Jones Gabrielle, Nodari Carolina Silva, Fabre Laëtitia, de Valk Henriette, Noel Harold, Cointe Aurélie, Bonacorsi Stéphane, Weill François-Xavier, Le Strat Yann
Emerg Infect Dis. 2025 May;31(13):117-128. doi: 10.3201/eid3113.241950.
Whole-genome sequencing (WGS) is routine for surveillance of Shiga toxin-producing Escherichia coli human isolates in France. Protocols use EnteroBase hierarchical clustering at <5 allelic differences (HC5) as screening for cluster detection. We assessed current implementation after 5 years for 1,002 sequenced isolates. From genomic distances of serotypes O26:H11, O157:H7, O80:H2, and O103:H2, we determined statistical thresholds for cluster determination and compared those with HC5 clusters. Thresholds varied by serotype, 5-16 allelic distances and 15-20 single-nucleotide polymorphisms, showing limits of a single-threshold approach. We confirmed validity of HC5 screening for 3 serotypes because statistical thresholds had limited effect on isolate clustering (high sensitivity and specificity). For O80:H2, results suggest that HC5 is less reliable, and other approaches should be explored. Public health officials should regularly assess WGS used for Shiga toxin-producing E. coli surveillance to account for serotype and genomic evolution and to interpret WGS-linked isolates in light of epidemiologic data.
在法国，全基因组测序（WGS）是监测产志贺毒素大肠杆菌人类分离株的常规方法。检测方案采用等位基因差异小于5个（HC5）的EnteroBase层次聚类法作为聚类检测的筛选方法。我们对1002株测序分离株在5年后的当前实施情况进行了评估。根据血清型O26:H11、O157:H7、O80:H2和O103:H2的基因组距离，我们确定了聚类判定的统计阈值，并将其与HC5聚类进行比较。阈值因血清型而异，为5至16个等位基因距离和15至20个单核苷酸多态性，这显示了单阈值方法的局限性。我们证实了HC5筛选对3种血清型的有效性，因为统计阈值对分离株聚类的影响有限（高灵敏度和特异性）。对于O80:H2，结果表明HC5的可靠性较低，应探索其他方法。公共卫生官员应定期评估用于产志贺毒素大肠杆菌监测的WGS，以考虑血清型和基因组进化，并根据流行病学数据解释与WGS相关的分离株。
