Hospitals

The microbiome of a patient hospital room

A new study proposes that understanding how microbes interact with patients, staff, and hospital surfaces within the microbiome of a hospital environment can contribute to a complete knowledge of healthcare associated infections and antibiotic resistance, and how to prevent both.

A foundational premise of Infection Prevention science is that contaminated environments increase the risk of transmission of healthcare associated infections, including those caused by multi-drug resistant organisms (i.e. “superbugs”), and that appropriate environmental cleaning and disinfection is critical and effective at maintaining a safe environment of care for both patients and healthcare workers.

Historically, few studies have focused on the hospital room microbiome and whether the data might adjust our approach to patient hygiene, room cleaning and/or other aspects of care that we and many healthcare facilities take for granted. Recently, however, a new study published in Science Translational Medicine proposes that understanding how microbes interact with patients, staff, and hospital surfaces within the microbiome of a hospital environment can contribute to a complete knowledge of healthcare associated infections and antibiotic resistance, and how to prevent both.

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In this study by Simon Lax and his team, bacterial cultures were collected from surfaces including floors, bed rails, countertops, faucet handles, and computer mice in occupied patient hospital rooms. The investigators also swabbed the hands and noses of patients and staff, along with the shoes, shirts, and cell phone of staff members. Over the course of a patient’s hospital stay, the study found that patient’s skin and room surfaces became “microbially similar”. Other studies (such as this one and this one) have observed the same thing concluding that our surroundings contribute to the make-up of our own microbial communities.

An interesting, and intuitively logical observation in this study was that non-ambulatory patients had less microbial diversity in nose, hand and patient zone (e.g. bedrail) samples, and less similarity to environmental surfaces, presumably since confinement to bed reduced their exposure.

 Another finding was that the longer patients stayed in their rooms, the more antibiotic-resistance genes the organisms in the environment acquired, though no association with antibiotic administration and resistance was observed except for topical antibiotics. The author suggested a reason for this in that the environment is inherently stressful for the bacteria due to regular cleaning so any organisms that survive would have a greater likelihood of being able to acquire genes that could be relevant. Two of the most resistant environmental colonizers were Escherichia coli and  – both dangerous to the health of the average person.

The hospital room microbiome has possibly the greatest potential to impact the most vulnerable patients such as in a neonatal intensive care unit (NICU).  The infants in a NICU are particularly susceptible to opportunistic infection.  Infected infants have high mortality rates, with the source of many NICU infections uncertain. Environmental testing in one NICU-specific study detected mainly skin and fecal bacteria and generally argued for the broader use of molecular testing for identification and tracking of bacteria diversity in NICUs to help keep our nation’s premature babies as safe as possible.

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In the Lax study, several bacterial samples taken more than 71 days apart were identical, leading the investigator to conclude that either ubiquitous skin-associated microbial strains had “seeded” the environment by sequential room occupants and staff, or that there were radically persistent bacteria in the environment despite cleaning with quaternary ammonium compounds daily and bleach at discharge.  The risk to patients from pathogens remaining in hospital rooms from previous patients is a finding now confirmed by multiple studies including these two studies.

Still, other researchers make observations regarding the effect of outdoor environmental and building factors on the microbiome of built environments such as hospitals, and how outdoor air and microbes contribute to indoor microbial communities.

Over the course of this study by Lax and team, roughly 10 percent of the 252 patients who participated were found to have healthcare-associated infections. This is consistent with Centers for Disease Control and Prevention statistics which reflect that hospital-acquired infections affect 5 to 10 percent of hospitalized patients in the U.S. per year.

However, the study did not find the causative bacteria in the room samples for any of the healthcare associated infections.  What this might mean that patients were “colonized” with the bacteria that caused their infections. Though, since not all surfaces were tested including patient linen, gowns and privacy curtains, it is not possible to rule out other environmental sources of these migrating microbes.

The precise amount of biological contamination on healthcare surfaces resulting in transmission or development of infection is not the same in every case.  However, we do know that environmental contamination that remains after a patient is discharged from a hospital room can pose a risk of infection to the next patient.  This, of course, includes multi-drug resistant organisms or “superbugs.” Also, we know that manual cleaning and disinfection of solid surfaces in the healthcare environment is often incomplete, leaving pathogens including Clostridium difficile, Enterobacteriaceae, and yeast.

Similarly, soft surfaces including patient bed linen, gowns, privacy curtains and scrubs can remain contaminated despite processing via industrial laundry facilities and become re-contaminated during handling, transport or storage per these studies – Cheng 2016 and Duffy 2014. 

The Lax study discussed here as well as others which focus on the interaction of the microbiome of the patient and the healthcare environment gives us a complete knowledge of bacterial resistance development, patient response to clinical treatments such as chemotherapy and antibiotic administration, and ultimately allows us to devise the best approaches to patient hygiene and environmental cleaning and disinfection.

The bottom line is that the findings from this study underscore the importance of patient and environmental hygiene to reduce infection risk.  It also validates what we know regarding the limitations of manual cleaning and disinfection that we have trusted for decades.

Instead, we now see the ongoing presence of dangerous pathogens in the hospital environment despite regular cleaning using standard protocols. As we look to develop the best infection prevention strategies and solutions, this type of fundamental science and objective data serves to underscore the importance of using and continuing to study novel technologies as adjuncts to manual cleaning such as UV light disinfection, HP vapor disinfection, antimicrobial soft and solid surfaces and silver ion based laundry treatment.  It also leaves key scientific and environmental questions on the table. Would novel antimicrobial treated solid and soft surfaces in our hospitals affect the findings? Would there be the same degree of shared patient and environmental bacteria and resistance genes if antimicrobial threaded or treated textiles covered the patient, providing a physical barrier between the patient and the rest of the patient’s inanimate environment?

It also leaves key scientific and environmental questions on the table. Would novel antimicrobial treated solid and soft surfaces in our hospitals affect the findings? Would there be the same degree of shared patient and environmental bacteria and resistance genes if antimicrobial threaded or treated textiles covered the patient, providing a physical barrier between the patient and the rest of the patient’s inanimate environment?