Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

Park, Sang-Cheol; Lee, Kihyun; Kim, Yeong Ouk; Won, Sungho; Chun, Jongsik

doi:10.3389/fmicb.2019.00834

Cited by 67 publications

(56 citation statements)

References 28 publications

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“…It is notable that many accessory genes were unique to a single strain (2797 genes, representing 34.1% of the pan-genome). The large accessory genome in our results is not uncommon and has been reported in different bacterial pathogens, including S. aureus 17,18 and Staphylococcus haemolyticus 19 . However, we recognize that pangenome sizes and precise characterization of core and accessory genes are greatly influenced by the phylogenetic distance, sequence quality of genomes, the number of genomes being compared, assembly and annotation methods, and choice of threshold values to define orthologous genes.…”

Section: Resultssupporting

confidence: 68%

Population genomics of Staphylococcus pseudintermedius in companion animals in the United States

et al. 2020

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Staphylococcus pseudintermedius is a commensal bacterium and a major opportunistic pathogen of dogs. The emergence of methicillin-resistant S. pseudintermedius (MRSP) is also becoming a serious concern. We carried out a population genomics study of 130 clinical S. pseudintermedius isolates from dogs and cats in the New England region of the United States. Results revealed the co-circulation of phylogenetically diverse lineages that have access to a large pool of accessory genes. Many MRSP and multidrug-resistant clones have emerged through multiple independent, horizontal acquisition of resistance determinants and frequent genetic exchange that disseminate DNA to the broader population. When compared to a Texas population, we found evidence of clonal expansion of MRSP lineages that have disseminated over large distances. These findings provide unprecedented insight into the diversification of a common cutaneous colonizer of man's oldest companion animal and the widespread circulation of multiple high-risk resistant clones.

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Section: Resultssupporting

confidence: 68%

Population genomics of Staphylococcus pseudintermedius in companion animals in the United States

et al. 2020

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“…Although our initial results revealed more open pangenome ( alpha ) in Clade B (0.762) than Clade A (0.807) or Clade C (0.806) or the whole collection (0.823), alpha was higher for small (<250) sample sizes here (Fig. 6) as indicated before 41 . Alpha estimates averaged across the sample size placed Clade C as more open than Clade A or Clade B (Table 3), highlighting a partial dependence of alpha on sample size that was removed once the sample sizes >250 when the relative rate of new genes became constant (Supplementary Fig.…”

Section: Resultssupporting

confidence: 49%

“…Previous work on E. coli 41 employed a metric of pangenome openness ( alpha ) that was similarly applied to our Roary pangenome results here to compare with previous findings that n = 648 Clade C isolates had a marginally more open genome (smaller alpha ) than n = 140 from Clade B, and both were more open than n = 70 Clade A isolates 31 . Although our initial results revealed more open pangenome ( alpha ) in Clade B (0.762) than Clade A (0.807) or Clade C (0.806) or the whole collection (0.823), alpha was higher for small (<250) sample sizes here (Fig.…”

Section: Resultsmentioning

confidence: 95%

“…Our analysis of this large collection’s core (3,712) and accessory (22,525) genes extended previous work showing that 283 predominantly ST131 isolates had 16,236 genes in an open pangenome with a core of 3,079 genes 46 , 21% less than the core genome count here. Nonetheless, ST131’s accessory genome may be streamlined: a more genetically diverse set of 1,509 E. coli including 266 ST131 had a core genome of 1,744 genes and a 62,753 cloud genes 29 , and an E. coli-Shigella core genome had 2,608 genes among a total of 128,193 genes 41 .…”

Section: Discussionmentioning

confidence: 99%

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An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Decano

Downing

2019

Sci Rep

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Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131’s origin, adaptation and spread is essential. E. coli ST131’s ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131’s population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.

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“…The pan-genome analysis showed that our ESBL-EC isolates had an expanding pan-genome and this result is consistent with those of previous studies in pan-genome analyses of E. coli [70,71]. An open pan-genomic trait of E. coli probably contributes to the diversity of species [39].…”

Section: Discussionsupporting

confidence: 91%

Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea

Kim

et al. 2020

Microorganisms

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The spread of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) has posed a critical health risk to both humans and animals, because resistance to beta-lactam antibiotics makes treatment for commonly infectious diseases more complicated. In this study, we report the prevalence and genetic characteristics of ESBL-ECs isolated from retail meat samples in Korea. A total of 1205 E. coli strains were isolated from 3234 raw meat samples, purchased from nationwide retail stores between 2015 and 2018. Antimicrobial susceptibility testing was performed for all isolates by a broth microdilution method, and the ESBL phenotype was determined according to the Clinical and Laboratory Standards Institute (CLSI) confirmatory method. All ESBL-EC isolates (n = 29) were subjected to whole-genome sequencing (WGS). The antimicrobial resistance genes, plasmid incompatibility types, E. coli phylogroups, and phylogenetic relations were investigated based on the WGS data. The prevalence of ESBL-ECs in chicken was significantly higher than that in other meat samples. The results in this study demonstrate that clonally diverse ESBL-ECs with a multidrug resistance phenotype were distributed nationwide, although their prevalence from retail meat was 0.9%. The dissemination of ESBL-ECs from retail meat poses a potential risk to consumers and food-handlers, suggesting that the continuous surveillance of ESBL-ECs in retail meat should be conducted at the national level.

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Large-Scale Genomics Reveals the Genetic Characteristics of Seven Species and Importance of Phylogenetic Distance for Estimating Pan-Genome Size

Cited by 67 publications

References 28 publications

Population genomics of Staphylococcus pseudintermedius in companion animals in the United States

Population genomics of Staphylococcus pseudintermedius in companion animals in the United States

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea

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