Climate, Oceans, Microbiomes, and Cholera National Science Board Vannevar Bush Award May 9, 2017 Rita R. Colwell, Ph.D., D.Sc. Distinguished University Professor University of Maryland, College Park and Johns Hopkins University Bloomberg School of Public Health
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Climate, Oceans, Microbiomes, and Cholera
National Science BoardVannevar Bush Award
May 9, 2017
Rita R. Colwell, Ph.D., D.Sc.Distinguished University Professor
University of Maryland, College Parkand
Johns Hopkins University Bloomberg School of Public Health
Model for the Transmission of Vibrio Cholerae from the Environment to Humans
G. Constantin de Magny
West Virginia UniversityCivil and Environmental Engineering
Chronology of cholera and satellites
Colwell (1996) Colwell (1996)
1996: Colwell’s coastal vibrio hypotheses
2001: Lobitz’s chlorophyll-SST
Several attempts to link satellite data with cholera
Classification of coastal and Inland cholera
Cholera and SST in the Indian OceanSix-month SST lead: R2 = 0.72
0 0.6+
R2
Lobitz et al., 2000, PNAS Vol. 97, No. 4 pp. 1438-1443
Vezzulli et al. Proc. Natl. Acad. Sci. USA 2016 113 (34) E5062-E5071 doi:10.1073/pnas.1609157113
Vezzulli et al. Proc. Natl. Acad. Sci. USA 2016 113 (34) E5062-E5071 doi:10.1073/pnas.1609157113
Theoretical framework for predicting cholera outbreaks in epidemic regions
Air
Air Temperature Rainfall
Below average fortwo previousmonths
Below average
Low RiskAvailableand intact
Cholera Outbreak Water and Sanitation Access
Above average for two previous months
Above average
High Risk Poor or Damaged
Small Chromosome Large Chromosome
Vibrio cholerae
Sequenced and published in 2000
Chromosome I (2,961,149 bp, 2,742 ORFs)Source: The Institute for Genomic Research
RC9 O1 Ctx+ Kenya 2740-80 O1 ElTor Env USNCTC8457 O1 ElTor 1910B33 O1 ElTor MzbMJ-1236 O1 hybrid biotype MO10 O139623-391587 O12VL426 albensisO395 O1 ClassicalAM-19226 O39 TMA21 non-O1 BrazilMAK757 O1 ElTor 1937 MZO-2 O14 MZO-3 O37 RC385 O135 Csp BayV51 O141 USV52 O37 Sudan
Chromosome II (1,072,315 bp, 1,093 ORFs)
RC9 O1 Ctx+ Kenya 2740-80 O1 ElTor Env USNCTC8457 O1 ElTor 1910B33 O1 ElTor MzbMJ-1236 O1 hybrid biotype MO10 O139623-391587 O12VL426 albensisO395 O1 ClassicalAM-19226 O39 TMA21 non-O1 BrazilMAK757 O1 ElTor 1937 MZO-2 O14 MZO-3 O37 RC385 O135 Csp BayV51 O141 USV52 O37 Sudan
Missing ORFs in V. cholerae strains (Reference: N16961; cutoff = 70% DNA similarity)Chun et al. Proc. Natl. Acad. Sci. USA 2009 106(36):15442-15447 doi:10.1073/pnas.0907787106
Microbes Extracted DNA DNA Sequencing
GENIUS®: Probabilistic Matching GENEBOOK® Library Raw Sequence Reads
ECIVRS
SESIYLA
NU
S® A
INE
G D
SIO
SMOC
Identified Bacteria
TetR
CIPR
mecActxA
GENEBOOK® Antibiotic Resistance & Virulence Factor Library
Applications: Pathogen detection for
health and wellness; food safety and probiotics biothreat and public health
surveillance; forensic and scientific
investigation
:BA L CE
G IVN RI ET SEST NG
& H NCI
C ER U
EA QEES S
R
Diarrheal Disease Study
National Institute of Cholera and Enteric DiseaseKolkata, India
www.niced.org.ind
Microbiomes of Diarrheal Subjects Compared to Healthy
DIA
RR
HEA
L PA
TIEN
TS
HEA
LTH
Y IN
DIV
IDU
ALS
Proteobacteria FirmicutesBacteroidetes
Polymicrobial Infection: Necrotizing Fasciitis
Neighbor-joining tree using 2,514 conserved full length predicted proteins
Strain level ID shows selective dissemination
Rel
ativ
e ab
unda
nce
of N
F st
rain
s
Aeromonas hydrophilaNF4
Aeromonas hydrophilaNF3
Aeromonas hydrophilaNF2
Aeromonas hydrophilaNF1
Relative distribution of four Aeromonas hydrophila strains NF1, 2, 3, and 4 into different metagenomic datasets derived from muscle, spleen and liver samples
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
0%
Mus
cle
1
Mus
cle
2
Mus
cle
4
Mus
cle
35
Spl
een
45
Spl
een
123
Live
r 1
Live
r 2
Live
r 3
Live
r 4
Live
r 5
Summary
Disease state patients often have multiple pathogenic organisms
Advances in microbial genomics and identification to strain level allow for better understanding of polymicrobial infections
Metagenomics can be used to explore biofilm/patient interactions in hospital settings
Metagenomic analysis for these studies was done with CosmosID and our curated database of >65,000 genomes, please contact me if you are interested in working together, or try it yourself:
app.cosmosid.com
A Simple, Sustainable Method for
Reducing Cholera
A Simple Solution for Cholera Prevention: Sari Filtration
Orange County Water District Study
Metagenomics and Public Health
The influent, secondary treated municipal wastewater of the AWPF treatment train is purified by a three-step process: microfiltration, reverse osmosis, and ultraviolet (UV) light with hydrogen peroxide. Initially the wastewater is screened at 4mmSodium hypochlorite as disinfectant is added prior to microfiltration. Hydrogen peroxide (H2O2) is added before UV treatment. The decarbonators remove CO2and raise the pH; addition of lime further stabilizes the purified water.
SodiumHypochlorite
influent
Filter Screens
Microfiltration (MF) process
Reverse Osmosis (RO)Process
H2O2
AWPF final product water
UltravioletIrradiation System
Decarbonators
Add’n Lime
Relative abundance and diversity of parasite DNA in MF-biofilm and Q1-water. The approximate relative abundance heat map was simplified, using the GENIUS bioinformatics algorithm and curated databases. The 99 relative abundance corresponds to sequences classified as Paramecium biaurelia strain v14, Thalassiosira, and Acanthamobea polyphaga based on observed frequency of DNA sequences identified. Parasite sequences were not found in the RO-biofilms.
Acanthamobeapolyphaga Thalassiosira
Paramecium biaureliastrain v14
Q1-water
MF-biofilm
RO-biofilm
99
30
9
2
0
Comparison of virus and bacteriophage DNA sequences
Adeno-associated
MF-biofilm
Q1-water
Pseudomonas
Klebsiella
Salmonella
Aeromonas
Burkholderia
Escherichia
Yersinia
Enterobacteria
Vibrio
Mycobacterium
Shigella
Stx1 Converting
Erwinia
Bacteroides
Lactococcus
Enterobacteria
Streptococcus
N=15
N=10N=4
Viral DNA 1709
Stx2 Converting
Roseophage
Yersinia
Escherichia
Lactococcus prophage
Phage-cdtl
Viral DNA 236
Salmonella
Enterococcus
Viral DNA 1241 RO-biofilm
N=0
bacteriophage
virus
Virus and bacteriophage DNA sequences comparison demonstrate the presence of bacteriophages and virus DNA in the membrane filter (MF)-biofilm and in the influent water, Q1. Note, the absence of bacteriophages and DNA viruses in the reverse osmosis (RO)-biofilm. Presence and absences of sequences (partial or complete) related to bacteriophage and viruses in MF-biofilm were compared to the Q1 water.
“When one tugs at a single thing in nature, he finds it hitched to the rest of the universe.”
John Muir(1838-1914)
Collaborators and Colleagues
Anwar Huq, ProfessorUniversity of Maryland,College Park, MD
Antarpreet Jutla, Assistant Professor, West Virginia UniversityMorgantown, WV
Dr. Nur HasanVice-President, Research and DevelopmentCosmosID, Inc.College Park, MD
Dr. Seon Young Choi,
Bioinformatic Scientist, CosmosID Inc.College Park, MD
Safe water is a global challenge
Courtesy of GB Nair, NICED, Kolkata, India
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