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This article was originally published in January 2023 and has been updated for inclusion in the Spring 2026 issue of Microcosm.

Though antibiotics are one of the most significant human innovations, their efficacy is eroded by the elusiveness of their microbial targets. Many bacteria require few or even single mutations to develop resistance to antibiotics. Unfortunately, once bacteria develop resistance, they don’t always keep it to themselves—bacterial cells can transfer their resistance genes to other bacteria around them.

Plasmids are one of the main vehicles for gene transfer among bacteria. These small, circular DNA loops can be transmitted through direct physical contact between bacterial cells, using a structure called a pilus. This process, a form of horizontal gene transfer known as conjugation, perpetuates the spread of plasmids across bacterial populations, which often contain antibiotic resistance genes. The result: resistance sweeps through a bacterial population, rendering infections caused by those bacteria exceedingly difficult to treat.

Plasmid Costs and Shareability: The Perfect Match

Holding on to a plasmid is not free for its bacterial host. Although some genes on the plasmid can be critical for survival—for example, antibiotic resistance genes—bacteria carrying plasmids often demonstrate less growth than their plasmid-free peers; this is known as a plasmid fitness cost. The causes of plasmid fitness cost are still not fully understood, although there is evidence for different possible mechanisms. One way that a plasmid might negatively impact its bacterial host is through genetic conflicts, where the plasmid of other genes that are important for growth. Conjugation itself can also contribute to the fitness cost, as it is an for the cell to perform.

Plasmid fitness costs are thought to influence how successful a plasmid can be in bacterial populations, as cells with costly plasmids can be outcompeted by those without. However, plasmids that are relatively “expensive” for their bacterial host can still be successful on an evolutionary timescale without antibiotic pressure—but the match between plasmid and host needs to be solid. A study published in 2023 used clinical isolates of Escherichia coli to explore what makes a and pinned good combinations down to how the plasmids evolve inside different hosts. “Good” hosts confer mutations to the plasmid that increase its transfer rate and decrease its fitness cost, which leads to increased transmission and maintenance. This allows certain plasmids to spread effectively in certain host populations.

Given that plasmids can spread even in the , and despite costs to their bacterial hosts, understanding why certain bacteria-plasmid combinations work better than others would be useful. Plasmid sharing in the absence of antibiotic pressure is generally concerning, as current best practice guides urge reduced use and abuse of antibiotics to relieve the selective pressure that could spur the spread of resistance genes. By understanding which plasmids are likely to be successful in which hosts, scientists could potentially predict particularly prolific and problematic combinations of bacterial hosts and resistance plasmids, and work to mitigate their incidence.

Use It or Lose It

The plasmid fitness cost can also lead to another outcome in the context of resistance plasmids—keep the plasmid backbone, but delete the expensive antimicrobial resistance genes when the antibiotic pressure is gone. This process, known as “,” can even drive the original, complete resistance plasmid to extinction, as the streamlined plasmid is transmitted between cells at a faster rate. The streamlined plasmid can also block further transmission of the complete plasmid, as cells that already have the streamlined version no longer take up the complete one containing resistance genes. There is no specific benefit to keeping the backbone around, but no cost, either.

The streamlining phenomenon has been explored in the well-studied , which confers resistance to antibiotics including ampicillin, chloramphenicol and streptomycin. Whether the same effect occurs in other plasmids is still unknown, partially because traditional experiments would miss the distinction between plasmid streamlining and complete loss of the plasmid. In such studies, bacteria are usually grown on media containing antibiotics to check if the plasmid is still there—only the carriers survive. However, bacteria with streamlined plasmids would also die, as even though the backbone is still there, the resistance genes are missing. Only by analyzing the genetic sequence of the whole plasmid can researchers identify streamlining events that eliminate resistance genes while leaving the backbone behind.

Beyond Conjugation: Alternative Ways to Share Plasmids

Although conjugation is considered the main way that bacteria transfer plasmids among themselves, it is certainly not the only mechanism used to do so. Some smaller plasmids lack genes encoding the entire repertoire of proteins needed for conjugation. This machinery includes proteins required to form the pilus, as well as enzymes that both cut circular plasmids into single DNA strands and lead them to the pilus for transfer to a recipient cell. Yet, even without these key pieces of the conjugation puzzle, plasmids can be transferred between cells.

One such plasmid is the of Salmonella enterica serovar Typhimurium, a particularly versatile bacterium that causes gastrointestinal infections in humans and other animals. The P3 plasmid carries resistance to 2 antibiotics and can also replicate without using host proteins like helicases and primases, but it is missing the conjugation machinery that is needed to jump between bacterial cells.

To get around this, the P3 plasmid often occurs alongside 2 other plasmids (P1 and P2) that each have their own conjugation machinery. Research published in the Journal of Bacteriology in 2022 showed that P3 encoded by the P2 plasmid to conjugatively transfer itself among bacterial cells. The spread is not limited to S. Typhimurium, either, as the researchers showed that P3 can be transferred to a broad range of bacteria isolated from the human gut, as well as environmental isolates. This suggests that the animal gut is a likely arena for the transfer of the P3 plasmid, and potentially others like it.

Detecting Plasmid Transmission in Clinical Settings

Plasmid transmission occurs in the "real world," but is surprisingly difficult to monitor in critical settings like hospitals. However, a recent study detailed the efforts at the University Hospital Münster in Germany, where researchers ramped up genomic surveillance efforts to include resistance plasmids, which are rarely monitored due to technical challenges. They by comparing the DNA sequences of plasmids across more than 400 multidrug-resistant bacteria isolated from patients, mostly belonging to the species E. coli and Klebsiella pneumoniae. By not routinely tracking plasmid transmission between different bacteria, the researchers estimated that they were missing approximately one-third of all plasmid transfer events occurring in their hospital environment.

The researchers also cross-referenced similarities in plasmid sequences with patient records to identify overlaps in hospital stays, or closer contacts like shared rooms, and infer routes of plasmid transmission between different bacteria. They identified 12 potential plasmid transmissions; 7 of these occurred in a single patient, while 5 occurred between patients. Indeed, plasmid transmission between different bacteria is likely to begin inside a single host, where bacteria are in close quarters, but the study could not pinpoint whether intra- or inter-patient transmission occurred first.

The study authors note that their findings may not be representative of other health care settings, as the prevalence and transmission of resistance genes to different antibiotics across the globe. The use of long-read DNA sequencing technology may also not be feasible for researchers in other health care settings to implement, raising a barrier to monitoring the spread of antibiotic resistance in resource-limited settings .

The Bottom Line

Altogether, studies that probe the mechanisms and dynamics of plasmid transfer among bacteria are vitally important. By understanding where, how and how often resistance plasmids are shared, we can continue to seek and develop solutions for emerging multidrug-resistant pathogens, as well as quantify risks and manage the world’s ever-growing populations of antibiotic-resistant pathogens.