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Dr. Meng Laboratory Research

Research Summaries

    1. Genomic Analyses of Multidrug-Resistant Salmonella Indiana, Typhimurium, and Enteritidis Isolates Using Minion and Miseq Sequencing Technologies
  • We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n=11), Typhimurium (n=8), and Enteritidis (n=6) using both MinION long-read and MiSeq short-read sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance, virulence potential, whole-genome phylogeny, and pan-genome. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.

    2. Benchmarking Long-Read Assemblers for Genomic Analyses of Bacterial Pathogens Using Oxford Nanopore Sequencing
  • Both simulated and real Oxford Nanopore long reads of bacterial pathogens spanning a wide range of genome sizes and GC contents were assembled using different assemblers, including Canu, Flye, Miniasm/Racon, Raven, Redbean, and Shasta. The assemblies were compared in terms of genome completeness and accuracy, antimicrobial resistance, virulence potential, phylogeny, and pan genome. Our study demonstrates that the overall best assembler was Raven, followed by Miniasm/Racon, although it does not indicate circularity.

    3. Benchmarking Hybrid Assembly Approaches for Genomic Analyses of Bacterial Pathogens Using Illumina and Oxford Nanopore Sequencing
  • We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing in terms of genome completeness/accuracy, antimicrobial resistance, virulence potential, multilocus sequence typing, phylogeny, and pan genome. Ten and 12 strains were selected for testing simulated (both mediocre- and low-quality) and real reads, respectively. Our research demonstrates the hybrid assembly pipeline of Unicycler as a superior approach for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.

    4. Polishing the Oxford Nanopore Long-Read Assemblies of Bacterial Pathogens with Illumina Short Reads to Improve Genomic Analyses
  • The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.

    5. Whole-Genome Sequencing of Salmonella enterica and Listeria spp. Isolates from Water Samples in South America
  • A total of 596 Salmonella enterica isolates and 120 Listeria spp. isolates from water samples in Chile have been sequenced, with 240 S. enterica isolates and 120 Listeria spp. isolates sequenced using MiSeq at JIFSAN and 356 S. enterica isolates sequenced using NextSeq at CFSAN. Serotype and antimicrobial resistance genes of each isolate were predicted. There were 142 antimicrobial-resistant S. enterica isolates, as predicted based on the WGS data. A total of 171 Salmonella isolates from water samples in Mexico have been sequenced using NextSeq at CFSAN, out of which 137 isolated were predicted to be antimicrobial-resistant. S. enterica serotypes were also predicted based on the WGS data, which showed a wide variety of serotypes among the isolates. Whole-genome phylogeny was analyzed to compare these isolates from the same site by calling single nucleotide polymorphisms. This study allows a comprehensive look at the microbial safety of Latin American surface waters associated with produce production.

    6. Whole-Genome Analysis of Shiga Toxin-Producing Escherichia coli and Salmonella spp. Isolates from Untreated Cattle and Poultry Manures in California and Arizona
  • Whole-genome analysis of Shiga toxin-producing Escherichia coli (STEC) and Salmonella spp. isolates from untreated cattle and poultry manures in California and Arizona were conducted. Based on the Illumina MiSeq sequence data of STEC (n=316) and Salmonella spp. (n=177) isolated from cattle (n=158) and poultry (n=66) manure samples, serotype, virulence genes, antimicrobial resistance genes, and plasmids of each isolate were predicted. Whole-genome phylogeny was analyzed to compare these isolates by calling single nucleotide polymorphisms. This study highlights genomic diversity among STEC and Salmonella spp. isolates from untreated animal manures, which provides critical genome-based data for risk assessment relevant to the Food Safety Modernization Act Produce Safety Rule.

    7. Whole-Genome Sequencing Analysis of Non-Top 7 STEC Serogroups Suggests Novel Serotypes and Relatedness to Human Clinical Isolates
  • A total of 284 isolates of non-top seven STEC from cattle feces were sequenced using Illumina MiSeq. When an isolate was unserotypable, Oxford Nanopore sequencing was applied to generate a hybrid assembly using reads from both sequencing platforms to determine corresponding novel O-antigen gene clusters. A SNP-based phylogenetic tree was built to examine the relatedness between these isolates and human clinical STEC isolates obtained from NCBI. About 80% (n=232) of the isolates carried stx2 only whereas 14% (n=40) contained stx1 only. Approximately 4% (n=12) of the isolates carried both. Phylogenetic analysis indicates that some isolates were closely related to clinical isolates. The results suggest non-top 7 SETC have the potential to cause human illness.

    8. Identification of Mobile Genetic Elements and Evolutionary Analysis Based on Long-Read Sequencing of Listeria monocytogenes in the Food Processing Environment
  • We have sequenced 17 non-outbreak ECII L. monocytogenes strains were isolated from seven different food processing facilities in the United States and using the complete genomes, the distinct mobile genetic elements such as prophages and plasmids were identified and characterized to test our evolutionary hypothesis. Additionally, 25 outbreak ECII strains recovered from the U.S. and South Africa were collected from the NCBI database for tip-dated phylogeny and evolutionary analysis. Combining long-read and short-read sequencing technologies, we closed and characterized genomes of Listeria monocytogenes epidemic clone II isolates from geographically dispersed food processing facilities and investigated the genetic relationship among isolates from different facilities. This study suggests that Nanopore sequencing when combined with MiSeq sequencing could accurately produce complete genomes and identify mobile genetic elements, and prophages and plasmids were important markers to study L. monocytogenes persistence and evolution.

    PUBLICATIONS/ABSTRACTS:
  • 1. Chen, Z., Kuang, D., Xu, X., González-Escalona, N., Erickson, D.L, Brown, E., Meng, J. Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies. PLOS ONE. Under Revision.
  • 2. Chen, Z., Peiman, A., Rivadeneira, P., Meng, J., Jay-Russell, M. Whole-genome analysis of Shiga toxin-producing Escherichia coli and Salmonella spp. isolates from untreated cattle and poultry manures in California and Arizona. International Association for Food Protection Annual Meeting, Cleveland, OH, 10/2020.
  • 3. Huang, X., Shi, X., Nagaraja, T.G., Meng, J. Whole genome sequencing analysis of non-top 7 STEC serogroups suggests novel serotypes and relatedness to human clinical isolates. International Association for Food Protection Annual Meeting, Cleveland, OH, 10/2020.
  • 4. Kwon, H.J., Chen, Z., Meng, J, Evans, P. Identification of mobile genetic elements and evolutionary analysis based on long-read sequencing of Listeria monocytogenes in the food processing environment. International Association for Food Protection Annual Meeting, Cleveland, OH, 10/2020.