The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains.

Four isolates (FSL S4-120^T, FSL S4-696, FSL S4-710, and FSL S4-965) of Gram-positive, motile, facultatively anaerobic, non-spore-forming bacilli that were phenotypically similar to species of the genusListeriawere isolated from soil, standing water and flowing water samples obtained from the natural environment in the Finger Lakes National Forest, New York, USA. The four isolates were closely related to one another and were determined to be the same species by whole genome DNA–DNA hybridization studies (>82 % relatedness at 55 °C and >76 % relatedness at 70 °C with 0.0–0.5 % divergence). 16S rRNA gene sequence analysis confirmed their close phylogenetic relatedness toListeria monocytogenesandListeria innocuaand more distant relatedness toListeria welshimeri, L. seeligeri, L. ivanoviiandL. grayi.Phylogenetic analysis of partial sequences forsigB, gap,andprsshowed that these isolates form a well-supported sistergroup toL. monocytogenes. The four isolates were sufficiently different fromL. monocytogenesandL. innocuaby DNA–DNA hybridization to warrant their designation as a new species of the genusListeria. The four isolates yielded positive reactions in the AccuProbe test that is purported to be specific forL. monocytogenes, did not fermentl-rhamnose, were non-haemolytic on blood agar media, and did not contain a homologue of theL. monocytogenesvirulence gene island. On the basis of their phenotypic characteristics and their genotypic distinctiveness fromL. monocytogenesandL. innocua,the four isolates should be classified as a new species within the genusListeria, for which the nameListeria marthiisp. nov. is proposed. The type strain ofL. marthiiis FSL S4-120^T(=ATCC BAA-1595^T=BEIR NR 9579^T=CCUG 56148^T).L. marthiihas not been associated with human or animal disease at this time.

For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. Therefore, we conducted a retrospective and prospective analysis. The retrospective study investigated isolates from 1 confirmed outbreak. Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included 58 isolates obtained in 2012, including isolates from 1 epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the outbreak-associated PFGE type. Additional putative outbreak clusters were detected in the retrospective and prospective analyses. This study demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.

Psychrotolerant spore-forming bacteria represent a major challenge to the goal of extending the shelf life of pasteurized dairy products. The objective of this study was to identify prominent phylogenetic groups of dairy-associated aerobic sporeformers and to characterize representative isolates for phenotypes relevant to growth in milk. Analysis of sequence data for a 632-nucleotide fragment ofrpoBshowed that 1,288 dairy-associated isolates (obtained from raw and pasteurized milk and from dairy farm environments) clustered into two major divisions representing (i) the genusPaenibacillus(737 isolates, including the speciesPaenibacillus odorifer,Paenibacillus graminis, andPaenibacillus amylolyticussensu lato) and (ii)Bacillus(n= 467) (e.g.,Bacillus licheniformissensu lato,Bacillus pumilus,Bacillus weihenstephanensis) and genera formerly classified asBacillus(n= 84) (e.g.,Viridibacillusspp.). When isolates representing the most commonrpoBallelic types (ATs) were tested for growth in skim milk broth at 6°C, 6/9Paenibacillusisolates, but only 2/8 isolates representingBacillussubtypes, grew >5 log CFU/ml over 21 days. In addition, 38/40Paenibacillusisolates but only 3/47Bacillusisolates tested were positive for β-galactosidase activity (including some isolates representingBacillus licheniformissensu lato, a common dairy-associated clade). Our study confirms thatPaenibacillusspp. are the predominant psychrotolerant sporeformers in fluid milk and provides 16S rRNA gene andrpoBsubtype data and phenotypic characteristics facilitating the identification of aerobic spore-forming spoilage organisms of concern. These data will be critical for the development of detection methods and control strategies that will reduce the introduction of psychrotolerant sporeformers and extend the shelf life of dairy products.