Antibiotic resistance genes are differentially mobilized according to resistance mechanism
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Antibiotic resistance genes are differentially mobilized according to resistance mechanism. / Nielsen, Tue Kjærgaard; Browne, Patrick Denis; Hansen, Lars Hestbjerg.
In: GigaScience, Vol. 11, giac072, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Antibiotic resistance genes are differentially mobilized according to resistance mechanism
AU - Nielsen, Tue Kjærgaard
AU - Browne, Patrick Denis
AU - Hansen, Lars Hestbjerg
N1 - Publisher Copyright: © 2022 The Author(s). Published by Oxford University Press GigaScience.
PY - 2022
Y1 - 2022
N2 - Background: Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes. Results: Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. Conclusions: In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
AB - Background: Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes. Results: Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons. Conclusions: In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.
KW - antibiotic resistance genes
KW - bioinformatics
KW - mobile genetic elements
U2 - 10.1093/gigascience/giac072
DO - 10.1093/gigascience/giac072
M3 - Journal article
C2 - 35906888
AN - SCOPUS:85135207500
VL - 11
JO - GigaScience
JF - GigaScience
SN - 2047-217X
M1 - giac072
ER -
ID: 318832764