Abstract
The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.
Highlights
Hospital-acquired infections (HAIs) represent a serious public health problem, affecting millions of people worldwide [1]
663 samples were collected during the six months. 502 (75.7%) samples contained classifiable sequences, while 161 (24.3%) did not present sequences after the filtering process
A relatively low number of sequences in most libraries was observed, which can be partially related to the rigorous filtering process, but most importantly, due to the intrinsic feature of the hospital environment presenting only a few number of microorganisms, as a consequence of its constant cleaning and sterilization procedures
Summary
Hospital-acquired infections (HAIs) represent a serious public health problem, affecting millions of people worldwide [1]. Known as nosocomial infections, they are the fifth leading cause of death in acute-care hospitals. In developing countries, where the burden of endemic healthcare-associated infection is significantly higher [4], the prevalence of HAIs varies between 5.7% and 19.1% [1]. One of the challenges in preventing HAIs is understanding the microbial diversity associated with the hospital environment, the sources of infectious agents and the routes of transmission. Understanding the hospital microbiome could be essential to maintaining low levels of HAI infections and to help improving healthcare assistance
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