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See detailPopulation structure and phenotypical traits of Campylobacter jejuni circulating in Luxembourg
Nennig, Morgane UL

Doctoral thesis (2022)

Campylobacter is the leading cause of bacterial gastroenteritis worldwide. The most prevalent species, C. jejuni, is a strict microaerobic, capnophilic, and thermotolerant pathogen. Given its growth ... [more ▼]

Campylobacter is the leading cause of bacterial gastroenteritis worldwide. The most prevalent species, C. jejuni, is a strict microaerobic, capnophilic, and thermotolerant pathogen. Given its growth requirements, the ability of C. jejuni to persist in food environments and be transmitted throughout food processing has long puzzled scientists. This study aimed to compare the different genetic profiles of C. jejuni strains, isolated in Luxembourg, at the core genome (cg) and whole genome (wg) levels to elucidate its genetic population structure. Using phenotypical assays in controlled conditions and functional genomics analyses from wgMLST data, the study also investigated the possible link between phenotypic traits and emergence or persistence of genotypes. A high concordance in strain clustering was observed between genomic lineage classifications and the epidemic and endemic signals, regardless the three cgMLST typing schemes used. The higher genome stability within genomic lineages supports the hypothesis of a clonal expansion with monomorphic patterns over time and sources. A high correlation was observed between phenotypes and host-specific or generalist clonal complexes for oxidative stress, adhesion to inert surfaces, biofilm formation, and acclimation to aerobic conditions responses. These data allowed the establishment of metaphenotypes specific to the genomic lineages. Functional genomic analysis revealed factors that may contribute to the spatiotemporal survival of recurrent strains. These results also suggest the selection of better-adapted and persistent C. jejuni strains to environmental stresses throughout the transmission to human. [less ▲]

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See detailInvestigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes
Nennig, Morgane UL; LLARENA, Ann-Katrin; HEROLD, Malte et al

in Frontiers in Cellular and Infection Microbiology (2021), 10

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 ... [more ▼]

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, emphasising the need to investigate their survival strategy in greater depth. [less ▲]

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