Table_2_Whole Resistome Analysis in Campylobacter jejuni and C. coli Genomes Available in Public Repositories.xlsx

Campylobacter spp. are the most frequent agent of human gastroenteritis worldwide, and the spread of multidrug-resistant strains makes the clinical treatment difficult. The current study presents the resistome analysis of 39,798 Campylobacter jejuni and 11,920 Campylobacter coli genomes available in public repositories. Determinants of resistance to β-lactams (Be) and tetracyclines (Te) were the most frequent for both species, with resistance to quinolones (Qu) as the third most important on C. jejuni and to aminoglycosides (Am) on C. coli. Moreover, resistance to Te, Qu, and Am was frequently found in co-occurrence with resistance to other antibiotic families. Geographical differences on clonal complexes distribution were found for C. jejuni and on resistome genotypes for both C. jejuni and C. coli species. Attending to the resistome patterns by isolation source, three main clusters of genomes were found on C. jejuni genomes at antimicrobial resistance gene level. The first cluster was formed by genomes from human, food production animals (e.g., sheep, cow, and chicken), and food (e.g., dairy products) isolates. The higher incidence of tet(O), associated with tetracycline resistance, and the gyrA (T86I) single-nucleotide polymorphism (SNP), associated with quinolone resistance, among genomes from this cluster could be due to the intense use of these antibiotics in veterinary and human clinical settings. Similarly, a high incidence of tet(O) genes of C. coli genomes from pig, cow, and turkey was found. Moreover, the cluster based on resistome patterns formed by C. jejuni and C. coli genomes of human, turkey, and chicken origin is in agreement with previous observations reporting chicken or poultry-related environments as the main source of human campylobacteriosis infections. Most clonal complexes (CCs) associated with chicken host specialization (e.g., ST-354, ST-573, ST-464, and ST-446) were the CCs with the highest prevalence of determinants of resistance to Be, Qu, and Te. Finally, a clear trend toward an increase in the occurrence of Te and Qu resistance determinants on C. jejuni, linked to the spread of the co-occurrence of the blaOXA–61 and tet(O)-tet(O/W/O) genes and the gyrA (T86I) SNP, was found from 2001 to date in Europe.

弯曲杆菌属（Campylobacter spp.）是全球范围内人类胃肠炎最常见的病原菌，多重耐药菌株的传播使得临床治疗难度大幅增加。本研究对公共数据库中收录的39798株空肠弯曲杆菌（Campylobacter jejuni）和11920株结肠弯曲杆菌（Campylobacter coli）的基因组开展了耐药组（resistome）分析。
β-内酰胺类（β-lactams，原文缩写Be）与四环素类（tetracyclines，原文缩写Te）耐药决定因子是两种弯曲杆菌最常见的耐药类型；其中，空肠弯曲杆菌的喹诺酮类（quinolones，原文缩写Qu）耐药性位列第三重要的耐药类型，而结肠弯曲杆菌则以氨基糖苷类（aminoglycosides，原文缩写Am）耐药性位居第三。此外，四环素类、喹诺酮类与氨基糖苷类耐药性常与其他抗生素家族的耐药性共同出现。
研究发现，空肠弯曲杆菌的克隆复合体（clonal complexes, CC）分布存在地理差异，而两种弯曲杆菌的耐药组基因型均存在地理差异。按分离来源划分耐药组模式后，在抗菌药物耐药基因层面，空肠弯曲杆菌的基因组可划分为3个主要类群。第一类群包含来自人类、食用动物（如绵羊、牛与鸡）以及食品（如乳制品）分离株的基因组。该类群基因组中，与四环素耐药相关的tet(O)基因以及与喹诺酮耐药相关的gyrA（T86I）单核苷酸多态性（single-nucleotide polymorphism, SNP）的检出率更高，这可能与兽医及人类临床诊疗场景中这类抗生素的大规模使用有关。
类似地，在来源于猪、牛与火鸡的结肠弯曲杆菌基因组中，tet(O)基因的检出率同样较高。此外，由人类、火鸡与鸡来源的空肠弯曲杆菌和结肠弯曲杆菌基因组所构成的耐药组类群，与既往研究发现鸡或家禽相关环境是人类弯曲杆菌感染主要传染源的结论一致。
多数与鸡宿主特异性相关的克隆复合体（如ST-354、ST-573、ST-464与ST-446），其β-内酰胺类、喹诺酮类与四环素类耐药决定因子的检出率均为最高。从2001年至今的欧洲地区数据中，研究还发现空肠弯曲杆菌的四环素类与喹诺酮类耐药决定因子检出率呈显著上升趋势，这与blaOXA-61、tet(O)-tet(O/W/O)基因以及gyrA（T86I）单核苷酸多态性的共同传播密切相关。