The Hospital Microbiome Project

hosp microbiome

I recently came across the Hospital Microbiome Project, a multidisciplinary, multinational project designed to investigate the hospital microbiome. The science of ‘microbiomics’ (considering the whole microbial population rather than the small subset that can be cultured) is beginning to revolutionise our understanding of microbiology and human disease (1,2). Environmental studies tend to evaluate the presence of a particular microbe of interest. Few have begun to evaluate the microbiome of the hospital, and how it interacts with patients. Furthermore, antibiotic resistance genes can be shared between various species through horizontal transmission. Indeed, a study from our group at King’s College London found that ‘outbreaks of resistance’ across different species could be identified in the ICU (3). It is not known whether environmental surfaces represent a reservoir for antibiotic resistance genes and an environment in which horizontal transmission can occur (4-6). Thus, the ‘resistome’ of hospital surfaces warrants further evaluation (4-6). This point is particularly important for multidrug-resistant Gram-negative rods, which are multiply antibiotic resistant through a variety of resistance mechanisms (7-8).

The Hospital Microbiome Project uses methods to assess both the microbiome and the resistome of the hospital environment. Patient, staff, water and air will be sampled and sequencing of 16S and 18S ribosomal DNA has been used to identify bacteria and fungi, respectively, and an oligonucleotide array to detect a range of resistance genes. The initial studies are tracking the development of the hospital microbiome in a new Chicago hospital, and of a single patient room in a German military hospital (9). Some initial results already published on the Hospital Microbiome website are fascinating, explaining the microbial populations in a hospital under construction.

I look forward to seeing more results from the project in due course. There’s a chance the findings could change the way we think about contamination of the hospital environment.


  1. Blottiere HM, de Vos WM, Ehrlich SD, Dore J. Human intestinal metagenomics: state of the art and future. Curr Opin Microbiol 2013; 16: 232-239.
  2. Rajpal DK, Brown JR. Modulating the human gut microbiome as an emerging therapeutic paradigm. Sci Prog 2013; 96: 224-236.
  3. Vlek AL, Cooper BS, Kypraios T, Cox A, Edgeworth JD, Auguet OT. Clustering of antimicrobial resistance outbreaks across bacterial species in the intensive care unit. Clin Infect Dis 2013; 57: 65-76.
  4. Molin S, Tolker-Nielsen T. Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure. Curr Opin Biotechnol 2003; 14: 255-261.
  5. Warnes SL, Highmore CJ, Keevil CW. Horizontal transfer of antibiotic resistance genes on abiotic touch surfaces: implications for public health. MBio 2012; 3:
  6. Mkrtchyan HV, Russell CA, Wang N, Cutler RR. Could public restrooms be an environment for bacterial resistomes? PLoS ONE 2013; 8: e54223.
  7. Karah N, Sundsfjord A, Towner K, Samuelsen O. Insights into the global molecular epidemiology of carbapenem non-susceptible clones of Acinetobacter baumannii. Drug Resist Updat 2012; 15: 237-247.
  8. Munoz-Price LS, Poirel L, Bonomo RA et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis 2013; 13: 785-796.
  9. Smith D, Alverdy J, An G et al. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci 2013; 8: 112-117.

Image credit: Hospital Microbiome Website.

3 thoughts on “The Hospital Microbiome Project

  1. Indeed, this type of approach that is discussed will revolutionize how infection control professionals, clinical microbiologists, and the overal medical community understand and work to prevent MDROs.


    • Thanks Rodney. I’m not so sure. I am certain there’s some very interesting things going on down there on hospital surfaces. But the bottom line is really whether patients acquire pathogens from surfaces (i.e. the culturable microbes that can cause infections). That said, I do wonder to what extent hospital surfaces are a reservoir for antibiotic resistance genes, which could be acquired directly or spread horizontal within biofilms (Molin & Tolker-Nielsen et al. Curr Opin Biotechnol 2003;14:255-61).


      • Well, ten years ago I would have agreed with you. And, the microbiologist in me still leans that way with regards to “culturable microbes that cause infections” but I’m keeping an open mind. I look forward to hard data that shows the story either way….


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