Exploring Bacterial Diversity in Hospital Environments by GS-FLX Titanium Pyrosequencing

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.

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

“…We compared 16S rRNA gene fragments recovered from the shower hose metagenomes against 16S rRNA gene sequences available from DWDS pipes located in Florida (75) and a surface in the intensive care unit (ICU) of a hospital ward in Spain (76). This analysis revealed distinct taxonomic profiles between these and our shower hose metagenomes (see Fig.…”

“…Members of these genera also have the ability to coaggregate with other community members, contributing to effective colonization and expansion of biofilms (84). In view of the frequent occurrence of Sphingomonadaceae in hospital tap water and their high survival in the air of the indoor environment, this group has been identified as a frequent contaminant of medical devices (67,69,76). Although these organisms were less abundant than mycobacteria in shower hose biofilms (see Fig.…”

Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

“…By parallel sequencing of short amplicons, typically 16S rRNA genes in bacteria and internal transcribed spacer (ITS) domains in fungi (8), it is possible to comprehensively profile the microbial composition of diverse environments. Microbial communities in intensive care units (ICUs) (9), hospitals (10), public restrooms (11), wineries (12), and office spaces (13) have been explored using high-throughput amplicon sequencing, advancing our knowledge of microbial trafficking and colonization in these systems. A recent report on bacterial communities on the surfaces in two NICUs demonstrated significant diversity and supported the hypothesis that colonies of pathogens on NICU surfaces may increase the risk of infection for premature infants (14).…”

PCR Technique for the Microbial Analysis of Inanimate Hospital Environment

“…The phylogenetic spectrum combined species associated with the outside environment, taxa closely related to potential human pathogens and beneicials as well as included 7 phyla and 76 genera [73]. A similar methodology was obtained by Poza et al [74], who ampliied a hypervariable region of the bacterial 16S rRNA gene to explore the bacterial diversity at inanimate surfaces of the ICU wards. Detected microbiota contained a total of 3000 operational taxonomic units.…”

“…Detected microbiota contained a total of 3000 operational taxonomic units. The identiied representatives were 16 canonical bacterial phyla, members of the phyla Firmicutes mainly Staphylococcus and Streptococcus and Actinobacteria mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae , the phylum Proteobacteria mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae , the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria, Proteobacteria mainly due to the high abundance of Enterobacteriaceae members [74]. 16 S rDNA PCR and sequencing was also employed in study of Xu et al [75], where 53 isolates from environmental water-associated sites in a haematology unit, and the outer surfaces of cleaning lotion containers sited throughout a tertiary referral hospital were investigated.…”