Hospital-associated microbiota and implications for nosocomial infections

Appropriate song to play while reading this post: Doctor! Doctor! – Thompson Twins

Despite the many hours we spend inside homes, offices, and other buildings, we still know very little about the microorganisms that live inside these walls. Health-care facilities are very important in this respect, because the humans inside these buildings are often immunocompromised: they are sick, either very young or at an advanced age, and receiving antibiotics or other medications. That makes them much more vulnerable to infections. If we want to improve the rate of nosocomial infections (infections that are acquired during a hospital stay), it is important to know which microbes live inside hospital buildings and equipment.

Simon Lax and Jack A. Gilbert wrote a timely review last week on this topic. In this paper in Trends in Molecular Medicine called “Hospital-associated microbiota and implications for nosocomial infections“, Lax and Gilbert give an excellent oversight of several studies that characterized hospital-associated microbial communities. In addition, they list studies documenting the spread of antimicrobial resistance within hospitals, and the discovery and characterization of emerging new nosocomial pathogens. Finally, they focus on improvement of indoor air quality and surface cleaning regimens.

Hospital-associated microbiota and implications for nosocomial infections – Simon Lax and Jack A. Gilbert – Trends in Molecular Medicine – doi:10.1016/j.molmed.2015.03.005


The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.


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Elisabeth Bik

After receiving my PhD at Utrecht University in The Netherlands, I worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, I joined the Department of Microbiology and Immunology at Stanford, where I have worked on the characterization of the microbiome of human oral, gastric, and intestinal samples, as well as samples from marine mammals. Since November 2016, I am the new Science Editor at uBiome, a microbiome genomics company enabling citizen science. But you might also find me working on the detection of science misconduct, at my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, on Twitter at @MicrobiomDigest.