Superbugs!
How bacteria develop resistance to antibiotics
Antibiotics are one of the miracles of modern medicine, allowing us to fight infections by pathogenic bacteria. They attack essential molecular machines in bacteria, stopping or slowing their action, ultimately slowing growth or killing the cell. Resistance to antibiotics is posing a new danger to our health care. Infections by resistant bacteria are difficult to treat as they evolved proteins that destroy or modify antibiotics, or evade the drugs. Evolution of resistance is very fast in bacteria as they multiply rapidly to generate large populations. Antibiotics can kill susceptible strains, leaving resistant ones to proliferate.
The illustration shows a cross section of a fragment of MRSA (methicillin-resistant Staphylococcus aureus) with proteins involved in antibiotic resistance 
. Select them on the painting to access more information. Each resistance protein contains a highlight for easier navigation. Use the menus to explore resistance by Antibiotic or by Mechanism. Explore the biological processes targeted by different antibiotic classes in the Antibiotics and MRSA view.
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Antibiotics and MRSA
Staphylococcus aureus can cause infections in the skin, throat, and digestive tract. MRSA (methicillin-resistant Staphylococcus aureus) is a strain of staph bacteria that has developed resistance mechanisms to evade almost all current antibiotics. The bacteria is shown in full on the EM-scan on the left and in detail in the illustration.
The following bacterial sections are highlighted on the illustration with the biological processes targeted by some antibiotics listed:
Cell Wall: 
Cell wall is the outer layer composed of a crosslinked network of peptidoglycan chains that protects the bacteria from osmotic pressure. Building of the cell wall is targeted by:
Cell Membrane:
Membrane is filled with protein pumps and enzymes that build the cell wall
Cytoplasm:
Cytoplasm is filled with DNA, ribosomes, enzymes, and other proteins key to bacterial life cycle. Cytoplasmic processes targeted by antibiotics:
- DNA Replication: Quinolones
- DNA Transcription: Rifampicin
- Protein Synthesis: Macrolides, Aminoglycosides, Fusidic acid
- Folic Acid Synthesis: Antifoliates
Beta-lactamase
Resistance against: Beta-lactam antibiotics 
Resistance mechanism: Destruction of antibiotic
Beta-lactamases are enzymes expressed by resistant bacteria that protect the Penicillin Binding Proteins (PBPs). They bind to beta-lactam antibiotics (e.g. penicillin) and break the reactive beta-lactam ring, destroying the antibiotics. PDB structure 1pio.
Penicillin Binding Protein 2a (PBP2a)
Resistance against: Beta-lactam antibiotics
Resistance mechanism: Mutation in the target site
PBP2a is a mutated form of PBP. It binds weakly to beta-lactam antibiotics (red), so it can cross-link the peptidoglycan chains in the presence of antibiotics. PDB structure 1mwu.
VanA
Resistance against: Vancomycin
Resistance mechanism: Alteration to the target
VanA is an enzyme that builds a new type of cell wall building block that does not bind vancomycin but can still be used by PBPs to create the cell wall. PDB structure 1e4e.
VanX
Resistance against: Vancomycin
Resistance mechanism: Alteration to the target
VanX works alongside VanA . It breaks down any of the vancomycin-susceptible building blocks of the cell wall while VanA produces the antibiotic-resistant kind. PDB structure 1r44.
TetM protein
Resistance against: Macrolide antibiotics
Resistance mechanism: Alteration of the target site
After erythromycin binds to the large subunit of the ribosome, the TetM protein (shown in magenta) reaches in and displaces it, restoring the ribosome to its normal function. PDB structure 3j9y.
rRNA Methyltransferase
Resistance against: Aminoglycoside antibiotics
Resistance mechanism: Alteration of the target site
rRNA Methyltransferases (shown in magenta) modify ribosomal RNA, providing resistance against aminoglycosides like streptomycin. PDB structure 4ox9.
Ribosomes
Ribosomes are target of many antibiotics including macrolides and aminoglycosides . The resistant bacteria express special enzymes such as TetM proteins and rRNA methyltransferases that modify the ribosomes restoring their protein-building capabilities.
FusB Protein
Resistance against: Fusidic acid
Resistance mechanism: Alteration of the target site
FusB protein binds to EF-G and protects it from fusidic acid. PDB structure 2mzw.
Aminoglycoside acetyltransferases
Resistance against: Aminoglycosides
Resistance mechanism: Chemical modification of antibiotic
Aminoglycoside acetyltransferases add acetyl groups to the aminoglycoside antibiotics, making them unable to bind to ribosomes. PDB structure 1bo4.
Topoisomerase
Resistance against: Quinolones
Resistance mechanism: Mutation in the target site
Topoisomerase II helps untangle DNA during replication. Quinolone antibiotics (shown in red) stop the action of this enzyme. Resistance occurs through mutations that block the antibiotic binding but allow the enzyme to function. PDB structure 3k9f.
RNA Polymerase
Resistance against: Rifampicin
Resistance mechanism: Mutation in the target site
RNA Polymerase transcribes the bacterial DNA. Rifampicin (shown in red) stops the elongation process. Resistance occurs through mutations that block the antibiotic binding but allow the enzyme to function. PDB structure 5uhc.
Dihydropteroate Synthase and Dihydrofolate Reductase
Resistance against: Antifoliates
Resistance mechanism: Mutation in the target site
Antifoliates inhibit enzymes along the folate metabolic pathway including dihydropteroate synthase (left) and dihydrofolate reductase (right). Resistance occurs through mutations that block the antibiotic binding but allow the enzyme to function. PDB structures 3tzf and 2w9s.
Multidrug Resistant Transporters
Multidrug Resistant Transporters are expressed by bacteria when toxins are detected inside cell. For example Sav1866 uses a scissor-like motion to transport antibiotics across the cell membrane. PDB structure 2onj.
Gene regulation in resistance
Cells use repressor proteins to regulate the genes involved in resistance, so that the proteins are made only when needed. The MecI repressor regulates the gene that encodes PBP2a. PDB structure 2d45.
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Beta-lactam antibioticsExamples: Protein Target: Beta-lactams contain an extremely reactive beta-lactam ring that attacks PBPs which are responsible for crosslinking the peptidoglycan chains in the bacterial cell wall to form a thick matrix. Disabling of the PBPs results in an incomplete cell wall that lyses under osmotic pressure. |
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VancomycinTarget: Vancomycin (purple) |
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Macrolide antibioticsExamples: Protein Target: Macrolides bind to the large subunit of the ribosomes preventing the extension of the nascent protein chain. |
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Aminoglycoside antibioticsExamples: Protein Target: Aminoglycosides bind to both the small and the large subunit of the ribosomes. In the small subunit, they interfere with the recognition of the matching tRNA, ultimately leading to mistakes in building the new protein chains. In the large subunit, they cause problems at the end of protein synthesis, blocking the recycling of ribosomes. |
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Fusidic acid
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Rifampicin
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QuinolonesExamples: Protein Target: Quinolones inhibit topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial DNA replication, transcription, repair, strand supercoiling repair, and recombination. |
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AntifolatesExamples: Protein Target: Antifolates inhibit enzymes along the folate metabolic pathway interfering with the synthesis of vitamin B9. |
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More information about targeted antibiotics |
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Related Molecule of the Month (MoM) article(s). Mouse over the icon to display the title |
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3D molecular view at RCSB PDB |
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