Microbiota shaping and bioburden monitoring of indoor antimicrobial surfaces

Indoor residents are constantly exposed to dynamic microbiota that have significant health effects. In addition to hand hygiene, cleaning, and disinfection, antimicrobial coatings (AMCs) can prevent the spread of infectious diseases in public areas. The sustainable use of antimicrobial-coated products requires an assessment of their pros and cons for human health and the environment. The toxicity and resistance risks of AMCs have been considered, but large-scale genetic studies on the microbial community compositions and resistomes of AMCs are scarce. The use of an AMC can reduce the total number of microbes on a surface but poses the risk of dysbiosis, microbial imbalance, such as the polarized growth of metallophilic, metal- and antimicrobial-resistant, and other survivor bacteria, and the overall reduction of microbial diversity. Loss of diversity may lead to the enrichment of harmful bacteria and an increased risk of communicable or immunological non-communicable inflammatory diseases (NCDs). In public buildings, such as kindergartens and nursing homes for the elderly, the use of AMCs is likely to increase due to epidemics and pandemics in recent years. Therefore, comprehensive metagenomic research is needed to monitor the effects of AMCs on indoor microbial community compositions and functions. Although the determination of good indoor microbiota and homeostasis is difficult, microbial communities that have health-protective or harmful effects can and should be identified using a metagenomic sequencing approach before the large-scale implementation of AMCs.

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens.

Introduction: The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. Methods: To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. Results and Discussion: In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.

Co-occurrence of antibiotic and metal resistance in long-term sewage sludge-amended soils: influence of application rates and pedo-climatic conditions.

Urban sewage sludge (USS) is increasingly being used as an alternative organic amendment in agriculture. Because USS originates mostly from human excreta, partially metabolized pharmaceuticals have also been considered in risk assessment studies after reuse. In this regard, we investigated the cumulative effect of five annual USS applications on the spread of antibiotic-resistant bacteria (ARB) and their subsequent resistance to toxic metals in two unvegetated soils. Eventually, USS contained bacterial strains resistant to all addressed antibiotics with indices of resistance varying between 0.25 for gentamicin to 38% for ampicillin and azithromycin. Sludge-amended soils showed also the emergence of resistome for all tested antibiotics compared to non-treated controls. In this regard, the increase of sludge dose generally correlated with ARB counts, while soil texture had no influence. On the other hand, the multi-antibiotic resistance (MAR) of 52 isolates selected from USS and different soil treatments was investigated for 10 most prescribed antibiotics. Nine isolates showed significant MAR index (≥ 0.3) and co-resistance to Cd, As and Be as well. However, events including an extreme flash flood and the termination of USS applications significantly disrupted ARB communities in all soil treatments. In any case, this study highlighted the risks of ARB spread in sludge-amended soils and a greater concern with the recent exacerbation of antibiotic overuse following COVID-19 outbreak.

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

Antimicrobial resistance (AMR) is a growing public health threat. Improved surveillance of AMR's genetic indicators in environmental reservoirs should lead to a more comprehensive understanding of the problem at a global scale, as with SARS-CoV-2 monitoring in sewage. However, the "best" monitoring approach is unclear. Some scientific works have emphasized monitoring for the abundance of already-known antimicrobial resistance genes (ARGs);others have emphasized monitoring for the potential of new ARGs to arise. The goal of this study was to examine which methods were employed by highly-cited papers studying AMR in environmental engineering and agricultural systems, thus providing insight into current and future methodological trends for monitoring ARGs. We searched recent (2018-2020) literature documenting AMR in five environmental matrices: wastewater, surface water, drinking water, stormwater, and livestock manure. We selected the most highly-cited papers across these matrices (89 papers from 17 809 initial results) and categorized them as using targeted methods (e.g., qPCR), non-targeted methods (e.g., shotgun metagenomics), or both. More than 80% of papers employed targeted methods. Only 33% employed non-targeted methods, and the use of targeted versus non-targeted methods varied by environmental matrix. We posit that improving AMR surveillance in environmental reservoirs requires assessing risk, and that different monitoring approaches imply different objectives for risk assessment. Targeted methods are appropriate for quantifying known threats, particularly in environmental matrices where direct human exposure is likely (e.g., drinking water). However, long-term studies employing non-targeted methods are needed to provide an understanding of how frequently new threats (i.e., novel ARGs) arise.