Research Publications (Food Safety)

Staphylococcus aureus is one of the most common etiological agents responsible for contagious bovine mastitis. Here, we report the draft whole-genome sequences, with annotations, of 27 S. aureus strains and 3 Staphylococcus species strains that were isolated from Holstein cows with intramammary infection in Canada.

We report here the draft genome sequence of a Listeria monocytogenes strain, core genome multilocus sequence typing (cgMLST) complex type 2521 (CT2521), isolated from ready-to-eat meat sausage related to a protracted and supraregional listeriosis outbreak (Sigma1) in Germany from 2014 to 2019.

Brucellaphage EF4 was isolated from elk feces. The 38,321-bp double-stranded DNA genome is predicted to contain 72 coding regions, 38 of which have been assigned predicted functions. This phage displays nucleotide similarity to other brucellaphages of the genus Perisivirus.

Campylobacter species are the leading cause of gastroenteritis worldwide and an emerging threat in developing countries. Here, we report the draft whole-genome sequences of 51 Campylobacter jejuni and 12 Campylobacter coli strains isolated from patients with gastroenteritis in Santiago, Chile.

Foodborne pathogens have been implicated in illnesses worldwide. Here, we report the complete closed genome sequences of 28 bacterial strains belonging to 18 different species. These genomes belong to known foodborne pathogens. The genomes were closed by a combination of long-read and short-read sequencing.

Here, we report the near-complete genome sequence of swine norovirus strain SwNoV/Sw1/2018/JP. The genome was genetically similar (90.2%) to that of the only other swine norovirus strain previously detected in Japan (SW/NV/swine43/JP). In conclusion, genome sequences of swine noroviruses in Japan have not been changed significantly in the past 15 years.

Here, we report 11 bacterial strains isolated from commercial corn-based poultry feed to determine their potential as hygienic indicator microorganisms through a comparison of genome sizes and distribution patterns of unique genes. These isolates belonged to the genera Klebsiella, Kosakonia, Pantoea, Stenotrophomonas, and Enterococcus.

Forty-eight Escherichia coli strains were chosen due to variable detection of stx or serogroup by PCR. Although all strains were initially determined to be Shiga toxin-producing Escherichia coli (STEC), their genomes revealed 11 isolates carrying stx1a, stx1b, stx2a, and/or stx2b. Assembled genome sizes varied between 4,667,418 and 5,556,121 bp, with N50 values between 79,648 and 294,166 bp and G+C contents between 50.3% and 51.4%.

Serratia marcescens ATCC 274 produces the red pigment prodigiosin and the biosurfactant serrawettin W1 at 30°C but not at 37°C. A complete, high-quality genome sequence of S. marcescens ATCC 274 was obtained and found to comprise a single 5,148,533-bp circular genome with 4,799 genes.

Here, we present 95 metagenome-assembled genomes (MAGs) that harbor antimicrobial resistance genes, isolated from samples obtained in a large advanced wastewater reclamation facility prior to microfiltration. The MAGs were not in abundance after filtration at the facility and represent a useful resource to the water treatment community at large.

A large outbreak of extensively drug-resistant (XDR) Salmonella enterica serotype Typhi infections is ongoing in Pakistan, predominantly in Sindh Province. Here, we report the sequencing and characterization of five XDR Salmonella Typhi isolates from the Punjab province of Pakistan that are closely related to the outbreak strain and carry the same IncY plasmid.

Salmonella enterica subsp. enterica isolates are the leading cause of foodborne illness worldwide. Here, we report the draft genomes of 26 Salmonella isolates of food and clinical origin, belonging to four serovars, associated with outbreaks from 1999 to 2006 in the south of Brazil.

This is an announcement for the genome sequence of a clinical isolate of Salmonella enterica subsp. arizonae isolated from the urine and prostate of a 6-year-old male Labrador retriever. This is one of the few reports of a Salmonella enterica subsp. arizonae isolate cultured from canine urine.

Five strains of Salmonella enterica subsp. enterica serovar Infantis and two strains of S. enterica subsp. enterica serovar Kentucky isolated in 2017 from Ecuadorian layer poultry farms were sequenced using Illumina MiSeq technology. These isolates were collected on layer farms in central Ecuador, one of the most important areas of egg production in the country. The genome sequences of these isolates show valuable information for surveillance purposes.

We present here the complete genome sequences of three Salmonella enterica subsp. enterica serovar Muenchen strains, LG24, LG25, and LG26. All three strains were isolated from almond drupes grown in an orchard in San Joaquin County, California, in 2016. These genomic sequences are nonidentical and will contribute to our understanding of S. enterica genomics.

Diverse Shiga toxin-producing Escherichia coli (STEC) strains have been isolated from several environmental samples. Rivers are associated with the distribution of STEC pathogens in the environment. Thus, we report the complete genome sequence of a locus of enterocyte effacement (LEE)-positive STEC O157:H7 strain isolated from the Mississippi River.

Salmonella enterica subsp. enterica serovar Enteritidis has been the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. Here, we report the draft genomes of 30 S. Enteritidis isolates originating from a variety of patients and implicated foods during outbreaks between 1999 and 2006 in Brazil.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne disease with worldwide outbreaks. STEC serotypes O157, O26, O45, O103, O111, O121, and O145 cause the most outbreaks. There is little published information regarding the other serotypes. We report the draft genome sequences for 11 uncommon STEC serotypes from Nebraska.

Vibrio cholerae is an aquatic organism and facultative human pathogen that typically resides in coastal areas and brackish water. Here, we report the complete genome sequence of V. cholerae strain RFB16, which was isolated from a freshwater lake in southwestern Pennsylvania.

Four wild-type Campylobacter jejuni strains isolated from the cecal contents of broiler chickens were sequenced. The average genome size was 1,622,170 bp, with 1,667 to 1,761 coding sequences and 47 to 51 RNAs. Multiple genes encoding motility, intestinal colonization, toxin production, stress tolerance, and multidrug resistance were present in all the strains.

Here, we present the annotated genome of Shemara, a siphophage of Salmonella enterica. The Shemara genome is 44 kb with 83 predicted protein-coding genes. At the nucleotide and amino acid levels, Shemara is most similar to phages in the Guernseyvirinae subfamily.

A human norovirus (HuNoV) strain was obtained from a patient with acute gastroenteritis, and its complete coding sequence was determined. The coding-complete viral genome, with three open reading frames, was 7,565 bp long, with a GC content of 49.9%. The genotype of the HuNoV strain obtained in this study was identified as GII.p12_GII.3.

Sixty-six Salmonella enterica serovar Typhimurium isolates carrying incompatibility group FIB (IncFIB) plasmids were sequenced to further characterize the IncFIB plasmid-encoded factors associated with virulence and antimicrobial resistance genes. In addition to the IncFIB plasmid, many of these isolates harbored additional plasmids encoding virulence and antimicrobial resistance genes.

Clostridium perfringens causes severe gastrointestinal diseases, which include necrotic enteritis (NE) in chickens, a deadly disease worldwide. We report here the draft genome sequence of Clostridium perfringens strain TAMU, which was used in developing an NE chicken challenge model. This C. perfringens TAMU genome sequence will aid in advancing potential intervention strategies to reduce NE pathogenesis.