Microbiology chapters
Bacterial genetics and mechanisms of antibiotic resistance
How bacteria store and swap genes: the chromosome, plasmids, transposons and bacteriophages, mutation, and the three ways genes move between bacteria (transformation, transduction, conjugation), with lysogenic conversion of toxin genes and how these processes spread antibiotic resistance.
- Bacteria carry genes on a single circular chromosome, on plasmids (extra circular DNA carrying antibiotic resistance, toxins and pili; R plasmids spread multiple resistance) and on mobile transposons ("jumping genes") that move between plasmid and chromosome.
- Genes move between bacteria by transformation (uptake of naked DNA: S. pneumoniae, Haemophilus, Neisseria; Griffith's experiment), transduction (carried by a bacteriophage: generalised or specialised; important in staphylococci) and conjugation (direct transfer through a sex pilus, usually of plasmids: the commonest route of resistance spread, especially among Gram-negatives).
- Lysogenic conversion: a prophage gives the bacterium new genes, notably toxins: diphtheria toxin (β-prophage), cholera toxin, botulinum toxin, Shiga-like toxin and streptococcal erythrogenic (scarlet fever) toxin; resistance mechanisms include β-lactamases, altered targets (MRSA: mecA → PBP2a), reduced entry and efflux pumps.
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Bacterial genetic material
- Chromosome: a single, circular, double-stranded DNA molecule in the nucleoid (no nuclear membrane, no histones of the eukaryotic type, few or no introns). Bacteria are haploid, so mutations show immediately.
- Plasmids: small, circular, self-replicating extra-chromosomal DNA. Not essential for life but carry useful genes:
- Antibiotic resistance (R plasmids = resistance genes + resistance transfer factor for conjugation).
- Toxins (E. coli LT and ST; S. aureus exfoliatin; anthrax toxin).
- Pili and adhesins; F (fertility) plasmid encodes the sex pilus.
- Bacteriocins, metabolic enzymes.
- Episomes can integrate into the chromosome (the F factor in Hfr cells).
- Transposons ("jumping genes"): DNA segments that move from one site to another (chromosome ↔ plasmid ↔ phage) using transposase; often carry resistance genes; flanked by insertion sequences. Integrons collect several resistance gene cassettes.
- Bacteriophages: viruses that infect bacteria; can carry bacterial or toxin genes.
Mutation
A heritable change in the DNA sequence.
- Spontaneous (replication errors) or induced by mutagens (UV light, X-rays, chemicals such as nitrous acid, alkylating agents, base analogues).
- Types: point mutations (base substitution: silent, missense, nonsense), frameshift (insertion or deletion), large deletions, transposon insertion.
- Antibiotics do not cause resistance mutations; they select resistant mutants already present. This is why TB is treated with several drugs (the chance of one bacillus carrying mutations to two drugs at once is tiny).
- Example: chromosomal mutations give resistance to rifampicin (rpoB), fluoroquinolones (gyrase genes) and streptomycin (ribosomal protein).
Gene transfer between bacteria
Horizontal gene transfer moves genes between existing bacteria (even between species), unlike vertical transfer to daughter cells.
| Feature | Transformation | Transduction | Conjugation |
|---|---|---|---|
| What carries DNA | Free (naked) DNA from dead bacteria | Bacteriophage | Direct cell contact via a sex pilus |
| Needs | Competent recipient | Phage infection | F⁺ (donor) with F plasmid; recipient F⁻ |
| Destroyed by DNase? | Yes | No (DNA inside phage coat) | No |
| Typical organisms | S. pneumoniae, H. influenzae, Neisseria, Bacillus | Staphylococci (penicillinase plasmids), Salmonella | Gram-negatives (E. coli, Klebsiella, Shigella, Pseudomonas); some Gram-positives |
| Importance | Capsule switching (vaccine escape), penicillin resistance in pneumococcus (mosaic PBP genes) | Toxin genes; penicillinase in S. aureus | Main route of multidrug resistance spread (R plasmids, ESBL, carbapenemase genes) |
Transformation = naked DNA. Transduction = phage. Conjugation = sex pilus.
Transformation and Griffith's experiment
Griffith (1928): live non-capsulated (rough) pneumococci became capsulated (smooth) and killed mice when mixed with heat-killed capsulated bacteria. Avery, MacLeod and McCarty later showed the "transforming principle" was DNA.
Transduction
- Generalised transduction: during the lytic cycle, a phage accidentally packages any piece of bacterial DNA and delivers it to another bacterium.
- Specialised transduction: a lysogenic (temperate) phage that was integrated next to particular genes takes only those neighbouring genes when it excises.
Lysogeny and lysogenic conversion
Temperate phages can integrate into the bacterial chromosome as a prophage (lysogeny) instead of killing the cell. Phage genes then change the bacterium's properties: lysogenic conversion.
| Toxin or feature | Organism |
|---|---|
| Diphtheria toxin (β-prophage) | Corynebacterium diphtheriae (only lysogenised strains are toxigenic) |
| Cholera toxin (CTX phage) | Vibrio cholerae |
| Botulinum toxin | Clostridium botulinum (types C, D) |
| Shiga-like toxin (verotoxin) | EHEC (E. coli O157:H7) |
| Erythrogenic (pyrogenic) toxin → scarlet fever | Streptococcus pyogenes |
| O antigen changes | Salmonella |
Lysogenic conversion toxins: "ABCDE": shigA-like toxin, Botulinum, Cholera, Diphtheria, Erythrogenic.
Conjugation
- F⁺ × F⁻: the donor with an F plasmid makes a sex pilus, contacts the recipient and passes a copy of the plasmid; the recipient becomes F⁺.
- Hfr (high frequency of recombination): the F factor has integrated into the chromosome, so the donor transfers chromosomal genes (used to map bacterial genes).
- R plasmids spread by conjugation carry several resistance genes at once (to many antibiotic classes), so one transfer can make a bacterium multidrug-resistant; conjugation occurs in the gut between different species.
Recombination
Incoming DNA is integrated into the recipient chromosome by homologous recombination (RecA protein) or site-specific recombination (phages, transposons).
Antibiotic resistance: genetic and biochemical basis
Genetic basis: chromosomal mutation (usually resistance to one drug; selected by treatment) or acquisition of new genes on plasmids and transposons (often several drugs; transferable).
| Biochemical mechanism | Examples |
|---|---|
| Enzymatic inactivation | β-lactamases (penicillinase of S. aureus, ESBLs in E. coli and Klebsiella, carbapenemases such as NDM-1), aminoglycoside-modifying enzymes, chloramphenicol acetyltransferase |
| Altered target | MRSA (mecA → PBP2a), penicillin-resistant pneumococci (altered PBPs), VRE (D-Ala-D-Lac), quinolone resistance (gyrase mutation), rifampicin (rpoB), macrolides (ribosomal methylation, erm) |
| Reduced permeability | Porin loss in Gram-negatives (Pseudomonas resistance to imipenem) |
| Efflux pumps | Tetracyclines, macrolides, fluoroquinolones |
| Bypass pathway | Sulphonamides, trimethoprim (extra resistant enzymes) |
For resistant organisms in Pakistan (ESBL, XDR typhoid, MDR-TB) and stewardship, see antibiotic resistance.
Suppose the chance that one bacillus carries a resistance mutation:
isoniazid ≈ 1 in 10⁶ bacilli; rifampicin ≈ 1 in 10⁸
A cavity may hold about 10⁸–10⁹ bacilli:
with one drug, about 10⁹ ÷ 10⁶ = 1,000 resistant bacilli survive → treatment fails
Chance of a bacillus resistant to both by chance mutation:
10⁻⁶ × 10⁻⁸ = 10⁻¹⁴ → essentially none in 10⁹ bacilli
So two or more effective drugs prevent selection of resistance.
These mutation rates are approximate teaching figures used to explain the principle.
Expect: features of plasmids and R factors, transposons, mutation vs gene transfer, transformation (naked DNA, Griffith, pneumococcus), transduction (phage, generalised vs specialised), conjugation (sex pilus, F⁺, Hfr, commonest route of resistance spread), lysogenic conversion with toxin examples (diphtheria, cholera, botulinum, Shiga-like, erythrogenic), biochemical mechanisms of resistance with MRSA, ESBL and VRE, and why multiple drugs are used in TB.
Quick revision
- Chromosome: single circular DNA. Plasmids: resistance, toxins, pili. Transposons: jumping genes.
- Transformation: naked DNA (DNase-sensitive); pneumococcus, Haemophilus, Neisseria.
- Transduction: phage; generalised vs specialised; staphylococci.
- Conjugation: sex pilus; F⁺ → F⁻; Hfr; main spread of multidrug resistance.
- Lysogenic conversion: diphtheria, cholera, botulinum, Shiga-like, erythrogenic toxins.
- Resistance: enzymes, altered targets, less entry, efflux.
- Antibiotics select, not cause, resistant mutants → combination therapy in TB.
Written by The House Job from standard microbiology references (Levinson's Review of Medical Microbiology and Immunology).
FAQ
What are the three ways bacteria transfer genes to each other?
Transformation (uptake of free DNA), transduction (transfer by a bacteriophage) and conjugation (direct transfer through a sex pilus).
What is lysogenic conversion?
A change in a bacterium's properties caused by genes from an integrated bacteriophage; for example, only lysogenised Corynebacterium diphtheriae produce diphtheria toxin.
Which gene transfer method needs a sex pilus?
Conjugation.
What is a transposon?
A piece of DNA that can move from one location to another within or between DNA molecules, often carrying antibiotic resistance genes.