# First rabbit gut microbial gene catalog and metagenomic insights into the resistome: links with antibiotic use

Caroline Achard, Yuliaxis Ramayo Caldas, Amine Ghozlane, Mathieu M. Almeida, Samuel Boucher, Stéphane Chatellier, Adeline Chaubet, Sylvie Combes, Catherine Denis, Benoit Dile, et al.

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## ► To cite this version:

Caroline Achard, Yuliaxis Ramayo Caldas, Amine Ghozlane, Mathieu M. Almeida, Samuel Boucher, et al.. First rabbit gut microbial gene catalog and metagenomic insights into the resistome: links with antibiotic use. 16. International Symposium on Microbial Ecology - ISME16, Aug 2016, Montréal, Canada. [hal-02792973](https://hal.inrae.fr/hal-02792973v1)

HAL Id: hal-02792973

https://hal.inrae.fr/hal-02792973v1

Submitted on 5 Jun 2020

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INRA
SCIENCE & IMPACT

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GenPhySE

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ICSA
Institut Carnot
sante Animale

# FIRST RABBIT GUT MICROBIAL GENE CATALOG AND METAGENOMIC INSIGHTS INTO THE RESISTOME : LINKS WITH ANTIBIOTIC USE

Caroline S. ACHARD<fnref n="1" />, Y. RAMAYO-CALDAS<fnref n="2" />, A. GHOZLANE<fnref n="3" />, M. ALMEIDA<fnref n="4" />, S. BOUCHER<fnref n="5" />, S. CHATELLIER<fnref n="6" />, A. CHAUBET<fnref n="7" />, S. COMBES<fnref n="1" />, C. DENIS<fnref n="2" />, B. DILE<fnref n="5" />, D. ESQUERRE<fnref n="7" />, B. GABINAUD<fnref n="1" />, B. LE NORMAND<fnref n="6" />, N. PONS<fnref n="3" />, E. RUPPE<fnref n="3" />, J. ESTELLE<fnref n="2" />, O. ZEMB<fnref n="1" />

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## INTRODUCTION

Microbial antibiotic resistance genes emerging in livestock are a major public health concern. It is crucial to consider the prevalence of Antibiotic Resistance Genes (ARG) in commensal microbes which represent the vast majority of the gut microbiota of healthy individuals and can convey ARG between animal and human. ARG can be carried by mobile genetic element and transferred between bacterial species, ending up in human pathogens.

## OBJECTIVES

* To generate a first rabbit gut microbial gene catalog.

* To characterize the gut resistome in French meat rabbit farming.

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## METHODS

Does fecal sampling
(Mai-Oct 2014)
DNA extraction
(Godon et al., 1997)

30 samples
from 30 farms

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HiSeq2500

Illumina sequencing

~ 64M
sequences
/ samples

Sequences processed with MOCAT
(Kultima et al, 2012)
* SOAPdenovo → Assembly
* MetaGeneMark → Geneprediction
* CD-HIT-EST → Redondancy reduction
* Read-mapping → BWA

6,2 M
gene
catalog

Annotation and abundance table

* ARG with ResFinder (Zankari et al., 2012)

* ARG prediction with a pairwise
comparative modelling approach
(PCM)

## RESULTS

### ANTIBIOTIC USES

A global link between antibiotic uses and the sum of the relative abundance of all ARG detected.

<figure><img src="image_9.png" /><figcaption>Figure 1: Number of different antimicrobial molecules used in the rabbit farm panel per class and administration mode.</figcaption></figure>

### RESFINDER → 80 ARG DETECTED

<figure><img src="image_10.png" /><figcaption>Figure 2: Number of ARG identified in the gene catalog using ResFinder per antibiotic class. * antibiotics not used</figcaption></figure>

<table><caption>Table 1: Antibiotic uses and ARG detected</caption><thead><tr><th>Farm</th><th># antibiotics used</th><th># detected ResFinder ARG</th><th>Sum of ResFinder ARG abundance</th></tr></thead><tbody><tr><td>02</td><td>0</td><td>17</td><td>5,49E+03</td></tr><tr><td>12</td><td>0</td><td>18</td><td>1,06E+04</td></tr><tr><td>05</td><td>0</td><td>23</td><td>1,09E+04</td></tr><tr><td>32</td><td>1</td><td>44</td><td>1,53E+04</td></tr><tr><td>26</td><td>0</td><td>43</td><td>2,22E+04</td></tr><tr><td>07</td><td>1</td><td>20</td><td>2,74E+04</td></tr><tr><td>33</td><td>0</td><td>18</td><td>3,78E+04</td></tr><tr><td>01</td><td>0</td><td>23</td><td>4,58E+04</td></tr><tr><td>16</td><td>4</td><td>18</td><td>5,19E+04</td></tr><tr><td>18</td><td>0</td><td>49</td><td>5,24E+04</td></tr><tr><td>15</td><td>4</td><td>16</td><td>5,71E+04</td></tr><tr><td>13</td><td>1</td><td>22</td><td>5,94E+04</td></tr><tr><td>27</td><td>3</td><td>20</td><td>6,35E+04</td></tr><tr><td>17</td><td>3</td><td>24</td><td>6,51E+04</td></tr><tr><td>04</td><td>2</td><td>21</td><td>6,55E+04</td></tr><tr><td>24</td><td>2</td><td>18</td><td>6,73E+04</td></tr><tr><td>23</td><td>4</td><td>19</td><td>6,85E+04</td></tr><tr><td>14</td><td>1</td><td>61</td><td>6,95E+04</td></tr><tr><td>30</td><td>8</td><td>28</td><td>7,17E+04</td></tr><tr><td>11</td><td>4</td><td>21</td><td>7,53E+04</td></tr><tr><td>22</td><td>5</td><td>62</td><td>7,71E+04</td></tr><tr><td>03</td><td>6</td><td>20</td><td>7,71E+04</td></tr><tr><td>19</td><td>4</td><td>23</td><td>7,78E+04</td></tr><tr><td>25</td><td>5</td><td>24</td><td>8,11E+04</td></tr><tr><td>31</td><td>8</td><td>34</td><td>8,38E+04</td></tr><tr><td>10</td><td>5</td><td>49</td><td>8,74E+04</td></tr><tr><td>28<sup>a</sup></td><td>0</td><td>68</td><td>9,04E+04</td></tr><tr><td>08<sup>b</sup></td><td>1</td><td>50</td><td>9,13E+04</td></tr><tr><td>21</td><td>6</td><td>68</td><td>1,07E+05</td></tr><tr><td>20</td><td>7</td><td>77</td><td>1,94E+05</td></tr></tbody></table>

<sup>a</sup> oral exposure to antibiotics until end-2013

<sup>b</sup> oral exposure to antibiotics until end-2012

<figure><img src="image_11.png" /><figcaption>Figure 4: ResFinder ARG relative abundance</figcaption></figure>

9 ARG differentially abundant (Wilcoxon test)

Non oral exposure to antibiotics

* RWA farms

* standard farms

<figure><img src="image_12.png" /><figcaption>Figure 3: Sum of relative abundances of all ARG in Raised Without Antibiotic (RWA) farms and in standard farm using antibiotics.</figcaption></figure>

## CONCLUSION

* First rabbit gut microbial gene catalog: 80 antibiotic resistance genes (ARG ResFinder) and 8235 ARG candidates (pairwise comparative modelling approach).

* Decreasing the antibiotic use decreases the global abundance of antibiotic resistance genes.

* Some antibiotic resistance genes persist in antibiotic farms reducing their antibiotic use: an active strategy is needed (see poster 328B)

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<footnote n="1">¹GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France</footnote>

<footnote n="2">²INRA, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France</footnote>

<footnote n="3">³INRA, US1367 MetaGenoPolis, Jouy-en-Josas, France</footnote>

<footnote n="4">⁴Center for Bioinformatics and Computational Biology, College Park, MD, USA</footnote>

<footnote n="5">⁵Labovet, Réseau Cristal, Beaupréau et Les Herbiers, France</footnote>

<footnote n="6">⁶Clinique Vétérinaire des Marches de Bretagne, Fougères et St Brice en Cogles, France</footnote>

<footnote n="7">⁷INRA, GeT-PlaGe, Castanet Tolosan, France.</footnote>