Research Publications (Food Safety)

Staphylococcus aureus bacteria are ranked among the top five foodborne pathogens in the United States. Here, we report the draft genome sequences of 62 S. aureus isolates that originated from the manufacturing environment of an Illinois bakery and were associated with outbreaks between 2010 and 2011 in the United States.

Salmonella enterica subsp. enterica serotype Choleraesuis is a foodborne pathogen with zoonotic potential. We report the draft genome sequence and a closed plasmid sequence from a plant-internalized S. Choleraesuis strain that was isolated from the pulp of a Spanish Galia melon purchased from a German supermarket in 2015.

We report the draft genome sequences of seven Vibrio cholerae isolates from patients. Four isolates were profiled as multilocus sequence type 69, serogroup O1, a subset of seventh-pandemic El Tor clonal isolates. Presented here are genome assemblies and evidence for major pathogenicity islands, virulence factors, and antimicrobial resistance genes.

Salmonella enterica serovar Enteritidis ODA 99-30581-13 is a relatively heat-resistant strain isolated from shell eggs. The strain has a 4,777,965-bp genome sequence (52.1% GC content) that was predicted to encode 4,455 proteins, including heat stress response proteins and stress response regulators; these may be involved in its heat resistance.

Here, we report the whole-genome sequence of multidrug-resistant Salmonella enterica serovar Cannstatt harboring mcr-1.1, isolated from a fatal sepsis case. Genomic analysis revealed that the isolate was sequence type 2390 carrying mcr-1.1, blaCTX-M-14, aac(3)IId, aac(6')Iaa, floR, qnrS1, sul2, tetA, and tetM. Three Inc plasmids were observed, including the IncX4 plasmid containing mcr-1.1.

Here, we report the closed genome sequences of two representative Listeria monocytogenes strains belonging to PCR serogroup IVb, which are related to two large outbreaks of human listeriosis that affected Germany in 2015 (Eta1) and 2018 to 2019 (Epsilon1a).

Desulfobulbus oligotrophicus Prop6 is a sulfate-reducing, propionate-oxidizing Deltabacterota (formerly Deltaproteobacteria) strain from sewage sludge. Desulfobulbus species are found in anoxic environments, in animal microbiota, and some produce the neurotoxin methylmercury. The 3.1-Mbp D. oligotrophicus genome sequence enables studies of diverse environmental adaptations and the evolutionary genomics of mercury methylation mechanisms.

Genome sequences of Escherichia coli O157:H7 originating from pigs are limited in the public databases. We sequenced 104 E. coli O157:H7 isolates from pig and cattle feces and pork production environments in Alberta, Canada. The information will aid studies investigating sources of E. coli O157:H7 contaminating pork and the associated environments.

Vibrio cholerae is a global health threat and a model enteric pathogen that causes the human disease cholera. Here, we report the complete genome sequence of the seventh-pandemic V. cholerae O1 El Tor strain C6706.

Sprouts have been implicated in numerous foodborne illness outbreaks. To better understand baseline microbial profiles of irrigation water and subsequent spent irrigation water of alfalfa sprouts, DNA from water was extracted, sequenced, and annotated with CosmosID and a custom pipeline to provide bacterial, fungal, protist, and antimicrobial resistance gene profiles.

Sphingobium barthaii KK22T is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of S. barthaii revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.

Salmonella enterica serovar Livingstone 1236H was isolated originally from peanut butter and represents a health risk in low-moisture foods. The current work presents the strain’s genome sequencing results, which show a 4,824,729-bp genome sequence and 4,435 protein coding sequences, including some that are involved in adaptation to low-moisture environments.

This study reports the complete genome sequence of bisphenol A-degrading bacterium Sphingobium sp. strain A3, which was isolated from a contaminated soil sample from the site of a factory fire in South Korea. The genome consists of a 6.53-Mbp chromosome and eight plasmid contigs (532,947 bp), with 6,406 protein-coding sequences and a GC content of 63.82%.

Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:– from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.

Burkholderia pseudomultivorans MPSB1 was isolated from a copper mined-out soil sample collected from Mogpog, Marinduque, Philippines. Here, we report the draft genome sequence with predicted gene inventories supporting rhizosphere bioremediation, such as heavy metal tolerance, phosphate solubilization, and siderophore production.

Enterohemorrhagic Escherichia coli (EHEC) isolates of serotype O157:H7 are serious foodborne zoonotic pathogens and prime targets for biocontrol using bacteriophages. We report on the complete genome sequences of 11 novel lytic bacteriophages, representing three viral genera, isolated from cattle in Hungary that target E. coli O157 strains.

Listeria monocytogenes serotype 7 lacks glycosidic constituents in wall teichoic acids. Here, we present the complete genome sequence of L. monocytogenes serotype 7 strain FSL R9-0915 and an analysis of genes known to affect L. monocytogenes antigenicity. This strain is used as a control strain in Listeria phage host range analyses.

Bacteriophages can be used as a biocontrol for the foodborne pathogen Listeria monocytogenes. Propagation of phages is a necessary step for their use in experimental studies and biocontrol applications. Here, we present the complete genomes of three Listeria monocytogenes strains commonly used as propagation hosts for Listeria phages.

We report the complete genome (3.9-Mb chromosome, 5.9-kb plasmid) of Clostridium botulinum CJ0611A1, a type A(B) strain isolated from carrot juice distributed in Canada and linked to an international 2006 foodborne botulism outbreak. This strain encodes a full-length bont/A1 gene and a truncated bont/B gene.

Escherichia coli serotype O157:H7 strain 20R2R is a derivative of clinical isolate PA20. Prophage excision from the coding region of a PA20 transcription factor restored RpoS-dependent biofilm formation in 20R2R, providing a model for O157:H7 stress adaptation when transitioning between clinical and environmental settings. We report here the complete 20R2R genome sequence.

Here, we announce the draft genome sequence of Enterobacter hormaechei 2B-MC1, isolated from a shrimp sample collected from a farmer’s market in Atlanta, Georgia. The assembled genome sequence observed was 4,661,561 bp long with a G+C content of 55.3%. The isolate harbored sul1, sul2, qnrA1, oqxB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id, and aph(3'')-Ib antibiotic resistance genes.

Aspergillus flavus is an agriculturally and medically important filamentous fungus that produces mycotoxins, including aflatoxins, which are potent carcinogens. Here, we generated short- and long-read transcript sequence data from the growth of A. flavus strain NRRL 3357 under both typical and stress conditions to produce a new annotation of its genome.

The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas.

The complete genome of Salmonella enterica subsp. enterica serovar Kottbus strain Kharkiv (serogroup C2-C3), which was isolated from a commercial pork production facility in Kharkiv, Ukraine, was assembled using long-read Nanopore sequences. A single circular contig (4,799,045 bp) comprised a complete chromosome encoding antibiotic resistance, highlighting the risk of cross-species livestock and human infection.

We present the complete genomes of four Brucella suis biovar 2 isolates that were obtained from wild boars in Switzerland in 2008 and 2009. Genomes were sequenced with PacBio technology, contained two chromosomes each, had a genome size of 3.3 Mbp, and contained more than 3,225 genes per genome.