Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasizing the need to investigate their survival strategy in greater depth.

空肠弯曲菌是细菌性肠胃炎的主要原因，自13年以来，它一直促使人们监测卢森堡的遗传状况。来自我们使用基于扩展MLST方案的基因分型策略的综合监测，包括GyrA 和 porA标记，在基因型的时间分布中发现了意外的地方性模式。我们旨在通过实施与全面和国际验证的计划相关的全基因组测序（WGS）来测试稳定谱系发生的假设。这项前期研究评估了四种基于WGS的分型方案，以使用该内部分型系统对一组先前被鉴定为复发性或零星特征的108个菌株进行分类。菌株收集包括人类感染的四个常见谱系（N = 67），最初是从ST-GyrA--porA在非人类样本中也检测到等位基因：兽医（N = 19），食物（N = 20）和环境（N = 2）。属于零星分布的另一组19个菌株完成了测试小组。所有菌株均使用Illumina技术通过WGS处理，并采用严格的标准过滤测序数据。我们在基因组比较中确保稳健性。应用了四种分型方案对菌株进行分类：（i）637个基因座的cgMLST SeqSphere +方案，（ii）1,343个基因座的cgMLST Oxford方案，（iii）678个基因座的cgMLST INNUENDO方案，以及（iv）wgMLST INNUENDO 2,795个基因座的计划。通过比较计算出的调整后的华莱士系数，可以确定打字方案之间的高度一致性。经过质量控制并使用这四种打字方案进行分析后，不管使用哪种方法，证实60个菌株是四个复发谱系的成员（分别为N = 32、12、7和9）。我们的结果表明，无论使用哪种分类方案，都可以检测到由谱系B（ST2254-GyrA9-porA1）在2014年或沿袭A（ST19-GyrA8porA7）。这些发现支持了稳定基因组的克隆扩增。弯曲杆菌人群表现出多宿主的特征，并占了十年来分离出的大多数临床菌株。这些复发的基因型表明在水库，水源或环境中存在持久性，强调需要更深入地研究其生存策略。