Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

Liao, Jingqiu; Guo, Xiaodong; Weller, Daniel; Pollak, Shaul; Buckley, Daniel H.; Wiedmann, Martin; Cordero, Otto X.

doi:10.1038/s41564-021-00935-7

Cited by 67 publications

(104 citation statements)

References 43 publications

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“…These CCs were also common among French isolates recovered from both food and clinical sources in the period from 2005 to 2013 [41]. The size of the core genome within our isolate population (2391 genes) is in line with the size of other reported core genomes for L. monocytogenes (2322 to 2562 genes) [39,[42][43][44][45][46]. The accessory genome in the present study, which generally encompasses a larger pool of genes compared to the core genome, included 7470 genes.…”

Section: Discussionsupporting

confidence: 86%

“…This study found that the pangenome and especially accessory genes of L. monocytogenes evolve at a faster rate than the core genome is seen to diversify [45]. The authors suggest that because of this difference in diversification rate, the accessory genome can be used as a further measure of diversity within a set of isolates [45]. Within our isolate set, a number of CC37 isolates possessing 0-2 pairwise SNP differences appeared to be identical or highly similar (Figure 2).…”

Section: Discussionmentioning

confidence: 69%

“…The accessory genome in the present study, which generally encompasses a larger pool of genes compared to the core genome, included 7470 genes. A recent study that looked at the pangenome of L. monocytogenes from soil samples across the United States suggested that pangenome openness is the consequence of adaptive evolutionary processes that enable bacteria to survive in variable environments [45]. This study found that the pangenome and especially accessory genes of L. monocytogenes evolve at a faster rate than the core genome is seen to diversify [45].…”

Section: Discussionmentioning

confidence: 81%

“…A recent study that looked at the pangenome of L. monocytogenes from soil samples across the United States suggested that pangenome openness is the consequence of adaptive evolutionary processes that enable bacteria to survive in variable environments [45]. This study found that the pangenome and especially accessory genes of L. monocytogenes evolve at a faster rate than the core genome is seen to diversify [45]. The authors suggest that because of this difference in diversification rate, the accessory genome can be used as a further measure of diversity within a set of isolates [45].…”

Section: Discussionmentioning

confidence: 99%

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Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Bland

Johnson

Waite‐Cusic

et al. 2021

Foods

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Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0–2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 69%

Section: Discussionmentioning

confidence: 81%

Section: Discussionmentioning

confidence: 99%

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Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Bland

Johnson

Waite‐Cusic

et al. 2021

Foods

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“…Our analysis suggests that while for some species the global gene pool consists of highly structured sets of well-defined pools, for other species the boundaries between pools are 'blurred', and the global gene pool appears to be a set of highly overlapping pools. Recent analyses have suggested that some microbial species have highly structured populations in which population structure plays a key role in shaping evolutionary dynamics 12,52,53 ; our work complexifies this picture, indicating that some species have highly interconnected evolutionary dynamics regardless of their population structure. This further emphasizes the need for future investigations on the role of population structure in microbial genome evolution.…”

supporting

confidence: 55%

Core genes can have higher recombination rates than accessory genes within global microbial populations

Steinberg

Kussell

2021

Preprint

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Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. Yet quantifying the impact of homologous recombination on different gene classes, which is critical to understanding how selection acts on variation to shape species diversity and genome structure, remains challenging. This is largely due to the dynamic nature of bacterial genomes, whose high intraspecies genome content diversity and complex phylogenetic relationships present difficulties for inferring rates of recombination, particularly for rare genes. In this work, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. Our analysis suggests that even well-resolved sequence clusters sampled from global populations interact with overlapping gene pools, which has implications for the role of population structure in genome evolution. We show that in a majority of species, core genes have shorter coalescence times and higher recombination rates than accessory genes, and that gene frequency is often positively correlated with increased recombination. Our results provide a new line of population genomic evidence supporting the hypothesis that core genes are under strong, purifying selection, and indicate that homologous recombination may play a key role in increasing the efficiency of selection in those parts of the genome most conserved within each species.

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Novel Predictive Machine Learning Approach for Identification of Microbial Niche and Microbial Communities from Omics Dataset of Kaveri River, Tamil-Nadu, India

Pandiyarajan,

Maheswaran,

Raj

et al. 2024

Lecture Notes in Networks and Systems

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Nationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution

Cited by 67 publications

References 43 publications

Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Application of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources

Core genes can have higher recombination rates than accessory genes within global microbial populations

Novel Predictive Machine Learning Approach for Identification of Microbial Niche and Microbial Communities from Omics Dataset of Kaveri River, Tamil-Nadu, India

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