Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.
MULTIFILE
Introduction F-ACT is a flexible version of Assertive Community Treatment to deliver care in a changing intensity depending on needs of individuals with severe mental illnesses (Van Veldhuizen, 2007). In 2016 a number of the FACT-teams in the Dutch region of Utrecht moved to locations in neighborhoods and started to work as one network team together with neighborhood based facilities in primary care (GP’s) and in the social domain (supported living, social district teams, etc.). This should create better chances on clinical, social and personal recovery of service users. Objectives This study describes the implementation, obstacles and outcomes for service users. The main question is whether this Collaborative Mental Health Care in the Community produces better outcome than regular FACT. Measures include (met/unmet) needs for care, quality of life, clinical, functional and personal recovery, and hospital admission days. Methods Data on care utilization regarding the innovation are compared to regular FACT. Qualitative interviews are conducted to gain insight in the experiences of service users, their family members and mental health care workers. Changes in outcome measures of service users in pilot areas (N=400) were compared to outcomes of users (matched on gender and level of functioning) in regular FACT teams in the period 2015-2018 (total N=800). Results Data-analyses will take place from January to March 2019. Initial analyses point at a greater feeling of holding and safety for service users in the pilot areas and less hospital admission days. Conclusions Preliminary results support the development from FACT to a community based collaborative care service.
