The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013

Shogan, Benjamin D.; Smith, Daniel P.; Packman, Aaron I.; Kelley, Scott T.; Landon, Emily; Bhangar, Seema; Vora, Gary J.; Jones, Rachael M.; Keegan, Kevin P.; Stephens, Brent; Ramos, Tiffanie; Kirkup, Benjamin C.; Levin, Hal; Rosenthal, Mariana; Foxman, Betsy; Chang, Eugene B.; Siegel, Jeffrey A.; Cobey, Sarah; An, Gary; Alverdy, John C.; Olsiewski, Paula; Martin, Michael R.; Marrs, Rachel; Hernandez, Mark; Christley, Scott; Morowitz, Michael J.; Weber, Stephen G.; Gilbert, Jack A.

doi:10.4056/sigs.4187859

Cited by 14 publications

(10 citation statements)

References 5 publications

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“…Over the past decade, molecular microbial diversity studies have shed new light on the spatial and temporal variation of microbial communities in the built environment (8)(9)(10)(11) . Recent work has revealed how microbial communities, or microbiomes, differ with different building systems (e.g., ventilation mechanisms) (5) , how new buildings are colonized by microorganisms (11,12) , and how the human microbiome both impacts and is impacted by the microbiome of homes (13) .…”

Section: Introductionmentioning

confidence: 99%

Geography and location are the primary drivers of office microbiome composition

Chase

Fouquier

Zare

et al. 2016

Preprint

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North Americans spend the majority of their time indoors where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs, and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidates several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ based on surface material (e.g., ceiling tile or carpet), but do differ based on the location in a room (e.g., ceiling or floor), two features which are often conflated, but which we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material were likely detecting differences based on different usage patterns. Next, we find that offices have cityspecific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but officespecific bacterial communities are less apparent. This differs from previous work which has suggested officespecific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. ImportanceOur study highlights several points that should impact the design of future studies of the microbiology of the BEs. focus sampling effort on surveying different locations in offices and in different cities, but not necessarily different materials or different offices in the same city. Next, disturbance due to repeat sampling, though detectable, is small compared to other variables, opening up a range of longitudinal study designs in the built environment. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples on all sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities.

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Section: Introductionmentioning

confidence: 99%

Geography and location are the primary drivers of office microbiome composition

Chase

Fouquier

Zare

et al. 2016

Preprint

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“…Notably, we have identified very few bla OXA ϩ isolates; therefore, our focus for environmental screening was on CPOs that were bla KPC ϩ or bla NDM ϩ by PCR. Environmental surveillance can be a useful tool to identify the source of an outbreak (6), to better understand the microbial communities within the hospital (7), and to evaluate the efficacy of environmental disinfection or other infection control measures (8). Sources of outbreaks are occasionally linked to aqueous locations such as sinks and drains (9)(10)(11)(12), where the presence of biofilms makes remediation challenging; sink engineering modifications have been proposed to tackle these problems (13,14).…”

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confidence: 99%

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

Weingarten

Johnson

Conlan

et al. 2018

mBio

163

114

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The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of bla KPC /bla NDM -positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with bla KPC -positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs), suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.IMPORTANCE Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gramnegative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections. A 5-year genomic and epidemiological survey was undertaken to study the CPOs in the patient-accessible environment, as well as in the plumbing system removed from the patient. This comprehensive survey revealed a vast, unappreciated reservoir of CPOs in wastewater, which was in contrast to the low positivity rate in both the patient population and the patient-accessible environment. While there were few patient-environmental isolate associations, there were plasmid backbones common to both populations. These results are relevant to all hospitals for which CPO colonization may not yet be defined through extensive surveillance.

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“…Understanding of the microbiology of air, the aerobiome, is an emerging field of discovery. High-throughput sequencing methods are being used to explore the spatiotemporal distribution of bacterial and fungal populations [1][2][3][4][5][6][7][8][9][10]. A variety of sampling methods have been used for studying the air microbiome [3,[11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

A simple novel device for air sampling by electrokinetic capture

Gordon¹,

Gandhi²,

Shekhawat

et al. 2015

Microbiome

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BackgroundA variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable.ResultsAn air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as “gold standard.” Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air.ConclusionsThis work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.

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The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013

Cited by 14 publications

References 5 publications

Geography and location are the primary drivers of office microbiome composition

Geography and location are the primary drivers of office microbiome composition

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

A simple novel device for air sampling by electrokinetic capture

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