Intrinsic and acquired antibiotic resistance


Genetically (inherently) insensitivity for a drug is intrinsic. Intrinsic mechanism is those specified by naturally occurring gene found on host chromosome such as beta-lactamase of gram negative bacteria and many multidrug resistance (MDR) efflux system.

Examples: gram negative has impermeability for glycopeptides because of the outer membrane, if a microorganism has no cell wall they are intrinsically resistant to penicillin, Klebsiella also produce cephalosporinase , Pseudomonas aeruginosa resistant to tetracycline, chloramphenicol, and quinolones because of chromosome codded active exporters.


Spontaneous Mutation

  • Occur spontaneously in any gene of bacteria
    • Mutation is rare event 10-9 to 10-8 compared with gene transfer 10-5 to 10-4
  • Frequency of mutation differs between genes
  • Point mutations arise at a rate of around 10-9 to 10-10 per base pair per generation, and although extremely low, the large overall population size during infection, and the short generation time, provides the opportunity for diversity to arise during a single infection.
  • For example mutation leading streptomycin, nalidixic acid resistance is common 10-8-10-10 cells per generation whereas vancomycin or polymixin B is very rare
  • Streptomycin require single mutation and fluoroquinolone resistance is gradual; different mutations required.
  • Depends on antibiotic, bacterial species, time of drug use (slow killing ability of drug), stress, fitting cost, other genetic factors.

Types of mutation:

  1. Point mutation
    1. Silent, missense, nonsense
  2. Deletion
  3. Insertion ( frame-shift)
  4. Duplication

Transition– purine (G or A) misplace with (G or A) or Cor T misplace with C or T

Transversion- Pyrimidine (C or T) misplace with a  purine (A or G)

Factors increase the mutation rate of antibiotic resistance genesmu rate.png

Spontaneous mutations may cause resistance by:

  • Altering the target protein to which the antibacterial agent binds by modifying or eliminating the binding site.
  • Up regulating the production of enzymes that inactivate the antimicrobial agent.
  • Down regulating or altering an outer membrane protein channel that the drug requires for cell entry.
  • Up regulating pumps that expel the drug from the cell.
  • The mutation rate of Salmonella enterica serotype Typhimurium for rifampin resistance increases under starvation conditions
  • These observations indicate that bacterial growth conditions have a dramatic effect on the mutation rate. Analysis of several model systems have demonstrated that stress-enhanced bacterial mutation is a regulated phenomenon
  • This increased mutation rate is typically conferred by alterations in the genes that constitute the mismatch repair (MMR) system (mutS, mutL, mutH, mutT, mutY, mutM, and uvrD)
    • Mutations in the MMR system also increases the prevalence of genetic recombination, providing diversity to antibiotic resistance mechanisms
  • Spontaneous mutations.Chromosomal mutations are quite rare (one in a population of 106–108 microorganisms) and commonly determine resistance to structurally related compounds
  • Resistance to quinolones in E. coli is caused by changes in at least seven amino acids in the gyrAgene or three amino acids in the parCgene [1], whereas only a single point mutation in the rpoBgene is associated with a complete resistance to rifampin

This section above is adapted from a paper ( \) which I was very happy to run into!! I had one of this “aha” moments.


Horizontal transfer (HGT)

HGT may occur between strains of the same species or between different bacterial species or genera. Mechanisms of genetic exchange include conjugation, transduction, and transformation. HGT is the primary mechanism for evolution in prokaryotes and is synergised by complex networks of transfer involving the microbiome.

The dominance of HGT on Salmonella evolution is apparent from the observation that S. Typhi and S. Typhimurium share an average nucleotide identity of around 99%, yet around 15% of their genes are serovar specific. Genes affected include prophage, pathogenicity islands, ICEs, transposons, IS elements, and plasmids.


  • Most important way to spread bacterial resistance genes
  • Transfer between donor and recipient using conjugative genetic elements( transposons or plasmids) requires direct cell-to-cell contact (conjugation bridge) usinf F pillus.
  • The process allows for the passage of more than one functional gene at a time, so that multiple resistance could occur within a single step.
  • Conjugation is thus an important and highly efficient process for transferring genes, and the acquisition of resistance by most pathogens is probably a result of this process.
  • Resistance is believed to be mediated either by resistance plasmids (R plasmids) or transposable elements (transposons)
  • F (fertility) factor Donor F+ and recipient F-
    • If f+ cells divides and one daughter does not get F+; then it kills itself
  • OriT opens double strand becames single and DNA gets transferred (Type IV secretion apparatus)
  • IS elements( insertion sequence); homolog with chromosome parts.OriT is one of them
  • Conjugation is the dominant mechanism, used by ICEs and plasmids, but likely plays an important role in transfer of other mobile genetic elements (MGEs), such as transposons.
  • Antibiotic-resistance genes are present on the chromosome or on plasmids in Salmonella, often associated with MGEs such as composite transposons or ICEs



  • Does not require viability of donor cell
  • DNA is transferred from a donor to a recipient by way of a host, a bacteriophage.
  • Hershey and Chase 1952- labelled protein code ( remained outside of the cell)
  • It is still unknown whether this process causes clinically observed resistance to antibiotics. Because this process is highly dependent on specific phages, it may occur only within certain bacterial species.
  • Only a limited amount of DNA that can be packed into the head of a phage can normally be transferred. Transduction therefore cannot be responsible for multiple drug resistance.


  • Does not require viability of donor cell
  • Involves the passage of DNA to a recipient through a specific medium.
  • Transferring genetic material is mostly observed in vitro at laboratory. Almost never occurs in nature.
  • One strand degrades, single strand gets into cell via uptake system- DNA aligns with homologous part of chromosome- heteroduplex DNA is repaired into DNA.
  • There are naturally transformable bacteria and chemically transformable ( that’s why we don’t see our interest MO in nature transforming)
  • Limited between species transfer
  • Uptake of naked DNA, Mediates exchange of any part of DNA

Genetic materials (to be cont..)




IS (Insertion Sequences) 

Genomic Islands