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

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

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Source attribution of French clinical isolates of Campylobacter jejuni Pr Philippe Lehours E. Berthenet, A. Thpault, M. Chemaly, K. Rivoal, A. Ducournau, A. Buissonnire, L. Bnjat, E. Bessede, F. Megraud, SK Sheppard. CHU de Bordeaux,

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Source attribution of French clinical isolates

  • f 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)

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Introduction: CNRCH activities

➔ Isolates from 2017

17 janvier 2019 Titre de votre présentation

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  • C. jejuni

5 399 64 12 5 475

  • C. coli

888 11 1 900

  • C. fetus

39 49 5 93

  • A. butzleri

78 78

  • C. lari

16 3 19

  • C. upsaliensis

7 1 8

  • A. cryaerophilus

7 7 Helicobacter spp 1 3 4 Other Campylobacter 6 2 3 11 Unknown 407 7 1 415 Total 6 848 140 22 7 010 Stool Total Blood Others

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Introduction: invasive isolates

➔ Isolates from 2017

17 janvier 2019 Titre de votre présentation

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  • C. jejuni

5 399 64 12 5 475

  • C. coli

888 11 1 900

  • C. fetus

39 49 5 93

  • A. butzleri

78 78

  • C. lari

16 3 19

  • C. upsaliensis

7 1 8

  • A. cryaerophilus

7 7 Helicobacter spp 1 3 4 Other Campylobacter 6 2 3 11 Unknown 407 7 1 415 Total 6 848 140 22 7 010 Stool Total Blood Others

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Introduction: invasive isolates

➔ An increasing proportion of invasive C.jejuni are received every year since 2013

17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

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Y e a r o f is o la tio n R a tio in v a s iv e C . je ju n i / C . je ju n i to ta l R a tio in v a s iv e C . fe tu s / C . fe tu s to ta l

2 0 1 0 2 0 1 2 2 0 1 4 2 0 1 6 0 .0 0 0 0 .0 0 5 0 .0 1 0 0 .0 1 5 0 .4 0 .5 0 .6 0 .7 0 .8

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Introduction: source attribution for C. jejuni

➔ Origin of infection: ➔ MLST based studies identify chicken as the main reservoir

17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

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70.9% 19.3% 8.6% 1.2% Switzerland 2011-2012 Germany 2011-2014 74% 16%

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Introduction: MLST limits

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Core genome tree

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Introduction: source attribution for C. jejuni

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France 2009 France 2015 51% 41% 8% 63% 24% 13%

➔ Origin of infection: ➔ Whole-genome based (15 markers) study identifies a role for ruminant

70.9% 19.3% 8.6% 1.2% 74% 16%

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Facts and aims

➔ Increasing numbers of invasive C. jejuni ➔ Attribution studies based on non-invasive C. jejuni

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Is there a different origin for invasive strains ?

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Material: reservoir strains

➔ 583 strains publicly available from 3 main reservoirs

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352 136 95 New Zealand UK USA Belgium Canada The Netherlands France

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Material: clinical strains (n=316)

➔ 118 French clinical strains previously published ➔ 198 French clinical strains newly sequenced (Illumina NextSeq500)

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invasive 172 non invasive 143 2009

  • 39

2011 17

  • 2012

18

  • 2013

33

  • 2014

35

  • 2015

32+1 78 2016 37 26

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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)

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Material: newly sequenced clinical strains

➔ 198 strains newly sequenced strains (Helixio) › filtration of contigs (in-house script – CNRCH)

17 janvier 2019 Source attribution of French clinical isolates of Campylobacter jejuni

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S iz e (in M b p )

1 .4 1 .5 1 .6 1 .7 1 .8 1 .9 2 .0

N u m b e r o f c o n tig s

2 0 4 0 6 0

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Material: dataset

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Core genome tree Plain circles = French isolates Empty circles = World isolates

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Methods

➔ 15 host-segregating markers ➔ Use of BIGSdb to identify alleles present in each strain ➔ Use of Structure software to investigate population structure › 10 repetitions for each analysis

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marker 1 marker 2 marker 3 … marker 14 marker 15 Strain 1 1 1 2 … 2 3 Strain 2 2 1 2 … 3 1

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Results: self attribution

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➔ Self-attribution >90%

C h ic k e n R um in a nt E n viro n m e n t t

S e lf A ttrib u tio n (c o rre c te d )

0 .0 0 .2 0 .4 0 .6 0 .8 1 .0

0 .9 7 0 .9 0 0 .9 1

c h ic k e n n = 2 0 ru m in a n t n = 2 0 e n v iro n m e n t n = 2 0

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Results: source attribution of recent French isolates (2014-2016)

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➔ Non invasive (ruminant and chicken) ➔ Invasive (mainly chicken)

S tra in s fro m 2 0 1 4 to 2 0 1 6

0 .0 0 .2 0 .4 0 .6 0 .8 1 .0

C h ic k e n R um inant E nviro nm ent

0 .6 0 0 .3 9 0 .2 1 0 .5 8 0 .1 9

in vasive n = 1 0 5 n o n in v a sive n = 1 0 4

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Results: source attribution of non invasive strains

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➔ 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

0 .0 0 .2 0 .4 0 .6 0 .8 1 .0

C h ic k e n R um in a nt E n viro n m e n t

2 0 0 9 n = 3 9 2 0 1 5 n = 7 8 2 0 1 6 n = 2 6

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Results: source attribution of invasive strains

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➔ Invasive: › mainly chicken › drop in ruminant part after 2014 › environment increases (>10%) after 2014

In v a s iv e S tra in s

0 .0 0 .2 0 .4 0 .6 0 .8 1 .0

C h ic k e n R um in a nt E n viro n m e n t 2 0 1 1 2 0 1 3 2 0 1 5 2 0 1 2 n = 1 8 2 0 1 4 n = 3 5 2 0 1 6 n = 3 7

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Conclusion for non invasive strains

➔ Chicken Ruminant in non invasive strains than thought › need for sampling campaign in bovine reservoir

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39% 58%

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Conclusion for invasive strains

➔ Recent switch in invasive strains (mainly chicken) ➔ Differences between invasive and non invasive strains › genome Wide Association Study

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In v a s iv e S tra in s

0 .0 0 .2 0 .4 0 .6 0 .8 1 .0

C h ick e n R um inant E nviro nm ent 2 0 12 2 0 14 2 0 16

Y e a r o f is o la tio n R a tio in v a s iv e C . je ju n i / C . je ju n i to ta l

2 0 1 0 2 0 1 2 2 0 1 4 2 0 1 6 0 .0 0 0 0 .0 0 5 0 .0 1 0 0 .0 1 5 0 .4 0 .5 0 .6 0 .7 0 .8

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Acknowledgements

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CNRCH-INSERM U1053 Lucie Bénejat-Bruhl Alice Buissonnière Astrid Ducournau Francis Mégraud Emilie Bessède External co-authors Amandine Thépault Katell Rivoal Marianne Chemaly Samuel K. Sheppard