Phenotypic characterization and analysis of complete genomes of two distinct strains of the proposed species “L. swaminathanii”

Abstract

Recently, a new Listeria species, “Listeria swaminathanii”, was proposed. Here, we phenotypically and genotypically characterize two additional strains that were previously obtained from soil samples and compare the results to the type strain. Complete genomes for both strains were assembled from hybrid Illumina and Nanopore sequencing reads and annotated. Further genomic analysis including average nucleotide identity (ANI) and detection of mobile genetic elements and genes of interest (e.g., virulence-associated) were conducted. The strains showed 98.7–98.8% ANI with the type strain. The UTK C1-0015 genome contained a partial monocin locus and a plasmid, while the UTK C1-0024 genome contained a full monocin locus and a prophage. Phenotypic characterization consistent with those performed on the proposed type strain was conducted to assess consistency of phenotypes across a greater diversity of the proposed species (n = 3 instead of n = 1). Only a few findings were notably different from those of the type strain, such as catalase activity, glycerol metabolism, starch metabolism, and growth at 41 °C. This study further expands our understanding of this newly proposed sensu stricto Listeria species.

Taxonomy, ecology, and relevance to food safety of the genus Listeria with a particular consideration of new Listeria species described between 2010 and 2022

“…Moreover, the L. swaminathanii type strain is catalase negative. However, two other isolates of this new species were shown to be catalase positive ( 26 ), suggesting that the catalase phenotype is variable in L. swaminathanii , similarly to what has been documented for L. monocytogenes ( 30 – 33 ). Although five new Listeria sensu stricto species have been described since 2010, none of them are pathogenic; L. monocytogenes and L. ivanovii are still considered the only pathogenic species.…”

“…Within Listeria sensu stricto , phylogenetic analyses show that L. monocytogenes share an MRCA with L. cossartiae , L. marthii , and L. swaminathanii ( Fig. 1 ) ( 19 , 26 ); the species L. ivanovii , L. seeligeri , and L. immobilis are the most distantly related to L. monocytogenes within Listeria sensu stricto. Listeria sensu stricto also seems to have a much lower genetic diversity as compared to each of the two clades within Listeria sensu lato that have more than one species ( Fig.…”

“…Given the genotypic and phenotypic similarity of the four newly described Listeria sensu stricto species ( L. cossartiae , L. farberi , L. immobilis [ 17 ], and L. swaminathanii [ 19 , 26 ]) to the six species described prior to 2021 ( L. monocytogenes , L. innocua , L. ivanovii , L. seeligeri , L. welshimeri , and L. marthii ), it is expected that the newly described sensu stricto species will grow to detectable levels and be detected by the currently available conventional detection methods for Listeria spp. (although more experimental work will be needed to confirm this supposition).…”

Soil Collected from a Single Great Smoky Mountains Trail Contains a Diversity of Listeria monocytogenes andListeriaspp.

“…type strains, suggesting they would qualify as a novel species. After the initial submission of this work, these novel species isolates were further characterized and determined to belong to the proposed novel species “ Listeria swaminathanii ” ( 34 , 35 ).…”