Table_2_Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli.xlsx

IntroductionCommensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.ObjectivesIn order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources.ResultsThe core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.ConclusionThis is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.

引言：多重耐药性（MDR）的大肠杆菌的共生和致病菌株，以及非伤寒沙门氏菌菌株，代表着来自家禽食品的日益增长的食源性疾病威胁。多重耐药性的沙门氏菌肠炎亚种和埃希氏菌从肉鸡中频繁分离，这两种肠道细菌的共存可能允许移动耐药决定子的交换。目标：为了理解可能的基因组关系，并首次洞察肠道细菌之间耐药基因的潜在相互作用，我们比较了来自肉鸡来源的沙门氏菌肠炎亚种和大肠杆菌的基因组多样性和移动耐药组。结果：对56株沙门氏菌肠炎亚种和90株大肠杆菌当代菌株的核心基因组MLST分析揭示了肉鸡大肠杆菌的高度基因组异质性。这还首次揭示了匈牙利流行的沙门氏菌肠炎亚种MDR克隆B2的基因组多样性。我们还鉴定了沙门氏菌肠炎亚种（ST7081和ST7082）和大肠杆菌（ST8702和ST10088）的新MDR谱系。抗生素耐药基因和质粒类型的比较分析揭示了大肠杆菌和沙门氏菌肠炎亚种的移动耐药组之间相对狭窄的界面。在两种物种中，发现了总体高流行的移动耐药基因tet(A)、aadA1和sul1。这种基因关联是沙门氏菌肠炎亚种流行克隆B2的质粒pSI54/04的特征。这些基因以及与同一亚型的IncI质粒在共栖的沙门氏菌肠炎亚种和大肠杆菌盲肠菌株中的共存表明，这些质粒家族在沙门氏菌肠炎亚种和大肠杆菌之间可能的耐药基因相互作用中起着重要作用。结论：这是对沙门氏菌肠炎亚种和大肠杆菌当代肉鸡菌株进行的首次比较基因组分析。移动耐药组的多样性表明，共生的大肠杆菌可能是沙门氏菌肠炎亚种耐药的潜在储存库，但迄今为止，只有少数质粒类型和移动耐药基因可以考虑为这两种物种之间可能交换的。在这些中，IncI1质粒可能对大肠杆菌和沙门氏菌肠炎亚种之间的微进化与遗传相互作用贡献最大。