Table 1.
Mechanisms of action of non-β-lactam antibiotics active against S. aureus and molecular basis of antibiotic resistance.
| Antibiotic Class/ Primary Agent |
Approve Year and Use | Primary Target and Mechanisms of Action |
Resistance Genes | Mechanism(s) of Resistance | Comments |
|---|---|---|---|---|---|
| Macrolides | Protein synthesis | ||||
| Erythromycin | 1952 [66]. SSTI (Resistance 1955) [67] |
Erythromycin binds to bacterial 23S rRNA in the 50S ribosomal subunit and stops protein synthesis by inhibiting the transpeptidation/translocation step of protein synthesis and assembly of the 50S ribosomal subunit [68,69]. The target site for macrolides is nucleotides A2058 and A2059 located in the V region of 23S rRNA and, rarely, nucleotide A752 located in domain II [70]. |
ermA [31], ermB, ermC [32], ermY [52], msr(F) [71], msrA [72], msrB, ereA, ereB, mphB, mphC [52] |
(i) Modification of the bacterial ribosome by 23S rRNA methyltransferase (encoded by erm genes) prevents the binding of erythromycin to ribosomal target [31,32]. (ii) Active efflux of macrolides from cells by ATP-binding-cassette family (ABC-F) transporters (encoded by msrA and msrB genes) protects ribosomes from inhibition [72,73]. (iii) Enzymatic hydrolysis of 14- and 15-membered lactone ring of macrolides by esterase (encoded by ere genes) prevents its binding to the antibiotic target site [74]. (iv) Phosphotransferases (encoded by mph genes) introduce phosphate to the 2′-hydroxyl group of the 14-, 15-, and 16-membered lactone rings of macrolides amino sugar, which interferes with the interaction of the antibiotic with nucleotide A2058 [52]. |
Modification of the bacterial ribosome and active efflux from the bacterial cell are important mechanisms of macrolide resistance in S. aureus. |
| Lincosamides | Protein synthesis | ||||
| Clindamycin | Discovered in 1966. SSTI caused by CA-MRSA [29] (Resistance 1968) [30] |
Clindamycin binds to bacterial 23S rRNA in the 50S ribosomal subunit and impedes both the assembly of ribosomes and the translation process [75]. |
ermA, ermB, ermC [76] cfr [41,42] |
(i) The rRNA methylase (encoded by erm genes) methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503) [77]. (ii) The acquired cfr gene encoded rRNA methyltransferase methylates an adenine residue of the 23S rRNA in the 50S ribosomal subunit [41], resulting in altered antibiotic binding sites within the ribosome. |
|
| Aminoglycosides | Protein synthesis | ||||
| Gentamicin | U.S. FDA 1971. Bacterial meningitis, sepsis of newborns, septicemia, UTI (Resistance 1975) [78,79] |
Gentamicin binds to the A-site on the 16S rRNA helix at the mRNA-tRNA decoding center of bacterial 30S ribosome subunit [80,81], causing the inhibition and inaccurate induction of translation, disrupting protein synthesis [82,83,84]. |
aac(6′)/aph(2″) aadD (AG O-adenyltransferase) [85] ant(4′) (AG O-nucleotidyltransferase(4′)) ant(9) (AG O-nucleotidyltransferase(9)) |
The bifunctional AMEs inactivate aminoglycosides by acetylating, phosphorylating, or adenylating amino or hydroxyl groups [51,85] Gentamicin, tobramycin and kanamycin resistance is generally mediated by a bifunctional AME AAC(6′)-APH(2″) (encoded by aac(6′)/aph(2″) gene) that specifies 6′-acetyltransferase [AAC(6′)] and/or 2″-phosphotransferase [APH(2″)] aminoglycoside modifying activities [36,37]. |
The aac(6′)/aph(2″) gene is most prevalent in aminoglycoside resistant S. aureus [86]. |
| Arbekacin (not used clinically in the U.S.) |
Japanese PMDA 1990 [87]. Pneumonia and sepsis due to MRSA. (Resistance 1979) [88] |
Arbekacin binds to both 50S and the 30S ribosomal subunits, resulting in codon misreading and inhibition of translation [89]. | aac(6′)-aph(2″) [88,90] | (i) A single base alteration (G1126A) of aac(6′)/aph(2″) gene resulted in one amino acid substitution S376N in AAC(6′)/APH(2″), which leads to arbekacin resistance in MRSA strain PRC104 [90]. (ii) β-lactam-inducible arbekacin resistance was reported in MRSA strain by the integration of Tn4001-IS257 hybrid structure containing aac(6′)/aph(2″) gene cointegrated into a region downstream of blaZ gene [91].(iii) The AAC(6′)/APH(2″) modify arbekacin by 6′-N-acetylation and/or 2″-O-phosphorylation of AGs that contain 6′-NH2 and/or 2″-OH [37,92]. |
Arbekacin is not inactivated by AMEs (3′)(APH), (4′)(AAD), or AAD(2″) and has a weak affinity to (6′-IV) (AAC) [93]. |
| Glycopeptides | Cell wall synthesis | ||||
| Vancomycin | 1958. Bacteremia, infective endocarditis, osteomyelitis, meningitis, pneumonia, sepsis, and complicated SSTI due to HA-MRSA and CA-MRSA [29]. (Resistance VISA in 1996 [28] and VRSA in 2002 [94]) |
Vancomycin bind to D-Ala-D-Ala termini moieties of Lipid II precursor of peptidoglycan through a series of hydrogen bonds, leading to conformational alteration that prevents incorporation of NAM- and NAG-peptide subunits to the growing peptidoglycan chain and consequent transpeptidation [95,96,97]. This alters membrane integrity and increases permeability, leading to bacterial death. |
vanA [97,98] Mutations in walKR, vraSR, graSR, and clpP Mutation in rpoB [99,100] SNPs in capB (E58K) and lytN (I16V) gene [101] |
(i) VRSA: The Tn1546-borne vanA gene cluster encodes 9 proteins (D-Ala:D-Lac ligases) that modify D-Ala-D-Ala termini of peptidoglycan chains to D-Ala-D-Lactate, thereby inhibiting target binding by vancomycin [102,103]. (ii) VISA: Mutations in TCSs like essential WalKR [104,105,106,107], VraSR [108,109,110], and GraSR [107,109,110,111,112] affect cell wall biosynthesis, resulting in reduced susceptibility to vancomycin. (iii) Mutation in rpoB (encoding RNA polymerase subunit B) [99,100]. (iv) Mutation in TCS walKR and proteolytic regulatory gene clpP leads to raised vancomycin resistance in laboratory VISA strain N315LR5P1 [113]. (v) SNPs in capB (E58K) gene (encoding tyrosine kinase) and lytN (I16V) gene (encoding N-acetylmuramyl-L-alanine amidase) cause increased S. aureus resistance to vancomycin in the absence of van genes [101]. |
VRSA is mediated by the vanA gene cluster, which is transferred from vancomycin-resistant Enterococcus [114]. |
| Teicoplanin (formerly known as teichomycin A2) |
1988. Approved in Europe for SSTI, pneumonia, and sepsis [115]. Never approved for use in the U.S. (Resistance 2000) [116] |
Teicoplanin inhibits peptidoglycan polymerization, leading to the inhibition of bacterial cell-wall synthesis. | tcaRAB [117,118], tcaA [119] | (i) The tcaRAB operon may be involved in increased teicoplanin resistance in S. aureus [118]. (ii) Mutation in tcaRAB may influence the transcription of the cell wall biosynthesis gene and may contribute to increasing teicoplanin resistance [117]. (iii) The tcaA gene within tcaRAB plays a relevant role in teicoplanin resistance in S. aureus clinical isolates [119]. |
BSAC recommended breakpoint for teicoplanin are susceptible (MIC ≤ 2 mg/L) and resistant (MIC > 2 mg/L). |
| Oxazolidinones | Protein synthesis | ||||
| Linezolid | U.S. FDA 2000. ABSSSI, pneumonia, BJI, catheter- related bacteremia [120] (Resistance 2001) [121] |
Linezolid binds to bacterial 23S rRNA in the 50S ribosome subunit, thereby preventing the formation of functional 70S ribosomal initiation complex with 30S subunit, mRNA, initiation factors, and N-formylmethionyl-tRNA (tRNAfMet) [122]. |
cfr [123] Mutations in 23S rRNA [121,124] |
(i) Acquisition of cfr gene encoding 23S rRNA methyltransferase [125], which modifies adenosine at position 2503 in 23S rRNA in the large ribosomal subunit [126]. (ii) The T2500A mutation in the 23S rRNA gene and loss of a single copy of rRNA [127]. (iii) Mutations G2576T, G2576T, G2447T in domain V of 23S rRNA [121,124] and amino acid changes in ribosomal proteins L3 and L4 [128] lead to conformational changes in the ribosome. |
|
| Tedizolid | U.S. FDA 2014; E.U. EMA 2015.ABSSSI and pneumonia | Tedizolid binds to 23S rRNA in the 50S ribosome subunit and prevents the formation of 70S ribosomal initial complex, resulting in inhibition of bacterial protein synthesis [129,130]. |
cfr rplC, rplD, rplV, rpoB [131] |
(i) Mutations in domain V region of 23S rRNA target confer resistance to tedizolid. (ii) Mutations in ribosomal proteins L3, L4, and L22 (encoded by rplC, rplD, and rplV genes, respectively) and the 23S rRNA target [132]. (iii) Mutation in rpoB corresponding to amino acid substitution D449N [131]. |
Mutation in L3, L4, and L22 also mediate PhLOPSa (phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A) resistance. |
| Contezolid | NMPA of China 2021 [133]. Complicated SSTI, ABSSSI (Resistance 2021) [134]. |
Contezolid binds to the 23S rRNA region adjacent to the peptidyl transferase center of the 50S ribosomal subunit and prevents the formation of a functional 70S initiation complex, thereby interfering with bacterial protein synthesis. | cfr, optrA | Contezolid exhibited limited activity against strains with linezolid resistance genes cfr and optrA [134]. | Contezolid has reduced hematologic toxicity compared to linezolid |
| Lipopeptides | Cell wall synthesis Cell membrane |
||||
| Daptomycin | U.S. FDA 2003. Bacteremia, ABSSSI (Nonsusceptible 2004) [135] |
Daptomycin complexes with Ca2+ to form oligomers that insert into bacterial membranes, resulting in depolarization, permeabilization, leakage of ions, and ultimately bacterial death [136]. Daptomycin disrupts the localization of cell wall synthesis enzymes such as MurG, further interfering with cell wall synthesis [137,138]. |
mprF, dltA [139,140], yycH, yycI [141], rpoB [99], walKR, vraSR, graSR [142,143] | (i) Alteration of the surface charge of cells due to mutation in mprF gene (encoding phosphatidylglycerol lysyltransferase) which leads to lysinylation of PG and translocation of lysyl-PG [144]. (ii) Mutation in TCSs walKR, vraSR, and graSR which are involved in cell wall synthesis and permeability are associated with daptomycin susceptibility in S. aureus [142,143]. (iii) Mutation in rpoB gene (encoding RNA polymerase) confers dual heteroresistance to daptomycin and vancomycin [99]. (iv) Mutations in yycH and yycI genes lead to the loss of protein functions essential for cell wall synthesis [141]. (v) dltA gene overexpression leads to electrostatic repulsion and indirectly reduces autolysin, resulting in daptomycin nonsusceptibility [139,140]. |
S. aureus strains with MIC ≤ 1 μg/mL are referred as daptomycin-susceptible (DAP-S) [145] and MIC >1 μg/mL as daptomycin-non susceptible [146]. |
| Lipoglycopeptides | Cell wall synthesis | ||||
| Telavancin (derivative of vancomycin. Addition of the hydrophobic side chain and hydrophilic group results in enhanced activity [147]. |
U.S. FDA 2009 and 2013 [148]. Complicated SSTI, pneumonia, BJI, ABSSSI, bacteremia [149]. |
Telavancin inhibits cell wall biosynthesis by binding to late-stage peptidoglycan synthesis, like vancomycin. Additionally, it depolarizes the bacterial cell membrane and disrupts its functional integrity [150]. | - | The vanA-mediated telavancin resistance is rare in MRSA [151]. |
|
| Tetracyclines | Protein synthesis | ||||
| Tetracycline | 1948 [152] SSTI (Resistance 1953) [44] |
Tetracycline binds to bacterial 30S ribosomal subunit and prevents the aminoacyl tRNA from binding to A site of the rRNA, resulting in inhibition of translation. To some extent, it also binds to the bacterial 50S ribosomal subunit [44,153,154]. | tetM, tetO, tetK [155], tetS/M, tetA | (i) Ribosomal protection: the tetM and tetO genes encode enzymes that destabilize the interaction between tetracyclines and their cellular target ribosome [44,45]. (ii) Active efflux: the tetK gene encodes efflux protein that couples the tetracycline with proton motive force to pump it out from the cell against the concentration gradient [44,155]. |
The tetK gene is normally found in S. aureus. |
| Doxycycline | U.S. FDA 1967 [156,157]. UTI, SSTI [27] |
Doxycycline inhibits bacterial protein synthesis by preventing the association of aminoacyl tRNA with the ribosome, an MoA similar to tetracycline. | tetK [158,159] | Active efflux by tetK encoded efflux [158,159]. | |
| Tigecycline | U.S. FDA 2005.ABSSSI, pneumonia | Tigecycline inhibits protein synthesis, an MoA similar to tetracycline but with enhanced binding. | tetM, tetO, tetX | The oxygen-dependent destruction of tigecycline is catalyzed by the enzyme TetX [160,161,162]. |
Tigecycline retains activity against both tetM and tetO. |
| Omadacycline (derived from tetracycline) [163] |
U.S. FDA 2018.ABSSSI, SSTI [164], pneumonia (CA-associated) | Omadacycline binds to bacterial 30S ribosomal subunit and inhibits protein synthesis, an MoA similar to tetracycline with enhanced binding like tigecycline [165]. |
- | Resistance mechanism not reported. | Unaffected by the presence of tetK active efflux gene and ribosomal protection tetM or tetO gene [166,167]. |
| Fusidane | Protein synthesis | ||||
| Fusidic acid | 1962. ABSSSI |
Fusidic acid binds to elongation factor G (EF-G) on the ribosome, thereby preventing the release of EF-G-guanosine diphosphate complex and delaying bacterial protein synthesis by inhibiting the next stage in translation [168,169]. | fusA [170], fusB [171,172], fusc, fusD | (i) Mutations in chromosomal fusA (encoding ribosomal translocase and translation elongation factor EF-G) [170] or fusE genes confer high-level resistance to fusidic acid. (ii) Mutation in acquired genes fusB (encoding an inducible protein that protects an in vitro translation) [171,172] and fusD genes mediate low-level resistance. These mutations affect the elongation factor EF-6. |
The fusc and fusD are homologs of fusB [173]. |
| Pleuromutilin | Protein synthesis | ||||
| Retapamulin |
U.S. FDA 2007. Impetigo [174] |
Retapamulin binds to domain V of 23S rRNA on the 50S ribosome subunit, thereby blocking peptide formation directly by interfering with substrate binding. | 23S rRNA | Resistance to retapamulin occurs due to mutations in the genes encoding 23S rRNA methyltransferase. | Retapamulin is a semisynthetic derivative of pleuromutilin |
| Fluoroquinolones | DNA replication | [46,175] | |||
| Ciprofloxacin (2nd-generation fluoroquinolone) |
U.S. FDA 1987.UTI | Ciprofloxacin target bacterial DNA topoisomerase IV and DNA gyrase, thus preventing it from supercoiling the bacterial DNA [176], which leads to inhibition of DNA replication [177,178]. |
gyrA [33], grlA [33], flqA (formerly ofx/cfx) [35], norA [58,179] | (i) Mutation in the genes grlA (encoding DNA topoisomerase IV subunit A) [33,34,35,46], gyrA (encoding DNA gyrase subunit A) [33,34,35], and flqA (linked to DNA topoisomerase IV) [35]. (ii) Mutations in the gene norA (encoding a membrane-associated active efflux pump NorA) [58,180]. |
Elevated norA expression potentiates evolution by increasing the fitness benefit provided by a mutation in DNA topoisomerase [179]. |
| Levofloxacin | U.S. FDA 1996. RTI, UTI, SSTI |
Levofloxacin inhibits bacterial DNA replication, an MoA similar to ciprofloxacin. | gyrA, grlA | (i) Mutation in the genes grlA and gyrA [181]. (ii) Mutations in the gene norA [180]. |
|
| Delafloxacin (previously referred to as ABT-492) [182] |
U.S. FDA 2017 [183]; E.U. EMA 2019. SSTI, ABSSSI (Resistance 2017) [184] |
Delafloxacin inhibits bacterial DNA replication by blocking both DNA topoisomerase IV and DNA gyrase, an MoA similar to ciprofloxacin [182]. | grlA | Point mutations in the grlA [185,186]. | Delafloxacin is not active substrate for S. aureus efflux pumps [185]. |
| Quinolones | DNA replication | ||||
| Ozenoxacin (topical quinolone without fluorine at C6-position) |
U.S. FDA 2017.Japanese PMDA 2016 [187]. SSTI (impetigo) caused by MRSA |
Ozenoxacin inhibits bacterial DNA replication by dual-targeting activity against DNA topoisomerase IV and DNA gyrase [35]. | grlA, grlB | Mutations in QRDR regions of grlA and gyrA are the primary cause of decreased susceptibility to ozenoxacin [35]. | Low MIC of ozenoxacin was observed for MSSA and MRSA strains with reduced susceptibility to nadifloxacin [187]. |
| Pyrimidine/ Sulfonamide |
Folate synthesis (DNA synthesis and protein synthesis) | ||||
| Trimethoprim–Sulfamethoxazole (TMP-SMX) | UTI, SSTI, and BJI due to CA-MRSA [29] | TMP binds and inhibits the dihydrofolate reductase, thereby preventing the conversion of dihydrofolic acid (DHF) to tetrahydrofolic acid (THF) [188]. THF is an essential precursor of the thymidine synthesis pathway and interference with this pathway results in inhibition of bacterial DNA synthesis. SMX inhibits bacterial dihydropteroate synthase, an enzyme involved upstream in the thymidine synthesis pathway, resulting in the inhibition of folic acid biosynthesis [188]. |
dfrA, dfrB [189], dfrD [189], dfrG [190], dfrK, dfrS1 [191,192] | (i) The acquisition of dfrA gene (encoding DHFR) and mutation of the chromosomal dfrB gene (encoding SaDHFR) are considered key determinants of TMP-SMX resistance [189,193,194,195]. (ii) Point mutation in the dfrB gene resulted in a single amino acid substitution Phe98Tyr of SaDHFR, which was associated with TMP-SMX resistance in S. aureus [189]. (iii) Transposon-located dfrA gene mediates TMP resistance [194,196]. (iv) The dfrG gene (encoding DHFR) mainly mediates the TMP resistance in S. aureus clinical isolates [190,195]. |
|
| Other classes | |||||
| Mupirocin (previously pseudomonic acid) |
Discovered in 1971 [197] while marketed for clinical use in the UK in 1985 and US in 1988 [198]. SSTI, nasal carriage of S. aureus (Resistance 1987) [199,200]. |
Mupirocin binds to bacterial isoleucyl transfer RNA (tRNA) synthetase, leading to depletion of isoleucyl–tRNA and accumulation of the corresponding uncharged tRNA. This results in the inhibition of protein and RNA synthesis [201]. | ileS [202,203,204], mupA [205,206], and mupB [207] | (i) Mutations in the chromosomal ileS gene (encoding native isoleucyl t-RNA synthetase) result in V588F or V631F alterations [202,203,204], which lead to low-level mupirocin resistance [205]. (ii) Acquisition of the plasmid-encoded mupA gene (encoding eukaryotic-like isoleucyl–tRNA synthetase variant) [208] confers high-level resistance to mupirocin [205,206]. (iii) Acquisition of the plasmid-encoded mupB gene (encoding eukaryotic-like isoleucyl–tRNA synthetase variant) confers high-level resistance to mupirocin [207]. |
Low-level mupirocin resistance (MIC 8–256 μg/mL) and high-level resistance (MIC ≥ 512 μg/mL) [209]. |
| Fosfomycin | Discovered in 1969 [210]. UTI |
Fosfomycin deactivates the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) and catalyzes the addition of phosphoenolpyruvate to UDP-N-acetylglucosamine (UDP-GlcNAc) to form UDP-N-acetylmuramic acid (UDP-MurNAc), thereby inhibiting bacterial cell-wall synthesis [211]. | fosB [54], glpT and uhpT [212,213,214], murA [213,215] tet38 [216], fosY [217] | (i) Thiol-S-transferase (encoded by fosB gene) catalyzes the inactivation of fosfomycin [53,54]. (ii) Mutations in fosfomycin uptake transporter proteins GlpT (Trp137/Arg) (encoded by glpT gene) [213] and UhpT (encoded by uhpT genes) [214] reduce the permeability and subsequently prevent fosfomycin from invading the bacterium [212,213]. (iii) Mutation in target enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (encoded by murA gene) reduces its affinity for fosfomycin [215]. (iv) The major facilitator superfamily efflux transporter Tet38 (encoded by tet38 gene) contributes to fosfomycin resistance [216]. (v) FosY protein, a putative bacillithiol transferase enzyme (encoded by fosY gene) confers resistance to fosfomycin in CC1 S. aureus [217]. |
|
| Rifampin | Discovered in 1965, introduced for therapy in Italy in 1968, and approved in the United States in 1971 [218]. Endocarditis; BJI [27]. |
Rifampin inhibits transcription (RNA synthesis) by binding to the β-subunit of the bacterial DNA-dependent RNA polymerase [219,220]. | rpoB [43,221] | (i) Mutations in the RRDR region of rpoB gene (encoding RNA polymerase) resulted in amino acid substitutions of Gln468/Arg, His481/Tyr, and Arg484/His and are associated with high-level resistance to rifampicin [43]. (ii) Mutation in the rpoB (N967I) gene causes the substitution Asn967/Ile in the β-subunit of RNA polymerase [221]. |
CLSI breakpoint of rifampicin susceptibility is ≤1 μg/mL [146]. |
–: not studied or reported, AAC: aminoglycoside acetyltransferase, ABSSSI: acute bacterial skin and skin structure infection, AG: aminoglycoside, AMEs: aminoglycoside-modifying enzymes, ANT: aminoglycoside nucleotidyltransferase, APH: aminoglycoside phosphotransferase, BJI: bone and joint infections, BSAC: British Society for Antimicrobial Chemotherapy, CLSI: Clinical and Laboratory Standards Institute, E.U. EMA: European Union European Medicine Agency, Japanese PMDA: Japanese Pharmaceutical and Medical Devices Agency, MRSA: methicillin-resistant S. aureus, MSSA: methicillin-sensitive S. aureus, PG: peptidoglycan, QRDR: quinolone-resistance-determining region, RRDR: rifampin-resistance-determining region, rRNA: ribosomal RNA, SaPI: S. aureus pathogenicity island, SMX: sulfamethoxazole, SSTI: skin and soft tissue infections, TCSs: two-component regulatory systems, TMP: trimethoprim, U.S. FDA: U.S. Food and Drug Administration, UTI: urinary tract infection, VISA: vancomycin intermediate-resistant S. aureus, VRSA: vancomycin-resistant S. aureus.