Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing

PLoS One. 2012;7(8):e44105. doi: 10.1371/journal.pone.0044105. Epub 2012 Aug 29.

Abstract

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Databases, Nucleic Acid
  • Environmental Microbiology*
  • Genetic Variation*
  • Hospitalization
  • Hospitals*
  • Humans
  • Intensive Care Units
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA / methods*
  • Spain
  • Temperature*
  • Titanium / chemistry*

Substances

  • RNA, Ribosomal, 16S
  • Titanium

Grant support

This work was supported by the Spanish Network for Research in Infectious Diseases (REIPI, RD06/0008/0025), grants from Fondo de Investigaciones Sanitarias (PI081368 and PS09/00687), SERGAS (PS07/90) and Xunta de Galicia (07CSA050916PR) to GB and a grant from SERGAS (PS08/24, Galicia, Spain) to MP. MP was supported by the Isidro Parga Pondal Program (Xunta de Galicia, Spain), CG by the Spanish Network for Research in Infectious Diseases (REIPI, RD025/0008), MJG by the project Consolider INGENIO CSD2007-0005 and INTA-CSIC (Madrid, Spain) and SRF, MT, JA and AF by Instituto de Salud Carlos III (Spain). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.