Climate, Oceans, Microbiomes, and Cholera · 2017-05-09 · V51 O141 US. V52 O37 Sudan. Chromosome II ( 1,072,315 bp, 1,093 ORFs) RC9 O1 Ctx+ Kenya . 2740-80 O1 ElTor Env US. NCTC8457

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