scholarly journals Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species

2004 ◽  
Vol 32 (8) ◽  
pp. 2386-2395 ◽  
Author(s):  
K. E. Nelson
Keyword(s):  
Listeria Monocytogenes ◽  
Core Genome ◽  
Whole Genome ◽  
The Core ◽  
Food Borne ◽  
Serotype 4B ◽  
Genome Comparisons

scholarly journals Growth of Listeria monocytogenes within a Caramel-Coated Apple Microenvironment

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Kathleen A. Glass ◽  
Max C. Golden ◽  
Brandon J. Wanless ◽  
Wendy Bedale ◽  
Charles Czuprynski
Keyword(s):  
Listeria Monocytogenes ◽  
Water Activity ◽  
Room Temperature ◽  
Slow Growth ◽  
Free Water ◽  
Storage Conditions ◽  
Pathogenic Bacterium ◽  
Content Type ◽  
The Core ◽  
Serotype 4B

ABSTRACT A 2014 multistate listeriosis outbreak was linked to consumption of caramel-coated apples, an unexpected and previously unreported vehicle for Listeria monocytogenes. This outbreak was unanticipated because both the pH of apples (<4.0) and the water activity of the caramel coating (<0.80) are too low to support Listeria growth. In this study, Granny Smith apples were inoculated with approximately 4 log10 CFU of L. monocytogenes (a cocktail of serotype 4b strains associated with the outbreak) on each apple's skin, stem, and calyx. Half of the apples had sticks inserted into the core, while the remaining apples were left intact. Apples were dipped into hot caramel and stored at either 7°C or 25°C for up to 11 or 28 days, respectively. Data revealed that apples with inserted sticks supported significantly more L. monocytogenes growth than apples without sticks under both storage conditions. Within 3 days at 25°C, L. monocytogenes populations increased >3 log10 in apples with sticks, whereas only a 1-log10 increase was observed even after 1 week for caramel-coated apples without sticks. When stored at 7°C, apples with sticks exhibited an approximately 1.5-log10 increase in L. monocytogenes levels at 28 days, whereas no growth was observed in apples without sticks. We infer that insertion of a stick into the apple accelerates the transfer of juice from the interior of the apple to its surface, creating a microenvironment at the apple-caramel interface where L. monocytogenes can rapidly grow to levels sufficient to cause disease when stored at room temperature. IMPORTANCE Neither caramel nor apples are a food where the pathogenic bacterium Listeria monocytogenes should grow, as caramel does not contain enough free water and apples are too acidic. Caramel-coated apples, however, were recently linked to a deadly outbreak of listeriosis. We hypothesized that inserting a stick into the apple releases juice to the interface between the apple and caramel, providing a more hospitable environment than either component alone. To test this hypothesis, apples were inoculated with L. monocytogenes prior to caramel dipping. Some apples had sticks inserted into them before dipping, while others did not. No growth of L. monocytogenes occurred on refrigerated caramel apples without sticks, whereas slow growth was observed on refrigerated caramel apples with sticks. In contrast, significant pathogen growth was observed within 3 days at room temperature on caramel apples with sticks inserted. Food producers should consider interfaces between components within foods as potential niches for pathogen growth.

scholarly journals Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

2015 ◽  
Vol 81 (17) ◽  
pp. 6024-6037 ◽  
Author(s):  
Matthew J. Stasiewicz ◽  
Haley F. Oliver ◽  
Martin Wiedmann ◽  
Henk C. den Bakker
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Content Type ◽  
Food Borne ◽  
Clonal Spread

ABSTRACTWhile the food-borne pathogenListeria monocytogenescan persist in food associated environments, there are no whole-genome sequence (WGS) based methods to differentiate persistent from sporadic strains. Whole-genome sequencing of 188 isolates from a longitudinal study ofL. monocytogenesin retail delis was used to (i) apply single-nucleotide polymorphism (SNP)-based phylogenetics for subtyping ofL. monocytogenes, (ii) use SNP counts to differentiate persistent from repeatedly reintroduced strains, and (iii) identify genetic determinants ofL. monocytogenespersistence. WGS analysis revealed three prophage regions that explained differences between three pairs of phylogenetically similar populations with pulsed-field gel electrophoresis types that differed by ≤3 bands. WGS-SNP-based phylogenetics found that putatively persistentL. monocytogenesrepresent SNP patterns (i) unique to a single retail deli, supporting persistence within the deli (11 clades), (ii) unique to a single state, supporting clonal spread within a state (7 clades), or (iii) spanning multiple states (5 clades). Isolates that formed one of 11 deli-specific clades differed by a median of 10 SNPs or fewer. Isolates from 12 putative persistence events had significantly fewer SNPs (median, 2 to 22 SNPs) than between isolates of the same subtype from other delis (median up to 77 SNPs), supporting persistence of the strain. In 13 events, nearly indistinguishable isolates (0 to 1 SNP) were found across multiple delis. No individual genes were enriched among persistent isolates compared to sporadic isolates. Our data show that WGS analysis improves food-borne pathogen subtyping and identification of persistent bacterial pathogens in food associated environments.

scholarly journals Conservation of Genomic Localization and Sequence Content of Sau3AI-Like Restriction-Modification Gene Cassettes among Listeria monocytogenes Epidemic Clone I and Selected Strains of Serotype 1/2a

2010 ◽  
Vol 76 (16) ◽  
pp. 5577-5584 ◽  
Author(s):  
Suleyman Yildirim ◽  
Driss Elhanafi ◽  
Wen Lin ◽  
Anthony D. Hitchins ◽  
Robin M. Siletzky ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Gene Cassette ◽  
Conclusive Evidence ◽  
Gene Encoding ◽  
Epidemic Clone ◽  
Food Borne ◽  
Serotype 1 ◽  
Serotype 4B ◽  
Clonal Population Structure ◽  
Restriction Modification

ABSTRACTListeria monocytogenesis a food-borne pathogen with a clonal population structure and apparently limited gene flow between strains of different lineages. Strains of epidemic clone I (ECI) have been responsible for numerous outbreaks and invariably have DNA that is resistant to digestion by Sau3AI, suggesting methylation of cytosine at GATC sites. A putative restriction-modification (RM) gene cassette has been identified in the genome of the ECI strain F2365 and all other tested ECI strains but is absent from other strains of the same serotype (4b). Homologous RM cassettes have not been reported amongL. monocytogenesisolates of other serotypes. Furthermore, conclusive evidence for the involvement of this RM cassette in the Sau3AI resistance phenotype of ECI strains has been lacking. In this study, we describe a highly conserved RM cassette in certain strains of serotypes 1/2a and 4a that have Sau3AI-resistant DNA. In these strains the RM cassette was in the same genomic location as in the ECI reference strain F2365. The cassette included a gene encoding a putative recombinase, suggesting insertion via site-specific recombination. Deletion of the RM cassette in the ECI strain F2365 and the serotype 1/2a strain A7 rendered the DNA of both strains susceptible to Sau3AI digestion, providing conclusive evidence that the cassette includes a gene required for methylation of cytosine at GATC sites in both strains. The findings suggest that, in addition to its presence in ECI strains, this RM cassette and the accompanying genomic DNA methylation is also encountered among selected strains of other lineages.

scholarly journals Genome Sequence of Listeria monocytogenes Strain F4244, a 4b Serotype

2017 ◽  
Vol 5 (49) ◽  
Author(s):  
Taylor W. Bailey ◽  
Naila C. do Nascimento ◽  
Arun K. Bhunia
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Illumina Sequencing ◽  
Foodborne Pathogen ◽  
Whole Genome ◽  
Content Type ◽  
Serotype 1 ◽  
Serotype 4B

ABSTRACT Listeria monocytogenes is an opportunistic invasive foodborne pathogen. Here, we performed whole-genome sequencing of L. monocytogenes strain F4244 (serotype 4b) using Illumina sequencing. The sequence showed 94.5% identity with strain F2365, serotype 4b, and 90.6% with EGD-e, serotype 1/2a.

scholarly journals CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

2020 ◽  
Author(s):  
Connor D Harris ◽  
Ellis L Torrance ◽  
Kasie Raymann ◽  
Louis-Marie Bobay
Keyword(s):  
Core Genome ◽  
Genomic Data ◽  
Data Sets ◽  
The Core ◽  
Genomic Analyses ◽  
Massive Accumulation ◽  
Genome Comparisons

Abstract The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

scholarly journals Comparative Proteomic Analysis of Listeria monocytogenes Strains F2365 and EGD

2008 ◽  
Vol 75 (2) ◽  
pp. 366-373 ◽  
Author(s):  
Janet R. Donaldson ◽  
Bindu Nanduri ◽  
Shane C. Burgess ◽  
Mark L. Lawrence
Keyword(s):  
Listeria Monocytogenes ◽  
Protein Identification ◽  
Altered Expression ◽  
Genetic Lineages ◽  
Multidimensional Protein Identification Technology ◽  
Food Borne ◽  
Flagellar Biosynthesis ◽  
Serotype 1 ◽  
Serotype 4B ◽  
Biological Differences

ABSTRACT Listeria monocytogenes is a gram-positive, food-borne pathogen that causes disease in both humans and animals. There are three major genetic lineages of L. monocytogenes and 13 serovars. To further our understanding of the differences that exist between different genetic lineages/serovars of L. monocytogenes, we analyzed the global protein expression of the serotype 1/2a strain EGD and the serotype 4b strain F2365 during early-stationary-phase growth at 37°C. Using multidimensional protein identification technology with electrospray ionization tandem mass spectrometry, we identified 1,754 proteins from EGD and 1,427 proteins from F2365, of which 1,077 were common to both. Analysis of proteins that had significantly altered expression between strains revealed potential biological differences between these two L. monocytogenes strains. In particular, the strains differed in expression of proteins involved in cell wall physiology and flagellar biosynthesis, as well as DNA repair proteins and stress response proteins.

scholarly journals DNA Probes for Unambiguous Identification of Listeria monocytogenes Epidemic Clone II Strains

2010 ◽  
Vol 76 (9) ◽  
pp. 3061-3068 ◽  
Author(s):  
Ying Cheng ◽  
J.-W. Kim ◽  
S. Lee ◽  
R. M. Siletzky ◽  
S. Kathariou
Keyword(s):  
United States ◽  
Listeria Monocytogenes ◽  
The United States ◽  
Dna Probes ◽  
Epidemic Clone ◽  
Clonal Group ◽  
Food Borne ◽  
Serotype 4B

ABSTRACT Listeria monocytogenes epidemic clone II (ECII) strains have been responsible for two major multistate outbreaks of food-borne listeriosis in the United States, but their prevalence and ecology remain poorly understood. In this study, we describe DNA probes that unambiguously identify this clonal group. These probes were able to differentiate ECII strains of outbreak, sporadic, or environmental origin from other L. monocytogenes strains of the same serotype (4b).

scholarly journals Whole-genome sequencing of Listeria monocytogenes serotype 4b isolated from ready-to-eat lentil salad in Algiers, Algeria

2020 ◽  
Vol 33 ◽  
pp. 100628 ◽  
Author(s):  
R. Drali ◽  
A. Deriet ◽  
B. Verhaegen ◽  
S.C.J. De Keersmaecker ◽  
N. Botteldoorn ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Serotype 4B

Phylogenomic grouping of Listeria monocytogenes

2015 ◽  
Vol 61 (9) ◽  
pp. 637-646 ◽  
Author(s):  
Swapnil Doijad ◽  
Markus Weigel ◽  
Sukhadeo Barbuddhe ◽  
Jochen Blom ◽  
Alexander Goesmann ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Epidemiological Studies ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Subsequent Evolution ◽  
Pathogenic Potential ◽  
Core Genes ◽  
Genome Typing

The precise delineation of lineages and clonal groups are a prerequisite to examine within-species genetic variations, particularly with respect to pathogenic potential. A whole-genome-based approach was used to subtype and subgroup isolates of Listeria monocytogenes. Core-genome typing was performed, employing 3 different approaches: total core genes (CG), high-scoring segment pairs (HSPs), and average nucleotide identity (ANI). Examination of 113 L. monocytogenes genomes available in-house and in public domains revealed 33 phylogenomic groups (PGs). Each PG could be differentiated into a number of genomic types (GTs), depending on the approach used: HSPs (n = 57 GTs), CG (n = 71 GTs), and ANI (n = 83 GTs). Demarcation of the PGs was concordant with the 4 known lineages and led to the identification of sublineages in the lineage groups I, II, and III. In addition, PG assignments had discriminatory power similar to multi-virulence-locus sequence typing types and clonal complexes of multilocus sequence typing. Clustering of genomically highly similar isolates from different countries, sources, and isolation dates using whole-genome-based PG suggested that dispersion of phylogenomic clones of L. monocytogenes preceded their subsequent evolution. Classification according to PG may act as a guideline for future epidemiological studies.

scholarly journals Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

2015 ◽  
Vol 53 (9) ◽  
pp. 2869-2876 ◽  
Author(s):  
Werner Ruppitsch ◽  
Ariane Pietzka ◽  
Karola Prior ◽  
Stefan Bletz ◽  
Haizpea Lasa Fernandez ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Core Genome ◽  
Target Genes ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Typing Scheme ◽  
Reference Strains

Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterizeListeria monocytogenesoutbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a newL. monocytogenestyping scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determined the breadth of theL. monocytogenespopulation based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67L. monocytogenesisolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated fiveL. monocytogenesgroups. Using all available NCBI RefSeq genomes (n= 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks.

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