Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria

This article belongs to the Collection Feature Papers in Molecular Microbiology.Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.This research was partially funded by the European Union’s Horizon 2020 Research and Innovation program, grant agreement No 773830: One Health European Joint Program.info:eu-repo/semantics/publishedVersio

Effects of subinhibitory quinolone concentrations onfunctionality, microbial community composition, and abundance of antibiotic resistant bacteria and qnrS in activated sludge

©2020 The AutorsWastewater treatment plants (WWTPs) are continuously exposed to sub-inhibitory concentrations of antibiotics that are thought to contribute to the spreading of antibiotic resistant bacteria and antibiotic resistance genes, which are eventually released to downstream environments through effluents. In order to understand the effects of sub-inhibitory concentrations of antibiotics on sludge microbiome and resistome, we spiked a conventional activated sludge (CAS) model system with ciprofloxacin, a common fluoroquinolone antibiotic, from 0.0001 mg/L (about twice the typical ciprofloxacin concentration observed in municipal wastewater) up to 0.1 mg/L (one order of magnitude below the clinical MIC for Enterobacteriaceae) for 151 days. The abundance of ciprofloxacin resistant bacteria and qnrS, a plasmid-associated gene that confers resistance to quinolones, in activated sludge and in effluents of control and spiked CAS reactors, showed no measurable effect of the antibiotic amendment. This was also true for the bacterial community structure and for indicators of WW treatment such as N removal efficiency. Surprisingly, temporal fluctuations in both reactors could explain the observed internal variability of these antibiotic resistance determinants better than the hypothesized antibiotic-driven selective pressure. Overall, this work shows that the core sludge microbiome in CAS systems is resilient to sub-inhibitory concentrations of ciprofloxacin at a functional, structural, and antibiotic resistance levels.1101

Fate and persistence of antibiotic-resistant bacteria and genes through a multi-barrier treatment facility for direct potable reuse

Given the availability of technological solutions and guidelines for safe drinking water, direct potable reuse of reclaimed water has become a promising option to overcome severe lack of potable water in arid regions. However, the growing awareness of the presence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) in corresponding raw wastes has led to new safety concerns. This study investigated the fate of ARB and intracellular and extracellular ARG after each treatment step of an advanced water treatment facility in Windhoek, Namibia. The New Goreangab Water Reclamation Plant (NGWRP) produces drinking water from domestic secondary wastewater treatment plant effluent and directly provides for roughly a quarter of Windhoek's potable water demand. Procedures to study resistance determinants were based on both molecular biology and culture-based microbiological methods. TaqMan real-time PCR was employed to detect and quantify intracellular resistance genes sul1, ermB, vanA, nptII and nptIII as well as extracellular resistance gene sul1. The NGWRP reduced the amount of both culturable bacterial indicators as well as the resistance genes to levels below the limit of detection in the final product. The main ozonation and the ultrafiltration had the highest removal efficiencies on both resistance determinants.3733901

Use of Novel Techniques in Plant Breeding and Practical Consequences Concerning Detection, Traceability, Labeling, and Risk Assessment

Genetically modified plants (GMP) are regulated by comprehensive EU legislation. Cisgenesis, intragenesis, oligo-directed mutagenesis (ODM), zinc-finger nucleases (ZFN), and agroinfiltration were examined concerning detection, traceability, labeling, and risk assessment. Similar transformation methods -- as in transgenesis using genetic elements from same or cross-compatible plant species -- characterize cisgenesis and intragenesis. Targeting the genome with ODM or ZFN minimizes unintended effects, but current data indicate limited efficiency and specificity; modifications are similar to those occurring during traditional plant breeding. The characteristics of plants produced by these techniques affect detection in the supply chains. Detection is possible when the target site is known, except for agroinfiltration that aims at transient expression of a gene/trait. The basis to assess potential risks arising from relevant plants and derived food and feed is similar to that of GMP. Depending on the specifics of the plant under investigation, data requirements for regulators may be reconsidered case-by-case

Factors associated with the prevalence of antibiotic resistance in the environment from a One Health perspective: Protocol for a systematic evidence map

This was developed within the FED-AMR project and is associated with WP6-T1 “Factors influencing the prevalence of antibiotic resistance in the environment”. It describes the protocol for a systematic evidence map of the scientific literature concerning factors associated with the prevalence of antibiotic resistance in the environment. This protocol adheres to the PRISMA-P statement: an established procedure for planning systematic evidence work. A key outcome of this systematic evidence map is to gather data items for future analysis work; potentially, this has application in identifying the main environmental risk factors associated with the presence and transmission of antibiotic resistance. This has important implications concerning risk mitigation for public and animal health