Validation of the Modified Clear Safety Salmonella for Detection of Salmonella enterica in Selected Poultry and Pet Food Matrixes and on Stainless Steel: AOAC Performance Tested MethodSM 111802.

BACKGROUND: The Clear Safety Salmonella method was modified to improve sample preparation, PCR reagents, library preparation, flow cell quality control, library loading mix, priming mix, and sequencing kit reagents and steps. OBJECTIVE: To evaluate the modified Clear Safety Salmonella method (manual and automated) via independent and method developer validation studies according to current AOAC INTERNATIONAL Validation Guidelines. METHOD: Performance of the modified Clear Safety Salmonella method (manual and automated) was assessed for selectivity (using 105 inclusive and 30 exclusive strains), probability of detection in matrixes, product consistency, stability, and robustness. The modified Clear Safety Salmonella method was compared with the appropriate reference method for Salmonella detection on 4 inch × 4 inch stainless steel environmental surfaces, and in chicken carcass rinse (30 mL), raw ground chicken (375 g), dry pet food (375 g), and ready-to-eat deli turkey breast (375 g). RESULTS: The modified Clear Safety Salmonella method (manual and automated) demonstrated no statistically significant differences between the candidate and reference method probability of detection or between the presumptive and confirmed results for all target food matrixes and the stainless steel surface. Additionally, the modified method (manual and automated) detected all 105 inclusivity organisms and excluded all 30 exclusivity organisms. The product consistency and kit stability studies showed no statistical differences between lots or over the term of the kit's shelf life. In robustness studies, changes in enrichment time, diluted sample volume, and sample volume for PCR did not show any statistical difference in terms of assay performance. CONCLUSIONS: The modified Clear Safety Salmonella method (both manual and automated) is statistically equivalent to or better than the reference methods. HIGHLIGHTS: The Clear Safety Salmonella method utilizes PCR amplification and targeted next-generation sequencing technology to selectively detect Salmonella enterica.

Validation of the Clear Safety Listeria Method for Detection of Listeria Species in Hot Dogs and on Environmental Surface Matrixes: AOAC Performance Tested MethodSM 091901.

BACKGROUND: The Clear Safety Listeria method utilizes polymerase chain reaction (PCR) amplification and targeted next-generation sequencing technology to detect Listeria species (L. monocytogenes, L. innocua, L. ivanovii, L. marthii, L. grayi, L. welshimeri, and L. seeligeri) in hot dogs and on selected environmental surfaces. OBJECTIVE: The aim was to validate the candidate method according to current AOAC guidelines. METHOD: The candidate method was compared to the reference method for hot dogs and the environmental surfaces. The method was also evaluated for inclusivity and exclusivity using 50 inclusivity strains and 30 exclusivity strains for each reported target. Product consistency and stability was tested and robustness was evaluated with changes in enrichment temperature, volume of sample treatment, and aliquot volume for PCR. RESULTS: The candidate method demonstrated no statistically significant differences using the probability of detection model between candidate and reference methods or between presumptive and confirmed results for all environmental surfaces and hot dogs. Additionally, the candidate method detected all inclusivity organisms and excluded all exclusivity organisms for each reported target. Product lots were shown to be consistent and data supported the kit's shelf life. Finally, the robustness study demonstrated no statistical differences when the volume of sample or the aliquot volume for PCR was altered. Increasing the incubation temperature to 37 ± 1 °C resulted in greater recovery of L. monocytogenes as compared to 35 ± 1 °C and 30 ± 1 °C. CONCLUSIONS: The Clear Safety Listeria method is statistically equivalent to the reference methods for the detection of L. monocytogenes and Listeria spp. in hot dogs and on selected environmental surfaces. HIGHLIGHTS: The Clear Safety Listeria method is an automated, highthroughput NGS-based method capable of detecting Listeria species in the hot dog and environmental samples within 28h.

Evaluation: A Qualitative Pilot Study of Novel Information Technology Infrastructure to Communicate Genetic Variant Updates.

BACKGROUND: Partners HealthCare Personalized Medicine developed GeneInsight Clinic (GIC), a tool designed to communicate updated variant information from laboratory geneticists to treating clinicians through automated alerts, categorized by level of variant interpretation change. OBJECTIVES: The study aimed to evaluate feedback from the initial users of the GIC, including the advantages and challenges to receiving this variant information and using this technology at the point of care. METHODS: Healthcare professionals from two clinics that ordered genetic testing for cardiomyopathy and related disorders were invited to participate in one-hour semi-structured interviews and/ or a one-hour focus group. Using a Grounded Theory approach, transcript concepts were coded and organized into themes. RESULTS: Two genetic counselors and two physicians from two treatment clinics participated in individual interviews. Focus group participants included one genetic counselor and four physicians. Analysis resulted in 8 major themes related to structuring and communicating variant knowledge, GIC's impact on the clinic, and suggestions for improvements. The interview analysis identified longitudinal patient care, family data, and growth in genetic testing content as potential challenges to optimization of the GIC infrastructure. DISCUSSION: Participants agreed that GIC implementation increased efficiency and effectiveness of the clinic through increased access to genetic variant information at the point of care. CONCLUSION: Development of information technology (IT) infrastructure to aid in the organization and management of genetic variant knowledge will be critical as the genetic field moves towards whole exome and whole genome sequencing. Findings from this study could be applied to future development of IT support for genetic variant knowledge management that would serve to improve clinicians' ability to manage and care for patients.

Everolimus and zoledronic acid in patients with renal cell carcinoma with bone metastases: a randomized first-line phase II trial.

BACKGROUND: Bone metastases from renal cell carcinoma (RCC) are a major cause of morbidity. Post hoc analysis has suggested that bone turnover markers can identify patients at risk of skeletal-related events (SREs) among those receiving zoledronic acid. This study sought to evaluate the effect on bone metastases of everolimus alone compared with everolimus plus zoledronic acid. PATIENTS AND METHODS: Thirty treatment-naive patients with RCC and ≥ 1 bone metastases were randomized 1:1 to everolimus (10 mg daily) versus everolimus plus zoledronic acid (4 mg intravenously 4-weekly). Bone-specific assessments were performed at baseline and at weeks 1, 4, 8, and 12. Treatment was continued on allocated arm until progression per RECIST 1.1 (Response Evaluation Criteria in Solid Tumors, version 1.1). The primary outcome measure was urine N-telopeptide (uNTX) level, with secondary measures of plasma C-telopeptide (CTX), quality of life (Functional Assessment of Cancer Therapy-Bone Pain [FACT-BP], Brief Pain Inventory [BPI]), progression-free survival (PFS), SREs, and safety. RESULTS: After 12 weeks, reduction in mean uNTX and CTX on everolimus plus zoledronic acid relative to everolimus was 68.4% (95% CI, 60.1%-74.9%; P < .0001) and 76.2% (95% CI, 67.3%-82.7%; P < .0001), respectively. There was no evidence of a difference for FACT-BP (P = .5), but evidence was favorable for BPI Severity (P = .05) and BPI Interference (P = .06). Median PFS was 7.5 months (95% CI, 3.4-11.2) on everolimus plus zoledronic acid and 5.4 months (95% CI, 3.2-6.3) on everolimus (P = .009). Median time to first SRE was 9.6 months (95% CI, 4.3-15.5) on everolimus plus zoledronic acid and 5.2 months (95% CI, 1.6-8.2) on everolimus (P = .03). CONCLUSION: In this RCC population, the addition of zoledronic acid to everolimus significantly reduced bone resorption markers and may prolong tumor control.

Potential Interactions between Salmonella enterica and Ralstonia solanacearum in tomato plants.

Over the past decade, the Eastern Shore of Virginia (ESV) has been implicated in at least four outbreaks of salmonellosis associated with tomato, all originating from the same serovar, Salmonella enterica serovar Newport. In addition to Salmonella Newport contamination, the devastating plant disease bacterial wilt, caused by the phytopathogen Ralstonia solanacearum, threatens the sustainability of ESV tomato production. Bacterial wilt is present in most ESV tomato fields and causes devastating yield losses each year. Although the connection between bacterial wilt and tomato-related salmonellosis outbreaks in ESV is of interest, the relationship between the two pathogens has never been investigated. In this study, tomato plants were root dip inoculated with one of four treatments: (i) 8 log CFU of Salmonella Newport per ml, (ii) 5 log CFU of R. solanacearum per ml, (iii) a coinoculation of 8 log CFU of Salmonella Newport per ml plus 5 log CFU of R. solanacearum per ml, and (iv) sterile water as control. Leaf, stem, and fruit samples were collected at the early-green-fruit stage, and S. enterica contamination in the internal tissues was detected. S. enterica was recovered in 1.4 and 2.9% of leaf samples from plants inoculated with Salmonella Newport only and from plants coinoculated with Salmonella Newport plus R. solanacearum, respectively. S. enterica was recovered from 1.7 and 3.5% of fruit samples from plants inoculated with Salmonella Newport only and from plants coinoculated with Salmonella Newport plus R. solanacearum, respectively. There were significantly more stem samples from plants coinoculated with Salmonella Newport plus R. solanacearum that were positive for S. enterica (18.6%) than stem samples collected from plants inoculated with Salmonella Newport only (5.7%). Results suggested that R. solanacearum could influence S. enterica survival and transportation throughout the internal tissues of tomato plants.

How physicians document outpatient visit notes in an electronic health record.

BACKGROUND: Clinical documentation, an essential process within electronic health records (EHRs), takes a significant amount of clinician time. How best to optimize documentation methods to deliver effective care remains unclear. OBJECTIVE: We evaluated whether EHR visit note documentation method was influenced by physician or practice characteristics, and the association of physician satisfaction with an EHR notes module. MEASUREMENTS: We surveyed primary care physicians (PCPs) and specialists, and used EHR and provider data to perform a multinomial logistic regression of visit notes from 2008. We measured physician documentation method use and satisfaction with an EHR notes module and determined the relationship between method and physician and practice characteristics. RESULTS: Of 1088 physicians, 85% used a single method to document the majority of their visits. PCPs predominantly documented using templates (60%) compared to 34% of specialists, while 38% of specialists predominantly dictated. Physicians affiliated with academic medical centers (OR 1.96, CI (1.23, 3.12)), based at a hospital (OR 1.57, 95% CI (1.04, 2.36)) and using the EHR for longer (OR 1.13, 95% CI (1.03, 1.25)) were more likely to dictate than use templates. Most physicians of 383 survey responders were satisfied with the EHR notes module, regardless of their preferred documentation method. CONCLUSIONS: Physicians predominantly utilized a single method of visit note documentation and were satisfied with their approach, but the approaches they chose varied. Demographic characteristics were associated with preferred documentation method. Further research should focus on why variation exists, and the quality of the documentation resulting from different methods used.

Usability of a novel clinician interface for genetic results.

The complexity and rapid growth of genetic data demand investment in information technology to support effective use of this information. Creating infrastructure to communicate genetic information to healthcare providers and enable them to manage that data can positively affect a patient's care in many ways. However, genetic data are complex and present many challenges. We report on the usability of a novel application designed to assist providers in receiving and managing a patient's genetic profile, including ongoing updated interpretations of the genetic variants in those patients. Because these interpretations are constantly evolving, managing them represents a challenge. We conducted usability tests with potential users of this application and reported findings to the application development team, many of which were addressed in subsequent versions. Clinicians were excited about the value this tool provides in pushing out variant updates to providers and overall gave the application high usability ratings, but had some difficulty interpreting elements of the interface. Many issues identified required relatively little development effort to fix suggesting that consistently incorporating this type of analysis in the development process can be highly beneficial. For genetic decision support applications, our findings suggest the importance of designing a system that can deliver the most current knowledge and highlight the significance of new genetic information for clinical care. Our results demonstrate that using a development and design process that is user focused helped optimize the value of this application for personalized medicine.

Analysis of user behavior in accessing electronic medical record systems in emergency departments.

Electronic patient tracking and records systems in emergency departments often connect to hospital information systems, ambulatory patient records and ancillary systems. The networked systems may not be fully interoperable and clinicians need to access data through different interfaces. This study was conducted to describe the interactive behavior of clinicians working with partially interoperable clinical information systems. We performed 78 hours of observation at two emergency departments, shadowing five physicians, ten nurses and four administrative staff. Actions related to viewing or recording data in any system or on paper were recorded. Collected data were compared along clinical roles and contrasted with findings across the two hospital sites. The findings suggest that differences in the levels of interoperability may affect the ways physicians and nurses interact with the systems. When tradeoffs in functionality are necessary for connecting ancillary systems, the effects on clinicians and staff need to be considered.