The Human Microbiome and Infection Prevention: How Gut Health, Dysbiosis, and Hospital Environments Influence HAIs and Antimicrobial Resistance

Microorganisms are widespread in humans, animals, and the environment. Microorganisms, such as bacteria, viruses, and fungi, all coexist within a human host. This collective of microorganisms is called the human microbiota.¹ Normally, the microbiota within a host acts as a protective barrier by preventing pathogens from taking root in the body.² Microbiome is defined as the genetic information of all the microorganisms that live in and outside our bodies.³ The impact of the microbiome is becoming an emerging science in infection prevention.

The microbiota is affected by both external and internal exposures. For example, an infant’s intestinal microbiota is initially influenced by vertical transmission from the mother.⁴ Additionally, dietary habits and exposure to external microorganisms impact the microbiota.

Hospitalization can have significant impacts on a patient's microbiome. Dietary changes during hospitalization can alter the function of normal gut flora. Stress and the need for parenteral nutrition vs the diet the individual normally has at home can result in decreased diversity and functionality of the microbiota. Additionally, medications, particularly antimicrobials, significantly alter the composition of the microbiota. A microbiome that was primed to defend against pathogenic microorganisms may be severely limited in its ability to perform those functions when a person is hospitalized.⁵ The microbiome influences the host’s immune system. From birth, the microbiome of an infant helps develop immune cells, such as T cells, B cells, and CD4 cells.⁴ Additionally, microbiomes have a role in the development of metabolic pathways, the nervous system, and inflammatory responses.

Historically, the role of the microbiome in medicine has not been considered. Microorganisms evolve alongside their hosts over time. This relationship between the host and the microbiome can directly affect many disease processes. For example, the health of the gut microbiome has been shown to directly affect the efficacy of chemotherapy and radiation treatments for certain cancers.⁴

Following the basic principles of infection prevention requires understanding that the development of health care–associated infections (HAIs) depends on having a susceptible host, a pathogen, and transmission. Most frequently, the source of the pathogens is exogenous, or from outside the body. However, we also know that many HAIs result from the endogenous microbiota. Studies have shown that 20% of patients who are colonized with a multidrug-resistant organism (MDRO) will develop an HAI with that same organism during their admission in an intensive care unit (ICU).²

Dysbiosis is an imbalance in the microbiota, characterized by decreased beneficial microorganisms and increased pathogenic microorganisms. A healthy gut microbiota prevents colonization by MDROs. However, antimicrobial administration can lead to overgrowth of exogenous pathogens and increase the risk of developing resistance. The persistence of resistance genes, known as the antibiotic resistome, can be transmitted between different species of microorganisms, leading to increased emergence of MDROs.² Not only is the patient who received the antimicrobials at risk, but studies have shown that resistance genes have been transmitted to other humans who had no prior exposure to antimicrobials.²

Even more concerning is that studies on the immediate effects of antimicrobials on microbiota show that these changes can persist for years after the medication is administered.²

A study of ICU patients found that those with changes in their microbiome reflecting increased levels of specific microorganisms associated with producing acids that harm the gut lining were at increased risk of developing ventilator-associated pneumonia.⁵ Other studies have shown similar findings, but these results still have limitations. However, there is a relationship between gut microbiome and negative outcomes during ICU admission.⁵

A person’s microbiota is influenced by many factors. The environment in which a person interacts also shapes that microbiota. The health care environment includes medical equipment, health care workers (HCWs), medications, and the actual rooms or spaces where health care activities are performed.

Studies have examined the effects of a health care environment on patients’ microbiota and microbiome, focusing on these potential areas of exposure. HCWs themselves may be among the main risks affecting patient microbiota. A study of HCWs sampled their hands, cell phones, and hospital scrubs, showing that all were contaminated with a similar distribution of the types of pathogens most frequently associated with.¹ In particular, 27% of HCW hands had samples that grew Clostridioides difficile.¹

Tozzo et al described a study in which patients admitted to an ICU were sampled on admission and again 10 days into their stay.¹ Their microbiota was compared over this time period. Initially, closer to admission, the patients had more similar microbiota. However, after day 10, patients’ microbiota were more varied. This study showed that during an ICU admission, endogenous microbiota were rapidly modified, and more pathogenic microbiota were introduced.¹

Respiratory tract infections may be linked to similar disruptions in the endogenous microbiome. The diversity of a patient’s microbiota is essential to maintaining the balance as well. If the microbiome distribution is less diverse, it is more likely to reflect a prevalence of pathogenic organisms. To demonstrate this, skin microbiomes of healthy patients compared with patients who developed ventilator-associated pneumonia found that the healthy microbiome was more diverse and included more protective species vs the microbiome of patients who developed an HAI.¹

Similarly, patients’ microbiota can influence the microbiome of their environment. We know that patients shed their microbiota into their environments, but how much does that change the environmental microbiome? A study compared the patient microbiome before and after ICU admission and found that environmental samples matched more closely in terms of organism types after admission. This shows that the patient microbiome impacted the environmental microbiome, demonstrating an exchange between them.¹

The microbiome of a health care environment changes over time, as does a patient’s. Studies comparing ICU rooms over time showed that the rooms’ microbiomes more closely resembled those of rooms closest to them but varied more when patient turnover was higher. Similarly, as a patient’s stay lengthened, the microbiota in medical devices near the patient’s room became increasingly similar to the patient’s.¹

With this knowledge of how the microbiome functions in humans and its important role in the body’s systems, interventions that modify the microbiome have been developed for disease management. The most widely known example is fecal microbiota transplant (FMT). FMT has been used to treat recurrent C difficile infection (CDI) for many years. C difficile is the leading cause of health care-associated diarrhea in the US.² Studies focused on FMT for treatment, or even prevention of CDI, have shown that after administration, the patient has an increase in the diversity of microorganisms and, importantly, an increase in the specific microbiome that is seemingly protective against toxin-producing C difficile.²

However, as many infection preventionists are aware, there are concerns with FMT—not only the perceived unpleasantness of the procedure itself but also the potential for exposure to pathogens from donor stool. Companies that have developed donor networks and prepackaged specimens have been under regulatory scrutiny, limiting FMT’s utilization in the current setting.⁷

Other examples of modifying the microbiome to improve immune function include the use of probiotics and phage interventions. Probiotics have been recommended as prophylactic treatments for many years. Although study findings have been inconsistent about their effectiveness, the use of probiotics remains common.² The goal of probiotics is like that of FMT: to boost the level of protective microbiota. However, ensuring that the appropriate microbiota is incorporated and that the route of administration is effective is challenging.²

Phage technology focuses on developing viruses that target the genetic characteristics of harmful bacteria, thereby eliminating or neutralizing pathogens. Bacteriophages are naturally occurring viruses that prey on bacteria. Current therapies are being developed using phage mechanisms to address some of the most common gut pathogens, including C difficile, Escherichia coli, and Listeria.⁶ Additionally, research is being conducted on utilizing phage therapies for the treatment of gastrointestinal cancers.⁶ Overall, if phage therapies are proven to be a successful and safe treatment option, their applications are countless and could provide a mechanism to reduce dysbiosis and prevent unnecessary antimicrobial use.

Traditional infection prevention and control tactics alone are not sufficient to prevent alterations in the microbiome. Antimicrobial and diagnostic stewardship efforts can support patient microbiome health alongside IPC strategies. Through appropriate testing, diagnosis, and medication administration, patients will receive the correct medication for their infection. This overall decreases antimicrobial resistance and helps prevent dysbiosis in those who do not need treatment.⁶

Outbreak investigations using genetic sequencing are becoming more common.⁶ Identifying matching organisms and potential sources can be done with precision, leading to more effective interventions. A barrier to this is the limited sequencing capabilities of most facility laboratories, which instead rely on health departments or reference labs. This increases the time to obtain results and the costs associated with the investigation.

Environmental cleaning and disinfection have been a tool for infection prevention from the beginning. More information on the microbiome of health care environments further stresses its importance in the chain of infection.¹ Advances in cleaning and disinfection can leverage this knowledge to develop innovative approaches. One example is the use of probiotic-infused cleaning solutions. Studies of a cleaning solution infused with spores of Bacillus species that inhibit the growth of pathogenic species have shown promising early results.¹

The investigators compared environmental samples before and after cleaning with traditional quaternary-based disinfectants and the probiotic-based solution. The results showed that after using the quaternary products, pathogenic bacteria remained significantly present on surfaces; however, after using the Bacillus-based product, the levels of the pathogenic microbiota were significantly reduced, but those of Bacillus remained unchanged.¹ Certainly, this concept needs further research, with an understanding of impacts on patients, but it is a promising consideration.

Conclusion

Patient microbiome diversity may serve as a biomarker for future treatments, enabling proactive identification of those at higher risk of HAI development. Targeted therapies can be included early in the admission or health care encounter to promote the endogenous protective microbiome and reduce the risk of dysbiosis.

Microbiota and microbiome are emerging areas of interest for IPC. Not only do current IPC strategies affect the microbiota of our patients and health care environments, but advancements in this area can provide targeted tools and interventions to reduce patient risk. Beyond the walls of our health care facilities, consideration must also be given to how changes in climate and animal populations impact microbiomes. Having this holistic One Health approach provides an overarching view of how these elements are connected and interrelated for the prevention of infectious diseases.

References

1. Tozzo P, Delicati A, Caenazzo L. Human microbiome and microbiota identification for preventing and controlling healthcare-associated infections: a systematic review. Front Public Health. 2022;10:989496. doi:10.3389/fpubh.2022.989496
2. Pettigrew MM, Johnson JK, Harris AD. The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance. Ann Epidemiol. 2016;26(5):342-347. doi:10.1016/j.annepidem.2016.02.007
3. Microbiome. National Institute of Environmental Health Sciences. Reviewed January 29, 2026. Accessed April 19, 2026. https://www.niehs.nih.gov/health/topics/science/microbiome
4. Ma L, Zhao HQ, Wu LB, Cheng ZL, Liu C. Impact of the microbiome on human, animal, and environmental health from a One Health perspective. Sci One Health. 2023;2:100037. doi:10.1016/j.soh.2023.100037
5. Elfiky SA, Ahmed SM, Elmenshawy AM, Sultan GM, Asser SL. Study of the gut microbiome as a novel target for prevention of hospital-associated infections in intensive care unit patients. Acute Crit Care. 2023;38(1):76-85. doi:10.4266/acc.2022.01116
6. Emencheta SC, Olovo CV, Eze OC, et al. The role of bacteriophages in the gut microbiota: implications for human health. Pharmaceutics. 2023;15(10):2416. doi:10.3390/pharmaceutics15102416