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 Single Nucleotide Polymorphism Genotyping Analysis Shows That Vaccination Can Limit the Number and Diversity of Recombinant Progeny of Infectious Laryngotracheitis Viruses from the United States

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Carlos A. Loncoman ◽  
Carol A. Hartley ◽  
Mauricio J. C. Coppo ◽  
Glenn F. Browning ◽  
Gabriela Beltrán ◽  
...  
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Viral Replication ◽  
The United States ◽  
Snp Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotyping Assay ◽  
Infectious Laryngotracheitis

ABSTRACT Infectious laryngotracheitis (ILTV; Gallid alphaherpesvirus 1) causes mild to severe respiratory disease in poultry worldwide. Recombination in this virus under natural (field) conditions was first described in 2012 and more recently has been studied under laboratory conditions. Previous studies have revealed that natural recombination is widespread in ILTV and have also demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In the United States, natural ILTV recombination has also been detected, but not as frequently as in Australia. To better understand recombination in ILTV strains originating from the United States, we developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two virulent U.S. field strains of ILTV (63140 and 1874c5) under experimental in vivo conditions. We also tested the capacity of the Innovax-ILT vaccine (a recombinant vaccine using herpesvirus of turkeys as a vector) and the Trachivax vaccine (a conventionally attenuated chicken embryo origin vaccine) to reduce recombination. The Trachivax vaccine prevented ILTV replication, and therefore recombination, in the trachea after challenge. The Innovax-ILT vaccine allowed the challenge viruses to replicate and to recombine, but at a significantly lower rate than in an unvaccinated group of birds. Our results demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination between these ILTV strains and also show that vaccination can limit the number and diversity of recombinant progeny viruses. IMPORTANCE Recombination allows alphaherpesviruses to evolve over time and become more virulent. Historically, characterization of viral vaccines in poultry have mainly focused on limiting clinical disease, rather than limiting virus replication, but such approaches can allow field viruses to persist and evolve in vaccinated populations. In this study, we vaccinated chickens with Gallid alphaherpesvirus 1 vaccines that are commercially available in the United States and then performed coinoculations with two field strains of virus to measure the ability of the vaccines to prevent field strains from replicating and recombining. We found that vaccination reduced viral replication, recombination, and diversity compared to those in unvaccinated chickens, although the extent to which this occurred differed between vaccines. We suggest that characterization of vaccines could include studies to examine the ability of vaccines to reduce viral recombination in order to limit the rise of new virulent field strains due to recombination, especially for those vaccines that are known not to prevent viral replication following challenge.

scholarly journals Genome-Wide Association Study Identifies Single Nucleotide Polymorphism Markers Associated with Mycelial Growth (at 15, 20, and 25°C), Mefenoxam Resistance, and Mating Type in Phytophthora infestans

2020 ◽  
Vol 110 (4) ◽  
pp. 822-833 ◽  
Author(s):  
D. A. Ayala-Usma ◽  
G. Danies ◽  
K. Myers ◽  
M. O. Bond ◽  
J. A. Romero-Navarro ◽  
...  
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Phytophthora Infestans ◽  
Mating Type ◽  
Mycelial Growth ◽  
Phenotypic Diversity ◽  
The United States ◽  
Central Mexico ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Phenotypic diversity among individuals defines the potential for evolutionary selection in a species. Phytophthora infestans epidemics are generally thought to be favored by moderate to low temperatures, but temperatures in many locations worldwide are expected to rise as a result of global climate change. Thus, we investigated variation among individuals of P. infestans for relative growth at different temperatures. Isolates of P. infestans came from three collections: (i) individual genotypes recently dominant in the United States, (ii) recently collected individuals from Central Mexico, and (iii) progeny of a recent sexual recombination event in the northeastern United States. In general, these isolates had optimal mycelial growth rates at 15 or 20°C. However, two individuals from Central Mexico grew better at higher temperatures than did most others and two individuals grew relatively less at higher temperatures than did most others. The isolates were also assessed for mefenoxam sensitivity and mating type. Each collection contained individuals of diverse sensitivities to mefenoxam and individuals of the A1 and A2 mating type. We then searched for genomic regions associated with phenotypic diversity using genotyping-by-sequencing. We found one single nucleotide polymorphism (SNP) associated with variability in mycelial growth at 20°C, two associated with variability in mycelial growth at 25°C, two associated with sensitivity to mefenoxam, and one associated with mating type. Interestingly, the SNPs associated with mefenoxam sensitivity were found in a gene-sparse region, whereas the SNPs associated with growth at the two temperatures and mating type were found both at more gene-dense regions.

scholarly journals Identification of the Paternal Parent of ‘Bing’ Sweet Cherry and Confirmation of Descendants Using Single Nucleotide Polymorphism Markers

2014 ◽  
Vol 139 (2) ◽  
pp. 148-156 ◽  
Author(s):  
Umesh R. Rosyara ◽  
Audrey M. Sebolt ◽  
Cameron Peace ◽  
Amy F. Iezzoni
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Sweet Cherry ◽  
Prunus Avium ◽  
The United States ◽  
Willamette Valley ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Paternal Parent

‘Bing’ is an iconic sweet cherry (Prunus avium L.) cultivar in the United States that even after more than 130 years of cultivation remains the most highly regarded dark sweet cherry and is the standard by which new sweet cherries are judged. ‘Bing’ has been repeatedly used as a parent in North American breeding programs and is found in the lineages of several important modern cultivars. The maternal parent of ‘Bing’ is reported to be ‘Black Republican’, an old cultivar commercially grown for fruit in the Willamette Valley, OR, after ≈1860 and now is usually only grown as a pollenizer cultivar; however, the paternal parent of ‘Bing’ is unknown. The objective of this study was to deduce the paternal parent of ‘Bing’ and validate the pedigree records for the relatives of ‘Bing’ using statistical algorithms that use genomewide single nucleotide polymorphism (SNP) data. With a high probability, it was determined that the sweet cherry cultivar Napoleon, also known as Royal Ann in the Pacific northwestern United States, a large, firm, blush-type, light-fleshed, and productive cherry, is the paternal parent of ‘Bing’. This parentage deduction results in an increase in the known relatedness among U.S. cultivated sweet cherry breeding germplasm because ‘Napoleon’ is an important founder previously known to be present in the ancestry of every self-compatible sweet cherry cultivar bred to date, directly and through ‘Bing’ and its descendants.

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 Genetic Characterization of Global Cultivated Potato Clones, Including Korean Potatoes, Using Genome-Wide Single Nucleotide Polymorphism Markers

2021 ◽  
Author(s):  
Kwang Ryong Jo ◽  
Seungho Cho ◽  
Ji-Hong Cho ◽  
Hyun-Jin Park ◽  
Jang-Gyu Choi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Abiotic Stress Tolerance ◽  
The United States ◽  
Extended Haplotype Homozygosity ◽  
Biotic And Abiotic Stress ◽  
Nucleotide Polymorphism ◽  
Extended Haplotype ◽  
Single Nucleotide ◽  
Population Structure Analysis

Abstract Characterizing the genetic diversity and population structure of breeding materials is essential for breeding to improve crop plants. The potato is an important non-cereal food crop worldwide, but breeding potatoes remains challenging owing to their auto-tetraploidy and highly heterozygous genome. We evaluated the genetic structure of a 110-line Korean potato germplasm using the SolCAP 8303 single nucleotide polymorphism (SNP) Infinium array and compared it with potato clones from other countries to understand the genetic landscape of cultivated potatoes. Following the tetraploid model, we conducted population structure analysis, revealing three subpopulations represented by two Korean potato groups and one separate foreign potato group within 110 lines. When analyzing 393 global potato clones, country/region-specific genetic patterns were revealed. The Korean potato clones exhibited higher heterozygosity than those from Japan, the United States, and other potato landraces. We also employed integrated extended haplotype homozygosity (iHS) and cross-population extended haplotype homozygosity (XP-EHH) to identify selection signatures spanning candidate genes associated with biotic and abiotic stress tolerance. Based on the informativeness of SNPs for dosage genotyping calls, 10 highly informative SNPs discriminating all 393 potatoes were identified. Our results could help understanding a potato breeding history that reflects regional adaptations and distinct market demands.

scholarly journals Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States

2013 ◽  
Vol 21 (2) ◽  
pp. 119-125 ◽  
Author(s):  
L. C. Pawloski ◽  
A. M. Queenan ◽  
P. K. Cassiday ◽  
A. S. Lynch ◽  
M. J. Harrison ◽  
...  
Keyword(s):  
United States ◽  
Bordetella Pertussis ◽  
Stop Codon ◽  
The United States ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Content Type ◽  
Routine Surveillance ◽  
Nucleotide Insertion ◽  
Positive Isolate

ABSTRACTPertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s.Bordetella pertussisisolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting thatB. pertussisis losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting andprnsequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481in theprngene (prnIS481positive). The firstprnIS481-positive isolate was found in 1994, and the nextprnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in theprngene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found inprn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficientB. pertussisisolates throughout the United States.

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