College of Agriculture & Natural Resources

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The collections in this community comprise faculty research works, as well as graduate theses and dissertations.

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    FOOD SAFETY IN THE ERA OF NEXT-GENERATION SEQUENCING: GENOMIC CHARACTERIZATION OF SHIGA TOXIN-PRODUCING ESCHERICHIA COLI AND METAGENOMIC SURVEILLANCE OF IRRIGATION SURFACE WATER
    (2023) Huang, Xinyang; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    In this study, we first utilized high-throughput next-generation sequencing (NGS) and bioinformatic analyses to characterize potential public health threats posed by non-top-7 Shiga toxin-producing Escherichia coli (STEC). NGS allowed us to detect virulence (n = 46) and antimicrobial resistance (AMR) (n = 27) factors within the genomes of the STEC strains, to make genome-wide comparisons with published human clinical isolates, and to characterize three novel O-antigen gene clusters. We found that the distribution of 33 virulence genes and 15 AMR determinants exhibited significant differences among serotypes (P < 0.05), and that 47 strains were genetically related to human clinical strains inferred from a pan-genome phylogenetic tree. We secondly developed a web tool, PhyloPlus, that allowed users to generate customized bacterial and archaeal phylogenies, which can be incorporated into their own microbial community studies. We also utilized two public datasets (human microbiome, n = 60; fermented food metagenomes, n = 62) to illustrate how application of phylogeny improved our analyses. We showed that the integration of phylogenies introduced alternative phylogeny-based diversity metrics and allowed more conservative null model constructions, thereby reducing potential inflation of type I errors. Finally, we employed deep metagenomic shotgun sequencing, and our developed web tool, to investigate on a collection of 404 surface water samples collected from four regions in Latin America. We reported the high detection rates of pathogenic and contaminant bacteria in these samples, including Salmonella (29.21%), Listeria (6.19%), and E. coli (35.64%), necessitating the monitoring and proper treatment on these surface waters. We also described the regional differences in terms of sample taxonomic composition and the resistome, and further presented key factors that drove the separation patterns for each sampling region. We utilized recent metagenomic assembly and binning algorithms to report the construction of 1,461 de-replicated metagenome-assembled genomes (MAGs) that were of at least medium quality. The incorporation of the MAGs into the taxonomic classifier Kraken2’s database led to a 12.85% increase in classifiable sequence reads. Additionally, we conducted network analysis on AMR genes and the genus-level taxonomy, based on assembled contigs, to provide information to better understand the dynamics of the transferring of AMR genes.
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    Isolation and characterization of antimicrobial resistant Staphylococcus aureus in retail ground meats
    (2010) Li, Yi; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Staphylococcus aureus is commonly present in humans and animals. It can cause a variety of suppurative infections, food intoxication and toxic shock syndrome. Antimicrobial resistant S. aureus, especially methicillin-resistant S. aureus (MRSA), have emerged and are a major public health concern. There is an increasing risk of food production animals serving as a reservoir and transmitting S. aureus and MRSA in community environments. Due to the increased food safety risk posed by MRSA in addition to its multidrug resistance, we were interested in determining the prevalence of S. aureus and MRSA in retail meat and investing the multidrug resistance of the S. aureus isolates. A survey study was conducted, involving 480 retail ground meat samples (231 ground pork and 249 ground beef) collected in the Washington DC area from March 2009 to March 2010. Approximately 42.08% (n = 202) of the samples were identified as S. aureus positive and one MRSA isolate was recovered from a ground beef sample. Antimicrobial resistance testing showed 53.34% of recovered S. aureus isolates exhibited different levels of antimicrobial resistance to CLI, CHL, GEN, LEVO, CIP, SYN and TGC. The MRSA isolate was resistant to 8 of 22 antimicrobials tested. PFGE fingerprinting identified the MRSA isolate as USA300 subtype, which also carried genes of virulence factors PVL and protein A. Our findings indicated that antimicrobial resistant S. aureus strains were common in retail ground beef and port, and that MRSA could also be present in such products that could potentially serve as a reservoir.