1) The document summarizes research on Campylobacter evolution and its relationship to intensive animal agriculture. 2) Key findings include that the rise of intensive cattle farming coincided with the emergence and rapid expansion of specialized cattle-associated Campylobacter lineages. 3) Genomic analysis identified genes associated with host adaptation in cattle-specialist lineages, including genes related to nutrition utilization and surface properties relevant to host colonization.

1. Evangelos Mourkas
Postdoctoral Researcher
The Milner Centre for Evolution
Department of Biology and Biochemistry
University of Bath
Bath, United Kingdom
e.mourkas@bath.ac.uk | Twitter: @CampyVet
The impact of animal agriculture
in the evolution of Campylobacter
www.CLIMB.ac.uk

2. 5 facts you may not know about Campylobacter
1. Leading cause of gastroenteritis in high income countries
2. Causes three times more cases than E. coli, Salmonella and Listeria combined
3. Carried in the faeces of chickens, pigs, cattle and wild animals
4. Around 1 in 7 people suffer from an infection at some point in their life
5. Estimated to be present in the faeces of 20% cattle worldwide

3. Campylobacter transmission dynamics
The Sun, February 2016
Mourkas, E (2020). Genomics and evolution of Campylobacter: host adaptation and the
emergence of globally disseminated lineages.
(Doctoral dissertation, University of Bath, Bath, UK)

4. The impact of animal agriculture on the environment
~50%
of Earth’s land area
~ 30%
of all freshwater
~ 15%
of global GHG emissions

5. Loss of Biodiversity
180
Million tones
230
Million tones
832
Million tones
Terrestrial Biomass

6. Impact of intensive agriculture on Campylobacter evolution
“Campy” “E.coli” “Staph” “Listeria”

7. Finding the source of human Campylobacter infection
952
22
42
45
177
682
48
1275
661692
61
206
354
257
1034
574
21
Sheppard et al. (2009) Clinical Infectious Diseases 48:1072–1078
Sheppard et al. (2010) Applied Environmental Microbiology 76, 5269-5277

8. Source attribution of human cases of campylobacteriosis :
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)
https://www.thelocal.no/20170706/sheep-poo-makes-norwegian-cyclists-sick
Contribution of cattle-associated Campylobacter to human disease
Thépault et al. (2017) AEM 83 (7) 1-13; doi:10.1128/AEM.03085-16

9. Signatures of host adaptation in Campylobacter
Sheppard et al. (2013) PNAS 110 (29) 11923-11927; doi:10.1073/pnas.1305559110

10. Contribution of cattle-associated Campylobacter to human disease
https://www.pnas.org/content/117/20/11018
https://microreact.org/project/1Kb4NSNnA/eef54366

11. Press media attention
Coverage Headline facts and figures
 95 articles across online and print
 439 million potential total news reach (monthly online
visitors to websites)
 Coverage in UK, US, Europe, India, Japan and
Australia
 Social media posts had 6279 impressions on Twitter;
the video interview with Evangelos had 920 views.
AVE* £4.1 million

12. Impact of intensive agriculture on Campylobacter evolution
3x1017 (300 quadrillion)
C. jejuni
30 kg
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117
 Impact on Campylobacter
evolution?
 Formidable & recent increase in niche
space
 Adaptation to high transmissibility /
lower environmental survival? 
promotion of host jumps? Virulence to
humans?
 Increased opportunity for interspecies
recombination

13. pubMLST
https://pubmlst.org/campylobacter/
 99,057 C. jejuni/coli isolates
 50,824 C. jejuni/coli genomes

14. Cattle-associated clinical isolates in pubMLST
https://pubmlst.org/campylobacter/
 ~4,500 MLST profiles of Campylobacter isolates from ruminants/ruminant products
 ~1,000 clinical isolates associated with the two major-cattle lineages

15. Cattle specialist C. jejuni emerged from host generalist ancestors
Population structure of C. jejuni
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

16. Emergence of cattle specialists coincides with intensive cattle farming
Hannah Ritchie and Max Roser (2013) – “Land Use”. Published online at
OurWorldInData.org. – Retrieved from: https://ourworlddata.org/land-use
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117
ST-61 complex
BayesianSkylineModel
Rapid clonal expansion

17. Population expansion of cattle-associated ST-61 lineage
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117
 Stepwise emergence of ST-61 lineage
 Gradual increase in “ST-61-like” alleles

18. Mechanisms of Horizontal Gene Transfer
Sheppard et al. (2018) Nat Rev Gen 19 (9) 549-565; doi:10.1038/s41576-018-0032-z

19. Using genomics to investigate the emergence of cattle specialists
Accessory genome variation
between ST-61 and ST-21
Identification of genes involved in
homologous recombination in ST-61
Are there genes specifically present in ST-61
but absent in ST-21?
Are there genes recombining in ST-61
but not ST-21?
Detection of homoplasies
How many of the candidate adaptive
genes in ST-61 are present or absent
in other cattle-associated lineages?

20. Identifying host adaptive genomic traits - homoplasies
Genetic bottleneck
Convergent evolution

21. Gene presence/absence – Homologous recombination
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

22. Identifying homoplasies
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117
HomoplasyFinder

23. Homoplasies
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

24. Gene loss and niche adaptation
Iranzo et al. (2019) Nat Coms 10, 5376;
doi:10.1038/s41467-019-13429-2
Morley et al. (2015) AEM 81 (11): 3641-3647;
doi:10.1128/AEM.00546-15

25. Gene loss associated with cattle specialism
https://nptel.ac.in/courses/102103015/module2/lec3/2.html
Genes cj1319-cj1332 →
Flagella glycosylation
(legionaminic acid biosynthesis)
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

26. Candidate cattle adaptive genes – Mechanisms and functions
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

27. Slide to introduce biofilm-cell hydrophobicity
Nothaft & Szymanski (2010) Nature Rev Micro 8, 765-778; doi:10.1038/nrmicro2383
Guerry et al. (2006) Mol Micro 60: 299-311; doi:10.1111/j.1365-2958.2006.05100.x
Menozzi et al. (1994) Infection and Immunity, 62 (10) 4261-4269;
doi:10.1128/IAI.62.10.4261-4269.1994
Joshua et al. (2006) Microbiology 152 (2) 387-396;
doi:10.1099/mic.0.28358-0

28. Reduced Hydrophobicity and Biofilm formation in cattle specialists
Cell hydrophobicity Autoagglutination
Biofilm
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117
Prof Dave Kelly
Dr Aidan Taylor

29. Name Alias % recomb Predicted function Predicted COG category description
cj0665c argG 37.38% argininosuccinate synthase Amino acid transport and metabolism genes
cj0709 ffh 22.21% signal recognition particle protein Intracellular trafficking and secretion genes
cj1082c thiD 79.56% phosphomethylpyrimidine kinase Coenzyme transport and metabolism genes
cj1349c - 62.24% putative fibronectin/fibrinogen-binding protein Transcription
cj1352 ceuB 14.96% enterochelin uptake permease Inorganic ion transport and metabolism genes
cj0641 pnk 21.98% inorganic polyphosphate/ATP-NAD kinase Carbohydrate transport and metabolism genes
cj1044c thiH 29.87% thiamine biosynthesis protein ThiH Coenzyme transport and metabolism genes
cj1350 mobA 92.87% putative molybdopterin-guanine dinucleotide biosynthesis protein Coenzyme transport and metabolism genes
cj1633 - 52.70% putative ATP-binding protein Translation
Identifying adaptation associated with allelic variation
 Vitamin B1 biosynthesis (thiD + thiH genes)
 Molybdenum metabolism associated (mobA gene)
 Fibronectin/fibrinogen-binding protein (cj1349c gene)
Mourkas et al. (2020) PNAS 117 (20) 11018-11028; doi:10.1073/pnas.1917168117

30. Nutrition ecology in cattle and chickens
Thiamine (Vitamin B1) supplements ↑ caeca
Molybdenum ↓ concentration supplements
(Polin et al., 1966, Bräunlich & Zintzen, 1976; Nell, 1980)
Thiamine (Vitamin B1) ↓ large intestine
Molybdenum ↑ large intestine
(Rérat & Jaquot, 1954; Rérat et al., 1956, 1958, 1959, Virtanen, 1963; Blakley, R.
2016, MSD. Veterinary Manual)

31. Conclusions
Understanding the ecology and evolution in Campylobacter by:
Quantitative analysis
• Accessory genome variation
• Average nucleotide identity
• Recombination
Qualitative analysis
• Zoom in gene function
• Test gene function in vitro in the lab

32. Acknowledgements
The Sheppard lab
Sam Sheppard
Ben Pascoe
Sion Bayliss
Jessica Calland
Leonardos Mageiros
Harry Thorpe
Martin Maiden
Alison Cody
Keith Jolley
James Bray
Dave Kelly
Aidan Taylor
Koji Yahara
Guillaume Méric
Julian Parkhill
Anne Ridley
William Miller
Craig Parker
Norval Strachan
Ken Forbes
Bruno Lopes