The global distribution and environmental drivers of the soil antibiotic resistome

Delgado‐Baquerizo, Manuel; Hu, Hang‐Wei; Maestre, Fernando T.; Guerra, Carlos A.; Eisenhauer, Nico; Eldridge, David J.; Zhu, Yan; Chen, Qinglin; Trivedi, Pankaj; Du, Shuai; Makhalanyane, Thulani P.; Verma, Jay Prakash; Gozalo, Beatriz; Ochoa, Victoria; Asensio, Sergio; Zaady, Eli; Illán, Javier Gutiérrez; Siebe, Christina; Grebenc, Tine; Zhou, Xiaobing; Liu, Yurong; Bamigboye, Adebola R.; Blanco‐Pastor, José Luis; Durán, Jorge; Rodríguez, Alexandra; Mamet, Steven D.; Alfaro, Fernando D.; Abades, Sebastián; Teixido, Alberto L.; Peñaloza-Bojacá, Gabriel F.; Molina‐Montenegro, Marco A.; Torres-Díaz, Cristián; Pérez, Cecilia A.; Gallardo, Antonio; García‐Velázquez, Laura; Hayes, Patrick E.; Neuhauser, Sigrid; He, Ji‐Zheng

doi:10.1186/s40168-022-01405-w

Cited by 34 publications

(18 citation statements)

References 44 publications

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“…5, S6; Table S4). HGT is known to be a major driver of AMR spread among diverse microbial species in the community ( 1 , 3 ). These findings may have implications for how we manage future medical and environmental impacts of AMR spread through time ( 26 ).…”

Section: Discussionmentioning

confidence: 99%

“…Microbial interactions (competition and facilitation) are important factors in shaping the temporal variation of ARGs and ARB ( 1 , 23 ). The proximate determinants for the development of antibiotic resistance and its subsequent spread are horizontal gene transfer and mutation, as well as diverse microbial assemblages that can harbour ARGs ( 3 , 5 ). In fact, we showed there is variation in ARGs and ARB with soil age in the Arctic glacier forefields, and this variation can be meditated through microbial diversity and HGT (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…5, Table S6). These soil edaphic variables can influence both the proximate and ultimate determinants of AMR through habitat filtering ( 3 , 9 , 30 ).…”

Section: Discussionmentioning

confidence: 99%

“…Soil represents a natural reservoir for antibiotic resistance genes (ARG) that are either intrinsically evolved in bacteria or acquired under selection pressure through mutation, and recombination and/or through horizontal gene transfer (HGT) ( 1–3 ). ARGs within bacteria primarily act as a deterrent to the antimicrobial products (antibiotics) secreted by competing microbes in anticipation of maximising their nutrient acquisition from the environment, and thereby pre-date anthropogenic antibiotic use ( 4 , 5 ).…”

Section: Introductionmentioning

confidence: 99%

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Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

Roy,

Dawson,

Bradley

et al. 2023

Preprint

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Antimicrobial resistance (AMR) is widespread in terrestrial ecosystems. However, the natural processes shaping the spatial and temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies in recently deglaciated pioneer and developing Arctic soils. We showed that antibiotic-resistant genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB) are abundant, exhibit a non-uniform distribution, and generally increase with soil age. Our analyses suggest a strong positive relationship between soil age and ARG and ARB, which we attribute to increased competition between microbes in older soils. We also observed a weak negative relationship between soil age and ARG diversity mediated by soil organic matter – suggesting facilitation due to the alleviation of nutrient limitation. The microbial processes regulating the spread of AMR in Arctic soils may be further susceptible to the effects of future climate change and human activities.TeaserThe spatial and temporal spread of antimicrobial resistance in Arctic soils is dependent on microbial interactions for nutrients

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…5, Table S6). These soil edaphic variables can influence both the proximate and ultimate determinants of AMR through habitat filtering ( 3 , 9 , 30 ).…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

Roy,

Dawson,

Bradley

et al. 2023

Preprint

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“…Besides their versatility, ARGs can be highly mobilized throughout microbial populations via transformation, transduction and conjugation, greatly enhancing their dissemination (Zheng et al, 2023). A recent global analysis of topsoil communities showed a widespread prevalence of ARGs worldwide, with efflux pumps being the most common class (Delgado-Baquerizo et al, 2022). This prevalence may be attributed to their rapid spread through the environment via aerosols, even in clouds, water runoff from agriculture and plastic waste.…”

Section: Why Do Microorganisms Produce Antibiotics and De Velop Antib...mentioning

confidence: 99%

The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms

Van Goethem,

Marasco,

Hong

et al. 2024

Microbial Biotechnology

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In the relentless battle for human health, the proliferation of antibiotic‐resistant bacteria has emerged as an impending catastrophe of unprecedented magnitude, potentially driving humanity towards the brink of an unparalleled healthcare crisis. The unyielding advance of antibiotic resistance looms as the foremost threat of the 21st century in clinical, agricultural and environmental arenas. Antibiotic resistance is projected to be the genesis of the next global pandemic, with grim estimations of tens of millions of lives lost annually by 2050. Amidst this impending calamity, our capacity to unearth novel antibiotics has languished, with the past four decades marred by a disheartening ‘antibiotic discovery void’. With nearly 80% of our current antibiotics originating from natural or semi‐synthetic sources, our responsibility is to cast our investigative nets into uncharted ecological niches teeming with microbial strife, the so‐called ‘microbial oases of interactions’. Within these oases of interactions, where microorganisms intensively compete for space and nutrients, a dynamic and ever‐evolving microbial ‘arms race’ is constantly in place. Such a continuous cycle of adaptation and counter‐adaptation is a fundamental aspect of microbial ecology and evolution, as well as the secrets to unique, undiscovered antibiotics, our last bastion against the relentless tide of resistance. In this context, it is imperative to invest in research to explore the competitive realms, like the plant rhizosphere, biological soil crusts, deep sea hydrothermal vents, marine snow and the most modern plastisphere, in which competitive interactions are at the base of the microorganisms' struggle for survival and dominance in their ecosystems: identify novel antibiotic by targeting microbial oases of interactions could represent a ‘missing piece of the puzzle’ in our fight against antibiotic resistance.

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Tackling Soil ARG‐Carrying Pathogens with Global‐Scale Metagenomics

Bin-hao

Wang

et al. 2023

Advanced Science

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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.

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The global distribution and environmental drivers of the soil antibiotic resistome

Cited by 34 publications

References 44 publications

Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

The antibiotic crisis: On the search for novel antibiotics and resistance mechanisms

Tackling Soil ARG‐Carrying Pathogens with Global‐Scale Metagenomics

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