Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Shen, Zhi Yong; Koh, Xiu Pei; Yu, Yan; Lau, S. S.

doi:10.3390/microorganisms8111713

Cited by 3 publications

(4 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Almost all E. coli or Shigella genomes were within HierCC cluster HC2350_1, and genomes with other taxonomic or Clade designations belonged to other HC2350 clusters. However, soon after the definition of the EcoRPlus collection, additional genomes of Escherichia which were related to Clade II were described from inter-tidal marine and fresh water sediments near Hong Kong [61, 66]. Furthermore, due to its numerical predominance, E. coli overshadows other Escherichia species and sub-species within EcoRPlus.…”

Section: Resultsmentioning

confidence: 99%

EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

Achtman

Zhou

Charlesworth

et al. 2022

Preprint

View full text Add to dashboard Cite

The definition of bacterial species is traditionally a taxonomic issue while defining bacterial populations is done with population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST alleles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate the ability of HierCC to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and revealed differences in vertical inheritance of O serogroups. Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.

show abstract

Section: Resultsmentioning

confidence: 99%

EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

Achtman

Zhou

Charlesworth

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Almost all E. coli or Shigella genomes were within HierCC cluster HC2350_1, and genomes with other taxonomic or clade designations belonged to other HC2350 clusters. However, soon after the definition of the EcoRPlus collection, additional genomes of Escherichia which were related to clade II were described from inter-tidal marine and fresh-water sediments near Hong Kong [ 66 , 70 ]. Furthermore, due to its numerical predominance, E. coli overshadows other Escherichia species and subspecies within EcoRPlus .…”

Section: Resultsmentioning

confidence: 99%

“…R. Soc. B 377: 20210240 collection, additional genomes of Escherichia which were related to clade II were described from inter-tidal marine and fresh-water sediments near Hong Kong[66,70]. Furthermore, due to its numerical predominance, E. coli overshadows other Escherichia species and subspecies within EcoRPlus.…”

mentioning

confidence: 99%

EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations

Achtman

Zhou

Charlesworth

et al. 2022

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase ( http://enterobase.warwick.ac.uk ) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus . HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella . Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.

show abstract

“…While our isolates were from Hong Kong, China, the host-associated clade II strains originated from Australia, Gabon, and United States ( Walk et al, 2009 ; Clermont et al, 2011 ; Lescat et al, 2013 ; Walk, 2015 ; Gangiredla et al, 2018 ). We previously demonstrated that two groups of clade II genomes displayed signatures of functional divergence that were reflective of ecological differentiation to occupy gastrointestinal and external environments, respectively ( Shen et al, 2020 ). The study included genomes of isolates in this study.…”

Section: Discussionmentioning

confidence: 99%

Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments

et al. 2022

Self Cite

View full text Add to dashboard Cite

Escherichia coli not only inhabit the large intestines of human and warm-blooded animals but could also persist in the external environment. However, current knowledge was largely based on host-associated strains. Moreover, cryptic Escherichia clades that were often misidentified as E. coli by conventional diagnostic methods were discovered. Failure to distinguish them from E. coli sensu stricto could lead to inaccurate conclusions about the population genetics of E. coli. Based on seven housekeeping genes, we determine the genetic and ecological diversity of E. coli and cryptic clades as they occupy aquatic habitats with different characteristics and human impact levels in subtropical Hong Kong. Contrary to previous reports, clade II was the most abundant cryptic lineage co-isolated with E. coli, being especially abundant in relatively pristine subtropical aquatic environments. The phylogenetically distinct cryptic clades and E. coli showed limited recombination and significant genetic divergence. Analyses indicated that these clade II strains were ecologically differentiated from typical E. coli; some may even represent novel environmental Escherichia clades that were closely related to the original clade II strains of fecal origins. E. coli of diverse origins exhibited clonality amidst divergent genotypes STs, echoing other studies in that recombination in housekeeping genes was insufficient to disrupt phylogenetic signals of the largely clonal E. coli. Notably, environmental E. coli were less diverse than fecal isolates despite contributing many new alleles and STs. Finally, we demonstrated that human activities influenced the distribution of E. coli and clade II in a small aquatic continuum. Moving from relatively pristine sites toward areas with higher human disturbance, the abundance of clade II isolates and new E. coli genotypes reduces, while E. coli bearing class I integrons and belonging to CCs of public health concern accumulates. Altogether, this work revealed the new genetic diversity of E. coli and cryptic clades embedded in selected subtropical aquatic habitats, especially relatively pristine sites, which will aid a more thorough understanding of the extent of their genetic and functional variations in relation to diverse habitats with varied conditions.

show abstract

Genetic Variation and Preliminary Indications of Divergent Niche Adaptation in Cryptic Clade II of Escherichia

Cited by 3 publications

References 48 publications

EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations

Genetic and Ecological Diversity of Escherichia coli and Cryptic Escherichia Clades in Subtropical Aquatic Environments

Contact Info

Product

Resources

About