By Joseph F. John, Jr., MD, FACP, FIDSA, FSHEA

Clinical Professor of Medicine and Microbiology, Medical University of South Carolina and Lowcountry Infectious Diseases, Charleston

Dr. John reports no financial relationships relevant to this field of study.

SYNOPSIS: Researchers observed nongrowing cells of Salmonella that remained persistent, resisted antibiotics, and retained infectivity.

SOURCE: Stapels DAC, Hill PWS, Westermann AJ, et al. Salmonella persisters undermine host immune defenses during antibiotic treatment. Science 2018;362:1156-1160.

Microbiologists in England, Germany, and the Netherlands recently have been studying the population of bacterial pathogens that lie dormant and metabolically inactive, as though dead. In her London lab, Sophie Helaine, senior author on this paper, showed in 2014 that nongrowing forms of one particular bacterial pathogen, Salmonella enterica, can enter macrophages and assume a nongrowing state known as persisters that does not respond to antibiotics. Earlier observations established that certain bacteria grown in vitro will have some cells that remains dormant, but these new observations about Salmonella were unique because the microbes could reassume pathogenicity.

Stapels and colleagues set out understand the metabolism of Salmonella persisters. Through the following set of experiments, they showed that antibiotic treatment of persisters after they infect bone-marrow macrophages selects an active set of persisters that can regrow and retain infectivity. Active persisters survive by expressing what is called a pathogenicity island that in Salmonella contains those genes that evade immune destruction.

In an elegant set of experiments using new molecular methods to detect gene expression even in single cells, researchers found that transcription and translation were retained in active persisters. Furthermore, they performed what is known as dual RNA sequencing of both bacterial and host cells. In so doing, the group demonstrated that genes translocated from the Salmonella pathogenicity island to host cells resulted in dampening of the immune response to the infecting Salmonella. Additional experiments on the type of macrophage altered to reduce immune reactivity allowed support of the hypothesis that downregulation of specific macrophages (M2 rather than M1 macrophages) by active persisters allows certain persisters to survive and reignite infection.

Taken together, this work on mechanisms of survival for a classic, major human pathogen highlights the cross talk between the bacterium and the host cell. In this case, active but nongrowing Salmonella retained the ability to make proteins that would depress the immune response, allowing Salmonella to resist antibiotic destruction and immune alteration.


Clinicians are familiar with some forms of bacterial trickery, such as spore formation to insure bacterial survival. Clinicians also know that certain bacteria, like Salmonella and Listeria, require an intracellular sanctuary not only to survive but also to produce disease. The work of these scientists seems momentous to me. It reinforces the complexity of the bacterial infection. It is only with newer molecular methods that the complexity of cross talk between host and pathogen could be culled. Some parts of the bacteria are crucial to promote survival vs. destruction, either through antibiosis or immune attack. Pathogenicity islands are a good example of a kind of secret bullet within the bacterial genome that fires with initial infection and alters the host response so that the dormant persister remains nonresponsive to antibiotics but also has sensitized the host genome to alter its immune response.

The implications of this work are profound. First, this new type of antimicrobial resistance, the nonresponsiveness of the persister, is very challenging. Therapeutics would have to be devised to turn on the persister and find a way for it to respond adversely to the antimicrobial. Second, even if the persister can be spurred to interact with the antimicrobial, there needs to be an adequate immune response to effect killing intracellularly. Perhaps interrupting specific parts of the pathogenicity island with a CRISPR insertion could allow the host cell to regain the upper hand. Finally, do these results suggest that there is even further interaction between microbial invader and host cell, other than the immune escape shown in this experimental design, that produces additional survival advantages?

Clinicians will need to adopt new terminology. In staphylococcal infection, we now have concern for another kind of persister, the small colony variant. But small colony variants, seen also in other genera, continue to metabolize. In the Salmonella persisters of this current work, we are facing a newly discovered entity that evades both antimicrobial attack and immune subversion. New imaging techniques will be required to help clinicians understand that certain cells remain infected even with bacterial cellular forms that only seem dead and really are just playing opossum.