Antimicrobial Resistance

Antimicrobial Resistance (AMR) -

Genomic Options to Advance Canada’s Action Plan

David Bailey, Ph.D.

President and CEO

Genome Alberta

Beef Value Chain Roundtable (BVCRT)

Ottawa, Ontario

4-5 March 2015

No Antimicrobials – What Would That Mean?

“If antibiotics stopped working, we would find that instead of 7% of deaths

being related to infection at the moment in the developed world, it would go

back up to about half (50%) of deaths, just because we couldn’t use

antibiotics.” ~ Dame Sally Davies, UK Chief Medical Officer (Feb 2015)

“In a world with few effective antibiotics, modern medical advances such as

surgery, transplants, and chemotherapy may no longer be viable due to the

threat of infection”

~ (USA) National Strategy for Combating Antibiotic-Resistant Bacteria (Sep 2014)

4-5 March 2015Beef Value Chain Roundtable (Ottawa, Ontario)

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Outline

Overview - Antimicrobial Resistance (AMR)

Canada’s AMR Action Plan - Key Focus Areas

Genomic Options

Closing Remarks


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Overview - AMR

What is Antimicrobial Resistance?

Resistance of a microbe (bacteria, fungi, viruses, parasites) to an

antimicrobial drug that was originally effective for treatment of

infections caused by it.

~ WHO Fact Sheet No. 194 (2014)


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The Economist (31-MAR-

2011)

Overview - AMR

Is Resistance A Natural Phenomenon?

YES - Evolution of resistant

strains is a natural

phenomenon but the use

and misuse of antimicrobial

drugs accelerates the

emergence of drug-

resistant strains.

~ WHO Fact Sheet No. 194 (2014)


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~ S

chm

ieder

and E

dw

ard

s (

2012)

“There has been a seven-fold increase in the incidence of Vancomycin-resistant

Enterococci infections between 2007-2012.”– AMR and Use in Canada (Oct 2014)

“Resistome”

The collection of all genes that directly

or indirectly contribute to antibiotic

resistance.

Categories

(1) Inactivation (of genes) bacteria

more resistant to antibiotics

(2) Inactivation (of genes) bacteria

more susceptible to antibiotics

Overview - AMR

How Does Resistance Develop?


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Resistance Mechanisms

1. Produce enzyme that degrades

antibiotic (= antibiotic inactivation)

2. Produce enzyme that alters

antibiotic (= target site alteration)

3. Overproduce antibiotic targets

(= target amplification)

4. Reduce intracellular accumulation

of antibiotic ( influx, efflux)

… option to improve

efficacy of current drugs

(1) VERTICAL

Natural resistance OR

Spontaneous mutation

(2) HORIZONTAL

Horizontal transfer of AMR genes

to same or different microbes

Overview - AMR

How is Antimicrobial Resistance Transferred?


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Bacteria have a

new generation

every 20 minutes!~ Dame Sally Davies

2015

AMR AMR

Mobile Genetic Elements

Overview - AMR

Why is AMR a Global Health Concern?

The rate at which

microbes are acquiring

resistance is GREATER

than the rate at which

antimicrobials are being

discovered.


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-- Antimicrobial Resistance – Global Report on Surveillance (World Health Organization, 2014)

“bacteria do not recognize borders”

– National (USA) Strategy for Combating

Antibiotic-Resistant Bacteria (Sep 2014)

Overview - AMR

Link between AMR in Humans and Livestock?

“Substantial evidence demonstrates that

use of antibiotics in animal agriculture

promotes the development of antibiotic-

resistant microbes in animals and that

retail meat can be a source of microbes,

including antibiotic-resistant microbes” ~

Report to the (USA) President on Combating Antibiotic Resistance

(Sep 2014)

Transfer of resistant microbes between

humans and livestock does occur

(genomics is helping to prove this point)


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“Worldwide, over 70% of

all antibiotics prescribed

are used on farm animals”

~ Dame Sally Davies 2015

“Up to half of antibiotic use in

humans and much of antibiotic

use in animals is unnecessary

and inappropriate and makes

everyone less safe.”

~ CDC 2013

Canada’s AMR Action Plan - Key Focus Areas

A Federal Framework For Action


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SURVEILLANCE

Detecting and monitoring trends and threats in order to

inform strategies to reduce the risks and impacts of

antimicrobial resistance (CNISP, CIPARS, CARSS)

STEWARDSHIP

Conserving the effectiveness of existing treatments

through infection prevention and control guidelines,

education and awareness, regulations, and oversight.

INNOVATION

Creating new solutions to counteract loss in

antimicrobial effectiveness through research and

development.

Genomic Options

Gene? Genome? Genomics?


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Gene is the basic physical and functional unit of heredity. Genes,

which are made up of DNA, act as instructions to make molecules

called proteins.

Genome is the complete set of genes or genetic material in a cell or

organism.

Genomics is the study of the structure, content, and evolution of

genomes, and includes analysis of the expression and function of

both genes and proteins.

Epigenetics relates to, or arises from, non-genetic influences on gene

expression.

Targeted manipulation of gut microbiome to promote growth

Probiotics inhibit pathogens by competing for colonization sites

or nutritional sources

Prebiotics selectively stimulate activity of a limited number of

bacteria in colon, which promotes growth

Genomic Options

Growth Promotion & Disease Control


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Eliminate use of antimicrobials for growth promotion

Reduce reliance on antimicrobials for disease control

Replacement breeding stock selected for fast and efficient growth

Continue search for compounds that could (?) replace antibiotics

Immunity modulating agents, bacteriophages & lysins,

phytodynamic

therapy (PDT), antimicrobial peptides (AMPs), pro-/pre-/synbiotics,

plant extracts, inhibitors targeting pathogenicity, feed enzymes, …

Improved infection control measures

Promote vaccine use

Antimicrobial Growth Promotants

As intended,

total

antimicrobial

use in livestock

dropped.

But use of

prescribed

antimicrobials

in livestock

went up!

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Cattle drug sales in Denmark

since 2001

0

10

20

30

40

50

60

70

Very High Importance High Importance Medium Importance

% o

f a

nti

mic

rob

ials

so

ld b

y

fee

dm

ills

an

d p

ha

rma

cie

s

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

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Genomic Options

Treat INDIVIDUALS, not all

Adopt animal management practices and technologies that quickly

identify sick individuals for closer inspection and treatment.


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Stop misuse and abuse of antimicrobials

Feed intake & behaviour monitoring

Precision Livestock Farming – “Virtual Shepherd”

AMR and Use in Canada

– A Federal Framework for Action

ACTION 3: Work with the animal agriculture

sector partners to strengthen the regulatory

framework on veterinary medicines and

medicated feeds, including facilitating

access to alternatives and encourage the

adoption of practices in order to reduce the

use of antimicrobials.

Track Temperature

Genomic Options

Miniaturized Equipment


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Point-of-need ID of microbes and treatment with correct antimicrobials

Methods of Identifying Microbes

(1) Biochemical

(2) Genetic tools (PCR, DNA

fingerprinting)

(3) Spectral analysis (mass

spectrometry, elastic light scattering,)

Laboratory Field

Miniaturize?

Point-of-need

ID of microbes

E. coli

Nanocoatings• OxiTitan – mineral based photocatalyst solution applied to textiles and

surfaces has proven action against AMR bacteria ( C. Difficile 10x in 24h)

• Nanoporous magnetic-like coating can trap and kill superbugs (S. aureus, )

Nanoparticles, nanosensors, nanocrystals, nanomechanical,• Accurate, economical, less time-consuming methods of detecting microbes

• Targeted delivery of nanomedicines using bispecific antibodies

Nano-metals (Ag, Au, Fe, Cu) and metallic oxides (Ag2O, TiO2, ZnO, …)

• Metal nanoparticles are effective against a broad spectrum of AMR bacteria

Nano-enabled antibiotics• A variety of nanosized carriers can be used as

drug delivery systems

Genomic Options

Nano-based Solutions


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Preventive Measures / Diagnosis / Therapies

Genomic Options

DNA Barcoding


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Rapid ID of microbes and treatment with correct antimicrobials

Animal Groups Land Plants

matK(1500 bp)

rbcL

CO1(648 bp)

Microbes

• Chaperonin-60

(cpn60)

• ?

DNA barcoding is a technique for characterizing species of

organisms using a short DNA sequence from a standard and

agreed-upon position in the genome. DNA barcode sequences

are very short relative to the entire genome and they can be

obtained reasonably quickly and cheaply.

Most antibiotics were discovered by

screening cultivable soil microorganisms

PROBLEM SOLUTION

1% cultivable 99% NOT

cultivable

iChip – isolate and

grow uncultured

bacteria in native soil

Genomic Options

Discover New Antibiotics


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End 30-year “discovery void”

50%

cultivableA New Antibiotic

(Teixobactin) Kills

Pathogens Without

Detectable Resistance

Ling, et. al. (2015)

NEW peptidoglycan

synthesis inhibitor

Construct

full-length

cDNA of

PEDV

Introduce

attenuating

mutations

Introduce

strategic

DIVA

mutations

Produce

new

vaccine

Genomic Options

New Vaccines / Therapeutics / Combinations


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Reduce reliance on antimicrobials and promote health

New Vaccines

‘Smart Vaccines’ use reverse genomics to develop

vaccines.

Porcine Epidemic Diarrhea Virus (PEDV)

~ VIDO-Intervac University of Saskatchewan

Therapeutics

Investigate candidates that interrupt

bacterial protein synthesis or disrupt

bacterial cell wall

Alternatives to small molecule

antibiotics: monoclonal antibodies,

synthetic antibodies, small inhibitory

oligonucleotides, antibacterial

peptides,

Combination Therapies

Combination therapies that target

both essential functions and

resistance factors are also promising

Differentiate Infected from

Vaccinated Animals

Genomic Options

Modern Tools for a Growing Challenge

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Genomic technologies can be used…

To develop novel antibiotics

Microbial whole-genome sequencing (WGS) allows for rapid id of resistance mechanisms

For surveillance

Microbial WGS provides insight into the history of emergence and spread of AMR

To study emergence of antibiotic resistance in real-time

To develop diagnostic tests and direct infection control measures

To study “Resistome”

Predict evolution of resistance

Understand link between resistance and virulence

Defining novel targets which inactivation make bacteria more susceptible to antibiotics

Closing Remarks

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Genomic Options

Growth promotion and disease control

Treat INDIVIDUALS, not all

Miniaturized Equipment

Nano-based solutions

DNA barcoding

Discover new antibiotics

New vaccines / Therapeutics / Combinations

Modern tools for a Growing Challenge

Solutions to AMR will require new and creative ways of

thinking, the integration of technologies and management

practices, and research investment dollars

Thank You

Acknowledgments

Susan Joyal – Consultant

Tim McAllister – AAFC

Reynold Bergen – BCRC

Cindy Bell – Genome Canada


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Antimicrobial Resistance

Health & Medicine