Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance

Parcey, Michael; Gayder, Steven; Morley-Senkler, Vivian; Bakkeren, Guus; Úrbez-Torres, J. R.; Ali, Shawkat; Castle, Alan J.; Svircev, A. M.

doi:10.1016/j.ygeno.2020.04.001

Cited by 34 publications

(37 citation statements)

References 57 publications

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“…The new CRISPR profile 5-60-38/D-n-α observed in the Portuguese isolate Ea 680, does not refute the high clonality of the Portuguese E. amylovora population neither a distinct origin from the other 35 isolates, since it was due to the likely recent acquisition of a single new spacer by CR2 and, therefore, can be used as a strain-specific marker to investigate the dispersion and prevalence of this strain in new outbreaks. These results are aligned with comparative genomics studies [35][36][37]. In fact, when comparing the profiles of the 35 E. amylovora Portuguese isolates with the strains described in these genomics studies, they fit in the 'Widely-Prevalent' clade, which is broadly distributed around the world, as mentioned above.…”

Section: Plos Onesupporting

confidence: 75%

“…Previous studies of comparative genomics, CRISPR and MLVA genotyping, have grouped E. amylovora in four different clades, all with the same epidemiological origin (North America), and mainly distinguished by their host preference (Amygdaloideae-or Rubus-infecting strains), supporting the high clonality observed within the species [33,35,37,[39][40][41]. Other studies have shown that E. amylovora strains display different levels of virulence [7-8, 36, 50-52].…”

Section: Introductionmentioning

confidence: 81%

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CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks

et al. 2021

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Fire blight is a destructive plant disease caused by Erwinia amylovora affecting pome fruit trees, and responsible for large yield declines, long phytosanitary confinements, and high economic losses. In Portugal, the first major fire blight outbreaks occurred in 2010 and 2011, and although later considered eradicated, the emergence of other outbreaks in recent years stressed the need to characterize the E. amylovora populations associated with these outbreaks. In this regard, CRISPR genotyping, assessment of three virulence markers, and semi-quantitative virulence bioassays, were carried out to determine the genotype, and assess the virulence of thirty-six E. amylovora isolates associated with outbreaks occurring between 2010 and 2017 and affecting apple and pear orchards located in the country central-west, known as the main producing region of pome fruits in Portugal. The data gathered reveal that 35 E. amylovora isolates belong to one of the widely-distributed CRISPR genotypes (5-24-38 / D-a-α) regardless the host species, year and region. Ea 680 was the single isolate revealing a new CRISPR genotype due to a novel CR2 spacer located closer to the leader sequence and therefore thought to be recently acquired. Regarding pathogenicity, although dot-blot hybridization assays showed the presence of key virulence factors, namely hrpL (T3SS), hrpN (T3E) and amsG from the amylovoran biosynthesis operon in all E. amylovora isolates studied, pathogenicity bioassays on immature pear slices allowed to distinguish four virulence levels, with most of the isolates revealing an intermediate to severe virulence phenotype. Regardless the clonal population structure of the E. amylovora associated to the outbreaks occurring in Portugal between 2010 and 2017, the different virulence phenotypes, suggests that E. amylovora may have been introduced at different instances into the country. This is the first study regarding E. amylovora in Portugal, and it discloses a novel CRISPR genotype for this bacterium.

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Section: Plos Onesupporting

confidence: 75%

Section: Introductionmentioning

confidence: 81%

CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks

et al. 2021

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“…1 ). This phylogeny is in strong agreement with the clade development resolved using whole chromosomal or plasmid pEA29 sequences ( 7 , 8 ). The major Amygdaloideae- infecting (AI) clades are composed of CRISPR groups Ia, Ib, II, III, and IV, with the Widely Prevalent clade comprising the Ia, Ib, and II as previously described ( Fig.…”

Section: Resultssupporting

confidence: 84%

“…The Widely Prevalent (WP) clade, the most commonly isolated group of E. amylovora , was disseminated globally through the movement of infected material in the early to mid 1900s ( 3 , 6 ). The Eastern North American (ENA) and Western North American (WNA) clades are found strictly in the continental USA and Canada in the eastern and western pome fruit growing regions, respectively ( 7 , 8 ). In the USA and Canada, control of E. amylovora infection is achieved through the application of the antibiotic streptomycin in spring ( 9 ).…”

Section: Introductionmentioning

confidence: 99%

“…In the USA and Canada, control of E. amylovora infection is achieved through the application of the antibiotic streptomycin in spring ( 9 ). This high antibiotic pressure has resulted in the development of streptomycin resistance (SmR) in the E. amylovora population, particularly prevalent in the WNA clade ( 2 , 7 ). Subsequently, research into alternatives to antibiotics, such as phage biocontrol, has increased ( 10 ).…”

Section: Introductionmentioning

confidence: 99%

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Function and Application of the CRISPR-Cas System in the Plant PathogenErwinia amylovora

Parcey

Gayder

Castle

et al. 2022

Appl Environ Microbiol

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Erwinia

Coutinho,

Shin

2023

Bergey's Manual of Systematics of Archaea and Bacteria

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er.win'i.a. N.L. fem. n. Erwinia , named after Erwin F. Smith. Proteobacteria / Gammaproteobacteria / Enterobacterales / Erwiniaceae / Erwinia Cells of the genus Erwinia are Gram‐stain‐negative rods, 0.5–1.0 × 1.0–3.0 μm, and occur alone or in pairs, sometimes in chains. Cells are motile by means of peritrichous flagella. They do not produce indole. They are mostly facultatively anaerobic, catalase‐positive, and oxidase‐ and urease‐negative. They utilize d ‐arabinose, fructose, fumarate, galactose, gluconate, glucose, glycerol, malate, β‐methyl‐glucoside, N‐ acetyl‐ d ‐glucosamine, ribose, trehalose, and succinate but not benzoate, butanol, l ‐fucose, glycogen, methanol, oxalate, propionate, or sorbose as the sole carbon sources. The major fatty acids are C 12:0 , C 14:0 , and C 16:0 . The known habitats are plants, where they cause vascular wilts and soft rots. They are also part of the epiphytic flora. They have also been isolated from insects and in one case from human skin. DNA G + C content (mol%) : 51.1–56.4%. Type species : Erwinia amylovora Winslow et al. 1920 AL (basonym: Micrococcus amylovorus Burrill 1882).

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Comparative genomic analysis of Erwinia amylovora reveals novel insights in phylogenetic arrangement, plasmid diversity, and streptomycin resistance

Cited by 34 publications

References 57 publications

CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks

CRISPR genotyping as complementary tool for epidemiological surveillance of Erwinia amylovora outbreaks

Function and Application of the CRISPR-Cas System in the Plant PathogenErwinia amylovora

Erwinia

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