The vast majority of antibiotic resistant genes (ARG) acquired by human pathogens have originated from the natural environment. Therefore, understanding factors that influence intrinsic levels of ARG in the environment could be epidemiologically significant. The selection for metal resistance often promotes AR in exposed organisms; however, the relationship between metal levels in nature and the intrinsic presence of ARG has not been fully assessed. Here, we quantified, using qPCR, the abundance of eleven ARG and compared their levels with geochemical conditions in randomly selected soils from a Scottish archive. Many ARG positively correlated with soil copper levels, with approximately half being highly significant (p<0.05); whereas chromium, nickel, lead, and iron also significantly correlated with specific ARG. Results show that geochemical metal conditions innately influence the potential for AR in soil. We suggest soil geochemical data might be used to estimate baseline gene presence on local, regional and global scales within epidemiological risk studies related to AR transmission from the environment.

Summary: The abundance of six tetracycline resistance genes tet (O) , tet (Q) , tet (W) , tet (M), tet (B) and tet (L), were quantified over time in wastewater lagoons at concentrated animal feeding operations (CAFO) to assess how feedlot operation affects resistance genes in downstream surface waters. Eight lagoons at five cattle feedlots in the Midwestern United States were monitored for 6 months. Resistance and 16S‐rRNA gene abundances were quantified using real‐time PCR, and physicochemical lagoon conditions, tetracycline levels, and other factors (e.g. feedlot size and weather conditions) were monitored over time. Lagoons were sorted according to antibiotic use practice at each site, and designated as ‘no‐use’, ‘mixed‐use’ or ‘high‐use’ for comparison. High‐use lagoons had significantly higher detected resistance gene levels (tet ^R ; 2.8 × 10 ⁶ copies ml ⁻¹ ) relative to no‐use lagoons (5.1 × 10 ³ copies ml ⁻¹ ; P < 0.01) and mixed‐use lagoons (7.3 × 10 ⁵ copies ml ⁻¹ ; P = 0.076). Bivariate correlation analysis on pooled data ( n = 54) confirmed that tet ^R level strongly correlated with feedlot area ( r = 0.67, P < 0.01) and ‘total’ bacterial 16S‐rRNA gene level in each lagoon ( r = 0.51, P < 0.01), which are both characteristic of large CAFOs. tet (M) was the most commonly detected gene, both in absolute number and normalized to 16S‐rRNA gene level, although tet (O), tet (Q) and tet (W) levels were also high in the mixed and high‐use lagoons. Finally, resistance gene levels were highly seasonal with abundances being 10–100 times greater in the autumn versus the summer. Results show that antibiotic use strategy strongly affects both the abundance and seasonal distribution of resistance genes in associated lagoons, which has implications on water quality and feedlot management practices.

Eroding foreshores endanger the floodplains of many estuaries, as such, effective and environmentally friendly interventions are sought to stabilise slopes and mitigate erosion. As a step in forestalling these losses, we developed laboratory microcosms to simulate tidal cycles and examined the mechanisms of erosion and failure on sandy foreshore slopes. As an experimental aim, we applied microbially induced calcite precipitation (MICP) to selected slopes and compared the effectiveness of this microbial geo-technological strategy to mitigate erosion and stabilise slopes. To assess shoreline stability, thirty cycles of slowly simulated tidal currents were applied to a sandy slope. Significant sediment detachment occurred as tides moved up the slope surface. For steeper slopes, one tidal event was sufficient to cause collapse of the slopes to the soil's angle of repose (similar to 35 degrees). Subsequent tidal cycles gradually eroded surface sediments further reducing slope angle (on an average 0.2 degrees per tidal event). These mechanisms were similar for all slopes irrespective of initial slope inclination. MICP was evaluated as a remedial measure by treating a steep slope of 53 degrees and an erosion-prone slope angle of 35 degrees with Sporosarcina pasteurii and cementation solution (0.7 M CaCl2 and urea) before tidal simulations. MICP produced 120 kg calcite per m(3) of soil, filling 9.9% of pore space. Cemented sand withstood up to 470 kPa unconfined compressive stress and showed significantly improved slope stability; both slopes showed negligible sediment erosion. With efforts towards optimisation for upscaling and further environmental considerations (including effect of slope saturation on MICP treatment, saline water and estuarine/coastal ecology amongst others), the MICP process demonstrates promise to protect foreshore slope sites. (C) 2015 Elsevier B.V. All rights reserved

Considerable debate exists over the primary cause of increased antibiotic resistance (AR) worldwide. Evidence suggests increasing AR results from overuse of antibiotics in medicine and therapeutic and nontherapeutic applications in agriculture. However, pollution also can influence environmental AR, particularly associated with heavy metal, pharmaceutical, and other waste releases, although the relative scale of the “pollution” contribution is poorly defined, which restricts targeted mitigation efforts. The question is “where to study and quantify AR from pollution versus other causes to best understand the pollution effect”. One useful site is Cuba because industrial pollution broadly exists; antibiotics are used sparingly in medicine and agriculture; and multiresistant bacterial infections are increasing in clinical settings without explanation. Within this context, we quantified 13 antibiotic resistance genes (ARG; indicators of AR potential), 6 heavy metals, 3 antibiotics, and 17 other organic pollutants at 8 locations along the Almendares River in western Havana at sites bracketing known waste discharge points, including a large solid waste landfill and various pharmaceutical factories. Significant correlations (p < 0.05) were found between sediment ARG levels, especially for tetracyclines and β-lactams (e.g., tet(M), tet(O), tet(Q), tet(W), bla_OXA), and sediment Cu and water column ampicillin levels in the river. Further, sediment ARG levels increased by up to 3 orders of magnitude downstream of the pharmaceutical factories and were highest where human population densities also were high. Although explicit links are not shown, results suggest that pollution has increased background AR levels in a setting where other causes of AR are less prevalent.

Editorial: Horizontal Gene Transfer Mediated Bacterial Antibiotic Resistance