Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp.

<i>Campylobacter </i>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 characterized the genetic diversity and accessory genome content of a collection of <i>Campylobacter</i> isolates from Cairo, Egypt. In total, 112 <i>Campylobacter</i> 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 were 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. Comparative genomics were used to quantify core and accessory genome sharing among isolates from the same country compared to sharing between countries. 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 <i>C. coli</i> isolates were multidrug resistant (MDR) compared to <i>C. jejuni. </i>This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies in the Egyptian market to combat such a threat.