Dataset Information

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

ABSTRACT: Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

SUBMITTER: Wang B

PROVIDER: S-EPMC10502870 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

Wang Binhao B Xu Jianming J Wang Yiling Y Stirling Erinne E Zhao Kankan K Lu Caiyu C Tan Xiangfeng X Kong Dedong D Yan Qingyun Q He Zhili Z Ruan Yunjie Y Ma Bin B

Advanced science (Weinheim, Baden-Wurttemberg, Germany) 20230709 26

Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembl ...[more]

PMID: 37424042

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Project description:BackgroundCryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions.ResultsOur metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation).ConclusionsOur genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.

Project description:BackgroundA global surplus of coronavirus disease 2019 (COVID-19) vaccines exists as a result of difficulties in aligning the demand and supply for vaccine manufacturing and delivery. World leaders have accelerated vaccine development, approval, production and distribution as a pragmatic approach to addressing the immediate public health challenges of the first two and a half years of the pandemic.Main bodyThe currently predominant, highly transmissible Omicron variant of severe acute respiratory syndrome coronavirus 2 has brought us closer to the threshold required to achieve herd immunity by greatly increasing rates of natural infection. Paradoxically, in parallel with rising vaccination levels in industrialized nations, this indirectly reduces the need for mass vaccine campaigns. Principal concerns that contribute to low vaccination rates which persist in several other countries, particularly of the Global South, are vaccine hesitancy and unequal access to vaccination. Social uncertainty fueled by fake news, misinformation, unfounded lay opinions and conspiracy theories has inevitably led to an erosion of public trust in vaccination.ConclusionTo address the current mismatch between supply and demand of COVID-19 vaccines, there should be a focus on three principles: decelerating vaccine production, increasing distribution across communities, and optimizing cost-effectiveness of distribution logistics. Slowing down and switching from large-scale production to effectively 'made to order' is a feasible option, which should be commensurate with management capacity. Transparent and evidence-based data should be widely and freely disseminated to the public through multimedia channels to mitigate miscommunication and conspiracy theories. Use of soon-to-expire stockpiles should be prioritized not only to enhance booster dose rollouts in adults but to expand immunization campaigns to children (especially those aged 5-11 years), subject to national approval. Future research should ideally aim to develop vaccines that only require basic, affordable storage and maintenance procedures as opposed to sophisticated and expensive protocols.

Dataset Information

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

Publications

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.

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