- Full list of author information is available at the end of the article. - So far there is no full agreement in the scientific community on the defin- ition of L. - monocytogenes persistence, however, the re- peated isolation over a long period of the same subtype from the same FPE has been proposed [3, 4]. - The persistence of such strains in the food system has also been observed to play a significant role in listeriosis outbreaks during the last decades [6–8].. - monocytogenes sub- types in a specific FPE may occur due to introduction(s) of resistant strain(s), and/or adaptation to the selection pressure met in the FPEs. - In addition, the adaptation to particular environmental niches may shelter them from sanitizers used in the food industry. - monocytogenes popula- tions and the complexity of the transmission pathways of persistent and transient strains in FPEs make the identification of the point of exposure source a critical. - industry in the past few decades [36]. - Recommended levels of QACs concentrations in the food industry are much higher than resistance levels conferred by these genes [39] and highly effective against the growth of planktonic bacteria [40]. - CC121, CC9, CC204) [20] on food processing plant surfaces, en- hancing cells persistence potentials in the food industry.. - The recently described cadA4 determinant [29] has been identified in the As- resistance island LGI2 of L. - genes only present in subgroups of the population). - monocytogenes isolates belonging to the prevalent pulsotypes repeatedly collected over time from food and FPEs of the three different French RTE seafood processing plants (A, B, C) (Additional file 1).. - An overview of the draft genomes quality, i.e. - depth and breadth of reads coverage, of the 94 L. - CDSs) varied from 2810 in the smallest genomes to 3100 in the largest ones. - To untangle the genetic relationships of the 94 L. - in the same environment for a long timeframe (over 2–. - The phylogenetic structure of the five L. - From the Phandango interactive visualization of the accessory genes based dis- tance tree, associated metadata and the pangenome matrix (Additional file 6), five major clusters represent- ing the CCs of L. - As observed in the SNP-based phylogenomic reconstruction, strains gathered within each cluster inde- pendently of the source or year of isolation. - transposon-related clusters of genes were identified in the accessory matrix and appeared to be the major loci of genetic diversity across different CCs. - Moreover, the intra-CC variations of the accessory genes content dis- criminated with higher resolution the genetic diversity observed in the core genome SNPs (Additional file 6).. - Gene clusters playing an important role in the survival of L. - For instance, a transposon harbouring Cd- and As-resistance cassettes was conserved in all CC204 isolates from this study and inserted in the yfbR gene. - 35.7 kbp) transposon inserted in the yfbR gene and recently identified in CC204 strains isolated from processing environment [17], as well as to the Listeria genomic island 2 (LGI2), previously de- scribed in the L. - The plasmidome of the 94 L. - monocytogenes genomes were de novo reconstructed and the gene content inves- tigated to untangle the MGEs contribution in the long- term survival of clonal groups. - On the other hand, the CC204 food and FPEs isolates from plant A were already plasmid- positive in the first sampling in 1999. - ANI) over ~ 99% of the sequence. - None of the plasmid sequences was found in two CC7 isolates from plant A as well as two CC204 isolates, one from each plant (A and B). - All these isolates were collected at the beginning of the sampling timeframe . - One of the first plasmid harbouring the cadA2C/. - See Additional file 8 for a detailed description of the main genetic com- ponents of plasmids.. - BLAST-based alignment of the closed 81.6 kbp plasmid reconstructed from CC7 strain C62-P3-LmUB3PA and the 2 contigs 90.8 kbp plasmid reconstructed from CC204 strain B7678-P1-LmUB3PA. - monocytogenes strains collected from food product and environment in the USA. - 4 BRIG comparison of the plasmids from this study and the public database PLSDB. - Interestingly, pGMI16–004 was found in the L. - Unique prophage profiles characterize persisting clones The prophage (φ) profiles of the 94 L. - Besides the chimeric nature of these regions, a major Listeria phage organism (homologous to more than 50% of the total number of CDS of the region) was identified in the majority (>. - 78%) of the pro- phage dataset. - although variants of the corresponding pro- phage length were observed (Table 2, Additional file 9).. - The majority of prophages detected in the L. - Moreover, the alignment of φcomK found in CC101, CC155 and CC204 showed high ANI values (above 94%) over ~ 70% of the sequences. - Only one-third of the φcomK sequence conserved in genomes from CC7 (homologous to phage A118) was aligned to the φcomK sequence with an ANI higher than 95% (Additional file 9). - 90%) for almost half of the φtRNA-Arg (ccg) se- quence (also homologous to phage A118) detected in genomes from CC121 isolated in the same plant (Add- itional file 9 and Additional file 10, Table 2). - This is consistent with the similarities observed in the pairwise comparison of prophages described above.. - Outside of the prophage regions, a cluster of 25 loci enriched in plant B was found to be part of a large (ca.. - This gene cluster included a number of CDSs specif- ically involved in the uptake, transport and utilization of primary carbon source (e.g. - The repeated introduc- tion of the same subtypes in FPEs and/or the ability of. - monocytogenes are recurrently isolated in the FPEs is still under discussion, as well as the dynamics of genetic elements potentially enhancing their persistence. - In the last decades, several. - Identify and characterize the CCs recur- ring in specific processing plants, along with the role of genetic elements contributing to their adaptation to the FPEs stressors may therefore boost the assessment of the L. - Persistent strains and newly introduced strains in the FPEs by raw material have been described in relation to specific STs or CCs . - Other authors suggested that the isolation of the same L. - monocytogenes strains in- cluded in the present study. - The only exceptions were single strains for CC155 (DSS836-CS1-LmUB3PA), CC101 (C1530-O-LmUB3PA) and CC121 (CS461-S1- LmUB3PA), considered as transient and likely reintro- duced in the FPEs due to the high genetic differences. - In addition, the presence of the CC204 clone in plants A and B during overlapping sampling timeframe would support the hypothesis of an inter-plant transmission L. - Plasmids encoding genes conferring increased toler- ance under multiple stress conditions related to food and FPEs were identified in the analysed L. - Previous authors also suggested the import- ance of plasmids in the contribution to the survival of L.. - Interestingly, this plasmid was identical to a plasmid identified in 6 out of 14 strains from CC155 mainly isolated in FPEs of the plant B. - The two strains lacking this plasmid were isolated at the beginning of the sampling.. - recombination of the 2 contigs identified in plasmids from CC204, accompanied by a deletion of around 9 kbp (9 CDSs) pre- or post-transfer from CC204 to CC7.. - not persistent) are probably reintroduced by raw material in the processing plants. - On the other hand, C1530-O-LmUB3PA genome presented the same prophage repertoire of the CC101 strains, although its pairwise differences from the persisting clone exceeded 25 SNPs. - Previous studies evidenced that φcomK are genetic markers involved in the niche-adaptation and persist- ence of L. - Highly conserved φcomK were detected in all the persisting clones ana- lysed in the present study. - More- over, most of the genes significantly enriched in the spe- cific plants were located in distinct prophages, suggesting that these regions include unique genetic markers possibly contributing to niche-specific adapta- tion of persisting clones.. - A cluster of 25 loci significantly enriched in the smoked-fish plant B was found to be included in a novel. - Functional annotation studies should be performed to fully evaluate the role of these genetic elements in the long-term survival of L. - Nanodrop® Spec- trophotometer and Qbit® fluorimeter were used to assess the quantity of the extracted gDNA. - Finally, a qualitative evaluation of the assembly is then performed by com- puting various metrics with QUAST [91]. - High-quality draft genomes of 94 L.monocytogenes strains were ob- tained with ARTwork pipeline (Additional file 3 and Additional file 4), whose source code is available at https://github.com/afelten-Anses/ARtWORK. - The pangenome of the 94 L. - Genes conserved in the 99% of the isolates will represent the “core genes” while the non-core genes (i.e. - Manual refinement of gene annotations and assessment of the synteny of. - total plasmid populations in a given environment) of the 94 L. - monocytogenes strains was de novo predicted using a combination of the bio- informatics tools plasmidSPAdes [58] and MOB-suite [59]. - major potential phage), the size of the phage region and specific phage- related keywords (e.g. - monocytogenes isolates included in the present study, associated metadata and sequence accessions.. - Overview of the genomes, CC, and quality parameters of de novo assembly and read mapping.. - List of genes enriched in the originating plant.. - NR participated in the design of the study and bioinformatics analyses and assisted in the drafting of the manuscript. - MYM and AB participated in the coordination of the study and edited the manuscript. - GMB participated in the design of the study and strains selection and subtyping. - The funding body played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - All the short pair-end reads of the 94 Listeria monocytogenes included in this study have been submitted to the European Nucleotide Archive (http://. - Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU. - Listeria monocytogenes lineages:. - Comparative genomics of the Listeria monocytogenes ST204 subgroup. - Stress survival islet 2, predominantly present in Listeria monocytogenes strains of sequence Type 121, is involved in the alkaline and oxidative stress responses. - New weapons to fight old enemies: novel strategies for the (bio) control of bacterial biofilms in the food industry. - Potential impact of the resistance to quaternary ammonium disinfectants on the persistence of Listeria monocytogenes in food processing environments. - Comparative analysis of plasmids in the genus Listeria. - Heavy metal resistance determinants of the foodborne pathogen Listeria monocytogenes. - Evolutionary dynamics of the accessory genome of Listeria monocytogenes.. - PHASTER: a better, faster version of the PHAST phage search tool. - Molecular studies on the ecology of Listeria monocytogenes in the smoked fish processing industry. - Processing-dependent and clonal contamination patterns of Listeria monocytogenes in the cured ham food chain revealed by genetic analysis.. - Evaluation of the international reference methods NF EN ISO 11290-1 and 11290-2 and an in-house method for the isolation of Listeria monocytogenes from retail seafood products in France
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