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Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes
Lin, Q.; Xavier, B.B.; Alako, B.T.F.; Mitchell, A.L.; Rajakani, S.G.; Glupczynski, Y.; Finn, R.D.; Cochrane, G.; Malhotra-Kumar, S. (2022). Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes. Communications Biology 5(1): 1217. https://dx.doi.org/10.1038/s42003-022-04187-x
In: Communications Biology. Nature Portfolio: Berlin. e-ISSN 2399-3642, more
Peer reviewed article  
Available in  Authors 
Keywords
    Marine/Coastal; Brackish water; Fresh water; Terrestrial
Authors  Top 
  • Lin, Q., more
  • Xavier, B.B., more
  • Alako, B.T.F.
  • Mitchell, A.L.
  • Rajakani, S.G., more
  • Glupczynski, Y., more
  • Finn, R.D.
  • Cochrane, G.
  • Malhotra-Kumar, S., more
Abstract
    Understanding the myriad pathways by which antimicrobial-resistance genes (ARGs) spread across biomes is necessary to counteract the global menace of antimicrobial resistance. We screened 17939 assembled metagenomic samples covering 21 biomes, differing in sequencing quality and depth, unevenly across 46 countries, 6 continents, and 14 years (2005-2019) for clinically crucial ARGs, mobile colistin resistance (mcr), carbapenem resistance (CR), and (extended-spectrum) beta-lactamase (ESBL and BL) genes. These ARGs were most frequent in human gut, oral and skin biomes, followed by anthropogenic (wastewater, bioreactor, compost, food), and natural biomes (freshwater, marine, sediment). Mcr-9 was the most prevalent mcr gene, spatially and temporally; blaOXA-233 and blaTEM-1 were the most prevalent CR and BL/ESBL genes, but blaGES-2 and blaTEM-116 showed the widest distribution. Redundancy analysis and Bayesian analysis showed ARG distribution was non-random and best-explained by potential host genera and biomes, followed by collection year, anthropogenic factors and collection countries. Preferential ARG occurrence, and potential transmission, between characteristically similar biomes indicate strong ecological boundaries. Our results provide a high-resolution global map of ARG distribution and importantly, identify checkpoint biomes wherein interventions aimed at disrupting ARGs dissemination are likely to be most effective in reducing dissemination and in the long term, the ARG global burden.
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