东非空肠弯曲菌跨国家比较基因组学：One Health 框架下的统一重分析
Cross-country comparative genomics of Campylobacter jejuni in East Africa: A harmonized One Health comparative genomic re-analysis
一项统一全基因组测序流程的 One Health 比较基因组重分析显示，埃塞俄比亚、肯尼亚和坦桑尼亚的 225 株公开空肠弯曲菌（Campylobacter jejuni）基因组中，blaOXA-193 检出率为 66.67%（150/225），tet(O) 为 18.22%（41/225），gyrA T86I 替换占 24.9%（56/225）。研究采用 ≥90% 核苷酸一致性和 ≥60% 基因覆盖度阈值筛查耐药与毒力基因，未检出获得性大环内酯耐药决定因子，毒力基因谱总体保守。
来源：Bioinformatics Advances · doi.org
Motivation
Campylobacter jejuni is a major foodborne zoonotic pathogen associated with antimicrobial resistance (AMR), particularly in low- and middle-income countries with limited genomic surveillance. We analysed 225 publicly available C.jejuni genomes from Ethiopia, Kenya, and Tanzania using a harmonized whole-genome sequencing workflow within a One Health framework. Analyses included genome assembly, annotation, AMR and virulence gene screening, plasmid replicon and mobile genetic element detection, multilocus sequence typing (MLST), phylogenetic reconstruction, principal component analysis (PCA), and minimum spanning tree (MST) analysis.
Results
Using thresholds of ≥ 90% nucleotide identity and ≥60% gene coverage, blaOXA-193 was detected in 66.67% (150/225) of genomes, tet(O) in 18.22% (41/225), tet(O/32/O) in 4.00% (9/225), and blaOXA-61 in 1.33% (3/225). The gyrA T86I substitution occurred in 24.9% (56/225) of isolates. The applied screening approach detected no acquired macrolide resistance determinants. Virulence-associated gene profiles were broadly conserved, with variation in selected genes. Three known plasmid replicon types and prophage-associated intA hits were identified. Phylogenomic analysis revealed 65 sequence types and substantial genetic overlap between poultry- and human-associated isolates, indicating relatedness but not proving direct transmission. These findings highlight the importance of integrated One Health genomic surveillance for monitoring AMR and genomic diversity of C. jejuni in East Africa.
Availability and implementation
data underlying this article will be shared on reasonable request to the corresponding author