Antibiotic Resistance

Three strategies of resistance

The framework. Bacteria defeat antibiotics in three ways: (1) enzymatic inactivation of the drug (beta-lactamases, aminoglycoside-modifying enzymes); (2) target modification, so the drug no longer binds (altered PBP, D-Ala-D-Lac, ribosomal methylation); and (3) reduced drug levels inside the cell (porin loss, efflux pumps). Resistance genes arise by chromosomal mutation and pass to daughter cells, but they spread fastest horizontally, often between species, on plasmids, phages and transposons.

Selection, not creation. Antibiotic exposure selects mutants or gene carriers that already exist. When a single mutation gives high-level resistance, as with rifampin (altered RNA polymerase), the drug is combined with others to treat an established infection.

Enzymatic inactivation

Beta-lactamases. These enzymes hydrolyze the beta-lactam ring. Staphylococcal penicillinase makes most S. aureus resistant to penicillin G and ampicillin. There are two counters: pair the drug with a beta-lactamase inhibitor (clavulanate, sulbactam, tazobactam, avibactam), or use a penicillinase-stable drug such as nafcillin or oxacillin, whose bulky side chain blocks the enzyme.

Extended-spectrum beta-lactamases (ESBLs). Found mainly in E. coli and Klebsiella, ESBLs hydrolyze penicillins, most cephalosporins (ceftriaxone included) and aztreonam, but clavulanate still inhibits them. Carbapenems are the treatment of choice for serious ESBL infection.

Carbapenemases (CRE). Carbapenem-resistant Enterobacterales, the "nightmare bacteria," make KPC or metallo-beta-lactamases such as NDM-1, which destroy nearly all beta-lactams, carbapenems included. Reserve agents are ceftazidime-avibactam, colistin and newer combinations. Avibactam inhibits KPC but not metallo-beta-lactamases, so ceftazidime-avibactam alone does not cover NDM-1 producers.

Aminoglycoside-modifying enzymes. These enzymes acetylate, phosphorylate or adenylate the drug so that it can no longer bind the 30S subunit. This is the most common mechanism of aminoglycoside resistance, and reduced uptake adds to it.

Target modification

MRSA. mecA, carried on the mobile SCCmec element, encodes PBP2a, a penicillin-binding protein with low affinity for beta-lactams. Every beta-lactam fails, nafcillin and oxacillin included, except ceftaroline, a 5th-generation cephalosporin that binds PBP2a. Treat with vancomycin, daptomycin or linezolid. Because nafcillin and oxacillin resist penicillinase, resistance to them defines MRSA.

VRE. Vancomycin-resistant enterococci carry vanA, which changes the terminus of peptidoglycan precursors from D-Ala-D-Ala to D-Ala-D-Lac, so vancomycin can no longer bind. Treat with linezolid, daptomycin or tigecycline. vanA sits on a transposon and has occasionally moved into S. aureus (VRSA).

Penicillin-resistant pneumococci. S. pneumoniae makes no beta-lactamase; it resists penicillin through altered PBPs, whose genes it has acquired by transformation. A beta-lactamase inhibitor therefore adds nothing.

erm and the D-test. The erm gene methylates 23S rRNA and blocks binding of macrolides, lincosamides (clindamycin) and streptogramin B, which is MLSB resistance. In inducible strains clindamycin appears active until a macrolide switches on the methylase. The D-test exposes this: an erythromycin disk flattens the adjacent clindamycin zone into a "D". A positive D-test means clindamycin should not be used.

Other target changes. Chromosomal mutations in DNA gyrase and topoisomerase IV cause fluoroquinolone resistance, often alongside efflux.

Keeping the drug out

Porins and efflux. Hydrophilic drugs cross the gram-negative outer membrane through porins. Loss of a porin such as Pseudomonas OprD blocks carbapenem entry. Efflux pumps actively expel tetracyclines and fluoroquinolones. Both mechanisms lower the intracellular drug concentration, and combined with a beta-lactamase they can give high-level resistance.

How resistance genes spread

Transformation. Competent bacteria take up naked DNA from the environment, released by dead cells: "SHiN," for S. pneumoniae, H. influenzae and Neisseria. No cell contact is needed, and adding DNase prevents it.

Transduction. A bacteriophage packages bacterial DNA, including resistance or toxin genes, and injects it into a new host. Generalized transduction occurs in the lytic cycle, when a phage mistakenly packages random host DNA. Specialized transduction occurs when a lysogenic prophage excises and carries the genes adjacent to its insertion site.

Conjugation. DNA passes through a sex pilus. F+ donors transfer the F plasmid, often carrying resistance genes, to F- recipients. An Hfr cell has F integrated into its chromosome and can transfer chromosomal genes; a plain F+ cell transfers only the plasmid. Resistance (R) plasmids carrying several resistance genes spread this way, making conjugation the main route of multidrug resistance.

Transposition. Transposons ("jumping genes") and insertion sequences excise and reinsert, moving resistance genes between plasmids and the chromosome. Plasmid-borne resistance can become chromosomal, and genes shuffle into new combinations.