Source attribution of French clinical isolates of Campylobacter - PowerPoint PPT Presentation

Source attribution of French clinical isolates of Campylobacter jejuni Pr Philippe Lehours E. Berthenet, A. Thépault, M. Chemaly, K. Rivoal, A. Ducournau, A. Buissonnière, L. Bénéjat, E. Bessede, F. Megraud, SK Sheppard. CHU de Bordeaux, laboratoire de Bactériologie, CNR des Campylobacters et des Hélicobacters INSERM U1053-UMR BaRITOn (Bordeaux), ANSES Ploufragan, University of Bath (UK)

Introduction: CNRCH activities ➔ Isolates from 2017 Stool Blood Others Total C. jejuni 5 399 64 12 5 475 C. coli 888 11 1 900 C. fetus 39 49 5 93 A. butzleri 78 0 0 78 C. lari 16 3 0 19 C. upsaliensis 7 1 0 8 A. cryaerophilus 7 0 0 7 Helicobacter spp 1 3 0 4 Other Campylobacter 6 2 3 11 Unknown 407 7 1 415 Total 6 848 140 22 7 010 2 17 janvier 2019 Titre de votre présentation

Introduction: invasive isolates ➔ Isolates from 2017 Stool Blood Others Total C. jejuni 5 399 64 12 5 475 C. coli 888 11 1 900 C. fetus 39 49 5 93 A. butzleri 78 0 0 78 C. lari 16 3 0 19 C. upsaliensis 7 1 0 8 A. cryaerophilus 7 0 0 7 Helicobacter spp 1 3 0 4 Other Campylobacter 6 2 3 11 Unknown 407 7 1 415 Total 6 848 140 22 7 010 3 17 janvier 2019 Titre de votre présentation

Introduction: invasive isolates ➔ An increasing proportion of invasive C.jejuni are received every year since 2013 0 .0 1 5 0 .8 0 .7 0 .0 1 0 R a tio in v a s iv e C . je ju n i R a tio in v a s iv e C . fe tu s 0 .6 / C . je ju n i to ta l / C . fe tu s to ta l 0 .0 0 5 0 .5 0 .0 0 0 0 .4 2 0 1 0 2 0 1 2 2 0 1 4 2 0 1 6 Y e a r o f is o la tio n 4 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Introduction: source attribution for C. jejuni ➔ Origin of infection: 19.3% 1.2% 8.6% 70.9% 16% 74% ➔ MLST based studies identify chicken as the main reservoir Switzerland 2011-2012 Germany 2011-2014 5 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Introduction: MLST limits Core genome tree 6 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Introduction: source attribution for C. jejuni ➔ Origin of infection: 19.3% 1.2% 8.6% 70.9% 16% 74% 8% 41% 51% 13% 24% 63% ➔ Whole-genome based (15 markers) study identifies a role for ruminant France France 2009 2015 7 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Facts and aims ➔ Increasing numbers of invasive C. jejuni ➔ Attribution studies based on non-invasive C. jejuni Is there a different origin for invasive strains ? 8 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Material: reservoir strains ➔ 583 strains publicly available from 3 main reservoirs 352 136 95 New Zealand UK USA Belgium Canada The Netherlands France 9 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Material: clinical strains (n=316) ➔ 118 French clinical strains previously published ➔ 198 French clinical strains newly sequenced (Illumina NextSeq500) invasive non invasive 172 143 2009 - 39 2011 17 - 2012 18 - 2013 33 - 2014 35 - 2015 32+1 78 2016 37 26 10 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Material: newly sequenced clinical strains ➔ 198 strains newly sequenced strains › Library prep (Nextera XT DNA Library Preparation Kit- Illumina) › Sequencing (NextSeq500 - Illumina) (Helixio, Clermont Ferrand) › De novo assembly (SPAdes) 11 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Material: newly sequenced clinical strains ➔ 198 strains newly sequenced strains (Helixio) › filtration of contigs (in-house script – CNRCH) 2 .0 6 0 N u m b e r o f c o n tig s 1 .9 S iz e (in M b p ) 1 .8 4 0 1 .7 1 .6 2 0 1 .5 1 .4 0 12 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Material: dataset Plain circles = French isolates Core genome tree Empty circles = World isolates 13 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Methods ➔ 15 host-segregating markers ➔ Use of BIGSdb to identify alleles present in each strain … marker 1 marker 2 marker 3 marker 14 marker 15 … Strain 1 1 1 2 2 3 … Strain 2 2 1 2 3 1 ➔ Use of Structure software to investigate population structure › 10 repetitions for each analysis 14 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Results: self attribution ➔ Self-attribution >90% S e lf A ttrib u tio n (c o rre c te d ) 1 .0 0 .8 0 .9 7 0 .9 0 0 .9 1 0 .6 E n viro n m e n t R um in a nt 0 .4 C h ic k e n 0 .2 0 .0 c h ic k e n ru m in a n t e n v iro n m e n t n = 2 0 n = 2 0 n = 2 0 15 t 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Results: source attribution of recent French isolates (2014-2016) ➔ Non invasive (ruminant and chicken) ➔ Invasive (mainly chicken) S tra in s fro m 2 0 1 4 to 2 0 1 6 1 .0 0 .1 9 0 .8 0 .5 8 0 .2 1 0 .6 E nviro nm ent R um inant 0 .4 C h ic k e n 0 .3 9 0 .6 0 0 .2 0 .0 n o n in v a sive in vasive n = 1 0 4 n = 1 0 5 16 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Results: source attribution of non invasive strains ➔ Non invasive › 50/50: chicken/ruminant › diminution of ruminant part after 2015 › environment part always bellow 10% N o n In v a s iv e S tra in s 1 .0 0 .8 C h ic k e n 0 .6 R um in a nt 0 .4 E n viro n m e n t 0 .2 0 .0 2 0 0 9 2 0 1 5 2 0 1 6 n = 3 9 n = 7 8 n = 2 6 17 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Results: source attribution of invasive strains ➔ Invasive: › mainly chicken › drop in ruminant part after 2014 › environment increases (>10%) after 2014 In v a s iv e S tra in s 1 .0 0 .8 0 .6 C h ic k e n R um in a nt 0 .4 E n viro n m e n t 0 .2 0 .0 2 0 1 2 2 0 1 4 2 0 1 6 2 0 1 1 2 0 1 3 2 0 1 5 n = 1 8 n = 3 5 n = 3 7 18 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Conclusion for non invasive strains ➔ Chicken Ruminant in non invasive strains than thought 58% 39% › need for sampling campaign in bovine reservoir 19 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Conclusion for invasive strains ➔ Recent switch in invasive strains (mainly chicken) In v a s iv e S tra in s 1 .0 0 .0 1 5 0 .8 0 .8 0 .7 0 .0 1 0 0 .6 C h ick e n R a tio in v a s iv e C . je ju n i 0 .6 R um inant / C . je ju n i to ta l 0 .4 E nviro nm ent 0 .0 0 5 0 .5 0 .2 0 .0 0 .0 0 0 0 .4 2 0 12 2 0 14 2 0 16 2 0 1 0 2 0 1 2 2 0 1 4 2 0 1 6 Y e a r o f is o la tio n ➔ Differences between invasive and non invasive strains › genome Wide Association Study 20 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

Acknowledgements CNRCH-INSERM U1053 External co-authors Lucie Bénejat-Bruhl Amandine Thépault Alice Buissonnière Katell Rivoal Astrid Ducournau Marianne Chemaly Francis Mégraud Emilie Bessède Samuel K. Sheppard 21 17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni