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Role of the metacommunity in the colonization of rabbit's intestinal tract to fight against antibiotic-resistant bacteria

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HAL Id: hal-02799866

https://hal.inrae.fr/hal-02799866

Submitted on 5 Jun 2020

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Role of the metacommunity in the colonization of

rabbit’s intestinal tract to fight against

antibiotic-resistant bacteria

Caroline Achard, Beatrice Gabinaud, Sylvie Combes, Véronique

Dupouy-Guiraute, Yuliaxis Ramayo Caldas, Catherine Denis, Maria Ballester,

Nathalie Le Floc’H, Samuel Boucher, Stéphane Chatellier, et al.

To cite this version:

Caroline Achard, Beatrice Gabinaud, Sylvie Combes, Véronique Dupouy-Guiraute, Yuliaxis Ramayo

Caldas, et al.. Role of the metacommunity in the colonization of rabbit’s intestinal tract to fight

against antibiotic-resistant bacteria. 16. International Symposium on Microbial Ecology - ISME16,

Aug 2016, Montréal, Canada. �hal-02799866�

(2)

Gut microbiota of the kits (local community)

Role of the metacommunity in the

colonization of rabbit's intestinal tract to

fight against antibiotic-resistant bacteria

Achard C.

1

, Gabinaud B.

1

, Combes S.

1

, Dupouy V.

2

, Ramayo-Caldas

Y

3

, Denis C.

3

, Ballester M.

3

, Le Floc’h N.

4

, Boucher S.

5

, Chatellier S.

6

,

Le Normand B.

6

, Bousquet-Melou A.

2

, Estellé J.

3

, Zemb O.

1

1INRA UMR 1388 GENPHYSE, Toulouse 2INRA UMR 1331 TOXALIM, Toulouse 3INRA UMR 1313 GABI, Jouy-en-josas 4INRA UMR 1348 PEGASE, Rennes

5Labovet, Reseau Cristal, Beaupréau et les herbiers 6Clinique Veterinaire des Marches de Bretagne 8Plateforme Genotoul, Toulouse

Introduction and objective

● The (ab) use of antibiotics in farming may favour antibiotic resistant microbes, which may poses a risk to public health.

● Since these microbes may persist even if antibiotics become infrequent, an active strategy is required to limit their diffusion across the farm. ● Competitive exclusion with foreign microbes added to the nest may limit the transmission of persistant resistant microbes to the kits.

Microbial metacommunity of the nest

Immigration rate of antibiotic resistant microbes/genes via coprophagy (natural behaviour)

1) Cultivable Enterobacteria

2) Total antibiotic resistance genes

19 does from farms using antibiotics

Ingestion of fecal pellet (i.e.natural behaviour occuring in normal practice)

A Adding feces free from

resistant microbes to the

clean nest (from does raised without antibiotics in farms A, B and C)

At weaning of the 114 kits (one kit per doe analyzed),

1) monitor antibiotic-resistant enterobacteria (counting on MacConkey petri dishes) 2) Quantify the antiresistance genes in total bacteria by qPCR

Methods and Experimental design

Limited ingestion of fecal pellet (nest cleaned daily)

p<0.05 Resistant 1.2 te tO (t e tr a cy cl in e ) p<0.05 N=4 N=3 N=3 N=4 N=5

feces containing antibiotic-resistant microbes A A A B C

Centre Toulouse Midi Pyrénées Chemin de Borde Rouge

CS 52627 • 31326 Castanet-Tolosan cedex Tél : +33(0) 05 62 28 50 20 100% 80% 60% 40% 20% 0 Normal practice

Enterobacteria resistant to tetracylcine (10 colonies per animal).

The proportion of tetracycline resistant Enterobacteria in lacting does (orange bars) is stable and similar in each group. Adding chosen fecal pellets to the nest (blue bars) limits the transmission of resistant microbes.

Nest Cleaned Adding Feces A Resistant Enterobacteria Adding Feces B Adding Feces C

Conclusions

● Changing the metacommunity of the nest changes the microbes colonizing the gut of the kits.

● The exclusion mecanism is not neutral and depends on the microbiota: Feces C seemed more efficient than Feces B.

● Some antibiotic resistance genes remained unaffected : the fecal community used for the competitive exclusion could be improved. 0.8 te tO (t e tr a cy cl in e ) 0.4 Normal practice Nest Cleaned Adding Feces A Adding Feces B Adding Feces C

Relative abundance of the microbial antibiotic resistance genes aphA3 (TOP) and tetO (BOTTOM) in the caecal content of the kits at weaning (normalized by the SSU). Adding Feces C decreased 6 out of the 20 antibiotic resistance genes that were quantified (vs 2 for Feces B). The does had similar levels of antibiotic resistance genes in each group (data not shown).

1.2 0.8 0.4 a a d E (a m in o g ly co si d e ) p<0.01

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