Studying the microbiology of the indoor environment

Kelley, Scott T.; Gilbert, Jack A.

doi:10.1186/gb-2013-14-2-202

Cited by 142 publications

(162 citation statements)

References 74 publications

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“…It is estimated that humans in industrialized countries spend as much as 90% of their lives indoors (1,2). Indeed, for billions of humans, the "great indoors" comprises the new human ecosystem.…”

mentioning

confidence: 99%

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

Gibbons

Schwartz

Fouquier

et al. 2015

Appl Environ Microbiol

107

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g Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in four public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late-successional community developed within 5 to 8 h on restroom floors and showed remarkable stability over weeks to months. Despite late-successional dominance by skin-and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human exclusion. Methicillin-resistant Staphylococcus aureus (MRSA)-associated virulence genes were found on floors but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophages, human papilloma virus, and herpesviruses, were significantly correlated with bacterial abundances and showed an unexpectedly low virus-to-bacterium ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.

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mentioning

confidence: 99%

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

Gibbons

Schwartz

Fouquier

et al. 2015

Appl Environ Microbiol

107

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“…The increasing ease and decreasing costs of high-throughput short-amplicon-sequencing technologies are propelling efforts to describe the microbial communities of surfaces on a massive scale (7). 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.…”

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confidence: 99%

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

2013

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Premature infants in neonatal intensive care units (NICUs) are highly susceptible to infection due to the immaturity of their immune systems, and nosocomial infections are a significant risk factor for death and poor neurodevelopmental outcome in this population. To investigate the impact of cleaning within a NICU, a high-throughput short-amplicon-sequencing approach was used to profile bacterial and fungal surface communities before and after cleaning. Intensive cleaning of surfaces in contact with neonates decreased the total bacterial load and the percentage of Streptococcus species with similar trends for total fungal load and Staphylococcus species; this may have clinical relevance since staphylococci and streptococci are the most common causes of nosocomial NICU infections. Surfaces generally had low levels of other taxa containing species that commonly cause nosocomial infections (e.g., Enterobacteriaceae) that were not significantly altered with cleaning. Several opportunistic yeasts were detected in the NICU environment, demonstrating that these NICU surfaces represent a potential vector for spreading fungal pathogens. These results underline the importance of routine cleaning as a means of managing the microbial ecosystem of NICUs and of future opportunities to minimize exposures of vulnerable neonates to potential pathogens and to use amplicon-sequencing tools for microbial surveillance and hygienic testing in hospital environments. P remature infants in neonatal intensive care units (NICUs) are highly vulnerable to infections due to the immaturity of virtually every aspect of their innate and adaptive immune systems. The importance of hospital surfaces and the cleaning of these surfaces in interrupting outbreaks of specific organisms in NICUs (1, 2) and in eliminating reservoirs of potential pathogens (3-5) has been emphasized. However, most studies to date have relied on culture-based techniques, which can give incomplete and biased assessments of mixed microbial communities (6).The increasing ease and decreasing costs of high-throughput short-amplicon-sequencing technologies are propelling efforts to describe the microbial communities of surfaces on a massive scale (7). 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).Stringent cleaning protocols for the surfaces in NICUs have been in place for many years, ...

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“…Culture media is defined as "a solid or liquid preparation used to grow, transport and store microorganisms" (Willey et al 2008, p. 110). Culture-based techniques are considered the standard for determining cell viability (Kelley and Gilbert 2013).…”

Section: Culture-based Methods Of Recoverymentioning

confidence: 99%

“…rDNA), for examining diversity can capture more organisms that culture-based studies miss, several orders of magnitude more diversity are found from these types of studies (Woese et al 1990;Kelley and Gilbert 2013). However, there are also limitations to culture-independent studies.…”

Section: Culture-based Methods Of Recoverymentioning

confidence: 99%

“…However geographic differences, in addition to technical differences, make comparing these studies difficult. It is established that external inputs to indoor environments, such as open windows, food, and soil can influence the diversity of microbial communities (Kelley et al 2013), and it is possible these factors are influencing differences in seasonal recovery of Pseudomonas species as well. Seasonal variability in Pseudomonas recovery indicates that microbial longitudinal studies must be carefully designed and consider climatic or environmental variables for greatest accuracy.…”

Section: Seasonal Variabilitymentioning

confidence: 99%

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Recovery and biogeography of Pseudomonas and Burkholderia species from the human home.

Purdy¹

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Studying the microbiology of the indoor environment

Abstract: The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health.

Cited by 142 publications

References 74 publications

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

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

Recovery and biogeography of Pseudomonas and Burkholderia species from the human home.

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