scholarly journals Harnessing Whole Genome Sequence Data for Facility-Specific Signatures for Listeria monocytogenes: A Case Study With Turkey Processing Plants in the United States

2021 ◽  
Vol 5 ◽  
Author(s):  
Phillip Brown ◽  
Yi Chen ◽  
Robin Siletzky ◽  
Cameron Parsons ◽  
Lee-Ann Jaykus ◽  
...  
Keyword(s):  
United States ◽  
Listeria Monocytogenes ◽  
Food Processing ◽  
Sequence Data ◽  
Allelic Variation ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Molecular Signatures ◽  
Processing Plants

Listeria monocytogenes is a Gram-positive foodborne pathogen responsible for the severe disease listeriosis and notorious for its ability to persist in food processing plants, leading to contamination of processed, ready-to-eat foods. L. monocytogenes persistence in various food processing environments (FPEs) has been extensively investigated by various subtyping tools, with increasing use of whole genome sequencing (WGS). However, major knowledge gaps remain. There is a need for facility-specific molecular signatures not only for adequate attribution of L. monocytogenes to a specific FPE but also for improved understanding of the ecology and evolution of L. monocytogenes in the food processing ecosystem. Furthermore, multiple strains can be recovered from a single FPE sample, but their diversity can be underestimated with common molecular subtyping tools. In this study we investigated a panel of 54 L. monocytogenes strains from four turkey processing plants in the United States. A combination of WGS and phenotypic assays was employed to assess strain persistence as well as identify facility-specific molecular signatures. Comparative analysis of allelic variation across the whole genome revealed that allelic profiles have the potential to be specific to individual processing plants. Certain allelic profiles remained associated with individual plants even when closely-related strains from other sources were included in the analysis. Furthermore, for certain sequence types (STs) based on the seven-locus multilocus sequence typing scheme, presence and location of premature stop codons in inlA, inlB length, prophage sequences, and the sequence content of a genomic hotspot could serve as plant-specific signatures. Interestingly, the analysis of different isolates from the same environmental sample revealed major differences not only in serotype and ST, but even in the sequence content of strains of the same ST. This study highlights the potential for WGS data to be deployed for identification of facility-specific signatures, thus facilitating the tracking of strain movement through the food chain. Furthermore, deployment of WGS for intra-sample strain analysis allows for a more complete environmental surveillance of L. monocytogenes in food processing facilities, reducing the risk of failing to detect strains that may be clinically relevant and potentially novel.

scholarly journals Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

2016 ◽  
Vol 2 (7) ◽  
pp. e1501714 ◽  
Author(s):  
Bridgett M. vonHoldt ◽  
James A. Cahill ◽  
Zhenxin Fan ◽  
Ilan Gronau ◽  
Jacqueline Robinson ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
North American ◽  
Sequence Data ◽  
The United States ◽  
Geographic Range ◽  
Whole Genome Sequence ◽  
Gray Wolf ◽  
Whole Genome ◽  
Eastern Wolf

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.

scholarly journals Whole Genome Sequence Analysis of Phage-Resistant Listeria monocytogenes Serotype 1/2a Strains from Turkey Processing Plants

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 199
Author(s):  
Phillip Brown ◽  
Yi Chen ◽  
Cameron Parsons ◽  
Eric Brown ◽  
Martin J. Loessner ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Phage Resistance ◽  
Whole Genome ◽  
Recombinant Phage ◽  
Processing Plants ◽  
Serotype 1 ◽  
Resistant Strains

Listeria monocytogenes is a Gram-positive bacterial pathogen and the causative agent of listeriosis, a severe foodborne infection. L. monocytogenes is notorious for its ability to persist in food processing environments (FPEs) via a variety of adaptive traits. Even though traits such as cold tolerance, biofilm formation and sanitizer resistance have been extensively investigated for their roles in persistence of L. monocytogenes in FPEs, much less is known about resistance to bacteriophages. Previous studies explored phage resistance mechanisms in laboratory-created mutants but it is imperative to investigate phage resistance that is naturally exhibited in FPE-derived strains. Here, we integrated the analysis of whole genome sequence data from a panel of serotype 1/2a strains of sequence types 321 and 391 from turkey processing plants, with the determination of cell surface substituents required for phage adsorption and phage infection assays with the four wide-host-range phages A511, P100, 20422-1 and 805405-1. Using a specific set of recombinant phage protein probes, we discovered that phage-resistant strains lacked one or both of the serogroup 1/2-specific wall teichoic acid carbohydrate decorations, N-acetylglucosamine and rhamnose. Furthermore, these phage-resistant strains harbored substitutions in lmo1080, lmo1081, and lmo2550, which mediate carbohydrate decoration of the wall teichoic acids.

scholarly journals Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States

2018 ◽  
Vol 92 (16) ◽  
Author(s):  
Ian E. H. Voorhees ◽  
Benjamin D. Dalziel ◽  
Amy Glaser ◽  
Edward J. Dubovi ◽  
Pablo R. Murcia ◽  
...  
Keyword(s):  
United States ◽  
Influenza A ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Canine Influenza Virus ◽  
Emerging Virus ◽  
Avian Origin ◽  
Canine Influenza ◽  
Comprehensive Surveillance

ABSTRACT Avian-origin H3N2 canine influenza virus (CIV) transferred to dogs in Asia around 2005, becoming enzootic throughout China and South Korea before reaching the United States in early 2015. To understand the posttransfer evolution and epidemiology of this virus, particularly the cause of recent and ongoing increases in incidence in the United States, we performed an integrated analysis of whole-genome sequence data from 64 newly sequenced viruses and comprehensive surveillance data. This revealed that the circulation of H3N2 CIV within the United States is typified by recurrent epidemic burst–fade-out dynamics driven by multiple introductions of virus from Asia. Although all major viral lineages displayed similar rates of genomic sequence evolution, H3N2 CIV consistently exhibited proportionally more nonsynonymous substitutions per site than those in avian reservoir viruses, which is indicative of a large-scale change in selection pressures. Despite these genotypic differences, we found no evidence of adaptive evolution or increased viral transmission, with epidemiological models indicating a basic reproductive number, R0, of between 1 and 1.5 across nearly all U.S. outbreaks, consistent with maintained but heterogeneous circulation. We propose that CIV's mode of viral circulation may have resulted in evolutionary cul-de-sacs, in which there is little opportunity for the selection of the more transmissible H3N2 CIV phenotypes necessary to enable circulation through a general dog population characterized by widespread contact heterogeneity. CIV must therefore rely on metapopulations of high host density (such as animal shelters and kennels) within the greater dog population and reintroduction from other populations or face complete epidemic extinction. IMPORTANCE The relatively recent appearance of influenza A virus (IAV) epidemics in dogs expands our understanding of IAV host range and ecology, providing useful and relevant models for understanding critical factors involved in viral emergence. Here we integrate viral whole-genome sequence analysis and comprehensive surveillance data to examine the evolution of the emerging avian-origin H3N2 canine influenza virus (CIV), particularly the factors driving ongoing circulation and recent increases in incidence of the virus within the United States. Our results provide a detailed understanding of how H3N2 CIV achieves sustained circulation within the United States despite widespread host contact heterogeneity and recurrent epidemic fade-out. Moreover, our findings suggest that the types and intensities of selection pressures an emerging virus experiences are highly dependent on host population structure and ecology and may inhibit an emerging virus from acquiring sustained epidemic or pandemic circulation.

scholarly journals Whole-Genome Sequence of Photobacterium damselae subsp. piscicida Strain 91-197, Isolated from Hybrid Striped Bass (Morone sp.) in the United States

2017 ◽  
Vol 5 (29) ◽  
Author(s):  
Yuki Teru ◽  
Jun-ichi Hikima ◽  
Tomoya Kono ◽  
Masahiro Sakai ◽  
Tomokazu Takano ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Striped Bass ◽  
The United States ◽  
Whole Genome Sequence ◽  
Economic Damage ◽  
Whole Genome ◽  
Content Type ◽  
Photobacterium Damselae ◽  
Causative Bacterium

ABSTRACT Photobacterium damselae subsp. piscicida is a causative bacterium of fish pasteurellosis, which has caused serious economic damage to aquaculture farms worldwide. Here, the whole-genome sequence of P. damselae subsp. piscicida 91-197, isolated in the United States, suggests that this genome consists of two chromosomes and two plasmids.

Listeria Prevalence and Listeria monocytogenes Serovar Diversity at Cull Cow and Bull Processing Plants in the United States†

2007 ◽  
Vol 70 (11) ◽  
pp. 2578-2582 ◽  
Author(s):  
MICHAEL N. GUERINI ◽  
DAYNA M. BRICHTA-HARHAY ◽  
STEVEN D. SHACKELFORD ◽  
TERRANCE M. ARTHUR ◽  
JOSEPH M. BOSILEVAC ◽  
...  
Keyword(s):  
United States ◽  
Listeria Monocytogenes ◽  
Causative Agent ◽  
Warm Season ◽  
The United States ◽  
Prevalence Data ◽  
Beef Processing ◽  
Processing Plants ◽  
Many Sources ◽  
Cull Cow

Listeria monocytogenes, the causative agent of epidemic and sporadic listeriosis, is routinely isolated from many sources, including cattle, yet information on the prevalence of Listeria in beef processing plants in the United States is minimal. From July 2005 through April 2006, four commercial cow and bull processing plants were sampled in the United States to determine the prevalence of Listeria and the serovar diversity of L. monocytogenes. Samples were collected during the summer, fall, winter, and spring. Listeria prevalence on hides was consistently higher during cooler weather (28 to 92% of samples) than during warmer weather (6 and 77% of samples). The Listeria prevalence data collected from preevisceration carcass ranged from undetectable in some warm season samples to as high as 71% during cooler weather. Listeria on postintervention carcasses in the chill cooler was normally undetectable, with the exception of summer and spring samples from one plant where >19% of the carcasses were positive for Listeria. On hides, L. monocytogenes serovar 1/2a was the predominant serovar observed, with serovars 1/2b and 4b present 2.5 times less often and serovar 1/2c not detected on any hides sampled. L. monocytogenes serovars 1/2a, 1/2c, and 4b were found on postintervention carcasses. This prevalence study demonstrates that Listeria species are more prevalent on hides during the winter and spring and that interventions being used in cow and bull processing plants appear to be effective in reducing or eliminating Listeria contamination on carcasses.

scholarly journals Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidalSalmonella

2018 ◽  
Author(s):  
Marcus Nguyen ◽  
S. Wesley Long ◽  
Patrick F. McDermott ◽  
Randall J. Olsen ◽  
Robert Olson ◽  
...  
Keyword(s):  
United States ◽  
Machine Learning ◽  
Prediction Models ◽  
The United States ◽  
Clinical Diagnostics ◽  
Gene Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Minimum Inhibitory Concentrations ◽  
Antimicrobial Resistance Gene

NontyphoidalSalmonellaspecies are the leading bacterial cause of food-borne disease in the United States. Whole genome sequences and paired antimicrobial susceptibility data are available forSalmonellastrains because of surveillance efforts from public health agencies. In this study, a collection of 5,278 nontyphoidalSalmonellagenomes, collected over 15 years in the United States, were used to generate XGBoost-based machine learning models for predicting minimum inhibitory concentrations (MICs) for 15 antibiotics. The MIC prediction models have average accuracies between 95-96% within ± 1 two-fold dilution factor and can predict MICs with noa prioriinformation about the underlying gene content or resistance phenotypes of the strains. By selecting diverse genomes for training sets, we show that highly accurate MIC prediction models can be generated with fewer than 500 genomes. We also show that our approach for predicting MICs is stable over time despite annual fluctuations in antimicrobial resistance gene content in the sampled genomes. Finally, using feature selection, we explore the important genomic regions identified by the models for predicting MICs. To date, this is one of the largest MIC modeling studies to be published. Our strategy for developing whole genome sequence-based models for surveillance and clinical diagnostics can be readily applied to other important human pathogens.

PRECOOKED FROZEN FOODS AND THE NEW HANDLING CODE1

1960 ◽  
Vol 23 (2) ◽  
pp. 54-58
Author(s):  
A. H. Robertson
Keyword(s):  
United States ◽  
Food Quality ◽  
Food Processing ◽  
The United States ◽  
Frozen Foods ◽  
Public Servants ◽  
Frozen Food ◽  
Early Use ◽  
Processing Plants ◽  
High Level

The origin of and membership in the Association of Food and Drug Officials of the United States is described. The formation in 1956 and the objectives of the Joint Committee on Frozen Foods in the above Association with representatives of the National Association of Frozen Food Packers is explained. The Committee was directed to prepare a model processing and handling code for uniform guidance of both industry and public servants. Industry has surveyed operations, including bacterial determinations on products at different stages of processing in several precooked frozen food processing plants. Any product consisting in part of meat, poultry, gravy, sauce or stuffing is readily subject initially to plant mishandling and should be processed with minimal delay. Sanitarians are urged to be practical, understanding, cautious and conservative when using the new tools in the recommended code; nevertheless, industry's familiarity with and early use of it will do much to maintain frozen food quality at a high level.

scholarly journals Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Sopio Chochua ◽  
Ben J. Metcalf ◽  
Zhongya Li ◽  
Joy Rivers ◽  
Saundra Mathis ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
The United States ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Group A Streptococci ◽  
Phylogenetic Clustering ◽  
Streptolysin O ◽  
Group A

ABSTRACTGroup A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing. Predictions were made for genotype, GAS carbohydrate, antimicrobial resistance, surface proteins (M family, fibronectin binding, T, R28), secreted virulence proteins (Sda1, Sic, exotoxins), hyaluronate capsule, and an upregulatedngaoperon (encodes NADase and streptolysin O) promoter (Pnga3). Sixty-four M protein gene (emm) types were identified among 69 clonal complexes (CCs), including one CC ofStreptococcus dysgalactiaesubsp.equisimilis.emmtypes predicted the presence or absence of activesofdeterminants and were segregated intosof-positive orsof-negative genetic complexes. Only one “emmtype switch” between strains was apparent.sof-negative strains showed a propensity to cause infections in the first quarter of the year, whilesof+strain infections were more likely in summer. Of 1,454 isolates, 808 (55.6%) were Pnga3 positive and 637 (78.9%) were accounted for by typesemm1,emm89, andemm12. Theoretical coverage of a 30-valent M vaccine combined with an M-related protein (Mrp) vaccine encompassed 98% of the isolates. WGS data predicted that 15.3, 13.8, 12.7, and 0.6% of the isolates were nonsusceptible to tetracycline, erythromycin plus clindamycin, erythromycin, and fluoroquinolones, respectively, with only 19 discordant phenotypic results. Close phylogenetic clustering ofemm59isolates was consistent with recent regional emergence. This study revealed strain traits informative for GAS disease incidence tracking, outbreak detection, vaccine strategy, and antimicrobial therapy.IMPORTANCEThe current population-based WGS data from GAS strains causing invasive disease in the United States provide insights important for prevention and control strategies. Strain distribution data support recently proposed multivalent M type-specific and conserved M-like protein vaccine formulations that could potentially protect against nearly all invasive U.S. strains. The three most prevalent clonal complexes share key polymorphisms in thengaoperon encoding two secreted virulence factors (NADase and streptolysin O) that have been previously associated with high strain virulence and transmissibility. We find thatStreptococcus pyogenesis phylogenetically subdivided into loosely defined multilocus sequence type-based clusters consisting of solelysof-negative orsof-positive strains; withsof-negative strains demonstrating differential seasonal preference for infection, consistent with the recently demonstrated differential seasonal preference based on phylogenetic clustering of full-length M proteins. This might relate to the differences in GAS strain compositions found in different geographic settings and could further inform prevention strategies.

scholarly journals Outbreaks of Adenovirus-associated Respiratory Illness on 5 College Campuses in the United States, 2018–2019

2020 ◽  
Author(s):  
Stephanie A Kujawski ◽  
Xiaoyan Lu ◽  
Eileen Schneider ◽  
David Blythe ◽  
Sameh Boktor ◽  
...  
Keyword(s):  
United States ◽  
Social History ◽  
Military Training ◽  
Respiratory Illness ◽  
The United States ◽  
College Campuses ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Acute Respiratory Illness ◽  
Symptom Presentation

Abstract Background Human adenoviruses (HAdVs) are commonly associated with acute respiratory illness. HAdV outbreaks are well documented in congregate military training settings, but less is known about outbreaks on college campuses. During fall 2018 and spring 2019, 5 United States (US) colleges reported increases in HAdV-associated respiratory illness. Investigations were performed to better understand HAdV epidemiology in this setting. Methods A case was defined as a student at one of the 5 colleges, with acute respiratory illness and laboratory-confirmed HAdV infection during October 2018–December 2018 or March–May 2019. Available respiratory specimens were typed by HAdV type-specific real-time polymerase chain reaction assays, and for a subset, whole genome sequencing was performed. We reviewed available medical records and cases were invited to complete a questionnaire, which included questions on symptom presentation, social history, and absenteeism. Results We identified 168 HAdV cases. Median age was 19 (range, 17–22) years and 102 cases (61%) were male. Eleven cases were hospitalized, 10 with pneumonia; 2 cases died. Among questionnaire respondents, 80% (75/94) missed ≥ 1 day of class because of their illness. Among those with a type identified (79%), HAdV types 4 and 7 were equally detected, with frequency of each varying by site. Genome types 4a1 and 7d were identified, respectively, by whole genome sequence analysis. Conclusions HAdV respiratory illness was associated with substantial morbidity and missed class time among young, generally healthy adults on 5 US college campuses. HAdVs should be considered a cause of respiratory illness outbreaks in congregate settings such as college campuses.

scholarly journals Prevalence of Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella in Two Geographically Distant Commercial Beef Processing Plants in the United States†

2004 ◽  
Vol 67 (2) ◽  
pp. 295-302 ◽  
Author(s):  
MILDRED RIVERA-BETANCOURT ◽  
STEVEN D. SHACKELFORD ◽  
TERRANCE M. ARTHUR ◽  
KURT E. WESTMORELAND ◽  
GINA BELLINGER ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Listeria Monocytogenes ◽  
The United States ◽  
Conveyor Belt ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Beef Processing ◽  
Processing Plants ◽  
Northern United States

For two large beef processing plants, one located in the southern United States (plant A) and one located in the northern United States (plant B), prevalence of Escherichia coli O157:H7, Listeria spp., Listeria monocytogenes, and Salmonella was determined for hide, carcass, and facility environmental samples over the course of 5 months. The prevalence of E. coli O157: H7 (68.1 versus 55.9%) and Salmonella (91.8 versus 50.3%) was higher (P < 0.05), and the prevalence of Listeria spp. (37.7 versus 75.5%) and L. monocytogenes (0.8 versus 18.7%) was lower (P < 0.05) for the hides of cattle slaughtered at plant A versus plant B. Similarly, the prevalence of Salmonella (52.0 versus 25.3%) was higher (P < 0.05) and the prevalence of Listeria spp. (12.0 versus 40.0%) and L. monocytogenes (1.3 versus 14.7%) was lower (P < 0.05) for the fence panels of the holding pens of plant A versus plant B. The prevalence of E. coli O157:H7 (3.1 versus 10.9%), Listeria spp. (4.5 versus 14.6%), and L. monocytogenes (0.0 versus 1.1%) was lower (P < 0.05) for preevisceration carcasses sampled at plant A versus plant B. Salmonella (both plants), Listeria spp. (plant B), and L. monocytogenes (plant B) were detected on fabrication floor conveyor belts (product contact surfaces) late during the production day. For plant B, 21 of 148 (14.2%) late-operational fabrication floor conveyor belt samples were L. monocytogenes positive. For plant B, E. coli O157:H7 and L. monocytogenes were detected in preoperational fabrication floor conveyor belt samples. Overall results suggest that there are regional differences in the prevalence of pathogens on the hides of cattle presented for harvest at commercial beef processing plants. While hide data may reflect the regional prevalence, the carcass data is indicative of differences in harvest practices and procedures in these plants.

Sign in / Sign up

Export Citation Format

Share Document