Antibiotic Resistance

In my last post, I discussed antibiotics. In this post, I'm going to discuss what happens when bacteria are resistant to antibiotics! Hooray! (not...)

Understand how antimicrobial resistance has arisen and spread in bacterial populations

Antimicrobial resistance in populations comes about due to selective pressures. Without selective pressures, only a small number of microbes will have resistance, but when exposed to an antimicrobial agent, only those microbes with resistance will be able to survive and reproduce, such that resistant microbes eventually become dominant in the population.

Antimicrobial resistance has probably been around for as long as there have been microbes. For example, some microbes living in soil secrete their own antimicrobial agents, so neighbouring microbes may have gained resistance. Of course, nowadays we are mainly interested in looking at resistance to conventional antibiotics. There are many reasons why microbes may be developing resistance: some doctors may be prescribing antibiotics unnecessarily, some patients may not be complying with treatment (allowing some microbes to survive and mutate), and the use of antibiotics in agriculture may be problematic. One of the more problematic agricultural antibiotics is avoparcin, which is a glycopeptide (like vancomycin), and gives cross-resistance to vancomycin. It has been hypothesised that vancomycin resistance might be linked to antibiotic use in animals.

Understand the genetics of antibiotic resistance

Sometimes, resistance is already coded within bacterial genes. Other times, mutations might be acquired from mutations, vertical transfer via chromosomes, or horizontal transfer via transfer of chromosomal genes or transfer of genes on mobile genetic elements. These mobile genetic elements include plasmids, transposons, and integrons. Plasmids are self-replicating circular dsDNA that come in a few varieties. Conjugative plasmids can transfer information between bacteria, while R plasmids (which may also be conjugative) encode antibiotic resistance. Transposons and integrons are linear dsDNA that cannot self-replicate. Integrons can integrate into transposons, and transposons can integrate into chromosomes or plasmids.

In the process of conjugation, two bacterial cells must first come together. Sometimes this occurs through retraction of a sex pilus, which is a structure that is present on some bacterial cells. A "conjugation tube" forms between the two bacteria, and plasmid DNA replication begins. While DNA replication occurs, the free DNA strand begins moving through the conjugation tube. In the recipient cell, the free strand is replicated. The end result is that each cell ends up with a full copy of the plasmid.

Know the five mechanisms of antibiotic resistance and some examples

The main mechanisms are as follows:

1. Decreased influx of antibiotic (e.g. permeability barriers)
2. Increased efflux of antibiotic (e.g. efflux pumps)
3. Antibiotic inactivation (e.g. beta-lactamases, aminoglycoside-modifying enzymes)
4. Antibiotic target site alteration (e.g. altered pencillin-binding-proteins / transpeptidases, altered DNA gyrase)
5. Antibiotic target amplification or alternate pathway (e.g. producing more folate to overcome folate synthesis inhibitors)

Be able to describe selected clinically important resistances

Streptococcus pneumoniae

S. pneumoniae is a common cause of ear infections, but since antibiotics don't penetrate the middle ear very well, there's a high chance that treatment isn't 100% effective. As such, a small number of bacteria are left hanging around and are able to mutate. Some S. pneumoniae has developed penicillin resistance via mutation of penicillin-binding proteins (i.e. antibiotic target site alteration). Since very high level resistance is unusual, it can usually be overcome by increasing the dose of penicillin.

Staphylococcus aureus

S. aureus has a particularly nasty form called MRSA (methicillin-resistant S. aureus), which is also known as a "superbug." MRSA contains the Staphylococcal Cassette Chromosome mec (SCCmec), which is a mobile genetic element that integrates into the S. aureus chromosome. SCCmec contains the antibiotic resistance gene mecA, which codes for PBP2a, which does not bind beta-lactam antibiotics. Usually alternative antibiotics, such as vancomycin, are required to treat this bad boy.

β-lactamase resistance in Gram negatives

Most beta-lactamase resistance is due to beta-lactamases in Gram-negative bacteria. Extended-spectrum beta-lactamases (ESBLs) are resistant to penicillins, cephalosporins, and monobactams (but not to carbapenems). ESBLs can be inhibited by clavulanic acid, which is why clavulanic acid is often packaged together with some antibiotics (e.g. amoxicillin-clavulanate). Some bacteria have carbapenemases which, as their name suggests, are also capable of hydrolysing carbapenems. Recently, a new carbapenemase, called New Delhi metallo-beta-lactamase (NDM-1), has been discovered. It is found on a plasmid encoding the bla_NDM gene, and has spread rapidly. If you have a superbug with this carbapenemase, you're pretty much stuck with the polymixins and tigecycline.

Other resistances

Aside from beta-lactams, bacteria have also developed resistance to some other antibiotics (sneaky buggers!). To defend against aminoglycosides, some bacteria have inactivating enzymes (e.g. streptomycin acetyltransferase) and/or have a decreased expression of porins, decreasing membrane permeability to aminoglycosides. To defend against the MLSB group (macrolides, lincosamide, streptogramin B), some bacteria methylate 16S rRNA to alter the binding site and/or have increased efflux through multidrug resistance (MDR) efflux pumps. Bacteria can also defend against tetracyclines by increasing efflux through a specific Tet pump.

Understand the implications of antibiotic resistance and strategies to address the problem

Obviously, antibiotic resistance is kind of problematic. When bacteria are resistant, it narrows down our treatment choices and we might be stuck with only very toxic drugs (or, worse still, no options at all). Some strategies that have been suggested to address this problem include:

• Use more specific agents if possible (rather than broad-spectrum)
• Avoid vancomycin unless necessary
• Only prescribe if required, and prescribe for the optimal duration
• Shorten hospital stays (less likelihood of a patient getting a nosocomial infection and needing antibiotics)
• Prevent infections (via immunisation, sanitation etc.)