The document summarizes research on Campylobacter jejuni associated with asymptomatic paediatric infection in the Peruvian Amazon. It finds that isolates from Peruvian children have a local gene pool and genotypes rarely seen globally. Lineages associated with asymptomatic infection are proliferating in the region. Though globally circulating strains are present, the regional accessory genome content differs. Poultry is identified as the predominant infection source for children in the Peruvian Amazon. Further sampling is needed to better understand regional differences and reservoirs.

1. Genomic epidemiology of Campylobacter
jejuni associated with asymptomatic
paediatric infection in the Peruvian Amazon
Ben Pascoe
b.pascoe@bath.ac.uk | Twitter: @benizao

2. Campylobacter: Human infection in the UK – predominantly by eating
undercooked contaminated poultry products
More often in young people, but more
severe in older people
Seasonal differences
Nichols et al 2012: BMJ Open e001179.

3. Is Campylobacter epidemiology the same all over the world?
 Over 50,000 WGS in pubMLST (>98,000 MLST profiles)
 + thousands of isolates uploaded to NCBI
> 75% genomes from UK / USA
https://pubmlst.org/campylobacter/

4. Historical evidence that epidemiology is different in LMICs
o Increased exposure: high-incidence
among young children (when sampled –
often no surveillance measures).Very
little documented in adults.
o Different sources? (Food and Env)
o Asymptomatic infection - isolation from
children and associated with growth
stunting.
o human-to-human transmission?
Calva et al 1988: The Lancet, 1:503-6; Coker et al 2002: Emerg Infect Dis. 8:237-44.

5. Local differences, global similarity
…Campylobacter is not always a food poisoning infection

6. https://www.medrxiv.org/content/10.1101/2020.04.26.20075689v1
https://microreact.org/project/CampyPeruOnly
https://microreact.org/project/CampyPeruContext

7. Symptomatic –vs- asymptomatic Peruvian isolates
Lee et al (2013) PLoS Neg Trop Diseases doi:10.1371
Pascoe et al (In press)

8. Proliferation of globally rare genotypes in Peruvian Amazon children

9. Not all STs/CCs are found everywhere
Pascoe et al (unpublished)
*How much is down to lack of sampling?
o Differences in global genetic diversity
o Some lineages (clusters) have only been seen
in certain regions

10. Globally disseminated ST-21 & ST-45 isolates are common in farmed
chicken and human disease

11. Peruvian Amazon paediatric isolates have a local gene pool

12. Lineages associated with asymptomatic infection in Peruvian
Amazon paediatric cases
Pascoe et al (In press) Plos NTD
See also: Schiaffino et al (2019) AAC; DOI: 10.1128/AAC.01911-18

13.  Common in (agricultural) avian and mammalian species
 Host specialists vs. generalist lineages
Estimating the source of human Campylobacter infection
1
0.5
0
` 1000 2000 3000 4000
1
0.5
0
1
0.5
0
500
0
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A
B
Sourceprobability
Human cases
Chicken is a major source
of human infection Sheppard et al. (2009) Clinical Infectious
Diseases 48:1072–1078

14. Greater proportion of French isolates
attributed to ruminant sources
60 – 80 % attributed to chicken
40 – 60 % to ruminant
4 – 10 % to wild birds & environment
(Sheppard et al., 2009, Kittl et al., 2013, Boysen et al., 2014, Mossong et al., 2016)
Differences between countries

15. Poultry is the predominant source of infection in Peruvian Amazon
children
Effective source attribution relies
on composition of your
comparison dataset:
-> rare STs/CCs poorly attributed
-> unsampled sources?

16. Mini-summary
 Globally circulating disease genotypes are found in the Peruvian
Amazon
 Proliferation of globally rare genotypes in Peruvian Amazon
children
 Peruvian Amazon paediatric isolates have a local gene pool
 Lineages associated with asymptomatic infection in Peruvian
Amazon paediatric cases
 Regional differences in accessory genome content (LOS/CPS types)
 Poultry is the predominant source of infection in Peruvian Amazon
children

17. What’s next?
 Global sampling (including continued sampling in Peru)
 Improve source attribution studies: local reservoir sampling
 Humans as a source?
 Other Campy species?
 Genetic elements associated with disease severity

18. Other sources of infection?
Reports of Campylobacter (jejuni and
other spp.) in small mammals, sea
mammals, domestic animals, variety
of wild bird species – including
penguins…

19. Human-adapted lineages? : ST403
This ST has also been sampled from
human infections in the Dutch
Antilles and is a poor colonizer of
avian hosts, typically lacking a gene
cluster (Cj1158-1159-1160)

20. o Very rare sequence type (only 14 genomes!)
o ALL from human clinical cases
Human-adapted lineages? : CC362 (ST2993)

22. Emerging MDR C. coli
Mourkas et al (2019) Environmental Microbiology;
Florez-Cuadrado et al (2017) Frontiers in Micro
Cross-species movement of erythromycin resistance

23. Local differences, global similarity
…Campylobacter is not always a food poisoning infection

24. Sion
Bayliss
Evangelos
Mourkas
Jessica
Calland
Europe:
David Kelly (Sheffield), Martin Maiden & Keith Jolley (Oxford), David
Aanensen (Oxford BDI), Jukka Corander (Oslo), Kaisa Haukka (Helsinki)
North America: USA & Canada
Madhusudan Grover (Mayo Clinic), Peter Evans & Mustafa Simmons
(FSIS), Criag Parker (USDA), Kerry Cooper (Arizona) Eduardo Taboada (PH
Canada)
South America: Peru
Margaret Kosek (John Hopkins/Lima)
Africa
Martin Antonio & Janghir Hossan (MRC Gambia), Sam Kariuki & Dayo
Adetifa (KEMRI), Isidore Bongkongu (PH Burkina Faso), Akousua Karikari
(Ghana), Mohamed ElHadidy (Zewail City)
Asia: Vietnam, Thailand
Stephen Baker (OUCRU), Taradon Luangtongkum (Chulalongkorn), Prapas
Patchanee (Chiang Mai)
Prof Sam Sheppard, University of Bath, UK
Thanks!