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Table 1 Genes related to antimicrobial resistance in S. suis

From: How Streptococcus suis escapes antibiotic treatments

Gene namesa

Relevant characteristicsb

Reference(s)

β-Lactams

 Target mutation

  pbp1a*1

PBP1a (A365S, P409T, V412F, E447A, N459D, H464Y, S477G, D479Q, A493T, K522Q, K255Q, N550D, S578A)

[65]

  pbp2b/pen(A)*1

PBP2b (K479T/A, D512E/Q/K/A, K513E/D, T515S)

[62, 65]

  pbp2X*1

PBP2x (M437L, S445T, T467S, Y525F, T551S, N569Q, L594Y/F, V596G)

[62, 65]

 Mutation in non-targeted genes

  mraY*1

Phospho-N-acetylmuramoyl-pentapeptide-transferase (M6I/L and either A4S/T or G8S)

[62]

Macrolides

 Target modification

  erm(A)*2

23S rRNA methyltransferase

[236]

  erm(B)*2

23S rRNA methyltransferase

[236]

  erm(C)*2

23S rRNA methyltransferase

[88]

  erm(G)*2

23S rRNA methyltransferase

[62]

  erm(T)

23S rRNA methyltransferase

[62]

  cfr*2

23S rRNA methyltransferase

[84]

 Antibiotic modification

  mph(B)

Macrolide 2'-phosphotransferase

[39]

  mph(C)

Macrolide 2'-phosphotransferase

[88]

 Efflux pump

  mef(A/E) / mel(D) (a.k.a. msr(D)) *3

MFS transporter / ABC F RPP

[31, 39, 88, 89]

Lincosamides

 Antibiotic modification

  lnu(A)

Lincosamide nucleotidyltransferase (adenylation)

[236]

  lnu(B)

Lincosamide nucleotidyltransferase (adenylation)

[39, 237]

  lnu(C)

Lincosamide nucleotidyltransferase (adenylation)

[145]

  lnu(E)

Lincosamide nucleotidyltransferase (adenylation)

[238]

 Target modification

  erm(A)*2

23S rRNA methyltransferase

[236]

  erm(B)*2

23S rRNA methyltransferase

[236]

  erm(C)*2

23S rRNA methyltransferase

[88]

  erm(G)*2

23S rRNA methyltransferase

[62]

  erm(T)

23S rRNA methyltransferase

[239]

  cfr*2

Ribosome methyltransferase

[84]

  lsa(E)*2

ABC-F RPP

[237]

  vga(F)*2

ABC-F RPP

[62]

  optrA*2

ABC-F RPP

[97, 115]

Pleuromutilin

 Target modification

  lsa(E)*2

ABC-F RPP

[145, 237]

  vga(F)*2

ABC-F RPP

[62]

Amphenicols

 Antibiotic modification

  cat(A)

Chloramphenicol acetyltransferase

[97, 143]

 Target modification

  optrA*2

ABC-F RPP

[33, 83, 97, 101, 115, 117]

  cfr*2

Ribosome methylase

[84]

 Efflux pump

  fexA

MFS transporter

[84]

Tetracyclines

 Target modification

  tet(M) [tet(M1), tet(M2), tet(M3)]*4

RPP antibiotic competition

[31, 51, 62]

  tet(O) (tetO1)*5

RPP, antibiotic competition

[31, 51]

  tet(O/32/O)*6

RPP, antibiotic competition

[31]

  tet(O/W/32/O)*6

RPP, antibiotic competition

[31]

  tet(S)

RPP, antibiotic competition

[31]

  tet(W)

RPP, antibiotic competition

[31, 51]

  tet(44)

RPP, antibiotic competition

[62]

 Efflux pump

  tet(B)

MFS transporter

[240]

  tet(K)

MFS transporter

[39]

  tet(L)

MFS transporter

[31, 51]

  tet(40)

MFS transporter

[31]

Trimethoprim

 Target modification

  dfrF

Trimethoprim-resistant dihydrofolate reductase

[62]

  dfrK

Trimethoprim-resistant dihydrofolate reductase

[62]

 Target mutation

  dhfr*1

Dihydrofolate reductase (I102L)

[62]

  dhfr promoter*1

Dihydrofolate reductase (A5G)

[62]

Aminoglycosides*7

 Antibiotic modification

  sat4

Streptothricin N-acetyltransferase

[116, 119]

  ant1

Aminoglycoside O-nucleotidyltransferase ANT

[62]

  ant(4’)-Ib

Aminoglycoside O-nucleotidyltransferase ANT

[62]

  ant(6)-Ia a.k.a. ant6, aadE (aadE1, aadE2)*8

Aminoglycoside O-nucleotidyltransferase ANT

[62, 89, 115, 116, 148]

  ant(6)-Ib

Aminoglycoside 6'-N-acetyltransferase

[62]

  ant(9’)-Ia, a.k.a. aad9

Aminoglycoside nucleotidyltransferase

[62, 116]

  aph(6)-Ia

Aminoglycoside O-phosphotransferase

[97]

  aph(3’)-IIIa a.k.a. aphA3

Aminoglycoside O-phosphotransferase

[116, 121]

  aac(6’)-aph(2’’) a.k.a. aacA, aphD*9

Aminoglycoside N-acetyltransferase—O-phosphotransferase

[97, 115]

  aac(6’)-Ie-aph(2’’)-Ia*9

Aminoglycoside N-acetyltransferase—O-phosphotransferase

[116]

Glycopeptides*10

 Target modification

  vanG

D-Ala-D-Ser ligase

[117, 121]

  vanT

D-ser producing serine racemase

[121]

  vanXY

D-Ala-D-Ala dipeptidase / D-Ala-D-Ala carboxypeptidase

[117, 121]

  vanZ

Putatively alters the binding of (lipo)glycopeptides to cells

[122]

Quinolones

 Target mutation

  parC*1

Topoisomerase IV (Ser79, Asp83)

[88, 131, 241]

  parE*1

Topoisomerase IV (Pro278)

[131]

  gyrA*1

DNA gyrase (Ser81, Glu85)

[62, 88, 131, 241]

  gyrB*1

DNA gyrase (Glu354, Asp315)

[62, 131]

 Efflux pump

  satAB

ABC transporter

[135]

  1. a *1 Mutated target gene. *2 AMR genes conferring resistance to several antibiotics. *3 The mef variants are not distinguished here. *4 Three tet(M) variants, tet(M1), tet(M2) and tet(M3), were identified in Hadjirin, et al., [62]. *5 A novel tet(O) variant designated tet(O1) was recently identified by Hadjirin, et al., [62]. *6 These are mosaic genes consisting of fragments of the tet genes mentioned in the order of 5’ to 3’. *7 There are two main nomenclatures in use for aminoglycoside-modifying enzymes (reviewed in Ramirez and Tolmasky [114]). Shortly, in the proposal of Shaw et al. [242], genes are identified by a three letter identifier followed by the site of modification in parentheses, then a Roman numeral indicating the resistance profile and, in some cases, a letter when multiple enzymes exist that modify the same position. In the proposal of Novick et al. [243], the genes are designated with three letters followed by a capital letter that identifies the site of modification and then a number to provide a unique identifier to different genes. The nomenclatures are interchangeably used in the literature, and both are provided in the table. *8 Two variants, aadE1 and aadE2, were recently reported by Hadjirin et al. [62]. *9 AAC(6´) enzymes can exist as fusion proteins linked to APH, ANT, or a different AAC, occupying the N- or C-terminal region and resulting in bifunctional enzymes. *10 There are six different molecular resistance types (named Van-A to Van-G) that confer resistance to glycopeptides by modifying the peptidoglycan structure and that can be organized in gene clusters. Reported individual genes are indicated. b Functions of the gene products, and, when appropriate, the substitutions in antibiotic targets reported in clinical antibiotic−resistant isolates are shown. Abbreviations: ABC, ATP-binding cassette; MFS, major facilitator family; PBP, penicillin-binding protein; RPP, ribosome protection protein.
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Veterinary Research

ISSN: 1297-9716