Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska

Thermokarst lakes are hotspots of antibiotic resistance genes in permafrost regions on the Qinghai-Tibet Plateau

Antibiotic resistance genes (ARGs) are natural products and emerging pollutants in remote environments, including permafrost regions that are rapidly thawing due to climate warming. We investigated the role of thermokarst lakes (including sediment and water) in reserving ARGs compared to permafrost soils across the permafrost regions on the Qinghai-Tibet Plateau. As intrinsically connected distinct environments, permafrost soil, lake sediment, and lake water harbored 1239 ARGs in total, while a considerable number of same ARGs (683 out of 1239) concurrently presented in all these environments. Soil and sediment had a higher number of ARGs than water. Multidrug resistance genes were the most diverse and abundant in all three environments, where cls, ropB, mdfA, fabI, and macB were the top five most abundant ARGs while with different orders. Soil and sediment had similar ARG profiles, and the alpha and beta diversity of ARGs in sediment were positively correlated with that in soil. The beta diversity of ARG profiles between sediment and soil was highly contributed by turnover component (89%). However, turnover and nestedness components were almost equality contributed (46%-54%) to the beta diversity of ARG profiles between soil and water as well as between sediment and water. The results suggested that thermokarst lake sediments might inherit the ARGs in permafrost soils. Water ARGs are the subset of soil ARGs and sediment ARGs to a certain degree with species turnover playing a significant role. When accounting the ARGs in sediment and water together, thermokarst lakes had a significantly higher number of ARGs than permafrost soils, suggesting that thermokarst lakes act as the hotspots of ARGs in permafrost regions. These findings are disturbing especially due to the fact that tremendous number of thermokarst lakes are forming under accelerating climate change.

Nanopore adaptive sampling enriches for antimicrobial resistance genes in microbial communities

Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures promoting their persistence. Genomic surveillance could provide insights into how these reservoirs change and impact public health. Enriching for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we tested the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and Flongle flow cells. Using adaptive sampling, we observed consistent enrichment by composition. On average, adaptive sampling resulted in a target composition 4× higher than without adaptive sampling. Despite a decrease in total sequencing output, adaptive sampling increased target yield in most replicates. We also demonstrate enrichment in a diverse community using an environmental sample. This method enables rapid and flexible genomic surveillance.

Real-time genomics for One Health

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.

Effects of freeze-thaw dynamics and microplastics on the distribution of antibiotic resistance genes in soil aggregates

This is the first study investigating the effects of freeze-thaw (FT) and microplastics (MPs) on the distribution of antibiotic resistance genes (ARGs) in soil aggregates (i.e., soil basic constituent and functional unit) via microcosm experiments. The results showed that FT significantly increased the total relative abundance of target ARGs in different aggregates due to the increase in intI1 and ARG host bacteria. However, polyethylene MPs (PE-MPs) hindered the increase in ARG abundance caused by FT. The host bacteria carrying ARGs and intI1 varied with aggregate size, and the highest number of hosts was observed in micro-aggregates (<0.25 mm). FT and MPs altered host bacteria abundance by affecting aggregate physicochemical properties and bacterial community and enhanced multiple antibiotic resistance via vertical gene transfer. Although the dominant factors affecting ARGs varied with aggregate size, intI1 was a co-dominant factor in various-sized aggregates. Furthermore, other than ARGs, FT, PE-MPs, and their integration promoted the proliferation of human pathogenic bacteria in aggregates. These findings suggested that FT and its integration with MPs significantly affected ARG distribution in soil aggregates. They amplified antibiotic resistance environmental risks, contributing to a profound understanding of soil antibiotic resistance in the boreal region.

Nanopore Adaptive Sampling Enriches for Antimicrobial Resistance Genes in Microbial Communities

Antimicrobial resistance (AMR) is a global public health threat. Environmental microbial communities act as reservoirs for AMR, containing genes associated with resistance, their precursors, and the selective pressures to encourage their persistence. Genomic surveillance could provide insight into how these reservoirs are changing and their impact on public health. The ability to enrich for AMR genomic signatures in complex microbial communities would strengthen surveillance efforts and reduce time-to-answer. Here, we test the ability of nanopore sequencing and adaptive sampling to enrich for AMR genes in a mock community of environmental origin. Our setup implemented the MinION mk1B, an NVIDIA Jetson Xavier GPU, and flongle flow cells. We observed consistent enrichment by composition when using adaptive sampling. On average, adaptive sampling resulted in a target composition that was 4x higher than a treatment without adaptive sampling. Despite a decrease in total sequencing output, the use of adaptive sampling increased target yield in most replicates.

An Update on Eukaryotic Viruses Revived from Ancient Permafrost

One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that have remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about "live" viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that "zombie viruses" are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from seven different ancient Siberian permafrost samples, one from the Lena river and one from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to five different clades infecting Acanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.

Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics

Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.

Antimicrobial Stewardship Program: Reducing Antibiotic's Spectrum of Activity Is not the Solution to Limit the Emergence of Multidrug-Resistant Bacteria

Overconsumption of antibiotics in hospitals has led to policy implementation, including the control of antibiotic prescriptions. The impact of these policies on the evolution of antimicrobial resistance remains uncertain. In this work, we review the possible limits of such policies and focus on the need for a more efficient approach. Establishing a causal relationship between the introduction of new antibiotics and the emergence of new resistance mechanisms is difficult. Several studies have demonstrated that many resistance mechanisms existed before the discovery of antibiotics. Overconsumption of antibiotics has worsened the phenomenon of resistance. Antibiotics are responsible for intestinal dysbiosis, which is suspected of being the source of bacterial resistance. The complexity of the intestinal microbiota composition, the impact of the pharmacokinetic properties of antibiotics, and the multiplicity of other factors involved in the acquisition and emergence of multidrug-resistant organisms, lead us to think that de-escalation, in the absence of studies proving its effectiveness, is not the solution to limiting the spread of multidrug-resistant organisms. More studies are needed to clarify the ecological risk caused by different antibiotic classes. In the meantime, we need to concentrate our efforts on limiting antibiotic prescriptions to patients who really need it, and work on reducing the duration of these treatments.

How Do the Players Play? A Post-Genomic Analysis Paradigm to Understand Aquatic Ecosystem Processes

Culture-independent and meta-omics sequencing methods have shed considerable light on the so-called “microbial dark matter” of Earth’s environmental microbiome, improving our understanding of phylogeny, the tree of life, and the vast functional diversity of microorganisms. This influx of sequence data has led to refined and reimagined hypotheses about the role and importance of microbial biomass, that paradoxically, sequencing approaches alone are unable to effectively test. Post-genomic approaches such as metabolomics are providing more sensitive and insightful data to unravel the fundamental operations and intricacies of microbial communities within aquatic systems. We assert that the implementation of integrated post-genomic approaches, specifically metabolomics and metatranscriptomics, is the new frontier of environmental microbiology and ecology, expanding conventional assessments toward a holistic systems biology understanding. Progressing beyond siloed phylogenetic assessments and cataloging of metabolites, toward integrated analysis of expression (metatranscriptomics) and activity (metabolomics) is the most effective approach to provide true insight into microbial contributions toward local and global ecosystem functions. This data in turn creates opportunity for improved regulatory guidelines, biomarker discovery and better integration of modeling frameworks. To that end, critical aquatic environmental issues related to climate change, such as ocean warming and acidification, contamination mitigation, and macro-organism health have reasonable opportunity of being addressed through such an integrative approach. Lastly, we argue that the “post-genomics” paradigm is well served to proactively address the systemic technical issues experienced throughout the genomics revolution and focus on collaborative assessment of field-wide experimental standards of sampling, bioinformatics and statistical treatments.