Genomic Epidemiology of Campylobacter in Peru

Genomic Epidemiology of Campylobacter to Improve Disease Control in Low and Middle Income Countries


Campylobacter is among the principal causes of bacterial enteritis worldwide and the progressive development of antimicrobial resistance among global isolates, particularly in low and middle income countries, has led the CDC to list drug-resistant Campylobacter at the top of its list of serious threats in 2019. The limited genomic study of Campylobacter done in low and middle income countries demonstrates important differences in the genomes of isolates from both humans and zoonotic sources, indicating that transmission dynamics differ in these settings compared to that seen in high income countries. The objective of this project is to inform targeted disease control measures to reduce the impact of campylobacteriosis and human MDR Campylobacter in low and middle income countries. Our central hypothesis is that industrially produced meat products are the principal source of campyobacteriosis and MDR Campylobacter in humans in this population. In order to test our central hypothesis we will:

1) identify host segregating features of Campylobacter from zoonotic sources in Peru;
2) characterize genomes of Campylobacter strains that cause disease in humans, evaluate the risk of household peron-to-person transmission and identify microbial genomic features associated with persistent asymptomatic human carriage; and
3) estimate the burden of campylobacteriosis and human MDR infections attributable to domestic and industrially derived zoonotic sources.

The proposed project will unite a highly complementary group of accomplished researchers with expertise in epidemiology, Campylobacter genomics, bioinformatics and microbial ecology to inform strategic and targeted disease control interventions for Campylobacter control in an area with one of the highest documented rates of human MDR Campylobacter infection. The project is innovative in its approach to link characterized human cases and zoonotic reservoirs in a high burden LMIC setting to local, regional, and global reference genomes to create robust evidence to drive policy and practice to improve the control of campylobacteriosis and the diminish the geographic expansion of MDR Campylobacter.


Meet the team

Project lead: Prof Margaret Kosek, University of Virginia & John Hopkins Bloomberg School of Public Health

Francesca Schiaffino, Universidad Peruana Cayetano Heredia & University of North Carolina Chapel Hill
Iquitos Satellite Laboratory (IQTLAB)

Craig Parker, Agriculture Research Services, United States Department of Agriculture, Produce Safety and Microbiology Research
Kerry Cooper, University of Arizona

UK: University of Oxford
Ben Pascoe, Big Data institute, University of Oxford
Professor Samuel Sheppard, Ineos Oxford Institute for Antimicrobial Research, University of Oxford
Evangelos Mourkas, Ineos Oxford Institute for Antimicrobial Research, University of Oxford




  1. Parker CT, Schiaffino F, Huynh S, Paredes Olortegui M, Peñataro Yori P, Garcia Bardales PF, Pinedo Vasquez T, Curico Huansi GE, Manzanares Villanueva K, Shapiama Lopez WV, Cooper KK, Kosek MN (2022) Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLoS Neglected Tropical Diseases doi: 10.1371/journal.pntd.0010815 [Publisher]
  2. Parker CT, Cooper KK, Schiaffino F, Miller WG, Huynh S, Gray HK, Paredes Olortegui M, Garcia Bardales PF, Rengifo Trigoso D, Penataro-Yori P & Kosek MN (2021) Genomic Characterization of Campylobacter jejuni Adapted to the Guinea Pig (Cavia porcellus) Host. Frontiers in Cellular and Infection Microbiology doi: 10.3389/fcimb.2021.607747 [Publisher]
  3. Pascoe B , Schiaffino F, Murray S, Méric G, Bayliss SC, Hitchings MD, Mourkas E, Calland JK, Burga R, Peñataro Yori P, Jolley KA, Cooper KK, Parker CT, Paredes Olortegui M, Kosek MN & Sheppard SK (2020) Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS Neglected Tropical Diseases doi: 10.1371/journal.pntd.0008533 [Publisher]