Publications by Colleges and Departments (MSU - Bozeman)
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Item Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidenc(Frontiers Media SA, 2022-01) Pettygrove, Brian A.; Smith, Heidi J.; Pallister, Kyler B.; Voyich, Jovanka M.; Stewart, Philip S.; Parker, Albert E.The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a large imaging dataset consisting of 16 independent CLSM microscopy experiments was leveraged. These experiments were designed to study interactions between human neutrophils and single cells or aggregates of Staphylococcus aureus (S. aureus) during the initial stages of biofilm formation. Results suggest that in untreated control experiments, variability differed substantially between growth phases (i.e., lag or exponential). When studying the effect of an antimicrobial treatment (in this case, neutrophil challenge), regardless of the inoculation level or of growth phase, variability changed as a frown-shaped function of treatment efficacy (i.e., the reduction in biofilm surface coverage). These findings were used to predict the best experimental designs for future imaging studies of early biofilms by considering differing (i) numbers of independent experiments; (ii) numbers of fields of view (FOV) per experiment; and (iii) frame capture rates per hour. A spreadsheet capable of assessing any user-specified design is included that requires the expected mean log reduction and variance components from user-generated experimental results. The methodology outlined in this study can assist researchers in designing their CLSM studies of antimicrobial treatments with a high level of statistical confidence.Item Evaluation of the Antimicrobial Efficacy of N-Acetyl-l-Cysteine, Rhamnolipids, and Usnic Acid—Novel Approaches to Fight Food-Borne Pathogens(MDPI, 2021) Chlumsky, Ondrej; Smith, Heidi J.; Parker, Albert E.; Brileya, Kristen; Wilking, James N.; Purkrtova, Sabina; Michova, Hana; Ulbrich, Pavel; Viktorova, Jitka; Demnerova, KaterinaIn the food industry, the increasing antimicrobial resistance of food-borne pathogens to conventional sanitizers poses the risk of food contamination and a decrease in product quality and safety. Therefore, we explored alternative antimicrobials N-Acetyl-L-cysteine (NAC), rhamnolipids (RLs), and usnic acid (UA) as a novel approach to prevent biofilm formation and reduce existing biofilms formed by important food-borne pathogens (three strains of Salmonella enterica and two strains of Escherichia coli, Listeria monocytogenes, Staphylococcus aureus). Their effectiveness was evaluated by determining minimum inhibitory concentrations needed for inhibition of bacterial growth, biofilm formation, metabolic activity, and biofilm reduction. Transmission electron microscopy and confocal scanning laser microscopy followed by image analysis were used to visualize and quantify the impact of tested substances on both planktonic and biofilm-associated cells. The in vitro cytotoxicity of the substances was determined as a half-maximal inhibitory concentration in five different cell lines. The results indicate relatively low cytotoxic effects of NAC in comparison to RLs and UA. In addition, NAC inhibited bacterial growth for all strains, while RLs showed overall lower inhibition and UA inhibited only the growth of Gram-positive bacteria. Even though tested substances did not remove the biofilms, NAC represents a promising tool in biofilm prevention.Item Quorum sensing inhibition as a promising method to control biofilm growth in metalworking fluids(2019-04) Ozcan, Safiye S.; Dieser, Markus; Parker, Albert E.; Balasubramanian, Narayanaganesh; Foreman, Christine M.Microbial contamination in metalworking systems is a critical problem. This study determined the microbial communities in metalworking fluids (MWFs) from two machining shops and investigated the effect of quorum sensing inhibition (QSI) on biofilm growth. In both operations, biofilm-associated and planktonic microbial communities were dominated by Pseudomonadales (60.2–99.7%). Rapid recolonization was observed even after dumping spent MWFs and meticulous cleaning. Using Pseudomonas aeruginosa PAO1 as a model biofilm organism, patulin (40 µM) and furanone C-30 (75 µM) were identified as effective QSI agents. Both agents had a substantially higher efficacy compared to α-amylase (extracellular polymeric substance degrading enzyme) and reduced biofilm formation by 63% and 76%, respectively, in MWF when compared to untreated controls. Reduced production of putatively identified homoserine lactones and quinoline in MWF treated with QS inhibitors support the effect of QSI on biofilm formation. The results highlight the effectiveness of QSI as a potential strategy to eradicate biofilms in MWFs.Item How long is enough? Identification of product dry-time as a primary driver of alcohol-based hand rub efficacy(2018-05) Suchomel, Miranda; Leslie, Rachel; Parker, Albert E.; Macinga, David R.Background The World Health Organization has called for the development of improved methodologies to evaluate alcohol-based handrub (ABHR) efficacy, including evaluation at “short application times and volumes that reflect actual use in healthcare facilities”. The objective of this study was to investigate variables influencing ABHR efficacy, under test conditions reflective of clinical use. Methods The test product (60% V/V 2-propanol) was evaluated according to a modified EN 1500 methodology, where application volumes of 1 mL, 2 mL, and 3 mL were rubbed until dry. Statistical analyses were performed to investigate the relative influences of product volume, hand size, and product dry-time on efficacy, and hand size and hand contamination on product dry-time. Results Mean log10 reduction factors (SD) were 1.99 (0.66), 2.96 (0.84) and 3.28 (0.96); and mean dry-times (SD) were 24 s (7 s), 50 s (14 s), and 67 s (20 s) at application volumes of 1 mL, 2 mL, and 3 mL, respectively (p ≤ 0.030). When data were examined at the individual volunteer level, there was a statistically significant correlation between dry-time and log reduction factor (p < 0.0001), independent of application volume. There was also a statistically significant correlation between hand surface area and dry-times (p = 0.047), but no correlation between hand surface area and efficacy (p = 0.698). Conclusions When keeping other variables such as alcohol type and concentration constant, product dry-time appears to be the primary driver of ABHR efficacy suggesting that dosing should be customized to each individual and focus on achieving a product dry-time delivering adequate efficacy.Item Community Engaged Cumulative Risk Assessment of Exposure to Inorganic Well Water Contaminants, Crow Reservation, Montana(2018-01) Eggers, Margaret J.; Doyle, John T.; Lefthand, M. J.; Young, Sara L.; Moore-Nall, Anita L.; Kindness, L.; Medicine, R. O.; Ford, Tim E.; Dietrich, E.; Parker, Albert E.; Hoover, J. H.; Camper, Anne K.An estimated 11 million people in the US have home wells with unsafe levels of hazardous metals and nitrate. The national scope of the health risk from consuming this water has not been assessed as home wells are largely unregulated and data on well water treatment and consumption are lacking. Here, we assessed health risks from consumption of contaminated well water on the Crow Reservation by conducting a community-engaged, cumulative risk assessment. Well water testing, surveys and interviews were used to collect data on contaminant concentrations, water treatment methods, well water consumption, and well and septic system protection and maintenance practices. Additive Hazard Index calculations show that the water in more than 39% of wells is unsafe due to uranium, manganese, nitrate, zinc and/or arsenic. Most families’ financial resources are limited, and 95% of participants do not employ water treatment technologies. Despite widespread high total dissolved solids, poor taste and odor, 80% of families consume their well water. Lack of environmental health literacy about well water safety, pre-existing health conditions and limited environmental enforcement also contribute to vulnerability. Ensuring access to safe drinking water and providing accompanying education are urgent public health priorities for Crow and other rural US families with low environmental health literacy and limited financial resources.Item Surface micropattern reduces colonization and medical device-associated infections(2017-11) Xu, Binjie; Wei, Qiuhua; Mettetal, M. Ryan; Han, Jie; Rau, Lindsey; Tie, Jinfeng; May, Rhea M.; Pathe, Eric T.; Reddy, Shravanthi T.; Sullivan, Lauren; Parker, Albert E.; Maul, Donald H.; Brennan, Anthony B.; Mann, Ethan E.PURPOSE: Surface microtopography offers a promising approach for infection control. The goal of this study was to provide evidence that micropatterned surfaces significantly reduce the potential risk of medical device-associated infections. METHODOLOGY: Micropatterned and smooth surfaces were challenged in vitro against the colonization and transference of two representative bacterial pathogens - Staphylococcus aureus and Pseudomonas aeruginosa. A percutaneous rat model was used to assess the effectiveness of the micropattern against device-associated S. aureus infections. After the percutaneous insertion of silicone rods into (healthy or immunocompromised) rats, their backs were inoculated with S. aureus. The bacterial burdens were determined in tissues under the rods and in the spleens. RESULTS: The micropatterns reduced adherence by S. aureus (92.3 and 90.5 % reduction for flat and cylindrical surfaces, respectively), while P. aeruginosa colonization was limited by 99.9 % (flat) and 95.5 % (cylindrical). The micropatterned surfaces restricted transference by 95.1 % for S. aureus and 94.9 % for P. aeruginosa, compared to smooth surfaces. Rats with micropatterned devices had substantially fewer S. aureus in subcutaneous tissues (91 %) and spleens (88 %) compared to those with smooth ones. In a follow-up study, immunocompromised rats with micropatterned devices had significantly lower bacterial burdens on devices (99.5 and 99.9 % reduction on external and internal segments, respectively), as well as in subcutaneous tissues (97.8 %) and spleens (90.7 %) compared to those with smooth devices. CONCLUSION: Micropatterned surfaces exhibited significantly reduced colonization and transference in vitro, as well as lower bacterial burdens in animal models. These results indicate that introducing this micropattern onto surfaces has high potential to reduce medical device-associated infections. KEYWORDS: hospital-acquired infections; infections; medical devices; micropatternsItem Who Goes in and Out of the Hospital Patient Room?(2017-06) Arbogast, James W.; Quinn, Jeff; Clark, Tracy; Moore, Lori; Thompson, Maria; Wagner, Pamela; Young, Elizabeth; Parker, Albert E.BACKGROUND: The objective of this study was to determine what percentage of entries and exits (E/E) in and out of the patient room should be attributed to healthcare workers (HCWs) in a wide variety of hospital units. This is a critical question for hospitals considering an automated monitoring system (AMS) to measure hand hygiene performance (HHP) as a complement to data from visual observation. HCWs often implicate others and do not perceive a need to change their HH behavior because they are convinced that visitors, patients, and others are responsible for very low HHP data. METHODS: Events (defined as patient room E/E) were observed and recorded by nurses not employed by the hospital. Observations were made in US and Canadian hospital units including emergency, ICU, medical surgical, oncology, and pediatrics. Observers classified events by: HCWs (e.g., nursing staff, aides, doctors, EVS, etc.), patients plus visitors, and other (e.g., clergy, hospice workers). Logistic regression was used to determine who was responsible for the most E/E events by category of individuals. RESULTS: Observers recorded a total of 14,876 E/E events in 29 units of 16 hospitals with units varying in size from 10 to 41 beds. 84.3% of all E/E were attributed to HCWs; 15.0% were from patients plus visitors and 0.7% from others. The odds are 6 to 1 that an E/E into a patient room is by a HCW (P < .0005). Pediatric units had the lowest percentage of HCWs E/E (76.7% total) CONCLUSIONS: This study demonstrates HCWs account for the greatest proportion of hospitalized patient room E/E. Further, the data show that others share a very small percentage of room E/E countering the argument that those individuals are responsible for the low unit HHP measured by AMS. This study demonstrates that other categories of individuals are not a deterrent to increasing unit-level HHP.Item Type and amount of organic amendments affect enhanced biogenic methane production from coal and microbial community structure(2018-01) Davis, Katherine J.; Shipeng, Lu; Barnhart, Elliott P.; Parker, Albert E.; Fields, Matthew W.; Gerlach, RobinSlow rates of coal-to-methane conversion limit biogenic methane production from coalbeds. This study demonstrates that rates of coal-to-methane conversion can be increased by the addition of small amounts of organic amendments. Algae, cyanobacteria, yeast cells, and granulated yeast extract were tested at two concentrations (0.1 and 0.5 g/L), and similar increases in total methane produced and methane production rates were observed for all amendments at a given concentration. In 0.1 g/L amended systems, the amount of carbon converted to methane minus the amount produced in coal only systems exceeded the amount of carbon added in the form of amendment, suggesting enhanced coal-to-methane conversion through amendment addition. The amount of methane produced in the 0.5 g/L amended systems did not exceed the amount of carbon added. While the archaeal communities did not vary significantly, the bacterial populations appeared to be strongly influenced by the presence of coal when 0.1 g/L of amendment was added; at an amendment concentration of 0.5 g/L the bacterial community composition appeared to be affected most strongly by the amendment type. Overall, the results suggest that small amounts of amendment are not only sufficient but possibly advantageous if faster in situ coal-to-methane production is to be promoted.Item An ensemble Kalman filter using the conjugate gradient sampler(2013) Bardsley, Johnathan Matheas; Solonen, Antti; Parker, Albert E.; Haario, Heikki; Howard, MarylesaThe ensemble Kalman filter (EnKF) is a technique for dynamic state estimation. EnKF approximates the standard extended Kalman filter (EKF) by creating an ensemble of model states whose mean and empirical covariance are then used within the EKF formulas. The technique has a number of advantages for large-scale, nonlinear problems. First, large-scale covariance matrices required within EKF are replaced by low-rank and low-storage approximations, making implementation of EnKF more efficient. Moreover, for a nonlinear state space model, implementation of EKF requires the associated tangent linear and adjoint codes, while implementation of EnKF does not. However, for EnKF to be effective, the choice of the ensemble members is extremely important. In this paper, we show how to use the conjugate gradient (CG) method, and the recently introduced CG sampler, to create the ensemble members at each filtering step. This requires the use of a variational formulation of EKF. The effectiveness of the method is demonstrated on both a large-scale linear, and a small-scale, nonlinear, chaotic problem. In our examples, the CG-EnKF performs better than the standard EnKF, especially when the ensemble size is small.Item Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis(2010) Folsom, James P.; Richards, Lee A.; Roe, Frank L.; Ehrlich, Garth D.; Parker, Albert E.; Mazurie, Aurélien J.; Stewart, Philip S.BACKGROUND: Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared rankings for a priori identified physiological marker genes between the biofilm and published data sets.RESULTS: Biofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database (www.ncbi.nlm.nih.gov/geo). By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h-1.CONCLUSIONS: Collectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity.