Etienne RuppéAP‐HP, Hôpital Bichat‐Claude BernardUMR 1137 IAME

Disclosures

Consultant for DaVolterra and MaaT Pharma

Received funds by bioMérieux

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1. The intestinal microbiota

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16S profiling and metagenomics allowed a more in‐depth vision of our microbiota

1. Huge number of bacterial cells (3.8x1013)1, pathogens are subdominant2. Great diversity (estimated hundreds of species)3. Mostly un(hardly)culturable bacteria

A 10M genes catalogue!2

1Sender, R. PLoS Biol. 14, e1002533 (2016);2Li, J. Nat. Biotechnol. 32, 834–841 (2014). 4

16S profiling and metagenomics allowed a more in‐depth vision of our microbiota

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Adapted from Sommer, F. & Bäckhed, F. Nat Rev Microbiol 11, 227‐238 (2013)

AllergyAlzheimerAtherosclerosisAutismBreast cancerCeliac diseaseCirrhosisColorectal cancerCrohn’sdiseaseEncephalopathyFrailty in seniorsHIVObesityParkinsonRheumatoid arthritisType 1 diabetesType 2 diabetesUlcerative colitis…You name it!

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Is there any left condition unliked to the intestinal microbiota?

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Antibiotics: barrier effect concentrations of resistant bacteria

Excretion of resistant bacteriaCross-transmissionSpread in environment

Carriage of resistantbacteriaSource of infectionGene transfer

AllergyAlzheimerAtherosclerosisAutismBreast cancerCeliac diseaseCirrhosisColorectal cancerCrohn’sdiseaseEncephalopathyFrailty in seniorsHIVObesityParkinsonRheumatoid arthritisType 1 diabetesType 2 diabetesUlcerative colitis…Resistance to antibiotics!

Adapted from Sommer, F. & Bäckhed, F. Nat Rev Microbiol 11, 227-238 (2013); Carlet, J. Antimicrob Resist Infect Control 1, 39 (2012).

The intestinal microbiota is the « epicentre of antibiotic resistance »

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2. The “barrier effect”

8Pamer, E. G. Science 352, 535–538 (2016).

The  intestinal microbiota opposes to the settlement and overgrowth of exgenous bacteria: introduction to the barrier effect or colonization resistance

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A consortium of 4 anaerobic bacteria collaborate to eradicate VRE from the gut in mice

1.Caballero, S. Cell Host & Microbe 21, 592–602.e4 (2017).

CBBP: C. bolteae, B. producta, B. sartorii and P. distasonis

Leo, S. et al. In preparation.

RNA extracted from feces cDNA synthesis and sequencing (Illumina) 16S and 23S analysis, multiple statistical analyses

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Some bacteria could be associated with a faster intestinal clearance of ESBL‐E. coli (but not with the acquisition)?

11Leo, S. et al. In preparation.

Some bacteria could be associated with a faster intestinal clearance of ESBL‐E. coli (but not with the acquisition)?

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3. Quantification of multidrug-resistant bacteria in the intestinal microbiota

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Have concentrations of resistant bacteria clinical consequences?

Bacterial translocation1

Urinary-tract infection2

Cross-transmission3

Long-term carriage4

Very low risk High risk

1Berg, R.D. et al. Infect Immun 33, 854-861 (1981); 2Ruppé, E. et al. Antimicrob. Agents Chemother. 2013, 57(9):4512; 3Donskey, C.J., et al. N Engl J Med 343, 1925-1932 (2000); 4Ruppé, E. et al. Clin Infect Dis. 61, 593–600 (2015).

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4. Actions!

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be creative!15

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BROWN!

Connelly S. J Appl Microbiol. 2017 Feb 28; 

P1A beta‐lactamase from Bacillus subtilis and its derivative P3A manufactured in E. coli (Asp276Asn): Ribaxamase

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Pre-treatment (D-4)

CRO+Ribaxamase (D4)

CRO (D4)

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Inactivation of the antibiotic in the colonusing engineered beta‐lactamases

18de Gunzburg, J. et al. bioRxiv 169813 (2017).

Inactivation of the antibiotic in the colonusing engineered active charcoal

19de Gunzburg, J. et al. bioRxiv 169813 (2017).

Inactivation of the antibiotic in the colonusing engineered active charcoal

201Ubeda, C. et al. Infect. Immun. 81, 965–973 (2013); 2Millan, B. et al. Clin. Infect. Dis. (2016). doi:10.1093/cid/ciw185

Num

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Mice1 Human2

Fecal material transplantation restores the barrier effect

7 health donors

Treatment (EtOH induced sporulation)

Encapsulation and storage at ‐80°C

SER‐109

21Khanna, S. et al. J Infect Dis. 214, 173–181 (2016). 21

Moving towards specific bacterial consortia

Khanna, S. et al. J Infect Dis. 214, 173–181 (2016).

The diversity of Enterobacteriaceae decreases (C), and Escherichia coli is restored as the prominent Enterobacteriaceae member. 

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Already in motion (almost)

Wrap upInterplay betweenpathogens, ATB,  resistance and commensals is far from beingunderstood

Several, complementarymethods are beingdeveloped: phages, colonicinactivation, FMT…

Let’s not forget to be cautious with the findings of metagenomic studies!

Yet new ideas to combat multidrug‐resistance emerge from a betterunderstanding of this interplay

Especially, preserving/restoring thebarrier effect in order to prevent theovergrowth of resistant bacteria

Indeed, lowering theconcentrations of resistantbacteria could have variousbenefits

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See you in Geneva for more metagenomics!

October 20-21 2018

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