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OBJECTIVES/GOALS: The Oregon Clinical and Translational Research Institute (OCTRI) Clinical Research Navigator program provides a single point of entry for clinical and translational research services, support, advice and guidance. We provide data to illustrate the Navigator model at OHSU and examine continued opportunities to optimize research resources. METHODS/STUDY POPULATION: Requests and activities performed by the OCTRI Navigator program, staffed by 3 FTE (2 Assistant Navigators and 1 Assistant Director) were analyzed. Navigator receives requests through multiple methods: a digital form (REDCap®), email, phone calls. Requests for services and support include focused need for a core or a broad request for multiple services for start-up: informatics, the clinical and translational research center, regulatory knowledge and support, recruitment, qualitative methods, community research, biostatistics or broad consultations. Requests are tracked in SPARCRequest. Navigator also supports wayfinding to institutional resources outside of the CTSA, matchmaking for sponsors seeking investigators, and serves as a connector and facilitator across programs. RESULTS/ANTICIPATED RESULTS: OCTRI Clinical Research Navigator triaged an average of 964 research requests for 613 projects with 388 unique investigators annually between 2018-2022. Navigator also fields more than 80 calls each year that are unrelated to CTSA projects. Project requests are examined to illustrate trends in projects requesting multiple services and display how Navigator simplifies project intake and connects researchers to resources they may have not recognized they needed. Project attributes including funding type and funding status are included in this review. DISCUSSION/SIGNIFICANCE: CTSA resources are essential to the infrastructure available to researchers. While absolute numbers of requests provide little insight into the impact each CTSA hub may have, the timing and clustering trends of projects with multiple program requests shows how a combination of technology and experienced staff can efficiently support researchers.

ABSTRACT: Objectives: This study aimed to sequence, assemble, and annotate three plasmids (two IncN and one IncI1) carrying the blaCTX-M-1 gene and assess their transferability rates between homologous and heterologous serovars and/or species of bacteria. Methods: First, the plasmids were sequenced, assembled, and annotated. They were then transferred from three donor strains (Escherichia coli/IncN, S. Heidelberg/IncN, and S. Heidelberg/IncI1) into nine recipient strains (S. Enteritidis, S. Heidelberg, S. Saintpaul, S. Cero, S. Infantis, S. Braenderup, E. coli 50, and E. coli 2010). The blaCTX-M-1 gene polymerase chain reaction (PCR), plasmid isolation, and antimicrobial susceptibility testing were used on the transconjugants to confirm the successful transfer of extended-spectrum beta lactamase (EBSL) plasmids into the recipient strains. Results: Both IncN plasmids were 42,407 bp in size and showed >99.4% similarity to the S. Bredeney pET1.2-IncN (GenBank accession CP043224.1), whereas the IncI1 plasmid was 107,635 bp in size and demonstrated >99.9% similarity to the E. coli pCOV33 plasmid (GenBank accession MG649046.1). Successful plasmid transfer was observed between donor ​E. coli (IncN) and all recipient strains except for E. coli 50 and between donor S. Heidelberg (IncN) and all recipient strains. Successful plasmid transfer was also observed between S. Heidelberg (IncI1) and E. coli 50. Conclusion: Transfer of the bla CTX-M-1 encoding IncN and IncI1 plasmids via conjugation is possible and yet occurs at different frequencies depending on the donor strain of bacteria, with S. Heidelberg (IncN) having the highest donor-dependent transfer frequency, followed by E. coli 9079 (IncN) and S. Heidelberg (IncI1).

ABSTRACT: In this study, we conducted a longitudinal sampling of peanut hull-based litter from a farm under a “no antibiotics ever” program. Our objective was to determine broiler management practices and environmental factors that are associated with the occurrence of food-borne pathogens (Salmonella and Campylobacter) and the abundance of commensal bacteria (Escherichia coli, Enterococcus spp., and Staphylococcus spp.). Litter (n = 288) was collected from 4 broiler houses over three consecutive flocks, starting with a complete house cleanout and fresh peanut hull. Litter was sampled at the beginning of each grow-out cycle and at the end of the cycle. Logistic and linear regression models were used to model the relationships between pathogen prevalence, commensal abundance and management practices, and environmental factors. The number of flocks raised on litter, grow-out period, broiler house, litter pH, litter moisture, and house temperature were associated with the prevalence of pathogens and the abundance of commensal bacteria in litter. The final logistic model for pathogens showed that a higher probability of detecting Salmonella in litter was associated with the number of flocks raised on litter and the grow-out period. A higher probability of detecting Campylobacter in litter was associated with the number of flocks raised on litter, broiler house and the sections of the house, and the pH of litter. Our results suggest that management practices and environmental factors affect Salmonella and Campylobacter differently and suggest that each pathogen will require its own tailored intervention to stop their persistence in broiler litter.

Abstract Effective management of wildlife populations threatened by disease requires accurate predictions about the consequences of intervention. However, generating such predictions is challenging, especially for organisms with complex life histories that are also threatened by climate change, such as montane amphibians. Cascades frogs (Rana cascadae) in northern California have experienced dramatic declines associated with the fungal pathogen Batrachochytrium dendrobatidis (Bd), and remnant populations are also threatened by changing climate conditions. We evaluated the population‐level impacts of treating Cascades frog metamorphs with the antifungal chemical itraconazole using a field experiment and population simulations. We explored the influence of larval habitat on these treatment effects by including metamorphs from different larval habitat types. We found that frogs treated with itraconazole were more than four times more likely to survive their first winter than untreated controls and had reduced Bd infection intensity compared to other surviving frogs from the same cohort in the following year. We also found an effect of larval habitat type on Bd infection in recently metamorphosed frogs, with the lowest levels of infection occurring in frogs emerging from larval habitats that tend to be intermediate in temperature and drying rate. Applying the differential apparent overwinter survival of treated and untreated metamorphs to population projections suggests that intermittent antifungal treatment of metamorphs has the potential to restore population viability. Our results indicate that in situ treatment of individual hosts may be a useful component of a comprehensive management strategy to reduce the risk of pathogen‐mediated population declines and extirpations.

Surgical antimicrobial prophylaxis is indicated when performing contaminated surgeries, when specific surgical implants are placed, and for prolonged surgical procedures. Unnecessary prophylactic antibiotics are often utilized for macaque surgeries, despite medical and veterinary guidelines. In this study we compared complication rates in macaques receiving peripheral lymph node (PLN) and laparoscopic biopsies, with and without antimicrobial prophylaxis. A majority of animals were SIV or SHIV infected at the time of surgery, so we also compared post-operative complication rates based on infection status. We found no significant difference in PLN biopsy complication rates for animals that received antimicrobial prophylaxis versus those that did not. Animals who underwent laparoscopic procedures and received prophylactic antibiotics had a higher complication rate than those who did not receive them. Complication rates did not differ significantly for SIV/SHIV infected versus uninfected animals for both laparoscopic biopsy procedures and PLN biopsy procedures. SIV/SHIV infected animals that underwent PLN biopsies had no significant difference in complication rates with and without antimicrobial prophylaxis, and SIV/SHIV infected animals receiving prophylactic antibiotics for laparoscopic biopsies had a higher complication rate than those that did not. This study suggests that perioperative prophylactic antibiotics have no role in the management of SIV/SHIV-infected and uninfected macaques undergoing clean, minimally invasive surgeries. Additionally, we recommend eliminating unnecessary antibiotic use in study animals due to their potential confounding impacts on research models and their potential to promote antimicrobial resistance.

ABSTRACT The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.

Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha−1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.

The use of educational digital games as supplemental tools to course instruction materials has increased over the last several decades and especially since the COVID-19 pandemic. Though these types of instructional games have been employed in the majority of STEM disciplines, less is known about how diverse populations of students interpret and define the value of these games towards achieving academic and professional pursuits. A mixed-method sequential exploratory research design method that was framed on the Technology Acceptance Model, Game-Based Learning Theory and Expectancy Value Theory was used to examine how 201 students perceived the usefulness of an intuitive education game that was designed to teach engineering mechanics used in designing civil structures. We found that students had different expectations of educational digital games than games designed for entertainment used outside of classroom environments. Several students thought that the ability to design their own structures and observe structure failure in real-time was a valuable asset in understanding how truss structures responded to physical loading conditions. However, few students thought the educational game would be useful for exam (14/26) or job interview (19/26) preparation. Students associated more value with engineering games that illustrate course content and mathematical calculations used in STEM courses than those that do not include these elements.

Since the onset of land application of poultry litter, transportation of microorganisms, antibiotics, and disinfectants to new locations has occurred. While some studies provide evidence that antimicrobial resistance (AMR), an evolutionary phenomenon, could be influenced by animal production systems, other research suggests AMR originates in the environment from non-anthropogenic sources. In addition, AMR impacts the effective prevention and treatment of poultry illnesses and is increasingly a threat to global public health. Therefore, there is a need to understand the dissemination of AMR genes to the environment, particularly those directly relevant to animal health using the One Health Approach. This review focuses on the potential movement of resistance genes to the soil via land application of poultry litter. Additionally, we highlight impacts of AMR on microbial ecology and explore hypotheses explaining gene movement pathways from U.S. broiler operations to the environment. Current approaches for decreasing antibiotic use in U.S. poultry operations are also described in this review.

Low-magnitude, high-frequency vibration has stimulated osteogenesis in mesenchymal stem cells when these cells were cultured in certain types of three-dimensional environments. However, results of osteogenesis are conflicting with some reports showing no effect of vibration at all. A large number of vibration studies using three-dimensional scaffolds employ scaffolds derived from natural sources. Since these natural sources potentially have inherent biochemical and microarchitectural cues, we explored the effect of low-magnitude, high-frequency vibration at low, medium, and high accelerations when mesenchymal stem cells were encapsulated in poly(ethylene glycol) diacrylate microspheres. Low and medium accelerations enhanced osteogenesis in mesenchymal stem cells while high accelerations inhibited it. These studies demonstrate that the isolated effect of vibration alone induces osteogenesis.

In this study, we investigated gene expression changes in three bacterial strains (Escherichia coli C3000, Escherichia coli O157:H7 B6914, and Enterococcus faecalis ATCC 29212), commonly used as indicators of water quality and as control strains in clinical, food, and water microbiology laboratories. Bacterial transcriptome responses from pure cultures were monitored in microcosms containing water amended with manure-derived dissolved organic matter (DOM), previously exposed to simulated sunlight for 12 h. We used RNA sequencing (RNA-seq) and quantitative real-time reverse transcriptase (qRT-PCR) to compare differentially expressed temporal transcripts between bacteria incubated in microcosms containing sunlight irradiated and non-irradiated DOM, for up to 24 h. In addition, we used whole genome sequencing simultaneously with RNA-seq to identify single nucleotide variants (SNV) acquired in bacterial populations during incubation. These results indicate that E. coli and E. faecalis have different mechanisms for removal of reactive oxygen species (ROS) produced from irradiated DOM. They are also able to produce micromolar concentrations of H2O2 from non-irradiated DOM, that should be detrimental to other bacteria present in the environment. Notably, this study provides an assessment of the role of two conjugative plasmids carried by the E. faecalis and highlights the differences in the overall survival dynamics of environmentally-relevant bacteria in the presence of naturally-produced ROS.

Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.

Objective: To investigate the role of a dedicated service corridor in intensive care unit (ICU) noise control and staff stress and satisfaction., Background: Shared corridors immediately adjacent to patient rooms are generally noisy due to a variety of activities, including service deliveries and pickups. The strategy of providing a dedicated service corridor is thought to reduce noise for patient care, but the extent to which it actually contributes to noise reduction in the patient care environment and in turn improves staff performance has not been previously documented., Methods: A before-and-after comparison was conducted in an adult cardiac ICU. The ICU was relocated from a traditional hospital environment to a new addition with a dedicated service corridor. A total of 118 nursing staff participated in the surveys regarding pre-move and post-move environmental comfort, stress, and satisfaction in the previous and new units. Acoustical measures of noise within the new ICU and a control environment of the previous unit were collected during four work days, along with on-site observations of corridor traffic., Results: Independent and paired sample t-tests of survey data showed that the perceived noise level was lower and staff reported less stress and more satisfaction in the new ICU (p < 0.01). Analyses of acoustical data confirmed that the new ICU was significantly quieter (p < 0.02). Observations revealed how the service corridor impacted patient care services and traffic., Conclusions: The addition of a dedicated service corridor works in the new unit for improving noise control and staff stress and satisfaction., Keywords: Critical care/intensive care, noise, satisfaction, staff, work environment.