Nguyet Kong

Nguyet Kong
University of California, Davis | UCD · Department of Population Health and Reproduction (VM)

Bachelor of Science

About

112
Publications
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Publications

Publications (112)
Article
Full-text available
Salmonella is a common food-associated bacterium that has substantial impact on worldwide human health and the global economy. This is the public release of 1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Salmonella genus.
Article
Full-text available
Background The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to e...
Technical Report
Full-text available
Next Generation Sequencing requires the input of high molecular weight genomic DNA to construct quality libraries for whole genome bacterial sequencing. Large scale sequencing projects, such as the 100K Pathogen Genome Project, require methods to rapidly assess the quantity and quality of the input DNA using high-throughput methods that are fast an...
Technical Report
Full-text available
The Agilent DNA Extraction Kit (p/n 200600) was compared to standard methods such as beadbeating and enzyme treatment for preparation of genomic DNA from the prokaryote Listeria monocytogenes. Using this extraction kit, with modifications, to lyse the bacteria and isolate high molecular weight DNA reproducibly yielded high quality DNA suitable for...
Technical Report
Full-text available
Next Generation Sequencing (NGS) requires the input of high molecular weight genomic DNA (gDNA) to construct quality libraries for large scale sequencing projects , such as the 100K Pathogen Genome Project. The assessment of DNA integrity is a critical first step in obtaining meaningful data, and intact DNA is a key element for successful library c...
Article
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic mat...
Article
Full-text available
A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic (N2-fixing) microbiota. Targeting these diazotrophs, w...
Preprint
Full-text available
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix...
Article
Full-text available
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA se...
Preprint
Full-text available
The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSC interaction with microbes at sites of tissue damage and inflammation is likely, especially in the gut, the consequences of bacterial association have yet to be elucidated. This study investigated the effect of Salmonella enteric...
Poster
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Non-jejuni Campylobacter species identification is quite challenging for a diagnostic microbiology laboratory due to suboptimal isolation protocols and lack of differentiating biochemical features. Here we applied whole genome sequencing in an outbreak investigation of a cryptic pathogen Campylobacter hyointestinalis subsp. hyointestinalis in great...
Article
Full-text available
Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Whole-genome sequencing revealed that the strain genetically encodes a novel multicomponent lantibiotic, velezensicidin.
Poster
Full-text available
Figure 1: 100K Pathogen Genome Project sample preparation workflow for multiplexed, short-read Illumina sequencing Figure 3: Detailed KAPA HTP Library Preparation protocol. The input into library construction is fragmented DNA or cDNA. Each enzymatic reaction is followed by a SPRI-bead cleanup. The "with-bead" protocol uses a single aliquot of SPRI...
Article
Full-text available
Prebiotic oligosaccharides are used to modulate enteric pathogens and reduce pathogen shedding. The interactions with prebiotics that alter Listeria monocytogenes infection are not yet clearly delineated. L. monocytogenes cellular invasion requires a concerted manipulation of host epithelial cell membrane receptors to initiate internalization and i...
Poster
Full-text available
Prebiotics and probiotics reduce and prevent GI infections by modulating the gut microbiome. Prebiotics proliferate beneficial gut bacteria while probiotics prevent the attachment and invasion of pathogens. However, the mechanisms of these intricate processes are inadequately understood that alter Salmonella infection dynamics. We hypothesized that...
Article
Full-text available
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS databas...
Poster
Full-text available
Next Generation Sequencing (NGS) is a process that can be used to construct DNAlibraries for large-scale sequencing projects. NGS utilizes the input of high molecular weight and intact genomicDNA(gDNA) to construct high-quality libraries. The assessment ofDNAintegrity is a key step in library construction. The Agilent 2200 TapeStation System with t...
Poster
Full-text available
The PacBio RS II provides for single molecular, real-time (SMRT) DNA technology to sequence genomes and detect DNA modifications. The quality control methods from gDNA input to the final library using the Agilent BioanalyzerSytem and Agilent TapeStation System were evaluated. Automated protocols of PacBio 10 kb library preparation produced librarie...
Article
Full-text available
Shigella is a major foodborne pathogen that infects humans and non-human primates and is the major cause of dysentery and reactive arthritis worldwide. This is the initial public release of 16 Shigella genome sequences from four species sequenced as part of the 100K Pathogen Genome Project.
Article
Full-text available
Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This is the release of a multidrug-resistant Campylobacter jejuni genome from an isolate that caused an abortion in a cow in northern California. This isolate is part of the 100K Pathogen Genome Project.
Article
Full-text available
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic...
Article
Full-text available
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra-and intergenomic...
Article
Full-text available
Listeria monocytogenes is a food-associated bacterium that is responsible for food-related illnesses worldwide. This is the initial public release of 306 L. monocytogenes genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in L. monocytogenes .
Article
Full-text available
Campylobacter is a food-associated bacterium and a leading cause of foodborne illness worldwide, being associated with poultry in the food supply. This is the initial public release of 202 Campylobacter genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Campylobacter genus.
Article
Full-text available
Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Da...
Article
Full-text available
Importance: Listeria monocytogenes is the causative agent of listeriosis, a disease which manifests as gastroenteritis, meningoencephalitis, and abortion. Amongst Salmonella, E. coli, Campylobacter, and Listeria-the most prevalent foodborne illnesses-infection by L. monocytogenes carries the highest mortality rate. The ability of L. monocytogenes...
Article
Full-text available
Importance: This study examined the link between public health and genomic variation of Campylobacter in relation to disease in humans, primates, and livestock. Use of large-scale whole genome sequencing enabled population level assessment to find new genes that are linked to livestock disease. With 184 Campylobacter genomes we assessed virulence...
Article
Full-text available
BACKGROUND: Helicobacter pylori, a gram-negative bacterium associated with a spectrum of benign and malignant gastric conditions, is one of the most genetically variable pathogens. Its genome encodes a large number of DNA methyltransferases targeting specific motif sequences of ∼4-15 bp. DNA base modifications epigenetically regulate gene expressio...
Article
Full-text available
Complex glycans cover the gut epithelial surface to protect the cell from the environment. Invasive pathogens must breach the glycan layer before initiating infection. While glycan degradation is crucial for infection, this process is inadequately understood. Salmonella contains 47 glycosyl hydrolases (GHs) that may degrade the glycan. We hypothesi...
Poster
Full-text available
The host gut epithelial membrane is shielded by complex glycans to protect the cell. Gastroenteritis begins when invasive pathogens bind and degrade the glycans at the epithelial barrier to gain access of host membrane. While glycan degradation is crucial for infection, this process is poorly understood. We hypothesized that Salmonella deploys its...
Technical Report
Full-text available
Next-generation whole genome sequencing of microbes demands rapid, robust, and scalable library construction workflows, capable of generating high-quality sequence data across a wide range of genome sizes, complexities and genomic GC content. In this Application Note, we describe a streamlined library preparation method that results in minimal bias...
Article
Full-text available
Vibrio parahaemolyticus is the leading cause of seafood-borne infections in the United States. We report complete genome sequences for two V. parahaemolyticus strains isolated in 2007, CDC_K4557 and FDA_R31 of clinical and oyster origin, respectively. These two sequences might assist in the investigation of differential virulence of this organism....
Technical Report
Full-text available
Automation of the PacBio 10 kb Template Preparation using the SMRTbell Template Prep kit for the sequencing of bacterial genomes on the Agilent Automated Liquid Handling Platform is described. Four bacterial genomes of differing GC content are used to prepare libraries without bias reading for next generation sequencing. The gDNA quality assessment...
Technical Report
Full-text available
A new method was developed to automate the KAPA HTP Library Preparation kit for microbial whole genome sequencing. This method uses the Agilent NGS Workstation, consisting of the NGS Bravo liquid handling platform with its accessories for heating, cooling, shaking, and magnetic bead manipulations in a 96-well format. User intervention in multistep...
Article
Full-text available
Mesenchymal stem cells (MSCs) are somatic, multipotent stromal cells with potent immunomodulatory and regenerative properties. Although MSCs have pattern recognition receptors and are modulated by Toll-like receptors (TLR) ligands, MSC-microbial interactions are poorly defined. The objectives of this study were to determine the effect of bacterial...
Article
Full-text available
Aims: Starter lactic acid bacteria in Cheddar cheese face physico-chemical stresses during manufacture and ageing that alter their abilities to survive and to interact with other bacterial populations. Nonstarter bacteria are derived from milk handling, cheese equipment and human contact during manufacture. Probiotic bacteria are added to foods fo...
Technical Report
Full-text available
Shearing of bacterial gDNA within a specific size range prior to sequencing library construction is a critical step in Next Generation Sequencing workflows. The quality control of the sheared bacterial gDNA is required in large multiplexed formats for large volume workflows, such as those used in the 100K Pathogen Genome Sequencing Project. Using t...
Technical Report
Full-text available
The initial step in Next Generation Sequencing is to construct a library from genomic DNA. To gain the optimum result, extracted DNA must be of high molecular weight with limited degradation. High-throughput sequencing projects, such as the 100K Pathogen Genome Project, require methods to rapidly assess the quantity and quality of genomic DNA extra...
Poster
Full-text available
Listeria monocytogenes is a gram positive, intracellular pathogen that infects immune-compromised populations and has ~50% mortality rate. It is responsible for numerous food-borne outbreaks worldwide each year and commonly persists in the environment. While L.monocytogenes is the only pathogenic species in this genus it is increasingly important t...
Poster
Full-text available
Salmonella enterica spp. enterica sv Typhimurium infection accounts for 1.3 billion foodborne disease cases worldwide. Gastroenteritis is initiated at the epithelial barrier where Salmonella binds receptors to initiate infection. As a protective mechanism, the host membrane is covered with complex glycans including mucin (glycoproteins) and the gly...
Poster
Full-text available
Salmonella is a food borne illness resulting in gastroenteritis in adults and children with increased mortality rates in newborns and children primarily, but also cause disease in adults. Historically, consumption of human milk promotes the growth of probiotics, sometimes suppressing gastrointestinal colonization by pathogens including Salmonella....
Article
Full-text available
Human milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk component...
Article
Despite the importance of neuraminidase (NA) activity in effective infection by influenza A viruses, limited information exists about the differences of substrate preferences of viral neuraminidases from different hosts or from different strains. Using a high-throughput screening format and a library of twenty α2-3- or α2-6-linked para-nitrophenol-...
Article
Oropharyngeal and cloacal swabs were collected from poultry sold in two live bird market (LBM) systems to estimate the prevalence of low pathogenicity avian influenza virus (LPAIV) shedding during the summer and fall of 2005. Random sampling was conducted in three LBMs in Minnesota where 50 birds were sampled twice weekly for 4 wk, and in three LBM...
Article
Full-text available
Avian influenza viruses (AIVs) pose a significant threat to public health, and viral subtypes circulating in natural avian reservoirs can contribute to the emergence of pathogenic influenza viruses in humans. We investigated the prevalence and distribution of AIVs in 8826 migratory and resident wild birds in North America along the Pacific flyway,...
Article
A duck-origin avian influenza virus (AIV) was used to study viral adaptation and transmission patterns in chickens (Gallus gallus domesticus) and Pekin ducks (Anas platyrhynchos domesticus). Inoculated birds were housed with naïve birds of the same species and all birds were monitored for infection. The inoculating duck virus was transmitted effect...
Article
Full-text available
The mitogen-activated protein kinase (MAPK) family is responsible for important signalling pathways which regulate cell activation, differentiation, apoptosis and immune responses. Studies have shown that influenza virus infection activates MAPK family members in mammals. While the extracellular signal-regulated kinase (ERK)1/2 is important for vir...