Reviewing major themes in hospital microbiome research

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Isabella O’Connor’
6 years ago
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Berkeley Department of Plant and Microbial Biology?

1 NAS/NAE/NAM Committee on Indoor Microbiomes 10/17/2016 Reviewing major themes in hospital microbiome research Brandon Bubba Brooks Banfield Lab, University of California Berkeley Department of Plant and Microbial Biology? samples, samples, samples, samples, samples, samples, samples, samples, samples, samples, samples, samples, samples, samples, samples

2 Why hospitals for room-occupant interaction studies? unique occupant populations environmental control of EVERYTHING GIF thanks to my former undergrad, Dylan Dahan, who is currently looking for PhD labs to join. He s great, you should hire him!

3 Why hospitals? = high frequency of HAIs & $$ lost In the US, 1/25 patients have at least 1 HAI Costs the US ~$30 BILLION/year

temperature ESKAPE organisms common 52% of samples culture positive for

4 It s difficult to clean hospitals single-use equipment box dead vs alive ward entry door two-step terminal cleaning 500 ppm chlorine treatment 12 month storage at room temperature ESKAPE organisms common 52% of samples culture positive for multidrug-resistance viability confirmed with multiple techniques after 12 mo! Hu et al., Hospital Infection 2015

5 Diversity varies in different zones of the hospital Poza et al., PloS ONE 2012

6 Surface microbes are likely sourced from humans Hewitt et al., PloS ONE 2013

7 Cleaning reduces microbial load bacterial fungal Bokulich et al., Clinical Microbiology 2013

8 Cleaning shifts the community structure PERMANOVA confirms: diffuse: Bokulich et al., Clinical Microbiology 2013

9 ESKAPE organisms relatively abundant = ESKAPE organisms Bokulich et al., Clinical Microbiology 2013

10 Low biomass, beware! Contaminants mislead you! Bokulich et al., Clinical Microbiology 2013

11 Hospitals vs other indoor microbiomes 1. Microbes overwhelmingly sourced from humans 1. Differences across zones 1. Cleaning/low biomass makes hospitals difficult to study 1. Microbes partially sourced from humans 1. Potentially more mixing 1. less cleaned/generally higher biomass in many cases

12 3-4 orders of magnitude biomass difference in NICU = wipes = > 4 µm bioaerosol (NIOSH cyclone) = 1-4 µm bioaerosol (NIOSH cyclone) Brooks et al., in prep

13 Touched surfaces have similar biomass = wipes = > 4 µm bioaerosol (NIOSH cyclone) = 1-4 µm bioaerosol (NIOSH cyclone) Brooks et al., in prep

14 Sink basin samples have the highest biomass = wipes = > 4 µm bioaerosol (NIOSH cyclone) = 1-4 µm bioaerosol (NIOSH cyclone) Brooks et al., in prep

15 Main entrance < incubator floor biomass = wipes = > 4 µm bioaerosol (NIOSH cyclone) = 1-4 µm bioaerosol (NIOSH cyclone) Brooks et al., in prep

16 Bioaerosols are higher in room than in entry hallway = wipes = > 4 µm bioaerosol (NIOSH cyclone) = 1-4 µm bioaerosol (NIOSH cyclone) Brooks et al., in prep

17 Hospitals vs other indoor microbiomes 1. Microbes overwhelmingly sourced from humans 1. Differences across zones 1. Cleaning/low biomass makes hospitals difficult to study 1. Occupancy drives biomass 1. Microbes partially sourced from humans 1. Potentially more mixing 1. less cleaned/generally higher biomass in many cases 1. Biomass drivers vary

18 Genomes are essential, strains are important! Infant Day of life (DOL) = Abx causes strain shift in Infant 5, day of life 4 = Abx causes strain shift, but original strain re-acquired/detected Raveh-Sadka et al., elife 2015

19 Loads of strain diversity, very few shared btw infants 4/149 strains shared!

20 Hospitals vs other indoor microbiomes 1. Microbes overwhelmingly sourced from humans 1. Differences across zones 1. Cleaning/low biomass makes hospitals difficult to study 1. Occupancy drives biomass 1. Numerous strains, not shared 1. Microbes partially sourced from humans 1. Potentially more mixing 1. less cleaned/generally higher biomass in many cases 1. Biomass drivers vary 1. Numerous strains, more shared

21 Project Framework Interventions: reservoirs dispersal engraftment

Conclusions, Hospitals vs other indoor microbiomes 1. Microbes overwhelmingly sourced from humans 1. Differences across zones 1. Cleaning/low biomass makes hospitals difficult to study 1.

22 Conclusions, Hospitals vs other indoor microbiomes 1. Microbes overwhelmingly sourced from humans 1. Differences across zones 1. Cleaning/low biomass makes hospitals difficult to study 1. Occupancy drives biomass 1. Numerous strains, not shared 1. Microbes partially sourced from humans 1. Potentially more mixing 1. less cleaned/generally higher biomass in many cases 1. Biomass drivers vary 1. Numerous strains, more shared reservoirs dispersal engraftment

23 Thanks for listening (!!!), plus my wish list Wish list more genomes, more strains! more quantitative approaches better controls larger cohorts with more metadata piggybacking on other projects Funding thanks to: Sloan NSF UC Berkeley Also thanks to: Jill Banfield Michael Morowitz Bill Nazaroff & lab 113 Crew (RIP) Gut Club Banfield Lab SPUR undergrads: Jennifer Yip Sophia Riemer Karina Soenjoyo Dylan Dahan Sample handling thanks to: Brian Firek Robyn Baker

24 EXTRA SLIDES

25 Architectural interventions, open the windows! reservoirs dispersal engraftment Kembel et al., ISME 2012

26 Monitor hospitals before, during, and after opening reservoirs dispersal engraftment Slide from Brent Stephens:

27 Monitor hospitals before, during, and after opening reservoirs dispersal engraftment Slide from Brent Stephens:

28 Lean microbes > obese at engraftment reservoirs dispersal engraftment Ridaura et al., Science 2013

Human-microbe mutualism: stability and resilience in health and disease

Human-microbe mutualism: stability and resilience in health and disease David A. Relman, Stanford University IOM Forum on Microbial Threats March 7, 2012 Our extended self : human-microbe mutualism (Based