Antimicrobial Resistance: Fitness gains hamper efforts to tackle drug resistance

  1. Shanta Dutta  Is a corresponding author
  1. National Institute of Cholera and Enteric Diseases, India

The effectiveness of the antibiotics used to treat diseases caused by bacteria is increasingly being limited by the spread of resistance to these drugs. For a long time it was thought that most of the mutations that lead to antimicrobial resistance in bacteria led to a reduction in fitness, which meant that the resistant bacteria did not grow as fast as those that were susceptible to antimicrobials. These fitness costs are important because they determine how quickly resistance is likely to develop, or to disappear if antibiotic use is discontinued (Andersson and Hughes, 2010). However, resistant bacteria often develop secondary mutations that can compensate for these fitness costs, and these mutations allow the bacteria to thrive, even in antimicrobial free environments (Lenski, 1998). When this occurs, resistance is likely to continue even if antibiotic use is stopped. This is why public health bodies around the world are so worried by the spread of antibiotic resistance.

Typhoid fever is caused by eating food or drinking water contaminated with Salmonella Typhi bacteria. According to the World Heath Organisation (WHO), the drug of choice for treating typhoid fever is ciprofloxacin, which belongs to the fluoroquinolone family of antibiotics (WHO, 2003). However, resistance to the fluoroquinolones is increasing all over the world (Parry and Beeching, 2009). Now, in eLife, Stephen Baker of the Oxford University Clinical Research Unit in Vietnam and co-workers in Vietnam and the UK have compared the fitness of various mutants of Salmonella Typhi that are resistant to fluoroquinolones with the fitness of a strain that is still susceptible to these drugs (Baker et al., 2013).

The fluoroquinolones target enzymes that untangle knots in bacterial genomes. Resistance to these antibiotics in Salmonella Typhi involves changes in these target enzymes that reduce the ability of the drugs to bind to them. These changes occur by substitution mutations in two genes, gyrA and/or parC, that encode these enzymes. Advances in site-directed mutagenesis allowed Baker and co-workers to construct eleven fluoroquinolone-resistant mutants and one susceptible control mutant with known nucleotide substitutions from a susceptible, weakened laboratory strain of Salmonella Typhi. The resistant mutants were generated by substitutions at two positions in the gyrA gene and one in the parC gene, which were introduced in combinations to create single, double or triple mutants. Seven of the eleven lab-engineered mutants have been found in clinical isolates, whilst the remaining four had not been observed in nature before.

To start each in vitro competition assay, a series of cultures containing equal numbers of bacteria from the susceptible parent strain and one of the 12 lab-engineered mutant strains were prepared. These cultures were then grown in the absence of any antibiotics for several generations. Every 24 hr, some of each culture mixture was removed and analysed (Figure 1). More culture was also diluted into fresh antibiotic-free growth media, and the entire process was repeated for a period of 15 days. Colony counting was used to calculate the number of bacterial generations during each period.

Fluoroquinolone-resistant mutants of Salmonella Typhi vs susceptible strains.

Fluoroquinolone-resistant mutants (red) with either one, two or three mutations in the gyrA and parC genes were cultured with a fluoroquinolone-susceptible parent strain (white) in liquid media that did not contain any antibiotics. Every 24 hr, over a period of 15 days, these growth cultures were subcultured into fresh antibiotic-free media, and samples were taken for colony counting and DNA extraction. Pyrosequencing of extracted DNA was used to determine the frequency of each mutation and the parent strain at each time-point, and to calculate the fitness of each mutant compared to the parent strain. Increases in fitness allowed some single and double mutants (red arrow) outcompeted the parent strain, while a reduction in fitness meant that the triple mutant lost out to the parent strain (blue arrow).

Whether each mutant had a selective advantage or disadvantage was determined from the frequency of the engineered mutated genes at each time point, which was measured by specific pyrosequencing with the extracted DNA. Statistical models were used to calculate the selection coefficient and fitness difference of each mutant when compared to the parent strain. Since the fate of a particular mutation depends on its interaction with its environment, including all the other genes found in the genome (Cordell, 2002), the effects of interactions between genes, often known as ‘epistasis’, were also calculated for the double and triple mutants.

Interestingly, six resistant mutants (two single mutants and the four double mutants tested) could outcompete the susceptible Salmonella Typhi parent strain. This indicates that these mutations conferred increased fitness, even in the absence of the antimicrobial. This goes against the dogma that resistance mutations always have a fitness cost, and can explain the frequent occurrence of certain resistant mutants in the antibiotic free environment. The single mutant with highest selective advantage (called S83F) contributed 1.3% more offspring per generation than the parent strain, and the most competitive double mutant (S83F-D87N, which has two changes within the gyrA gene) contributed 7.4% more offspring per generation. In contrast, the triple mutant (S83F-D87G-S80I) contributed 1% less offspring per generation than the parent strain: this indicates a negative interaction between these mutations, with the third mutation wiping out the fitness advantage of the double mutants.

Since Salmonella Typhi lives within host cells during an infection, and is restricted to humans, the results obtained in this in vitro experimental system using a weakened, lab strain would not be the same with wild strain and ex vivo or in vivo models. However, as acknowledged by Baker et al., all models have their own inherent limitations and currently there are no available systems (except humans and primates) that exactly mimic Salmonella Typhi infection cycle.

The process of evolution in any organism is determined by the order in which mutations occur (Kimura, 1985). Baker et al. have concluded that single mutations in gyrA gene that reduce susceptibility to fluoroquinolones (especially the S83F mutation) provide the starting point for the evolution of more resistant double mutants, which maintain the resistance, even in the absence of antibiotics. This would contribute to the global spread of fluoroquinolone-resistant Salmonella Typhi, and would also undermine efforts to control the spread of drug-resistant typhoid through the prudent use of antimicrobial drugs.


    1. Lenski RE
    Bacterial evolution and the cost of antibiotic resistance
    International Microbiology 1:265–270.
    1. WHO
    (2003) Background document: the diagnosis, prevention and treatment of typhoid fever
    19–23, Background document: the diagnosis, prevention and treatment of typhoid fever, Geneva, World Health Organization, Available at: ,

Article and author information

Author details

  1. Shanta Dutta

    Bacteriology Division, National Institute of Cholera and Enteric Diseases, Kolkata, India
    For correspondence
    Competing interests
    The author declares that no competing interests exist.

Publication history

  1. Version of Record published: December 10, 2013 (version 1)


© 2013, Dutta

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.


  • 550
    Page views
  • 62
  • 2

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Shanta Dutta
Antimicrobial Resistance: Fitness gains hamper efforts to tackle drug resistance
eLife 2:e01809.

Further reading

  1. Resistance to antimicrobial drugs is not driven solely by the excessive use of these drugs.

    1. Epidemiology and Global Health
    2. Evolutionary Biology
    Marta Matuszewska et al.
    Research Article

    Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here, we fully characterise the evolutionary dynamics of these MGEs using a collection of 1180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline, and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398 have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.