Mining the gut microbiota for solutions to infectious

disease and antibiotic resistance

Dr. Cormac Gahan

c.gahan@ucc.ie

Probiota, Dublin, 2020

http://apc.ucc.ie

This Presentation

• Scale of the problem – Infectious Disease & Antimicrobial Resistance

• Key study on sepsis in India

• Understanding mechanismsC. difficileL. monocytogenesS. Typhimurium

• Future Perspectives

Work from APC Microbiome Ireland & Other Published Sources

• Metabolism > Liver• Energy extraction –

fat deposition• Immune regulation• Barrier to infection

The Human Superorganism

http://apc.ucc.ie

Scale of the Problem – Infectious Disease & Sepsis

Harvard School of Public Health

1990 2010• Mortality due to respiratory tract infection and diarrheal disease remains significant

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Scale of the Problem – Infectious Disease & Sepsis

• Mortality due to respiratory tract infection and diarrheal disease remains significant

• Foodborne/diarrheal disease a particular concern but potentially a target for interventions

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Scale of the Problem – Infectious Disease & Sepsis

• Mortality due to respiratory tract infection and diarrheal disease remains significant

• Foodborne/diarrheal disease a particular concern but potentially a target for interventions

Disability-adjusted Life years (DALYs)

WHO 2017. Burden of foodborne disease in the European region.

*

*

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Scale of the Problem – Infectious Disease & Sepsis

• First global analysis of sepsis

• Found that the global burden of sepsis in 2017 was 48.9 million cases and 11 million deaths

• Twice that of previous ‘estimates’

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Scale of the Problem – Antibiotic Resistance

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Scale of the Problem – Antibiotic Resistance

Antibiotic resistance genes (incl carbapenem resistance) reside in the gut

Wyres & Holt. 2018. Curr Opin Microbiol.

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Rationale for Microbiota-sourced Therapeutics

C. difficile + FMT

Germ-free mice susceptible to infection

Clinical data ‘Probiotics’

Significant need for microbiota-based therapies to reduce:

• Incidence of infection (incl. foodborne)

• Rates of sepsis (immune modulation?)

• Carriage of Anti-microbial resistance

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Evidence: Synbiotic Reduces Sepsis

• Synbiotic = Lb. plantarum + fructooligosaccharide

• Reduced risk of sepsis by 40%• Reduced respiratory tract

infection• Prevention better than cure• Would reduce need for

antibiotic

http://apc.ucc.ie

This Presentation

• Scale of the problem – Infectious Disease & Antimicrobial Resistance

• Key study on sepsis in India

• Understanding mechanismsC. difficileL. monocytogenesS. Typhimurium

• Future Perspectives

Work from APC Microbiome Ireland & Other Published Sources

• Metabolism > Liver• Energy extraction –

fat deposition• Immune regulation• Barrier to infection

The Human Superorganism

http://apc.ucc.ie

Colonization Resistance

Ducarmon et al., 2018. Micro. & Mol. Biol. Rev

http://apc.ucc.ie

Colonization Resistance – Clostridioides difficile

C. difficile + FMT

• 81-96% cure rates

• Better than antibiotic standard of care treatments

• Effective in critically ill patients

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Clostridioides difficile

Buffie et al., Nature. 2015 ; Brown et al. BMC Gastro 2018

C. scindens Treatment with FMT

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Overlaid with Clostridium difficile

Bacillus thuringiensis

Thuricin CD; a two component bacteriocin

30,000 sporeformers

Rea et al., 2010 PNAS; Rea et al. 2011 PNAS; Rea et al. 2014 Microbiology

Thuricin CD

Colin Hill Paul Ross

Bacteriocin (Thuricin) inhibits C. difficile

apc.ucc.ie

C. difficile target

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8

6

4

2

0

0 60 120 180

Log cfu/ml

min

Control

Thuricin CD

Clostridium difficile 106

8

6

4

2

0

0 60 120 180

Log cfu/ml

min

Control

Thuricin CD

Lactobacillus paracasei 338

8

6

4

2

0

0 60 120 180

Log cfu/ml

min

Control

Thuricin CD

Bifidobacterium lactis BB12

Multifors Human Gut

Fermentation model

Control Thuricin Vancomycin

Control Thuricin

Mouse Infection

Model

Thuricin specifically targets C. difficile & is active in vivo

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Probiotic mechanisms & Listeria monocytogenesInfectious Cycle

Corr et al., PNAS 2007

Colin Hill

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Sinead Corr, Christian Riedel, Yin Li, Paul O’TooleLb. salivariusUCC118 produces a bacteriocin active against Listeria

Claesson, M et al. PNAS. 2006. 103:6718-23.

Flynn, S et al. Microbiology. 2002. 148:973-984

Creation of UCC118 Bac- mutant

b

0

20

40

60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

ol

aa

b

0

20

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60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

ol

aa

b

0

20

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60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

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aa

b

0

20

40

60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

ol

aa

UCC118 Bac-

Probiotic mechanisms & Listeria monocytogenes

http://apc.ucc.ie

Sinead Corr, Christian Riedel, Yin Li, Paul O’Toole

UCC118 Bac-

Placebo

Pat Casey, Sinead Corr

b

0

20

40

60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

ol

aa

b

0

20

40

60

80

100

120

L. monocytogenes

EGDe

CF

U/ L

iver

as a

% o

f co

ntr

ol

aa

UCC118 Bac-

Listeria w/t

Listeria Immune

Placebo UCC118

Immune strain no longer

susceptible to UCC118 in

vivo

Corr et al., PNAS 2007

Probiotic mechanisms & Listeria monocytogenes

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Specific Commensals & Listeria monocytogenesT0

Microbiota Perturbation

(Antibiotics or Diet)

STOP

T1 T2 T3 T4

Analyze for Return of Colonization Resistance

Susceptible to Infection

Resistant to Infection

Resistant to Infection

List

eria

/ sp

leen

4-strain consortium of

Clostridium spp. protected

against Listeriainfection

Becattini et al., 2017 J Exp med

Eric Pamer LabSloan-Kettering Institute

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Role of diet in colonization resistance

Oral L. monocytogenes Infection

Las Heras et al., 2019 Microbiome

Host Immune

Response

Low Fat Chow High Fat

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A commensal enhances colonization resistance

Oral L. monocytogenesInfection

Las Heras et al., 2019 Microbiome

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Role of diet in colonization resistance to Salmonella

1 Day Post-infection

High fat

Low fat

High fat + E. coli

Low fat + E. coli

Wotzka et al. 2019 Nat MicrobiolWD Hardt Lab

ETH-Zurich

• High Fat Diet promotes Salmonella survival in the gut

• Linked to elevated bile acid production

• Commensal E. coli (probiotic) protected against this effect

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Understanding Colonization Resistance & Rational Probiotic Selection

Ducarmon et al., 2018. Micro. & Mol. Biol. Rev

C. scindens

ThuracinUCC118

ClostridiaE. coli

Work ongoing in APC

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Conclusions & Future Directions

• Probiotics a very real prospect for preventing infectious disease

• Probiotics a prospect for reducing carriage of resistant bacteria

• Understanding mechanisms important to optimise selection

• Increased appreciation of mechanisms is necessary

• Understand shared mechanisms – resistance to multiple pathogens

• Role of microbiota in sepsis / immune regulation?

Paul CotterRaul Rubio

Silvia MelgarColin Hill

Adam ClooneyFeargal Ryan Justine RudkinNuno PinheiroCara Hueston

Vanessa las Heras

Sinead Corr, Paul O’Toole, Christian Riedel, Pat Casey

Paul Ross, Mary Rea

Thank-you!