Representative integrons

Integron captures and carries resistance genes by site-specific recombination. According to their integrase (intI) genes, integrons can be divided into classes 1, 2 and 3. Resistance genes are located on gene cassettes, which are captured and integrated into the integrons during recombination events.

Table 1|List of representative integrons

CategoryDesignationAccession numberResistance genesDRFASTA sequenceGene listGBK-annotationSQN-annotationManual annotationGene organization
Concise class 1 integron In0 U49101 qacED1, and sul1 CGACA
Concise class 1 integron In0 CP025705 sul1, floR, strA, and strB ATCGC
Concise class 1 integron In2 AF071413 aadA1a, qacED1, and sul1 TCCAT
Concise class 1 integron In4 U12338 aacC1e, aadA2, cmlA1, qacED1, and sul1 CATGG
Concise class 1 integron In28 AF313472 blaCARB-2, cmlA1d, aadA1a, and qacED1 CAGTT
Concise class 1 integron In127 AF261825 aadA2, qacED1, sul1, tetA(G), and blaCARB-2 ACTTG
Concise class 1 integron In127 CP030075 aadA2, qacED1, sul1, mph(E), blaVIM-4, aacA7, and aacA4 GAGTC
Concise class 1 integron In173 CP021775 blaGES-1
Concise class 1 integron In191 KF534788 dfrA14b CTGTT
Concise class 1 integron In244 KC543497 aacA4', and blaIMP-9
Concise class 1 integron In280 JQ010984 aadB3, blaOXA-21, qacED1, and sul1
Concise class 1 integron In363 AY963803 dfrA1, qacED1, sul1, tetA(G), and sul3 CCATG
Concise class 1 integron In384 CP047981 dfrA12, qacED1, sul1, chrA, mphR(A), and aphA1 CCGGT
Concise class 1 integron In1154 KJ588780 aacA7, and blaIMP-1 AGCAT
Concise class 1 integron In1212 MF344573 aacA7, qacED1, and sul1
Concise class 1 integron In1222 KU160531 qnrVC4, qacF, aacA4'-17, cmlA1g, blaOXA-10, aadA1e, dfrA14b, and mph(A) TCGTT
Concise class 1 integron In1223 KX784502 blaIMP-1, aacA4', and aadA6 GCGGG
Concise class 1 integron In1328 KX196168 aacA4, aadB, blaGES-24, blaOXA-2, qacED1, sul1, tetA(G), strA, and strB GAGTC
Concise class 1 integron In1589 MN961666 blaIMP-26, qacG2, aacA4'-41, arr3, qacED1, and sul1 GCGAG
Concise class 1 integron In1684 MN823992 aacA4, blaOXA-1, catB3, arr3, blaTEM-1, blaCTX-M-3, and sul1
Concise class 1 integron In1718 CP042860 aacA4-CR, blaOXA-1, catB3, arr3, qacED1, and sul1
Concise class 1 integron In1776 MN423364 dfrA12, qacED1, and sul1
Concise class 1 integron In1784 CP054623 aadB, aacA3, blaCARB-53, qacED1, sul1, and mer CACGA
Concise class 1 integron In1789 CP054581 aacA4'-17, blaCARB-2, aadA2, qacED1, and floR
Concise class 1 integron In1793 CP059345 qacG2, aadA6, qacED1, and sul1
Concise class 1 integron In1795 CP054843 blaGES-1, aacA4', aphA15, qacED1, and tetA(G) GAGTC
Complex class 1 integron In27 EF219134 dfrA12, aadA2, qacED1, sul1, qnrB2, chrA, and mph(A) GTGAC
Complex class 1 integron In37 AY259086 aacA4cr, blaOXA-1, catB3, arr3, qacED1, sul1, and qnrA1 CTGTT
Complex class 1 integron In207 MG764550 dfrA25, qacED1, sul1, qnrB, and blaKPC-2
Complex class 1 integron In469 CP059345 arr3, dfrA27, aadA16, qacED1, sul1, blaPER-1, and aphA6
Complex class 1 integron In609 MN821366 aacA4'-17, catB8, qacED1, sul1, and blaCTX-M-9
Complex class 1 integron In615 KY978628 aacA27, aacC3, arr7, qacED1, sul1, qnrB4, and blaDHA-1
Complex class 1 integron In834 JX141473 qacH4, blaOXA-10, aadA1e, qacED1, sul1, catA2, chrA, and tetA(A)
Complex class 1 integron In1007 JX469383 aacA4cr, blaOXA-1, catB3, arr3, dfrA27, qacED1, sul1, bleMBL, blaNDM-1, and qnrA1 CTGTT
Complex class 1 integron In1021 CP042858 aacA4cr, arr3, dfrA27, aadA16, qacED1, sul1, bleMBL, blaNDM-3, and chrA
Complex class 1 integron In1079 CP054844 aacA4-12, blaOXA-101, aadA5, qacED1, sul1, and blaPER-1
Complex class 1 integron In1130 CP010378 dfrB3, qacED1, sul1, and qnrB2 CATGG
Complex class 1 integron In1395 MF144194 catB3q, aadA1a, qacED1, sul1, mph(E), and qnrVC6 CAGTT
Class 2 integron In2-4 AP002527 dfrA1, and aadA1y GTGCG
Class 2 integron In2-8 DQ176450 aadB4, catB2, dfrA1, and aadA1y
Class 2 integron In2-15 DQ533990 None
Class 2 integron In2-16 CP042861 dfrA1, aadA1a, qacED1, sul1, bleMBL, and blaNDM-1
Class 2 integron In2-76 MG764552 dfrA1
Class 3 integron In3-1 AF416297 blaIMP-1, and aacA4'-3
Class 3 integron In3-2 AY219651 blaGES-1, and aacA4'-3
Class 1 integron In469 CP059345 aadA16, qacED1, blaPER-1, and sul1
Class 1 integron In1793 CP059345 qacG2, aadA6, qacED1, and sul1
Complex class 1 integron In2129 CP096912 blaIMP-1, aacA4'-10, arr-3, aadA1a, qacED1,, and sul1
Complex class 1 integron In1782 MN961670 arr3, aadA1a, qacED1, sul1, and pncA
Complex class 1 integron In1783 MN961670 blaIMP-89, qacG2, aacA4', qacED1, sul1, and floR
Complex class 1 integron In1771 CP045554 blaIMP-1, aacA4', blaOXA-21, and aadA1a
Complex class 1 integron In1768 CP045551 blaIMP-1, aacA4', qacF2,, and blaOXA-21
Complex class 1 integron In1792 CP059995 blaIMP-91, blaOXA-10, aadB, aacA4, qacED1, and sul1
Complex class 1 integron In2092 CP096975 blaIMP-92, aacA4'-3, and aadA2
Complex class 1 integron In2091 CP096916 blaIMP-8
Complex class 1 integron In1762 MN629346 blaIMP-8, qacG2, aacA4'-41, qacED1, and sul1
Complex class 1 integron In1769 CP097103 bla OXA-10, aacA27, qacED1, and sul1
Complex class 1 integron In1886 MN961673 bla IMP-1, and aacA4
Complex class 1 integron In2098 CP096823 blaIMP-1, aacA3, qacED1, and aacA4
Complex class 1 integron In2089 CP097104 blaIMP-34, aacA5, qacED1, and aacA4
Complex class 1 integron In2131 CP096914 blaIMP-1, aacA4', and aacA4'-45
Complex class 1 integron In2099 CP096910 blaIMP-1, aacA7, and aadB
Complex class 1 integron In1590 CP096370 blaIMP-4, qacG2, aacA4'-42, aacA64, catB3, qacED1, and sul1

Fig. 1|Evolution of Tn402-related class 1 integrons

Class 1 integrons are frequently present among antibiotics-resistant isolates of Enterobacteriaceae and Pseudomonas. Evolution of class 1 integrons is associated with Tn402 and involves three major steps 1-3.

Step I: Insertion of chromosomal ancestor class 1 integron into Tn402 with a complete tni transposition module to generate a hybrid structure flanked by IRi (inverted repeat at the integrase end) and IRt (inverted repeat at the tni end), combining the ability of integron to capture gene cassettes to the self-mobility of Tn402, which might occur prior to or concomitant with antibiotic era including capture of qacE (quaternary ammonium compound resistance) occurred around the same time.

Step II: Capture of sul1 (sulfonamide resistance), orf5 and orf6, and then formation of 3'-conserved region (3'-CS) due to deletion events between qacE and sul1.

Step III: Various deletion or insertion events within 3'-CS and/or tni.

Most class 1 integrons from clinical contexts carry modifications at their 5'- and 3'-terminal regions, especially including partial or complete deletions of tni, which impairs their self-mobility; nevertheless, they are often inserted within mobile genetic elements such as plasmids and transposons, facilitating their rapid spread in the community and within hospitals.

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Fig. 2|Prototypes of complex class 1 integrons

Please note that In1395 (Table 1) as a complex class 1 integron contains prototype 5'-CS (intI1–attI1), 3'-CS1 (qacED1–sul1), and 3'-CS2 (qacED1–sul1–orf5–orf6). 5'-CS and 3'-CS2 in a complex class 1 integron correspond to 5'-CS and 3'-CS in a concise class 1 integron.

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Table 2|Promoters of class 1 integrons

PromoterVariants-35 sequenceSpacer-10 sequenceRef.
PcPcW (Weak)TGGACA17TAAGCTU49101
PcPcH1 (Hybrid 1)TGGACA17TAAACTM95287
PcPcH2 (Hybrid 2)TTGACA17TAAGCTU13880
PcPcS (Strong)TTGACA17TAAACTU12441
PcPcSS (Super-Strong)TTGATA17TAAACT4
PcPcIn42TTGGCA17TAAACTAJ243491
PcPcIn116TTGACA17TGAACTAJ621187
PcPcPUOTCGACA17TAAACTS68049
P2P2TTGTTA17TACAGTU42226
P2P2m1 (Mutated)TTGTTA17GACAGTDQ315788
P2P2m2 (Mutated)TTGTTA17TACACA5
P2P2m3 (Mutated)TTGTTA17TACAAT6

Modified from a previous publication 7. The most frequent Pc variant was PcW (41.7%), followed by PcH1 (28%), PcS (24.3%) and PcH2 (4.4%). The four other Pc variants, all more recently described, were extremely rare. The Pc variants possessing different expression efficiencies: PcW, PcH1, PcWTGN-10, PcH2, and PcS from the weakest to the strongest. The second base upstream of the -10 hexamer of Pc can be replaced by a G or A or a T instead of C, respectively, generating PcWTGN-10, PcWTAN-10 and PcWTTN-10.

Download an example of PcWTGN-10.

PcWTGN-10 is a promoter containing the -35 and -10 sequences of PcW with the extended -10 TGN motif 7. The PcW variant PcWTGN-10 is much stronger than the weak promoter PcW due to the C to G mutation 2 bp upstream of the -10 element 7.

attI and attC sites

Integrase IntI recognizes two different types of recombination site attI (integron attachment site) and attC (recognition site for integrase), and it catalyzes integration or excision of gene cassettes through site-specific recombination commonly between one attI site and one or more attC sites 8, 9. These sites are long inverted-repeat-containing sequences of variable length and sequence, and each inverted repeat begins with a core sequence RYYYAAC (or most commonly GCCTAAC) and ends with an inverted core sequence GTTRRRY (or most commonly GTTAGGC) as described previously 10, 11, which would form imperfect cruciform structures and be required for capture of resistance genes.

RYYYAAC-Nz-GTTRRRY

GCCTAAC-Nz-GTTAGGC

GCCTAAC-Nx-GCCTAAC-Ny-GCCTAAC-Nx-GTTAGGC

References

1.    Rowe-Magnus, D. A., Guerout, A. M. & Mazel, D. Bacterial resistance evolution by recruitment of super-integron gene cassettes. Mol Microbiol 2002; 43: 1657-1669.
2.    Gillings, M. et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J Bacteriol 2008; 190: 5095-5100.
3.    Gillings MR. Integrons: past, present, and future. Microbiol Mol Biol Rev 2014; 78: 257-277.
4.    Brizio A, Conceicao T, Pimentel M et al. High-level expression of IMP-5 carbapenemase owing to point mutation in the -35 promoter region of class 1 integron among Pseudomonas aeruginosa clinical isolates. Int J Antimicrob Agents 2006; 27: 27-31.
5.    Lindstedt BA, Heir E, Nygard I et al. Characterization of class I integrons in clinical strains of Salmonella enterica subsp. enterica serovars Typhimurium and Enteritidis from Norwegian hospitals. J Med Microbiol 2003; 52: 141-9.
6.    Vinue L, Jove T, Torres C et al. Diversity of class 1 integron gene cassette Pc promoter variants in clinical Escherichia coli strains and description of a new P2 promoter variant. Int J Antimicrob Agents 2011; 38: 526-9.
7.    Jove T, Da Re S, Denis F et al. Inverse correlation between promoter strength and excision activity in class 1 integrons. PLoS Genet 2010; 6: e1000793.
8.    Partridge SR, Recchia GD, Scaramuzzi C et al. Definition of the attI1 site of class 1 integrons. Microbiology 2000; 146 (Pt 11): 2855-64.
9.    Hall RM, Collis CM. Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol Microbiol 1995; 15: 593-600.
10.    Stokes HW, O'Gorman DB, Recchia GD et al. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol Microbiol 1997; 26: 731-45.
11.    Francia MV, Avila P, de la Cruz F et al. A hot spot in plasmid F for site-specific recombination mediated by Tn21 integron integrase. J Bacteriol 1997; 179: 4419-25.