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  • Inda Diaz, Juan Salvador,1984Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,CARe - Centrum för antibiotikaresistensforskning,Department of Mathematical Sciences,Centre for antibiotic resistance research, CARe (author)

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes

  • Article/chapterEnglish2023

Publisher, publication year, extent ...

  • 2023-03-08
  • Springer Science and Business Media LLC,2023
  • electronicrdacarrier

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  • LIBRIS-ID:oai:research.chalmers.se:9162e26f-564a-4c51-ad2f-8631ff5dd55b
  • https://doi.org/10.1186/s40168-023-01479-0DOI
  • https://research.chalmers.se/publication/535209URI
  • https://gup.ub.gu.se/publication/325304URI

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  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants. RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs. CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Lund, David,1994Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,CARe - Centrum för antibiotikaresistensforskning,Department of Mathematical Sciences,Centre for antibiotic resistance research, CARe(Swepub:cth)dlund (author)
  • Parras Moltó, Marcos,1988Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences(Swepub:cth)parras (author)
  • Johnning, Anna,1985Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences(Swepub:gu)xjannz (author)
  • Bengtsson-Palme, Johan,1985Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Centre for antibiotic resistance research, CARe,Institute of Biomedicine, Department of Infectious Medicine(Swepub:gu)xbengg (author)
  • Kristiansson, Erik,1978Gothenburg University,Göteborgs universitet,CARe - Centrum för antibiotikaresistensforskning,Institutionen för matematiska vetenskaper,Centre for antibiotic resistance research, CARe,Department of Mathematical Sciences(Swepub:gu)xkrier (author)
  • Göteborgs universitetInstitutionen för matematiska vetenskaper (creator_code:org_t)

Related titles

  • In:Microbiome: Springer Science and Business Media LLC11:1, s. 44-2049-2618

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Chalmers University of Technology
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