Salmonella 4,[5],12:i:- currently circulating in swine in the US Midwest are likely to be part of an emerging multidrug-resistant clade first reported in Europe, and can carry plasmid-mediated resistance genes that may be transmitted horizontally to other bacteria, and thus may represent a public health concern.

b Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis of S. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmental S. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of the S. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method for S. Enteritidis. Foodborne bacterial pathogen characterization, surveillance, and outbreak detection is an important function of the public health laboratory (1). Current practices involve time-and laborintensive phenotypic typing, including biochemical profiling, phage typing, serotyping, and antimicrobial susceptibility testing. In addition, a variety of species-specific molecular methods for advanced characterization are utilized, including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA), and virulence gene typing (2). Often, it is necessary to combine results from multiple techniques to provide an adequate level of discrimination in order to identify outbreak clusters within routine clinical surveillance isolates.Salmonella is an important foodborne pathogen that is estimated to be responsible for approximately 1 million cases of illness and more than 450 deaths annually in the United States (3). Salmonella enterica serovar Enteritidis is responsible for 36% of Salmonella outbreaks in the United States, and in 1990, it replaced Salmonella enterica serovar Typhimurium as the most frequently reported serotype of Salmonella worldwide (4, 5). It is estimated that approximately 64% of S. Enteritidis clinical cases are attributable to contaminated eggs and 18% to poultry products (5, 6).There is limited genetic variation between the strains of S. Enteritidis, which reduces the utility of current subtyping methods (7-9). For example, PFGE, the gold standard s...

Four ready-to-eat smoked fish plants were monitored for 2 years to study Listeria contamination patterns and the impact of plant-specific Listeria control strategies, including employee training and targeted sanitation procedures, on Listeria contamination patterns. Samples from the processing plant environment and from raw and finished product were collected monthly and tested for Listeria spp. and Listeria monocytogenes. Before implementation of intervention strategies, 19.2% of raw product samples (n = 276), 8.7% of finished product samples (n = 275), and 26.1% of environmental samples (n = 617) tested positive for Listeria spp. During and after implementation of Listeria control strategies, 19.0% of raw product samples (n = 242), 7.0% of finished product samples (n = 244), and 19.5% of environmental samples (n = 527) were positive for Listeria spp. In one of the four fish plants (plant 4), no environmental samples were positive for L. monocytogenes, and this plant was thus excluded from statistical analyses. Based on data pooled from plants 1, 2, and 3, environmental Listeria spp. prevalence was significantly lower (P < 0.05) for nonfood contact surfaces and the finished product area and for the overall core environmental samples after implementation of control strategies. Listeria prevalence for floor drains was similar before and after implementation of controls (49.6 and 54.2%, respectively). Regression analysis revealed a significant positive relationship (P < 0.05) between L. monocytogenes prevalence in the environment and in finished products before implementation of control strategies; however, this relationship was absolved by implementation of Listeria control strategies. Molecular subtyping (EcoRI ribotyping) revealed that specific L. monocytogenes ribotypes persisted in three processing plants over time. These persistent ribotypes were responsible for all six finished product contamination events detected in plant 1. Ribotype data also indicated that incoming raw material is only rarely a direct source of finished product contamination. While these data indicate that plant-specific Listeria control strategies can reduce cross-contamination and prevalence of Listeria spp. and L. monocytogenes in the plant environment, elimination of persistent L. monocytogenes strains remains a considerable challenge.

Contamination of dairy products with Listeria monocytogenes is a concern because multiple human listeriosis outbreaks have been linked to contaminated cheese and dairy products. Dairy production on farmstead operations may be a particular concern because L. monocytogenes is also an animal pathogen that can be shed by ruminants with and without clinical symptoms; physical proximity between production animal and dairy processing facilities may thus provide a higher risk for introduction of L. monocytogenes into the dairy production process. To better understand the risks of L. monocytogenes contamination associated with farmstead dairy production, samples from a farmstead dairy processing operation and the milking barn of the directly adjacent dairy sheep operation were tested for L. monocytogenes over a 3-yr period. Prevalence of L. monocytogenes for samples collected on the farm (n = 85) and the dairy production facility (n = 674) was 9.4 and 2.7%, respectively. Molecular subtyping using automated EcoRI ribotyping of L. monocytogenes isolates revealed that distinct subtypes were associated with the dairy production facility and the farm's milking parlor. Although a total of 5 and 4 different ribotypes were identified among isolates obtained from the dairy production facility and the milking parlor, respectively, only 1 ribotype (DUP-1030A) was isolated from both. Different ribotypes were predominant among isolates from the dairy production facility (ribotype DUP-1052A, representing 15 of 18 isolates) and the farm's milking parlor (ribotype DUP-1039A, representing 4 of 8 isolates); each of these ribotypes appeared to persist over time in the respective area. Our data support that i) in farmstead dairy processing facilities, L. monocytogenes present on the farm can largely be prevented from being introduced into the processing facility; and ii) L. monocytogenes can persist on farm and in processing areas, providing a potential high-risk source for contamination. Preventing cross contamination between dairy production and processing facilities and control of persistent L. monocytogenes are thus critical to assuring the microbial safety of farmstead dairy products.

The results of this investigation suggest that A. butzleri should be considered an agent that can cause outbreaks of foodborne illness. Rigorous investigation of outbreaks of undetermined etiology is valuable for incrementally increasing our understanding of emerging agents causing foodborne illnesses.