Essential Science: Year-long survey tracks microbes in hospitals

Posted Jun 12, 2017 by Tim Sandle
Understanding the types of microorganisms found in a typical hospital and whether they are pathogens is an important part of good governance. Such investigations need to go further and understand changes over time.
A physician talks to the mother of a patient at pediatric hospital in Havana  Cuba on December 30  2...
A physician talks to the mother of a patient at pediatric hospital in Havana, Cuba on December 30, 2010
, AFP/File
To explore the longer-term profile and associated changes with the microbial profile of hospitals, microbiologists from the University of Chicago Medical Center embarked on a twelve-month study. No area was left unsampled; samples were taken of patients, medical and nursing staff and surfaces. The aim was to lay down a benchmark to help hospitals to understand how to encourage beneficial microbial interactions and decrease potentially harmful contact.
HAIs - Hospital-Acquired (Nosocomial) Infections
Superbugs are a particular problem in hospitals. Where healthy people can carry colonies of the organisms, those who are immunosuppressed are often vulnerable. The organism are invisible and can survive on surfaces for up to three days. In addition they can be transferred when one infected person simply touches another, or when the patient touches something on which the pathogen resides like a stethoscope, a TV remote, a computer mouse, or shared athletic equipment.
The hospital microbiome project
Discussing the aims further, the principal scientist Dr. Jack Gilbert explains: "The Hospital Microbiome Project is the single biggest microbiome analysis of a hospital performed, and one of the largest microbiome studies ever.” A microbiome refers to the microorganism found within a given ecological niche. It is more than a simple list of species; more so it is an understanding of how the community interacts and changes.
The study
For the study, the microbiologist constructed a map of microbial exchange and interaction throughout a hospital environment. This required several factors to be inputted, such as the ecology of a building; the type of microbial ecosystem; points where patients could interact with certain microorganisms and so on.
What also made the study interesting was that it was undertaken at a newly opened hospital, which allowed the changes over time to be correlated against an expansion of hospital activities as well as measuring changes in relation to seasonality. The hospital was the University of Chicago Medicine Center for Care and Discovery.
Across the time period the microbiologists took over 10,000 samples. With these microbial DNA was found in 6,523. The types of areas sampled included patient care rooms and adjoining nursing stations. These areas were located on different floors. With the samples of patients, sites selected included the hands, nostrils and armpits of patients. Samples were additionally taken of staff, to assess the interactions between staff and patient’s. With nursing staff there was a focus on hand cleanliness.
Alongside these samples were taken of things like bedrails or faucet handles (surfaces likely to have been touched by the patient). Samples were also taken pre- and post-cleaning, to assess the cleaning of wards and beds in-between patients.
The key findings
The interesting changes were when hospital opened compared with the hospital in later use. Bacteria including Acinetobacter and Pseudomonas, were abundant during construction and pre-opening preparations. These were soon replaced by human skin-associated organisms like Corynebacterium, Staphylococcus and Streptococcus, which are likely to be brought in by patients or staff. Over time the overall diversity of organisms increased.
H. pylori is a helix-shaped (classified as a curved rod  not spirochaete) Gram-negative bacterium ab...
H. pylori is a helix-shaped (classified as a curved rod, not spirochaete) Gram-negative bacterium about 3 μm long with a diameter of about 0.5 μm.
Institute for Systems Biology
Also of interest was the movement of microorganisms. Here a common pattern was, on a patient's first day in the hospital, bacteria tended to transfer from surfaces in the patient's to the patient. However, for all subsequent days the majority of bacteria moved in the opposite direction (that is from the patient to the room). This meant that quickly the patient's microbiome starts to takes over the hospital space.
Furthermore with patients, whether a patient was given an antibiotic (orally or intravenously) prior to or during admission had almost no impact on the skin microbiome. With patients subjected to extended stays (periods of months) potentially harmful bacteria, like Staphylococcus aureus and Staphylococcus epidermidis, began to acquire genes that led to antibiotic resistance. This has been attributed to selective pressures.
Microbes: Staphylococcus is a common bacteria which can cause anything from a simple boil to horribl...
Microbes: Staphylococcus is a common bacteria which can cause anything from a simple boil to horrible flesh-eating infections
Vano Shlamov, AFP/File
It was further found that as the heat and humidity increased during the summer, hospital staff shared more bacteria with each other. There was also, according to a statistical measure called dynamic Bayesian network analysis, an indication that hospital staff were more likely to be a source of bacteria on the skin of patients than the reverse. All of these results are interesting and suggest further study is needed. With such studies better infection and contamination control measures can be put in place to support hospitals and to protect patients.
The findings are published in the journal Science Translational Medicine, under the title of “Bacterial colonization and succession in a newly opened hospital.”
Essential Science
This article is part of Digital Journal's regular Essential Science columns. Each week Tim Sandle explores a topical and important scientific issue. Last week we delved into a new technique that looks at reducing skin aging, by applying methylene blue. The week before we explored the use of bioelectricity as a powerful way of killing pathogenic bacteria. The week before we looked at how nanotechnology can be used to rapidly and non-invasively treat broken bones.