Analysis of Additional Virulence Genes and Virulence Gene Regions in Listeria monocytogenes Confirms the Epidemiologic Relevance of Multi-Virulence-Locus Sequence Typing

2008 ◽  
Vol 71 (12) ◽  
pp. 2559-2566 ◽  
Author(s):  
SARA LOMONACO ◽  
YI CHEN ◽  
STEPHEN J. KNABEL
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Virulence Genes ◽  
Virulence Gene ◽  
The Other ◽  
Evolutionary Divergence ◽  
Gene Sequences ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Molecular Subtyping

Previous molecular subtyping studies have defined four epidemic clones (ECs) of Listeria monocytogenes (ECI, ECII, ECIII, and ECIV). Partial sequences of eight virulence genes were previously shown to be identical within individual ECs of L. monocytogenes. The present study was conducted to determine if the sequences of other virulence genes and virulence gene regions are also conserved within these ECs. Six additional virulence genes—bsh, hly, inlJ, lplA1, pgdA, and srtA—and three additional virulence gene regions of actA, inlA, and inlB were selected based on their role in L. monocytogenes virulence, and intragenic regions of each gene were sequenced. Sequencing was performed on a diverse set of 44 to 48 L. monocytogenes strains. Results demonstrated that the sequenced regions of the nine virulence genes were identical within each of the ECs, and 257 new single nucleotide polymorphism (SNPs) were identified. ECIII (lineage II) was easily distinguishable from the other ECs, as 238 SNPs were observed in ECIII due to its significant evolutionary divergence from lineage I. With regard to the other ECs, there were 5 SNPs that represented an informative set, since these SNPs were able to differentiate specific ECs from all other unrelated strains used in this study. This study confirms our previous finding that virulence gene sequences are highly conserved within individual ECs and contain stable SNPs that can be used to very accurately differentiate ECs of L. monocytogenes from each other and from other diverse strains.

scholarly journals Novel Multiplex Single Nucleotide Polymorphism-Based Method for Identifying Epidemic Clones of Listeria monocytogenes

2011 ◽  
Vol 77 (17) ◽  
pp. 6290-6294 ◽  
Author(s):  
Sara Lomonaco ◽  
Stephen J. Knabel ◽  
Alessandra Dalmasso ◽  
Tiziana Civera ◽  
Maria Teresa Bottero
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
High Throughput Screening ◽  
Virulence Genes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACTA novel primer extension-based, multiplex minisequencing assay targeting six highly informative single nucleotide polymorphisms (SNPs) in four virulence genes correctly identified and differentiated all four epidemic clones (ECs) ofListeria monocytogenesand 9 other strains initially misclassified as non-ECs. This assay allows rapid, accurate, and high-throughput screening for all known ECs ofL. monocytogenes.

scholarly journals Revelation by Single-Nucleotide Polymorphism Genotyping That Mutations Leading to a Premature Stop Codon in inlA Are Common among Listeria monocytogenes Isolates from Ready-To-Eat Foods but Not Human Listeriosis Cases

2010 ◽  
Vol 76 (9) ◽  
pp. 2783-2790 ◽  
Author(s):  
A. Van Stelten ◽  
J. M. Simpson ◽  
T. J. Ward ◽  
K. K. Nightingale
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Stop Codon ◽  
Human Health Risk ◽  
Premature Stop Codon ◽  
The United States ◽  
Nucleotide Polymorphism ◽  
Pathogenic Potential ◽  
Single Nucleotide

ABSTRACT Listeria monocytogenes utilizes internalin A (InlA; encoded by inlA) to cross the intestinal barrier to establish a systemic infection. Multiple naturally occurring mutations leading to a premature stop codon (PMSC) in inlA have been reported worldwide, and these mutations are causally associated with attenuated virulence. Five inlA PMSC mutations recently discovered among isolates from France and the United States were included as additional markers in our previously described inlA single-nucleotide polymorphism (SNP) genotyping assay. This assay was used to screen >1,000 L. monocytogenes isolates from ready-to-eat (RTE) foods (n = 502) and human listeriosis cases (n = 507) for 18 inlA PMSC mutations. A significantly (P < 0.0001) greater proportion of RTE food isolates (45.0%) carried a PMSC mutation in inlA compared to human clinical isolates (5.1%). The proportion of L. monocytogenes with or without PMSC mutations in inlA was similar among isolates from different RTE food categories except for deli meats, which included a marginally higher proportion (P = 0.12) of isolates carrying a PMSC in inlA. We also analyzed the distribution of epidemic clone (EC) strains, which have been linked to the majority of listeriosis outbreaks worldwide and are overrepresented among sporadic cases in the United States. We observed a significant (P < 0.05) overrepresentation of EC strains in deli and seafood salads and a significant (P < 0.05) underrepresentation of EC strains in smoked seafood. These results provide important data to predict the human health risk of exposure to L. monocytogenes strains that differ in pathogenic potential through consumption of contaminated RTE foods.

scholarly journals Development and Implementation of a Multiplex Single-Nucleotide Polymorphism Genotyping Assay for Detection of Virulence-Attenuating Mutations in the Listeria monocytogenes Virulence-Associated Gene inlA

2008 ◽  
Vol 74 (23) ◽  
pp. 7365-7375 ◽  
Author(s):  
A. Van Stelten ◽  
K. K. Nightingale
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Snp Genotyping ◽  
Regulatory Agencies ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotyping Assay ◽  
Virulence Attenuation

ABSTRACT The virulence factor internalin A (InlA) facilitates the uptake of Listeria monocytogenes by epithelial cells that express the human isoform of E-cadherin. Previous studies identified naturally occurring premature stop codon (PMSC) mutations in inlA and demonstrated that these mutations are responsible for virulence attenuation. We assembled >1,700 L. monocytogenes isolates from diverse sources representing 90 EcoRI ribotypes. A subset of this isolate collection was selected based on ribotype frequency and characterized by a Caco-2 cell invasion assay. The sequencing of inlA genes from isolates with attenuated invasion capacities revealed three novel inlA PMSCs which had not been identified previously among U.S. isolates. Since ribotypes include isolates with and without inlA PMSCs, we developed a multiplex single-nucleotide polymorphism (SNP) genotyping assay to detect isolates with virulence-attenuating PMSC mutations in inlA. The SNP genotyping assay detects all inlA PMSC mutations that have been reported worldwide and verified in this study to date by the extension of unlabeled primers with fluorescently labeled dideoxynucleoside triphosphates. We implemented the SNP genotyping assay to characterize human clinical and food isolates representing common ribotypes associated with novel inlA PMSC mutations. PMSCs in inlA were significantly (ribotypes DUP-1039C and DUP-1045B; P < 0.001) or marginally (ribotype DUP-1062D; P = 0.11) more common among food isolates than human clinical isolates. SNP genotyping revealed a fourth novel PMSC mutation among U.S. L. monocytogenes isolates, which was observed previously among isolates from France and Portugal. This SNP genotyping assay may be implemented by regulatory agencies and the food industry to differentiate L. monocytogenes isolates carrying virulence-attenuating PMSC mutations in inlA from strains representing the most significant health risk.

scholarly journals New insight on the Xq28 association with systemic sclerosis

2013 ◽  
Vol 72 (12) ◽  
pp. 2032-2038 ◽  
Author(s):  
F David Carmona ◽  
M Carmen Cénit ◽  
Lina-Marcela Diaz-Gallo ◽  
Jasper C A Broen ◽  
Carmen P Simeón ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Systemic Sclerosis ◽  
Meta Analysis ◽  
Conditional Logistic Regression ◽  
Statistical Significance ◽  
The Other ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Conditional Logistic Regression Analysis

ObjectiveTo evaluate whether the systemic sclerosis (SSc)-associated IRAK1 non-synonymous single-nucleotide polymorphism rs1059702 is responsible for the Xq28 association with SSc or whether there are other independent signals in the nearby methyl-CpG-binding protein 2 gene (MECP2).MethodsWe analysed a total of 3065 women with SSc and 2630 unaffected controls from five independent Caucasian cohorts. Four tag single-nucleotide polymorphisms of MECP2 (rs3027935, rs17435, rs5987201 and rs5945175) and the IRAK1 variant rs1059702 were genotyped using TaqMan predesigned assays. A meta-analysis including all cohorts was performed to test the overall effect of these Xq28 polymorphisms on SSc.ResultsIRAK1 rs1059702 and MECP2 rs17435 were associated specifically with diffuse cutaneous SSc (PFDR=4.12×10−3, OR=1.27, 95% CI 1.09 to 1.47, and PFDR=5.26×10−4, OR=1.30, 95% CI 1.14 to 1.48, respectively), but conditional logistic regression analysis showed that the association of IRAK1 rs1059702 with this subtype was explained by that of MECP2 rs17435. On the other hand, IRAK1 rs1059702 was consistently associated with presence of pulmonary fibrosis (PF), because statistical significance was observed when comparing SSc patients PF+ versus controls (PFDR=0.039, OR=1.30, 95% CI 1.07 to 1.58) and SSc patients PF+ versus SSc patients PF− (p=0.025, OR=1.26, 95% CI 1.03 to 1.55).ConclusionsOur data clearly suggest the existence of two independent signals within the Xq28 region, one located in IRAK1 related to PF and another in MECP2 related to diffuse cutaneous SSc, indicating that both genes may have an impact on the clinical outcome of the disease.

scholarly journals Evaluation of F-Measure and Feature Analysis of C5.0 Implementation on Single Nucleotide Polymorphism Calling

2018 ◽  
Vol 1 (1) ◽  
pp. 1
Author(s):  
Lailan Sahrina Hasibuan ◽  
Sita Nabila ◽  
Nurul Hudachair ◽  
Muhammad Abrar Istiadi
Keyword(s):  
Single Nucleotide Polymorphism ◽  
The Other ◽  
Training Dataset ◽  
Final Decision ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rule Based ◽  
Snp Calling ◽  
Single Nucleotide Polymorphism Calling ◽  
F Measure

Data growing in molecular biology has increased rapidly since Next-Generation Sequencing (NGS) technology introduced in 2000, the latest technology used to sequence DNA with high throughput. Single Nucleotide Polymorphism (SNP) is a marker based on DNA which can be used to identify organism specifically. SNPs are usually exploited for optimizing parents selection in producing high-quality seed for plant breeding. This paper discusses SNP calling underlying NGS data of cultivated soybean (Glycine max [L]. Merr) using C5.0, an improved rule-based algorithm of C4.5. The evaluation illustrated that C5.0 is better than the other rule-based algorithm CART based on f-measure. The value of f-measure using C5.0 and CART are 0.63 and 0.58. Besides of that, C5.0 is robust for imbalanced training dataset up to 1:17 but it is suffer in large training dataset. C5.0’s performance may be increased by applying bagging or the other ensemble technique as improvement of CART by applying bagging in final decision. The other important thing is using appropriate features in representing SNP candidates. Based on information gain of C5.0, this paper recommends error probability, homopolymer left, mismatch alt and mean nearby qual as features for SNP calling.

scholarly journals Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

2015 ◽  
Vol 53 (10) ◽  
pp. 3334-3340 ◽  
Author(s):  
Angela J. Taylor ◽  
Victoria Lappi ◽  
William J. Wolfgang ◽  
Pascal Lapierre ◽  
Michael J. Palumbo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Molecular Subtyping ◽  
Foodborne Outbreaks

Salmonella entericaserovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis ofS. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmentalS. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of theS. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method forS. Enteritidis.

Association analysis of GH1 and CRP loci polymorphisms with reproductive traits in native Pulawska gilts and sows

2020 ◽  
Vol 100 (4) ◽  
pp. 650-656
Author(s):  
M. Babicz ◽  
M. Pastwa ◽  
A. Kozubska-Sobocińska ◽  
B. Danielak-Czech ◽  
E. Skrzypczak ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Single Nucleotide Polymorphism ◽  
Sexual Activity ◽  
Reproductive Traits ◽  
The Other ◽  
Nucleotide Polymorphism ◽  
C Reactive Protein ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Reactive Protein

The objective of the study was to analyse the association of growth hormone (GH1) and C-reactive protein (CRP) loci polymorphisms with reproductive traits in native Pulawska gilts and sows. In the GH1 locus, two mutations were identified: one in the second intron [single-nucleotide polymorphism (SNP) = rs340429823 in.742C>T, MspI], and one in the second exon (SNP = rs340087546 c.566G>A, HaeII). In the CRP locus, two mutations were found in exon 2 (SNP = rs340175625, NM_213844.2: c.1271A>G, BstNI; and SNP = rs80928546, NM_213844.2: c.788C>T, HinfI). Analysis of sexual activity showed that intensity of external estrus signs differed significantly (P ≤ 0.05) and was the most manifested in gilts with the CT (GH1_MspI) genotype during the second estrus. In case of the CRP gene, statistically significant differences (P ≤ 0.05) were found in terms of the duration of farrowing. The longest farrowings were reported for the GG (CRP_HinfI) and the TT (CRP_BstNI) genotypes and the shortest for the AA (CRP_HinfI) and CC (CRP_BstNI). The most numerous first litters were produced by sows with the AA genotype (CRP_HinfI), with significant differences (P ≤ 0.05) between the AA and GG genotypes. In turn, the CC homozygotes (CRP_BstNI) differed significantly (P ≤ 0.05) in terms of the number of piglets born and reared to day 21 in the second litters compared to the other genotype groups.

Listeria monocytogenes in Cooked Chicken: Detection of an Outbreak in the United Kingdom (2016 to 2017) and Analysis of L. monocytogenes from Unrelated Monitoring of Foods (2013 to 2017)

2020 ◽  
Vol 83 (12) ◽  
pp. 2041-2052 ◽  
Author(s):  
J. McLAUCHLIN ◽  
H. AIRD ◽  
C. AMAR ◽  
C. BARKER ◽  
T. DALLMAN ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Disease Risk ◽  
Communicable Disease ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Linkage ◽  
Single Nucleotide

ABSTRACT In England and Wales, Public Health England applies whole genome sequencing to cultures of Listeria monocytogenes recovered from human cases of listeriosis, foods, and food production environments. Following the routine inspection of a small retailer in February and March 2016, two unopened packs of cooked chicken produced by the same manufacturer were found to be contaminated with L. monocytogenes at levels of 340 and 20 CFU/g. A public recall of this product was issued in March 2016. Early in 2017, a less than five single-nucleotide polymorphism single-linkage cluster was detected between the L. monocytogenes isolates from the two cooked chicken products and cultures from five cases of human listeriosis in England and Scotland with onsets of illness between March 2016 and February 2017. Epidemiological data provided further supportive evidence that this cluster was an outbreak linked to a manufacturer of cooked chicken whose products were supplied to the small retailer that initiated the outbreak investigation. Unrelated to this outbreak, 34 L. monocytogenes isolates recovered from routine food monitoring of 2,007 samples of cooked chicken during 2013 to 2017 were analyzed by whole genome sequencing. Previously undetected fewer than five single-nucleotide polymorphism single-linkage clusters were identified between cultures from cooked chicken and with those from two clusters and two sporadic cases of human listeriosis that were consistent with foodborne transmission. This analysis identified linkage of L. monocytogenes clusters within specific food chains more readily than traditional manual tracing. Linking of data associated with L. monocytogenes cultures from cases of listeriosis with those from unrelated food testing is a unique source of information for communicable disease risk assessment, epidemiological studies, and disease prevention and control. This report provides further evidence that should act as a reminder of the association between cooked chicken consumption and human listeriosis. HIGHLIGHTS

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