Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

<em>Campylobacter </em>is the most common cause of bacterial gastroenteritis worldwide and diarrheal disease is a major cause of child morbidity, growth faltering, and mortality in low- and middle-income countries (LMICs). Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory genome content of a collection of <em>Campylobacter</em> isolates from Cairo metropolitan area, Egypt. In total, 112 <em>Campylobacter</em> isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24) and patients (n=57) suffering from gastroenteritis. Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialist CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented with a total absence of CC61. Core and accessory genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory genome sharing was significantly higher among isolates from the same country, particularly CC21 which demonstrated greater local geographical clustering. In contrast, no geographic clustering was noted in either the core or accessory genomes of the CC828, suggesting a highly admixed population. A greater proportion of <em>C. coli</em> isolates were multidrug resistant (MDR) compared to <em>C. jejuni. </em>Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of AMR among this important pathogen.