrence by 40-50% with evidence of individual variability in responsiveness. A ≥10% decrease in mammography-determined breast density (BD) after 12–18 months of TAM use has been associated with clinical benefit. Early determination of changes in BD may offer a strategy to tailor hormone therapy in non-responders; for responders, it may encourage adherence. Fat-water decomposition MRI (FWD-MRI) is an accurate and fast (< 5 minutes) method for measuring BD without ionizing radiation or contrast agent. Here, we examined whether change in FWD-MRI-derived BD predicts decrease in BD at earlier time points than observable with a 12-month measure of BD. Methods: The study population included a subset of 44 pre- and post-menopausal women receiving TAM for treatment of early-stage breast cancer or prevention who were enrolled in a randomized, placebo-controlled trial of diindolylmethane. Eligibility for this analysis included participants with FWD-MRI scans at baseline, 6 and 12 months. Median time on TAM at baseline was 13 months (IQR, 5–26 months). All MRI images were acquired on a 1.5T GE Signa NV-CV/i scanner. Automated breast segmentation was performed using MATLAB software and validated against manual ROI drawings. MRI-based BD was calculated as the ratio of breast voxels with <80% apparent fat fraction (Fra80) over the entire breast, a measure previously shown by our group to be highly correlated with mammography-derived BD. For 40 participants, the unaffected, contralateral breast was analyzed. For 4 patients with two unaffected breasts, BD data from the left breast were analyzed. Change in BD was conservatively defined as > 2 times the test-retest variability of Fra80 (0.032). McNemar's test was used to test the association between change from baseline to 6 months and change from baseline to 12 months. Results and Discussion: At 12 months, 15 (34%) participants had a decrease in BD, whereas 29 (66%) remained unchanged or increased. Of these 29, 28 also had no decrease at 6 months (specificity = 97%), and 9 of the 15 women who showed a decrease at 12 months had a decrease at 6 months (sensitivity = 60%; McNemar's test, P = 0.06). Conversely, for those women with a measured decrease in BD from baseline to 6 months, 9 of 10 had a measured decrease at 12 months. A study limitation is inclusion of participants on TAM for varying duration as the greatest change in BD likely would have occurred earlier. Ongoing efforts will focus on FWD-MRI for measures of change in BD in patients initiating TAM. Conclusion: Use of the specified cut point would fail to detect a decrease in BD at 12 months in 40% of women. However, a decrease in BD from baseline to 6 months was highly associated with decrease from baseline to 12 months and in some women may be useful as an early biomarker of effect. Ongoing effort is needed to determine the impact of factors such as baseline BD, menopausal status, and time on TAM in misclassification of BD change using the 6-month measure. Acknowledgement: NIH grants CA149417, CA161534. Citation Format: Ding J, Thompson PA, Wertheim BC, Roe DJ, Marron MT, Altbach MI, Galons J-P, Wang F, Thomson CA, Huang C, Stopeck A. Breast density change at 6 months is associated with change at 12 months as measured by fat-water decomposition MRI in women on tamoxifen [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-19.

Objective Breast density(BD) is a measure of the distribution of variable tissue types within the breast and higher BD has been shown to positively correlate with breast cancer risk. As such, the accurate measurement of BD has become a priority for risk assessment and for evaluating the effects of prevention strategies aimed at reducing BD. Mammography(MG) is the most common method of BD determination but is limited by the exposure to ionizing radiation, particularly for studies requiring repeated measures. BD derived from fat-water decomposition magnetic resonance imaging(FWMRI-BD) has been proposed as an alternative, safe, and quantitative method for BD. To optimize its use, we developed a new FWMRI-BD that is automated, more accurate and reliable. In this study, we compare our automated method to digital MG and a previous reported algorithm for MRI derived BD. Methods From a completed prevention trial, 42 pre- and post-menopausal patients receiving tamoxifen therapy for early stage breast cancer or as primary chemoprevention were identified. Patients had undergone prior digital MG within 6 months from the date of MRI scan and MG-BD was calculated using a well-established method(Cumulus). MRI scans were performed on a 1.5T GE Signa NV-CV/i scanner using an axial radial IDEAL-GRASE sequence to generate quantitative fat fraction maps of the entire breast. Total acquisition time was < 5 min and automated breast segmentation was applied to all scans. Only the contralateral, unaffected breast was analyzed. Pearson correlation analysis compared BD as measured by MG(range 0-100%) and FWMRI based methods. BD by FWMRI was initially calculated as the ratio of breast voxels with<80% apparent fat fraction(Fra80). Fra80 had been previously shown by our group to correlate with MG-BD(Spearman ρ=0.86, p<0.001). Here, BD was calculated using a new algorithm(FraG+W) that accounts for the total amount of fibroglandular tissue and water content in the breast after correction for fat-water signal intensity bias and fat-water signal shine-through. Reliability of FWMRI measurements was tested in 24 repeated scans from 9 patients and evaluated using intra-class correlation(ICC) analysis. Results Table 1 shows the correlation and reliability analysis results between MG-BD and FWMRI-BD. Both FWMRI-BD measures(Fra80 and FraG+W) were strongly correlated with MG-BD. More importantly, they exhibit superior test-retest reliability(ICC>0.98) compared to MG-BD values from the literature(reported ICC range 0.91-0.95). FraG+W showed improvement over Fra80 in all measures tested including correlation to MG-BD, dynamic range, standard errors and ICC. Table 1. Accuracy and Reliability of the FWMRI-BD measuresFWMRI-BDFra80FraG+WPearson correlation coefficient* with MG-BDR=0.86R=0.94Test-retest reliabilitystandard error0.02300.0134dynamic range0.0902 – 0.65370.0736 – 0.6588standard error/ dynamic range4.1%2.3%ICC [95% confidence interval]0.985 [0.966,0.993]0.990 [0.976,0.995]* All P-values < 1e-10 Conclusion The refined and automated FWMRI-BD that quantifies the entire fibroglandular and water content of the breast(FraG+W) strongly correlates with MG-BD and is more accurate and reliable than previous FWMRI-BD method. Acknowledgement NIH grants CA149417, CA161534. Citation Format: Ding J, Thompson PA, Gao Y, Marron MT, Wertheim BC, Altbach MI, Galons J-P, Roe DJ, Wang F, Maskarinec G, Thomson CA, Stopeck A, Huang C. Accurate and reliable automated breast density measurements with no ionizing radiation using fat-water decomposition MRI [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-02-03.

We aimed to evaluate post-treatment inflammatory biomarkers, namely C-reactive protein (CRP), interleukin-6 (IL6), monocytes chemoattractant protein-1 (MCP1), leptin and adiponectin, in relation to overall survival (OS) in stage II-III colorectal cancer (CRC) patients. Methods: Participants were incident, invasive CRC cases who were 22-74 years of age, diagnosed between 1997-2008 from the populationbased Seattle Colon Cancer Family Registry. We included stage II-III cases who were at the greatest risk for disease progression. Further restriction to 308 participants with a blood draw 1-3 years after diagnosis was made to preclude acute treatment effects. We measured concentrations of all five markers in EDTA-plasma samples using the Meso Scale Discovery immunoassays. Biomarker levels were logtransformed to ensure normality. We also divided patients into sexspecific quartiles for each marker to test for a dose-effect of a biomarker on disease progression. Mortality and cause of death were assessed through linkage to the National Death Index. We used Cox proportional hazard regression to estimate hazard ratios (HR) and 95% confidence intervals (CI) for associations of post-treatment inflammatory markers with OS. HRs were adjusted for potential confounders selected a priori, including age at blood draw, sex, body mass index, plasma storage time, the time between diagnosis and blood draw, and stage at diagnosis. Results: Elevated CRP levels were associated with poorer OS (HR ¼ 1.32 per unit increase of log-CRP, 95% CI ¼ 1.13-1.55). For circulating IL6, a dose-response relationship with survival was evident: compared with the lowest quartile of IL6, the 2nd, 3rd and 4th quartiles were significantly associated with OS, with HRs (95% CIs) of 2.72 (1.42-5.21), 4.23 (2.24-7.99), and 6.80 (3.56-12.96) respectively (p for trend < 0.0001). For MCP1, we observed a 2-fold increase in the risk of overall mortality per unit increase in log-MCP1 (HR ¼ 2.17, 95% CI ¼ 1.39-3.39). Circulating levels of leptin and adiponectin were not significantly associated with OS. Conclusions: Circulating inflammatory markers, specifically CRP, IL6, and MCP1, are prognostic markers in stage II/III CRC patients and should be considered for incorporation into studies of CRC outcomes.