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.

Evaluating Climate Warming Effects on Soil Resistome and Pathogenome: Future Risks for Agriculture and Human Health

“…The ARG-assigned reads were further taxonomically annotated in order to identify microbial hosts of ARGs using Kraken2 (v2.1.3) with default settings 17 . The identification of pathogenic species was based on the taxonomic matching with the pathogen list curated by the previous study 18 .…”

Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China

“…uk/20121212135622/http://www.bis.gov.uk/assets/foresight/docs/infectious-diseases/ t16.pdf, accessed on 15 November 2023) [68]. Pathogen Host Interaction (PHI) database (http://www.phi-base.org/, accessed on 3 December 2023) was applied to investigate the interaction between hosts and pathogens [69].…”

Coated Bacteria: Advanced Living Materials for Microbial Therapy

“…16 Note that engineered bacteria also suffer from potential risk of gene mutation or contamination via horizontal gene transfer. 17 On the contrary, surface decoration is capable to flexibly modify bacteria with diverse compositions and functional motifs, such as synthetic small molecules, polymers, and nanoparticles, and endow bacteria-based living materials with new exogenous functions. 18,19 Despite these elegant achievements, engineered living materials prepared by conventional surface modification are difficult to endow the modified bacteria with multiple functions to simultaneously address the issues suffered during in vivo applications.…”

“…As a typical way of introducing new functions to bacteria, genetic engineering is able to manipulate bacterial behaviors and enhance the treatment efficacy by controllably producing therapeutic molecules or factors. , However, due to the poor understanding and lack of suitable genetic engineering tools, the number of bacteria that can be genetically engineered is limited . Note that engineered bacteria also suffer from potential risk of gene mutation or contamination via horizontal gene transfer . On the contrary, surface decoration is capable to flexibly modify bacteria with diverse compositions and functional motifs, such as synthetic small molecules, polymers, and nanoparticles, and endow bacteria-based living materials with new exogenous functions. , Despite these elegant achievements, engineered living materials prepared by conventional surface modification are difficult to endow the modified bacteria with multiple functions to simultaneously address the issues suffered during in vivo applications .…”