Mechanisms of resistance to antimicrobials

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Some organisms are intrinsically resistant to many (or even all) antimicrobial agents. Some microbiologists call this "primary resistance". Other organisms acquire resistance, either by mutating or by sharing the resistance genes of resistant organisms. This should not be confused with the term "clinical resistance" which refers to the failure of an antimicrobial to eradicate infection, despite the apparent ability of the agent to kill the 'bug' in vitro. A wide variety of problems can account for clinical resistance, such as impaired host immunity, inadequate drug delivery, and foreign material in the site of a wound.

Antimicrobial resistance is an ever-increasing problem in hospitals, especially in intensive care units. The problem is so severe that some authorities believe that we are entering the "post-antibiotic era" where widespread bacterial resistance will render most antibiotics ineffective.

What are the reasons for this resistance?
No-one is sure, but the principle cause appears to be inappropriate and profligate use of antibiotics, especially in the hospital environment. Several studies have shown widespread misuse of antibiotics. Another major problem is spread of infecting organisms from patient to patient. This is usually done by the nurses, doctors and others caring for the patient. The major method of spread is on contaminated hands. Over a hundred years after Semmelweiss we still have not learnt the lesson he taught. Semmelweiss reduced mortality rates substantially in his hospital by insisting that students wash their hands before moving from the autopsy room to the maternity wards, and was consequently hounded from office and died (ironically, of septicaemia) in a mental institution.

The main methods of resistance

The following very simplistic picture shows two important features of many bacteria:

  1. They have porin proteins that act as channels into the bacterium for a variety of substances, and
  2. They contain penicillin-binding proteins (PBP's) that are vital for cell wall synthesis.

Now let's see how a beta lactam such as penicillin disturbs this process:

The beta lactam enters the bacterium via the porin and binds to the PBP, inhibiting cell wall synthesis. The bacterium then dies. There are several ways that the bacterium can side-step this attack, and we will use these as a model for all resistance mechanisms, even in other organisms such as fungi and viruses. Mechanisms are as follows:

1. Diminished transport into the bacterium

The bacterium on the left has lost the porin that normally transports the antibiotic into the cell. In a normal environment, such a loss would be a disaster for the bacterium as it would lose its competitive edge over other bacteria. Here it is a boon, as it will survive while other porin-rich bacteria will be killed by the antibiotic!
The bacterium on the right has an even better solution. It has a pump that pumps out the beta lactam as fast as it comes in. An elegant form of resistance!

2. An altered binding site

This bacterium has a slightly altered PBP. The PBP can still carry out its function, but is no longer inhibited by the penicillin, which cannot bind to it. The bacterium carries on unscathed.

3. Enzymes that break down the antibiotic

This is an important method of resistance for many bacteria. Beta lactams are for example broken down by beta lactamases . There is a whole host of beta lactamases, and new ones seem to be discovered every day. Although more attention has been focussed on beta lactamases than on other enzymes that destroy antibiotics, there are many such enzymes that break down aminoglycosides, chloramphenicol, and so on.

Fortunately for us, there are several substances such as clavulanic acid that can be used to inhibit beta lactamases. But the wily bacteria have managed to get around this too, using a variety of methods!

There are several classifications of beta lactamases. A recent one is that of Bush, Jacoby & Medeiros { Antimicrob Agents Chemother 1995(39)1211-33 } which combines features of several other classifications. They define four groups:

  1. Cephalosporinases, not inhibited by clavulanic acid
  2. Penicillinases, inhibited by clavulanic acid
  3. Metallo-beta-lactamases
  4. penicillinases, not inhibited by clavulanic acid
A variety of gram-negative bacteria contains the group 1 enzymes. The Amp C cephalosporinases are common and although initially found in bacterial chromosomes, they have now moved to plasmids in E. coli and Klebsiella pneumoniae. They are resistant to most antibiotics including first, second and third generation cephalosporins, and also to penicillins, cephamycins, monobactams and combinations of beta lactams + beta-lactamase inhibitors.

Group two includes a vast array of enzymes including the common TEM beta lactamases (group 2b), and the extended spectrum beta lactamases (group 2be) which are still inhibited by clavulanic acid but show resistance to expanded spectrum cephalosporins and aztreonam. Of note is group 2br which contains enzymes that show reduced binding to clavulanic acid.

The metallo-beta-lactamases from Group 3 are quite capable of hydrolysing carbapenems such as imipenem. These are found in organisms such as Stenotrophomonas maltophilia, and also some Aeromonas, Bacteroides and Pseudomonas aeruginosa. Group four penicillinases are uncommon (found in e.g. P. cepacia).

Older classifications relied heavily on whether beta lactamases were found on bacterial chromosomes or on extrachromosomal DNA (plasmids). Expression of genes for chromosomal beta lactamases is often regulated, and they are only induced when a beta lactam is present, while plasmid beta lactamases are produced all the time. One does however encounter chromosomal genes that are "de-repressed" all the time, and churn out beta lactamase willy nilly. The major problem with classifications that stressed the location of the gene is that the genes jump from chromosome to plasmid and vice versa. (They also jump around within the genome of the bacterium itself).

4. Another method of resistance - an alternative pathway!

For the fourth method of resistance, we consider another antimicrobial agent and how bacteria combat it. The agent is trimethoprim . Bacteria need to make their own folic acid, and they normally do this using a vital pathway that involves the enzyme dihydrofolate reductase. Trimethoprim inhibits this bacterial enzyme, preventing folate synthesis and thus interfering with the ability to make DNA. But some wily bacteria bypass this step by acquiring a new enzyme that bypasses the old, inhibited dihydrofolate reductase. The new enzyme comes from (you guessed it) plasmids.

Fungal resistance mechanisms

Patients in ICU are often very susceptible to fungal infection, and as we have gained the ability to sustain the lives of sicker and sicker people, we have noticed many more fungal infections in ICU. There are not many antifungal agents, they have been used frequently, and now we are seeing more and more resistance. The common mechanisms for resistance in fungi are just those we discussed above: changes in the binding site of the antifungal agent, and decreased accumulation of the antifungal within the cell due to decreased permeability and/or a pump that gets rid of this agent.

Methods for testing in vitro fungal resistance have been argued about for years. Now National Committee for Clinical Laboratory Standards macro- and microdilution broth methods have been widely accepted {Alexander & Perfect, 1997}.

Amphotericin B (AB) is generally an excellent antifungal. AB binds ergosterol causing leaks in the fungal cell membrane, and may also stimulate host immunity. Ergosterol-deficient fungi seem to be resistant to the action of AB. Primary resistance is seen in fungi such as Pseudallescheria boydii as well as certain species of Candida e.g. C. lusitaniae. Although some have alleged that prior azole therapy may deplete fungal membranes of ergosterol and thus decrease the effectiveness of AB, evidence for this is scanty.

Resistance to azoles such as fluconazole (a "triazole") can be either due to acquired fungal resistance to the agent or to acquisition of a different strain. Long-term fluconazole therapy, especially in AIDS patients is often associated with resistance. Long-term prophylaxis with this agent may result in colonisation with intrinsically resistant organisms such as C. krusei. Azoles act on lanosterol 14-alpha demethylase, inhibiting ergosterol synthesis. (They may act on other enzymes too). Resistance to azoles is associated with defects in enzymes on the biosynthetic pathway for ergosterol, or to decreased intracellular concentrations of the drugs. Both impermeability and pumps that remove the drug from the fungal cell have been described. Much work has been done on the pumps, of which there are two main categories, the ABC and MFS transporters. (These stand for "ATP-binding cassette" and "major facilitator superfamily"). Azole cross-resistance is probably common.

Fluoropyrimidines such as 5-flucytosine (FC) are useful antifungals for certain species & strains of Cryptococcus and Candida, and for chromomycosis. Secondary resistance is common. FC is converted within fungal cells (but not mammalian cells) to fluorouracil which ultimately results in abnormal fungal RNA as well as interfering with DNA synthesis. Loss of one or more of several enzymes may confer resistance to FC.

Newer antifungals such as echinocandin B analogues, and possibly pradimicins have not yet been thoroughly investigated regarding fungal resistance.

Resistance in specific organisms

This is discussed elsewhere


  1. New Horizons August 1996 Vol 4 No 3 pp319-392.
    Numerous state-of the art articles on antimicrobial resistance in the intensive care unit.
  2. American Journal of Medicine July 1997 Vol 103 pp51-59
    Pitout JDD, Sanders CC, Sanders WE
    A fairly good article that focuses on beta lactam resistance.
  3. Clinical Infectious Diseases October 1996 Vol 23 pp790-794.
    Cassadevall A.
    A pertinent discussion of the current crisis in infectious disease.
  4. Drugs November 1997 Vol 54 No 5 pp657-678.
    Alexander BD & Perfect JR.
    A comprehensive discussion of antifungal resistance with a fair section on ways of combating this.