Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Abstract

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.

Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study

“…While cgMLST is the reference method for the surveillance of Campylobacter spp., the combination of mass spectrometry and artificial intelligence may be a suitable tool to make a pre-selection of what need to be sequenced. Indeed, it has been shown recently that genetic lineages were frequently identified in human infection over-time in Luxembourg [19]. Using the same lineage isolates of Nennig et al (2021), we pushed the study at the clone level, confirmed by three cgMLST schemes and by comparing the pangenome (wgMLST).…”

“…Indeed, it has been shown recently that genetic lineages were frequently identified in human infection over-time in Luxembourg [19]. Using the same lineage isolates of Nennig et al (2021), we pushed the study at the clone level, confirmed by three cgMLST schemes and by comparing the pangenome (wgMLST). Eleven specific MALDI-TOF profiles have been linked to specific lineages identified over-time in Luxembourg.…”

“…Among these isolates, a total of 74 were identified in a previous study, Nennig et al (2021), as belonging to four different lineages, i.e., A (n = 34), B (n = 15), C (n = 15) and D (n = 10), based on their ST-gyrA-porA combination and their frequency in human infection over time. Three clones, defined as a set of independent isolated bacteria with similar genotypic characteristic, were identified in isolates (Lineage A (n = 31), B (n = 12) and D (n = 9)), by complete genomic analysis, including 3 cgMLST schemes and whole genome MLST (wgMLST).…”

“…For C. jejuni, three main cgMLST typing schemes were developed, i.e., the Oxford scheme with 1343 loci [16]; the one from Ridom SeqSphere+ software (Ridom GmbH, Münster, Germany) with 637 loci, resulting into complex type (CT), and the INNUENDO scheme with 678 loci [17,18]. All showed high concordance when compared together [19]. However, the existence of different typing methods with different typing schemes underlines there is not a unique standard subtyping methodology for Campylobacter [20] and the lack of a common nomenclature.…”

Multi-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni

“…Because the core genome contained only conserved genes and was relatively small in this elucidation here, this might lead to different phylogenetic relationships between them. In addition, other studies have also tried to distinguish the closely related C. jejuni genomes based on the core or whole-genome sequencing type schemes and found that some clinical strain genomes are more stable than others for over a decade ( Cody et al, 2013 ; Nennig et al, 2021 ). It is known that C. jejuni has a high genetic diversity with very few repeat sequences and virtually no inserted or phage-associated sequence in the genome ( Parkhill et al, 2000 ).…”