Reference : Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four ...
Scientific journals : Article
Life sciences : Microbiology
Systems Biomedicine
http://hdl.handle.net/10993/50825
Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes
English
Nennig, Morgane mailto [University of Luxembourg > Faculty of Science, Technology and Medecine (FSTM) > > ; Laboratoire National de Santé > Microbiology > Epidemiology and Microbial Genomics > ; INRAE - Oniris]
LLARENA, Ann-Katrin mailto [Norwegian University of Life Sciences > Faculty of Veterinary Medicine]
HEROLD, Malte mailto [Laboratoire National de Santé > Microbiology > Epidemiology and Microbial Genomics]
MOSSONG, Joël mailto [Laboratoire National de Santé > Microbiology > Epidemiology and Microbial Genomics]
PENNY, Christian mailto [Luxembourg Institute of Science & Technology - LIST > Environmental Research and Innovation Department]
LOSCH, Serge mailto [Veterinary Services Administration > Laboratoire de Médecine Vétérinaire de l’Etat]
TRESSE, Odile mailto [INRAE - Oniris]
Ragimbeau, Catherine mailto [Laboratoire National de Santé > Microbiology > Epidemiology and Microbial Genomics]
8-Jan-2021
Frontiers in Cellular and Infection Microbiology
Frontiers Media SA
10
Molecular Bacterial Pathogenesis
Yes (verified by ORBilu)
International
2235-2988
2235-2988
[en] whole genome sequencing ; Campylobacter jejuni ; typing schemes ; WGS typing scheme comparison ; recurring genotypes ; clones ; core genome MLST ; whole genome MLST
[en] 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.
Laboratoire National de Santé ; INRAE - Oniris (France)
Fonds National de la Recherche - FnR ; RFI Food for Tomorrow of Région Pays de la Loire - France
CampylOmic
http://hdl.handle.net/10993/50825
10.3389/fcimb.2020.608020
https://www.frontiersin.org/articles/10.3389/fcimb.2020.608020/full
The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcimb.2020.608020/full#supplementary-material
FnR ; FNR11684203 > Catherine Ragimbeau > CampylOmic > One Health Genomics Of Campylobacter Jejuni In Luxembourg > 15/03/2018 > 14/03/2022 > 2017

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