Last data update: May 20, 2024. (Total: 46824 publications since 2009)
Records 1-5 (of 5 Records) |
Query Trace: Smith RJ [original query] |
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Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.
Bharat A , Petkau A , Avery BP , Chen J , Folster J , Carson CA , Kearney A , Nadon C , Mabon P , Thiessen J , Alexander DC , Allen V , ElBailey S , Bekal S , German GJ , Haldane D , Hoang L , Chui L , Minion J , Zahariadis G , VanDomselaar G , Reid-Smith RJ , Mulvey MR . Microorganisms 2022 10 (2) Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5100%), a specificity of 99.7% (98.6100%), a positive predictive value of 95.4% (68.2100%), and a negative predictive value of 99.1% (95.6100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles. 2022 by the authors. Licensee MDPI, Basel, Switzerland. |
The Fire and Tree Mortality Database, for empirical modeling of individual tree mortality after fire
Cansler CA , Hood SM , Varner JM , van Mantgem PJ , Agne MC , Andrus RA , Ayres MP , Ayres BD , Bakker JD , Battaglia MA , Bentz BJ , Breece CR , Brown JK , Cluck DR , Coleman TW , Corace RG3rd , Covington WW , Cram DS , Cronan JB , Crouse JE , Das AJ , Davis RS , Dickinson DM , Fitzgerald SA , Fule PZ , Ganio LM , Grayson LM , Halpern CB , Hanula JL , Harvey BJ , Kevin Hiers J , Huffman DW , Keifer M , Keyser TL , Kobziar LN , Kolb TE , Kolden CA , Kopper KE , Kreitler JR , Kreye JK , Latimer AM , Lerch AP , Lombardero MJ , McDaniel VL , McHugh CW , McMillin JD , Moghaddas JJ , O'Brien JJ , Perrakis DDB , Peterson DW , Prichard SJ , Progar RA , Raffa KF , Reinhardt ED , Restaino JC , Roccaforte JP , Rogers BM , Ryan KC , Safford HD , Santoro AE , Shearman TM , Shumate AM , Sieg CH , Smith SL , Smith RJ , Stephenson NL , Stuever M , Stevens JT , Stoddard MT , Thies WG , Vaillant NM , Weiss SA , Westlind DJ , Woolley TJ , Wright MC . Sci Data 2020 7 (1) 194 Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring from 1981-2016. Additional variables such as insect attack are included when available. The FTM database can be used to evaluate individual fire-caused mortality models for pre-fire planning and post-fire decision support, to develop improved models, and to explore general patterns of individual fire-induced tree death. The database can also be used to identify knowledge gaps that could be addressed in future research. |
Airborne fiber size characterization in exposure estimation: evaluation of a modified transmission electron microcopy protocol for asbestos and potential use for carbon nanotubes and nanofibers
Dement JM , Kuempel ED , Zumwalde RD , Ristich AM , Fernback JE , Smith RJ . Am J Ind Med 2015 58 (5) 494-508 BACKGROUND: Airborne fiber size has been shown to be an important factor relative to adverse lung effects of asbestos and suggested in animal studies of carbon nanotubes and nanofibers (CNT/CNF). MATERIALS AND METHODS: The International Standards Organization (ISO) transmission electron microscopy (TEM) method for asbestos was modified to increase the statistical precision of fiber size determinations, improve efficiency, and reduce analysis costs. Comparisons of the fiber size distributions and exposure indices by laboratory and counting method were performed. RESULTS: No significant differences in size distributions by the ISO and modified ISO methods were observed. Small but statistically-significant inter-lab differences in the proportion of fibers in some size bins were found, but these differences had little impact on the summary exposure indices. The modified ISO method produced slightly more precise estimates of the long fiber fraction (>15 mum). CONCLUSIONS: The modified ISO method may be useful for estimating size-specific structure exposures, including CNT/CNF, for risk assessment research. |
The impact of media coverage on the transmission dynamics of human influenza
Tchuenche JM , Dube N , Bhunu CP , Smith RJ , Bauch CT . BMC Public Health 2011 11 Suppl 1 S5 BACKGROUND: There is an urgent need to understand how the provision of information influences individual risk perception and how this in turn shapes the evolution of epidemics. Individuals are influenced by information in complex and unpredictable ways. Emerging infectious diseases, such as the recent swine flu epidemic, may be particular hotspots for a media-fueled rush to vaccination; conversely, seasonal diseases may receive little media attention, despite their high mortality rate, due to their perceived lack of newness. METHODS: We formulate a deterministic transmission and vaccination model to investigate the effects of media coverage on the transmission dynamics of influenza. The population is subdivided into different classes according to their disease status. The compartmental model includes the effect of media coverage on reporting the number of infections as well as the number of individuals successfully vaccinated. RESULTS: A threshold parameter (the basic reproductive ratio) is analytically derived and used to discuss the local stability of the disease-free steady state. The impact of costs that can be incurred, which include vaccination, education, implementation and campaigns on media coverage, are also investigated using optimal control theory. A simplified version of the model with pulse vaccination shows that the media can trigger a vaccinating panic if the vaccine is imperfect and simplified messages result in the vaccinated mixing with the infectives without regard to disease risk. CONCLUSIONS: The effects of media on an outbreak are complex. Simplified understandings of disease epidemiology, propogated through media soundbites, may make the disease significantly worse. |
Contributions of dust exposure and cigarette smoking to emphysema severity in coal miners in the United States
Kuempel ED , Wheeler MW , Smith RJ , Vallyathan V , Green FH . Am J Respir Crit Care Med 2009 180 (3) 257-64 RATIONALE: Previous studies have shown associations between dust exposure or lung burden and emphysema in coal miners, although the separate contributions of various predictors have not been clearly demonstrated. OBJECTIVES: To quantitatively evaluate the relationship between cumulative exposure to respirable coal mine dust, cigarette smoking, and other factors on emphysema severity. METHODS: The study group included 722 autopsied coal miners and nonminers in the United States. Data on work history, smoking, race, and age at death were obtained from medical records and questionnaire completed by next-of-kin. Emphysema was classified and graded using a standardized schema. Job-specific mean concentrations of respirable coal mine dust were matched with work histories to estimate cumulative exposure. Relationships between various metrics of dust exposure (including cumulative exposure and lung dust burden) and emphysema severity were investigated in weighted least squares regression models. MEASUREMENTS AND MAIN RESULTS: Emphysema severity was significantly elevated in coal miners compared with nonminers among ever- and never-smokers (P < 0.0001). Cumulative exposure to respirable coal mine dust or coal dust retained in the lungs were significant predictors of emphysema severity (P < 0.0001) after accounting for cigarette smoking, age at death, and race. The contributions of coal mine dust exposure and cigarette smoking were similar in predicting emphysema severity averaged over this cohort. CONCLUSIONS: Coal dust exposure, cigarette smoking, age, and race are significant and additive predictors of emphysema severity in this study. |
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