Global similarity and local differences in Campylobacter jejuni lineages associated with asymptomatic paediatric infection from the Peruvian Amazon

<i>Campylobacter</i> is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- to middle-income countries, where infection can be fatal, surveillance is rare and the genotypes responsible for disease have not been identified. The epidemiology of disease is different to the developed world, where infection is mostly associated with consumption of contaminated meat products. Infection is endemic among children and asymptomatic carriage is thought to be common. Widespread malnutrition encourages asymptomatic colonisation stunting childhood growth, leading to poor cognitive and physical development. Here, we sequence the genomes of a collection of <i>C. jejuni</i> isolates sampled from children in the Peruvian Amazon to investigate genetic differences between them and a global reference collection. In addition to common global disease lineages, we identified local genotypes rarely seen before. Asymptomatic isolates were not restricted to specific ecological groups or genotypes and chicken was the primary source of infection. Hidden reservoirs of bacterial diversity can help us understand the genetics underlying differences in the presentation of disease and will inform work to improve infant health globally.<br>