Case-based surveillance of antimicrobial resistance in the ACORN (A Clinically Oriented Antimicrobial Resistance Surveillance Network) study.
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ABSTRACT:
SUBMITTER: van Doorn HR
PROVIDER: S-EPMC7134533 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
Case-based surveillance of antimicrobial resistance in the ACORN (A Clinically Oriented Antimicrobial Resistance Surveillance Network) study.
van Doorn H Rogier HR Ashley Elizabeth A EA Turner Paul P
JAC-antimicrobial resistance 20200312 1
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Project description:Background: Antimicrobial resistance (AMR) / drug resistant infections (DRIs) are a major global health priority. Surveillance data is critical to inform infection treatment guidelines, monitor trends, and to assess interventions. However, most existing AMR / DRI surveillance systems are passive and pathogen-based with many potential biases. Addition of clinical and patient outcome data would provide considerable added value to pathogen-based surveillance. Methods: The aim of the ACORN project is to develop an efficient clinically-oriented AMR surveillance system, implemented alongside routine clinical care in hospitals in low- and middle-income country settings. In an initial pilot phase, clinical and microbiology data will be collected from patients presenting with clinically suspected meningitis, pneumonia, or sepsis. Community-acquired infections will be identified by daily review of new admissions, and hospital-acquired infections will be enrolled during weekly point prevalence surveys, on surveillance wards. Clinical variables will be collected at enrolment, hospital discharge, and at day 28 post-enrolment using an electronic questionnaire on a mobile device. These data will be merged with laboratory data onsite using a flexible automated computer script. Specific target pathogens will be Streptococcus pneumoniae, Staphylococcus aureus, Salmonella spp ., Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii. A bespoke browser-based app will provide sites with fully interactive data visualisation, analysis, and reporting tools. Discussion: ACORN will generate data on the burden of DRI which can be used to inform local treatment guidelines / national policy and serve as indicators to measure the impact of interventions. Following development, testing and iteration of the surveillance tools during an initial six-month pilot phase, a wider rollout is planned.
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Project description:Wastewater-based surveillance is increasingly recognized as an important approach to monitoring population-level antimicrobial resistance (AMR). In this exploratory study, we examined the use of metagenomics to evaluate AMR using untreated wastewater samples routinely collected by the Niger national polio surveillance program. Forty-eight stored samples from two seasons each year over 4 years (2016-2019) in three regions were selected for inclusion in this study and processed using unbiased DNA deep sequencing. Normalized number of reads of genetic determinants for different antibiotic classes were compared over time, by season, and by location. Correlations in resistance were examined among classes. Changes in reads per million per year were demonstrated for several classes, including decreases over time in resistance determinants for phenicols (-3.3, 95% CI: -8.7 to -0.1, P = 0.029) and increases over time for aminocoumarins (3.8, 95% CI: 0.0 to 11.4, P = 0.043), fluoroquinolones (6.8, 95% CI: 0.0 to 20.5, P = 0.048), and beta-lactams (0.85, 95% CI: 0.1 to 1.7, P = 0.006). Sulfonamide resistance was higher in the post-rainy season compared with the dry season (5.2-fold change, 95% CI: 3.4 to 7.9, P < 0.001). No differences were detected when comparing other classes by season or by site for any antibiotic class. Positive correlations were identified in genetic determinants of resistance among several antibiotic classes. These results demonstrate the potential utility of leveraging existing wastewater sample collection in this setting for AMR surveillance.
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Project description:Canada has implemented on-farm antimicrobial resistance (AMR) surveillance systems for food-producing animals under the Canadian Integrated Program for Antimicrobial Resistance (CIPARS); however, dairy cattle have not been included in that program yet. The objective of this manuscript was to describe the development and implementation of the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR). An Expert Panel (EP) of researchers was created to lead the development of the dairy surveillance system. The EP initiated a draft document outlining the essential elements of the surveillance framework. This document was then circulated to a Steering Committee (SC), which provided recommendations used by the EP to finalize the framework. CaDNetASR has the following components: (1) a herd-level antimicrobial use quantification system; (2) annually administered risk factor questionnaires; and (3) methods for herd-level detection of AMR in three sentinel enteric pathogens (generic Escherichia coli, Campylobacter spp., and Salmonella spp.) recovered from pooled fecal samples collected from calves, heifers, cows, and the manure pit. A total of 144 dairy farms were recruited in five Canadian provinces (British-Columbia, Alberta, Ontario, Québec, and Nova-Scotia), with the help of local herd veterinarians and regional field workers, and in September 2019, the surveillance system was launched. 97.1 and 94.4% of samples were positive for E. coli, 63.8, and 49.1% of samples were positive for Campylobacter spp., and 5.0 and 7.7% of samples were positive for Salmonella spp., in 2019 and 2020, respectively. E. coli was equally distributed among all sample types. However, it was more likely that Campylobacter spp. were recovered from heifer and cow samples. On the other hand, it was more common to isolate Salmonella spp. from the manure pit compared to samples from calves, heifers, or cows. CaDNetASR will continue sampling until 2022 after which time this system will be integrated into CIPARS. CaDNetASR will provide online access to farmers and veterinarians interested in visualizing benchmarking metrics regarding AMU practices and their relationship to AMR and animal health in dairy herds. This will provide an opportunity to enhance antimicrobial stewardship practices on dairy farms in Canada.
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