Metagenomic tracking of antibiotic resistance genes through a pre‐harvest vegetable production system: an integrated lab‐, microcosm‐ and greenhouse‐scale analysis

Summary: Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory‐, microcosm‐ and greenhouse‐scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG‐mobile genetic element co‐occurrences (n = 945). Radishes grown in manure‐ or compost‐amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic‐treated beef amendments. The findings emphasize that additional barriers, such as post‐harvest processes, merit further study to minimize potential exposure to consumers

Integrated metagenomic assessment of multiple pre-harvest control points on lettuce resistomes at field-scale

An integrated understanding of factors influencing the occurrence, distribution, and fate of antibiotic resistance genes (ARGs) in vegetable production systems is needed to inform the design and development of strategies for mitigating the potential for antibiotic resistance propagation in the food chain. The goal of the present study was to holistically track antibiotic resistance and associated microbiomes at three distinct pre-harvest control points in an agroecosystem in order to identify the potential impacts of key agricultural management strategies. Samples were collected over the course of a single growing season (67 d) from field-scale plots amended with various organic and inorganic amendments at agronomic rates. Dairy-derived manure and compost amendment samples (n= 14), soil samples (n= 27), and lettuce samples (n= 12) were analyzed via shotgun metagenomics to assess multiple pre-harvest factors as hypothetical control points that shape lettuce resistomes. Pre-harvest factors of interest included manure collection during/post antibiotic use, manure composting, and soil amendment soil with organic (stockpiled manure/compost) versus chemical fertilizer. Microbial community resistome and taxonomic compositions were unique from amendment to soil to lettuce surface according to dissimilarity analysis. The highest resistome alpha diversity (i.e., unique ARGs, n=642) was detected in amendment samples prior to soil application, while the composted manure had the lowest total ARG relative abundance (i.e., 16S rRNA gene-normalized). Regardless of amendment type, soils acted as an apparent ecological buffer, i.e., soil resistome and taxonomic profiles returned to background conditions 120 d-post amendment application. Effects of amendment conditions surprisingly re-emerged in lettuce phyllosphere resistomes, with the highest total ARG relative abundances recovered on the surface of lettuce plants grown in organically-fertilized soils (i.e. compost- and manure-amended soils). Co-occurrence analysis identified 55 unique ARGs found both in the soil amendments and on lettuce surfaces. Among these, arnA and pmrF were the most abundant ARGs co-occurring with mobile genetic elements (MGE). Other prominent ARG-MGE co-occurrences throughout this pre-harvest lettuce production chain included: TetM to transposon (Clostridiodies difficile) in the manure amendment and TriC to plasmid (Ralstonia solanacearum) on the lettuce surfaces. This suggests that, even with imposing manure management and post-amendment wait periods in agricultural systems, ARGs originating from manure can still be found on crop surfaces. This study demonstrates a comprehensive approach to identifying key control points for the propagation of ARGs in vegetable production systems, identifying potential ARG-MGE combinations that could inform future surveillance. The findings suggest that additional pre-harvest and potentially post-harvest interventions may be warranted to minimize risk of propagating antibiotic resistance in the food chain

Minimally invasive lumbopelvic instrumentation for traumatic sacrolisthesis in an elderly patient

PURPOSE: We present a novel minimally invasive technique for lumbopelvic instrumentation in selected elderly patients suffering from traumatic sacrolisthesis. An 82-year-old female suffered from sacrolisthesis after a fall. She developed significant low back pain and bilateral lower extremity radiculopathy. Preoperative radiographs and magnetic resonance imaging sequences demonstrated the fracture dislocation between S1 and S2 with compromise of the spinal canal. Lumbopelvic instrumentation was sought to offer fixation and allow mobilization; however, open lumbopelvic instrumentation techniques have significant morbidity, especially in this patient population of elderly patients with medical comorbidities. METHODS: A minimally invasive technique employing percutaneous pedicle screws at L5 and S1 coupled with percutaneous S2 iliac screws was employed. RESULTS AND CONCLUSIONS: The patient tolerated the procedure well without any complications or morbidity. At the last follow-up of 14 months, she was ambulating without assistance with near total resolution of back pain and radicular pain. Radiographs obtained at 8 months’ follow-up demonstrated fusion across the fracture line. Although further follow-up data is still needed to establish the durability of this technique in the long-term, this minimally invasive technique for lumbopelvic instrumentation can be considered as an option in elderly patients with traumatic sacrolisthesis, whose need for early mobilization and medical comorbidities preclude the use of an open lumbopelvic fixation procedure. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00586-012-2204-4) contains supplementary material, which is available to authorized users