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

Abstract

Campylobacter 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 Campylobacter isolates from Cairo, Egypt. In total, 112 Campylobacter 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 C. coli isolates were multidrug resistant (MDR) compared to C. jejuni. 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.

Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio

“…Similar trends were observed in published studies ( Ocejo et al, 2019 ; Cobo-Díaz et al, 2021 ; Hailu et al, 2021 ; Hull et al, 2021 ). As previously described ( Ocejo et al, 2019 ; Mouftah et al, 2021 ), blaOXA-193 was the most predominant ARG to beta-lactam compared to other beta-lactamase encoding genes ( blaOXA-449, -461, -603, and 61 ; <10%). However, some other studies have reported blaOXA-61 being predominant in Campylobacter ( Cobo-Díaz et al, 2021 ; Hull et al, 2021 ).…”

Prevalence and genetic characterization of Campylobacter from clinical poultry cases in China

“…This observation prompted the formulation of a hypothesis suggesting that C. jejuni isolates from diseased chickens may be more resistant to β-lactams than isolates from diseased ducks and diseased geese. Mouftah et al also found a high prevalence of the bla OXA-605 gene in C. jejuni from broiler carcasses ( 44 ).…”