https://orcid.org/0000-0003-3889-4313
Figures & data
Table 1 Major Features of the 17 AGEs Characterized in This Work
Figure 2 Massive gene acquisition and loss across whole-genomes of seven related ICEs Tn6512, Tn6860, Tn6861, Tn6862, Tn6863, Tn6864, and Tn6865.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue or light orange denotes regions of homology (nucleotide identity ≥90%), light pink (nucleotide identity <90%). The seven Tn6512-related ICEs are listed at vertical coordinates, while the 10 genomic regions/sites (numbers in circles) with major modular differences (for details in Table S5) are shown at horizontal coordinates. Please also refer to the detailed genetic organization of the accessory modules inserted within regions 1, 5, 6, 7, 9, and 10, plus site 4 (Figure S1), site 3 (), and region 8 ( and S1).
Figure 3 Organization of Tn6896 from Tn6864, and comparison to related regions.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within Tn6864. Accession number of Tn6309Citation48 used as reference is KX710094.
Figure 4 Comparison of MDR regions from Tn6860, Tn6861, Tn6862, Tn6863, Tn6864, and Tn6865.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue or light orange denotes regions of homology (nucleotide identity ≥90%), light pink (nucleotide identity ˂90%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PROV275 and PROV023, Tn6863, Tn6864, and the chromosomes of strains PROV002 and WCHPr000369, respectively. Accession numbers of ISCR1–blaPER-4 unit,Citation49 Tn6502a,Citation50 Tn501,Citation51 ISCR2–tet(X6) unit,Citation11 and Tn5393cCitation52 used as reference are KU133341, KF914891, Z00027, CP047340, and AF262622, respectively.
Figure 5 Comparison of three related IMEs Tn6872, Tn6873, and Tn6874.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥90%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains NCTC6933, PROV013, and BML2496, respectively. Accession number of Tn6872 used as reference is LR134189.
Figure 6 Organization of MDR regions from Tn6873 and Tn6874, and comparison to related regions.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PROV013 and BML2496, respectively. Accession numbers of Tn6581c,Citation22 Tn4352,Citation53 and Tn5393cCitation52 used as reference are CO042857, CP04285, and AF262622, respectively.
Figure 7 Comparison of two related IMEs Tn6875 and Tn6876.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains FDAARGOS_87 and PROV013, respectively. Accession number of Tn6875 used as reference is CP031508.
Figure 8 Comparison of Tn7 and its four derivatives.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PROV087, PROV023, MF1, and Pr-15-2-50, respectively. Accession number of Tn7Citation47 used as reference is KX117211.
Figure 9 Comparison of MDR regions from four Tn7 derivatives.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue or light orange denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PROV087, MF1, PROV023, and Pr-15-2-50, respectively. Accession numbers of Tn1722,Citation54 Tn5393c,Citation52 chrA–orf98 unit,Citation22 Tn2,Citation55 Tn6502a,Citation50 Tn4352,Citation53 Tn1548,Citation56 and Tn125Citation57 used as reference are X61367, AF262622, CP042858, HM749967, KF914891, CP042858, AF550415, and JN872328, respectively.
Figure 10 Comparison of Tn1696 and its three derivatives.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains BML2496, PROV002, and PROV013, respectively. Accession numbers of Tn1696,Citation35 Tn6338,Citation36 and Tn6909Citation22 used as reference are U12338, KY270853, and CP032168, respectively.
Figure 11 Comparison of Tn21 and its three derivatives.
Notes: Genes are denoted by arrows. Genes, AGEs, and other features are colored based on their functional classification. Shading in light blue denotes regions of homology (nucleotide identity ≥95%). Numbers in brackets indicate nucleotide positions within the chromosomes of strains PROV013, MF1, and PROV087, respectively. Accession numbers of Tn21Citation35 and Tn6975Citation37 used as reference are AF071413 and CP041301, respectively.
