Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions

Fritsch, Lena; Felten, Arnaud; Palma, Federica Di; Mariet, Jean-François; Radomski, Nicolas; Mistou, Michel‐Yves; Augustin, Jean-Christophe; Guillier, Laurent

doi:10.1016/j.ijfoodmicro.2018.11.028

Cited by 43 publications

(32 citation statements)

References 61 publications

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“…genes in 0% ≤ strains < 15%). These observations are consistent with previous comparative genomics studies unravelling the L. monocytogenes pangenome [48,49,54,55]. From the Phandango interactive visualization of the accessory genes based distance tree, associated metadata and the pangenome matrix (Additional file 6), five major clusters representing the CCs of L. monocytogenes genomes were identified.…”

Section: Pangenomic Extraction and Clustering Of Accessory Genes Revesupporting

confidence: 88%

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

et al. 2020

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Background: Listeria monocytogenes Clonal Complexes (CCs) have been epidemiologically associated with foods, especially ready-to-eat (RTE) products for which the most likely source of contamination depends on the occurrence of persisting clones in food-processing environments (FPEs). As the ability of L. monocytogenes to adapt to environmental stressors met in the food chain challenges the efforts to its eradication from FPEs, the threat of persistent strains to the food industry and public health authorities continues to rise. In this study, 94 food and FPEs L. monocytogenes isolates, representing persistent subtypes contaminating three French seafood facilities over 2-6 years, were whole-genome sequenced to characterize their genetic diversity and determine the biomarkers associated with long-term survival in FPEs. Results: Food and FPEs isolates belonged to five CCs, comprising long-term intra-and inter-plant persisting clones. Mobile genetic elements (MGEs) such as plasmids, prophages and transposons were highly conserved within CCs, some of which harboured genes for resistance to chemical compounds and biocides used in the processing plants. Some of these genes were found in a 90.8 kbp plasmid, predicted to be" mobilizable", identical in isolates from CC204 and CC155, and highly similar to an 81.6 kbp plasmid from isolates belonging to CC7. These similarities suggest horizontal transfer between isolates, accompanied by deletion and homologous recombination in isolates from CC7. Prophage profiles characterized persistent clonal strains and several prophage-loci were plant-associated. Notably, a persistent clone from CC101 harboured a novel 31.5 kbp genomic island that we named Listeria genomic island 3 (LGI3), composed by plant-associated loci and chromosomally integrating cadmium-resistance determinants cadA1C. Conclusions: Genome-wide analysis indicated that inter-and intra-plant persisting clones harbour conserved MGEs, likely acquired in FPEs and maintained by selective pressures. The presence of closely related plasmids in L. monocytogenes CCs supports the hypothesis of horizontal gene transfer conferring enhanced survival to FPEassociated stressors, especially in hard-to-clean harbourage sites. Investigating the MGEs evolutionary and transmission dynamics provides additional resolution to trace-back potentially persistent clones. The biomarkers herein discovered provide new tools for better designing effective strategies for the removal or reduction of resident L. monocytogenes in FPEs to prevent contamination of RTE seafood.

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Section: Pangenomic Extraction and Clustering Of Accessory Genes Revesupporting

confidence: 88%

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

et al. 2020

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“…Within a range from 51 Listeria monocytogenes [29] to 3701 Streptococcus pneumoniae strains [35] and without consensus on the appropriated size of genome dataset, most of the microbial GWAS includes around 500 samples under clonal and/or panmictic status (Table 6) [43]. Contrary to human GWAS focusing on the effects of individual SNPs, microbial GWAS has also to access phenotype associations based on presence/absence of genes alongside SNPs [43].…”

Section: Methodsmentioning

confidence: 99%

“…Following the first tool computing GWAS with a correction of Eukaryotic population structure based on SNPs (PLINK) [27], combinations of different methods have been implemented in the recently developed microbial GWAS. Over the last 10 years, microbial GWAS was implemented to explore a diversity of biological problems: genetic backgrounds of microbial origin [28], persistence [29], host preference [30], virulence [31, 32], and antibiotic resistance [33–42]. In comparison to human GWAS, the confounding factors of the microbial GWAS include genome selection, homologous recombination events, population structure, as well as genome wide significance [43].…”

Section: Introductionmentioning

confidence: 99%

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Nova

Durimel

et al. 2019

BMC Genomics

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BackgroundSalmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).ResultsBased on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.ConclusionsOur results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.

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“…The IT-OTH-CP-36 genome was compared to all the CC121 genomes available from the ANSES Laboratory for Food Safety database, including 107 genomes described by Félix et al [ 27 ], 54 genomes described by Henri et al [ 18 ], 6 by Fritsch et al [ 61 ], 29 by Palma et al [ 25 ], 143 genomes from the Liseq collection [ 17 ] and 21 new genomes specifically sequenced in the framework of this study. These genomes included 11 genomes of strains from Ireland, four from Republic of North Macedonia, four from France and two from Czech Republic.…”

Section: Methodsmentioning

confidence: 99%

First Report on the Finding of Listeria mnocytogenes ST121 Strain in a Dolphin Brain

et al. 2020

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Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes the foodborne illness, listeriosis. Clonal complexes (CC), such as CC121, are overrepresented in the food production industry, and are rarely reported in animals and the environment. Working within a European-wide project, we investigated the routes by which strains are transmitted from environments and animals to food and the food production environment (FPE). In this context, we report, for the first time, the occurrence of a ST121 (CC121) strain isolated from a dolphin brain. The genome was compared with the genomes of 376 CC121 strains. Genomic comparisons showed that 16 strains isolated from food were the closest to the dolphin strain. Like most of the food strains analyzed here, the dolphin strain included genomic features (transposon Tn6188, plasmid pLM6179), both described as being associated with the strain’s adaptation to the FPE. Like all 376 strains, the dolphin strain contained a truncated actA gene and inlA gene, both described as being associated with attenuated virulence. Despite this fact, the strain was able to cross blood-brain barrier in immunosuppressed dolphin exposed polychlorinated biphenyl and invaded by parasites. Our data suggest that the dolphin was infected by a food-related strain released into the Mediterranean Sea.

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Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions

Cited by 43 publications

References 61 publications

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

First Report on the Finding of Listeria mnocytogenes ST121 Strain in a Dolphin Brain

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