Soil Collected from a Single Great Smoky Mountains Trail Contains a Diversity of Listeria monocytogenes and<i>Listeria</i>spp.

Claxton, Michelle L.; Hudson, Lauren K.; Bryan, Daniel W.; Denes, Thomas G.

doi:10.1128/spectrum.01431-22

“…cayugensis , although being isolated from fewer sites, was detected in two states, North Carolina and Georgia (USA). L. swaminathanii was detected at only one site in the Great Smoky Mountains with an elevation of 587 m in the state of North Carolina (USA) ( 20 , 44 ). Overall, 5 of the 10 Listeria sensu stricto species have only been isolated in the USA, including L. marthii , which was first described in 2010, and four species ( L. cossartiae , L. farberi , L. immobilis , and L. swaminathanii ) that were described in 2022.…”

Section: Ecology and Distributionmentioning

confidence: 99%

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

Orsi,

Liao,

Carlin

et al. 2024

mBio

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Since 2010, the genus Listeria has had the addition of 22 new species that more than tripled the number of species identified until 2010. Sixteen of these 22 new species are distantly related to the type species, Listeria monocytogenes , and several of these present phenotypes that distinguish them from classical Listeria species ( L. monocytogenes , Listeria innocua , Listeria ivanovii, Listeria seeligeri , Listeria welshimeri , and Listeria grayi ). These 22 newly described species also show that Listeria is more genetically diverse than previously estimated. While future studies and surveys are needed to clarify the distribution of these species, at least some of these species may not be widely spread, while other species may be frequently found spread to human-related settings (e.g., farms and processing facilities), and others may be adapted to specific environmental habitats. Here, we review the taxonomic, phylogenetic, and ecological characteristics of these new Listeria species identified since 2010 and re-iterate the suggestion of re-classification of some species into three new genera: Murraya , Mesolisteria , and Paenilisteria . We also provide a review of current detection issues and the relevance to food safety related to the identification of these new species. For example, several new non-pathogenic species could be misidentified as the pathogen L. monocytogenes , based on methods that do not target L. monocytogenes -specific virulence genes/factors, leading to unnecessary product recalls. Moreover, eight species in the proposed new genus Mesolisteria are not good indicators of environmental conditions that could allow L. monocytogenes to grow since Mesolisteria species are unable to grow at low temperatures.

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Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest

Wang,

Schamp,

Hudson

et al. 2024

Microbiol Spectr

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Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis ( n = 8; n represents the number of distinct strains), L. monocytogenes ( n = 3), “ Listeria swaminathanii ” (Lsw) ( n = 1), Listeria marthii ( n = 1), and Listeria booriae ( n = 1). Most strains ( n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated ( P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens. IMPORTANCE As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.

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Whole-Genome Sequencing and Metagenomics Reveals Diversity and Prevalence of Soil Listeria spp. in the Nantahala National Forest

Wang,

Schamp,

Hudson

et al. 2023

Preprint

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Background. Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. Whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates is the current standard for surveillance and identifying outbreaks. WGS of Listeria isolates can assist in understanding the diversity of Listeria species. The capability of precise detection and characterization of Listeria spp. strains in the natural environment is important for identifying transmission routes that can lead to food contamination and human illness. Recently, metagenomic sequencing has emerged as a promising tool for the direct detection of Listeria spp. in environmental samples. The objective of this study was to use a practical hybrid approach that can provide valuable information on the occurrence of Listeria spp. in soil environments in the southern Appalachian region of the United States. Results. This study involved soil sampling from four locations across varying altitudes in the Nantahala National Forest. Forty-two Listeria spp. isolates and 12 metagenomes of soil bacterial communities were obtained. Analysis of the isolates genomes revealed 14 distinct strains, representing a diversity of Listeria species. The predominant species isolated was L. cossartiae subsp. cayugensis (n = 8), with the other species including L. monocytogenes (n = 3), ‘L. swaminathanii’ (n = 1), L. marthii (n = 1), and L. booriae (n = 1). Most distinct strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the ‘L. swaminathanii’ strain was isolated from two different altitudes. Metagenomic analysis demonstrated a decline in both bacterial community diversity and relative abundance of Listeria spp. with increasing altitude. Of the soil factors assessed, pH and cation exchange capacity were significantly positively correlated with the abundance of Listeria spp. in soil as detected by metagenomics. Conclusions. By integrating culture-independent metagenomics with culture-based WGS, this study provides insights into the diversity and prevalence of Listeria spp. in the Nantahala National Forest. These findings contribute to the current knowledge on the distribution of Listeria spp. in the natural environment and offer a potential culture-independent method for tracking the transmission of foodborne pathogens.

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

Cited by 3 publications

References 81 publications

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

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

Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest

Whole-Genome Sequencing and Metagenomics Reveals Diversity and Prevalence of Soil Listeria spp. in the Nantahala National Forest

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