The microbiome of a patient hospital room
By SUE BARNES
Jul 2, 2017 at 4:00 PM


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.

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.

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?


Sue Barnes
Sue Barnes
Sue Barnes, RN, CIC, FAPIC is Board Certified in Infection Control and Prevention, and was granted the designation of Fellow of APIC in 2015 (FAPIC). She has been in the field of Infection Prevention since 1989. She has participated in the development
of a number of APIC guides and served as a speaker for organizations including AORN and APIC. In addition, Sue has been published in journals including AORN Journal, American Journal of Infection Control, The Joint Commission Source for Compliance
Strategies and The Permanente Journal. She served on the National APIC Board of Directors from 2010 to 2012, and the San Francisco chapter board of directors for the past 10 years.
Having recently retired from Kaiser Permanente after almost 30 years as the National Leader for Infection Prevention, Sue embarked on a clinical consulting business in the field of Infection Prevention and Control. She works exclusively for companies and
organizations who share a passion for contributing to the evolution of the field and profession of Infection Prevention and Control, especially through innovation. These include both professional organizations and strategic vendor partners.


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