Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum ß-Lactamase in Escherichia coli from Different Animal Sources.

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum ß-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, blaCTX-M-15, blaTEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Simulating Woodchip Bioreactor Performance Using a Dual-Porosity Model.

There is a general understanding in the scientific community as to how denitrifying bioreactors operate, but we lack a quantitative understanding of the details of the denitrification process acting within them and comprehensive models for simulating their performance. We hypothesized that nitrate transport through woodchip bioreactors would be best described by a dual-porosity transport model where the bioreactor water is divided into a mobile domain (i.e., the water between the woodchips where it is free to flow and solute movement is by advection and dispersion) and an immobile domain of water (i.e., the water mostly within the woodchips that is stagnant and where solute movement is by diffusion alone). We calibrated the dual-porosity model contained in the HYDRUS model for a woodchip bioreactor using the results of a Br breakthrough experiment where we treated Br as a conservative nonadsorbing tracer. We then used the resulting model parameters to describe 2 yr of NO transport and denitrification within a bioreactor supplied by tile drainage. The only model parameters fitted to the NO data were either the zero- or first-order denitrification rate and its temperature dependence. The bioreactor denitrified 2.23 kg N (38%) of the NO entering it in 2013 and 3.73 kg N (49%) of the NO that entered it in 2014. The dual-porosity model fit the NO data very well, with fitted zero-order reaction rates of 8.7 and 6.8 mg N L d in 2013 and 2014, respectively, and corresponding first-order reaction rates of 0.99 and 1.02 d. For the 2-yr data set, both reaction rate models fit the data equally well. Consistent model parameters fitted for the 2 yr indicated that the model used was robust and a promising approach for modeling fate and transport of NO in woodchip bioreactors.

In situ bioreactors and deep drain-pipe installation to reduce nitrate losses in artificially drained fields.

Nitrate in water removed from fields by subsurface drain ('tile') systems is often at concentrations exceeding the 10 mg N L(-1) maximum contaminant level (MCL) set by the USEPA for drinking water and has been implicated in contributing to the hypoxia problem within the northern Gulf of Mexico. Because previous research shows that N fertilizer management alone is not sufficient for reducing NO(3) concentrations in subsurface drainage below the MCL, additional approaches are needed. In this field study, we compared the NO(3) losses in tile drainage from a conventional drainage system (CN) consisting of a free-flowing pipe installed 1.2 m below the soil surface to losses in tile drainage from two alternative drainage designs. The alternative treatments were a deep tile (DT), where the tile drain was installed 0.6 m deeper than the conventional tile depth, but with the outlet maintained at 1.2 m, and a denitrification wall (DW), where trenches excavated parallel to the tile and filled with woodchips serve as additional carbon sources to increase denitrification. Four replicate 30.5- by 42.7-m field plots were installed for each treatment in 1999 and a corn-soybean rotation initiated in 2000. Over 5 yr (2001-2005) the tile flow from the DW treatment had annual average NO(3) concentrations significantly lower than the CN treatment (8.8 vs. 22.1 mg N L(-1)). This represented an annual reduction in NO(3) mass loss of 29 kg N ha(-1) or a 55% reduction in nitrate mass lost in tile drainage for the DW treatment. The DT treatment did not consistently lower NO(3) concentrations, nor reduce the annual NO(3) mass loss in drainage. The DT treatment did exhibit lower NO(3) concentrations in tile drainage than the CN treatment during late summer when tile flow rates were minimal. There was no difference in crop yields for any of the treatments. Thus, denitrification walls are able to substantially reduce NO(3) concentrations in tile drainage for at least 5 yr.