Table 2.
Examples of MGEs carrying AMR genes found in S. suis genomes
| MGE | Hosts | AMR genes | Integration site (s) | Integrase family | References |
|---|---|---|---|---|---|
| ICEs | |||||
| Tn916 | |||||
| Tn916 | S. suis, S. agalactiae, S. pneumoniae, S. mutants, E. faecalis, C. difficile | tet(M) | llmO | Tyrosine | [145] |
| dICE_Tn916 | S. suis | tet(O) | [145] | ||
| dICE_Tn916 | S. suis | tet(M) | [145] | ||
| Tn5252 | |||||
| ICE_Tn5252_rplL*1 | S. suis, S. agalactiae, S. pneumoniae, S. pyogenes | tet(O), tet(O/W/32/O), tet(40), erm(B), aph(3’)-IIIa, ant(9’), ant(6’)-Ia, sat4 | rplL | Tyrosine | [89, 145] |
| ICE_Tn5252_rumA*1 | S. suis, S. agalactiae, S. pneumoniae, S. pyogenes | tet(M), tet(L), tet(O), tet(O/W/32/O), erm(B), aph(3’)-III, ant(6’)-Ia, sat4 | rumA | Tyrosine | [89, 97, 143, 145] |
| ICE_Tn5252_mutT*1 | S. suis | tet(L), tet(O), tet(O/W/32/O), erm(B), msr(C), mef(A) | mutT | Tyrosine | [89, 145] |
| ICE_Tn5252_rbgA*1 | S. suis | erm(B) | rbgA | Tyrosine | [145] |
| ICE_Tn5252_ llmO *1 | S. suis | tet(M) | llmO | Tyrosine | [145] |
| dICE_Tn5252 | S. suis | tet(O), tet(40) | rplL | Tyrosine | [145] |
| Partial_Tn5252 | S. suis | tet(O/W/32/O), erm(B), aph(3’)-IIIa, ant(9’), sat4 | rplL | Tyrosine | [145] |
| ICESsD9*2*3 | S. suis, E. faecalis | tet(O), erm(B) | rplL | Tyrosine | [143, 149] |
| ICESsu32457*2*4 | S. suis, S. agalactiae, S. pneumoniae, S. pyogenes | tet(40), tet(O/W/32/O), erm(B), ant(6’)-Ia, aph(3’) | rplL | Tyrosine | [143, 150, 244] |
| ICESsuSC216*2 | S. suis | tet(O), erm(B), optrA, aadD | rplL | Tyrosine | [97] |
| Tandem_ICESsuSC317*2 | S. suis | tet(L), tet(O), optrA | rumA | SR | [97] |
| ICESsuBSB6*2 | |||||
| S. suis | tet(O/W/32/O), erm(B), aph(3’)-IIIa, ant(6’)-Ia, sat4, vanG operon | rplL | Tyrosine | [121] | |
| ICESsuJH1308-2*2 | S. suis | tet(M), ant(6’)-Ia | rplL | Tyrosine | [89] |
| ICESsuJH1301*2 | S. suis | tet(O), erm(B), aph(3’)-III | rplL | Tyrosine | [89] |
| Tn1549 | |||||
| dICE_Tn1549_rplL | S. suis | tet(O/W/32/O) | rplL | Tyrosine | [145] |
| ICE_Tn1549_rbgA | S. suis | erm(B) | rbgA | Tyrosine | [145] |
| Tn1549 | S. suis | vanB operon | hsdM | Tyrosine | [89] |
| ICESp1108 | S. suis, S. agalactiae, S. pneumoniae,S. pyogenes | tet(L), tet(W), erm(B), lnu(B), erm(TR), ant(6’)-Ia, cat | rumA | Tyrosine | [89] |
| vanG | |||||
| ICE_vanG_lysS | S. suis | tet(W) | lysS | [145] | |
| TnGBS2 | |||||
| ICE_TnGBS2 | S. suis, S. agalactiae | tet(L), aph(3’)-IIIa, ant(6) | Diverse insertion sites, but not rplL | Tyrosine | [145, 245] |
| ICESsuTYPE3_rplL | S. suis, S. agalactiae, S. pneumoniae, S. pyogenes | tet(L), tet(W), erm(B), lnu(B), ant(6’)-Ia, cat | rplL | Tyrosine | [89] |
| IMEs | |||||
| Integrated in MGEs | |||||
| IME_PPI*3 | S. suis, S. thermophilus | tet(O), tet(40), erm(B) | PPI | SR | [145] |
| IME_SNF2*3 | S. suis | tet(O), erm(B) | SNF2 | SR | [145] |
| Integrated in chromosome | |||||
| IME_SsuNSUI181_tRNALeu | S. suis | aph(3’)-IIIa, ant(6)-Ia, sat4, vanZ | tRNA-leu | Tyrosine | [145] |
| IME_SsuNSUI231_rpsI | S. suis | tet(O) | rpsI | Tyrosine | [145] |
| IME_HTH-XRE-reg | S. suis | ant(6)-Ia | HTH-XRE regulator | SR | [145] |
| Prophages | |||||
| Prophage_rumA | S. suis | tet(O/W/32/O), tet(W), erm(B), lnu(B), lnu(C), lsa(E), mef(A), ant(6’)-Ib, aph(3’)-IIIa, ant(9’), sat4 | rumA | [145] | |
| ΦSC181 | S. suis | mef(A), aacA, aphD, cat, optrA | rumA | [97] | |
| Φm46.1*4 | S. suis, S. pyogenes | tet(O), mef(A) | rumA | Site-specific recombinase | [89, 97] |
| ΦSsu1135/10 | S. suis | erm(B), ant(6’)-Ia, aph(3)-IIIa | rumA | [170] | |
| ΦSsUD.1 | S. suis, S. pyogenes | tet(W), erm(B), ant(6’)-Ia, aph(3’)-III, sat4 | rumA | [89, 97, 170] | |
| ΦJH1301 | S. suis | mef(A), ant(6’)-Ia, cat, sat4 | cysM / rumA / SSU1958 | [89] |
ICEs, IMEs, and prophages are listed including the identified AMR genes, integration site, and integrase family (if known). ICEs are organized in families according to their conjugation module, and IMEs are grouped into two categories (indicated in bold). The presence of these elements in other bacterial species is notified. The table is not intended to be exhaustive but illustrative; for further information, see Bellanger et al. [144]
MGEs, mobile genetic elements; AMR, antimicrobial resistance; ICEs, integrative and conjugative elements; llmO, luciferase-like monooxygenase gene; SNF2, SNF2-family helicase; rplL, 50S ribosomal protein L7/L12; rum, RNA uracil methyltransferase; mutT, MutT/NUDIX hydrolase-family protein; rbgA, ribosome biogenesis GTPase A; dICE, derivative ICE; SR, serine recombinase; hsdM, type I restriction system adenine methylase; rplU, 50S ribosomal protein L21; IMEs, integrative and mobile elements; PPI, peptidyl-prolyl isomerase; rpsI, 30S ribosomal protein S9; HTH_XRE, helix-turn-helix XRE-family-like proteins; cysM, cysteine synthase.*1ICEs belonging to sub-family Tn5252. *2ICEs belonging to sub-family ICESa2603. *3MGEs studied for transfer between bacteria. erm(TR) genes include erm(B), erm(T) and an erm(A) subclass*4Prophage Φm46.1 is located in S. suis in tandem with several ICEs but can also behave as an independent element [89].