Investigating the distribution of strains of Erwinia amylovora and streptomycin resistance in apple orchards in New York using CRISPR profiles: a six-year follow-up

Plant Disease ◽  
2021 ◽  
Author(s):  
Anna Wallis ◽  
Isabella Magna Yannuzzi ◽  
Mei-Wah Choi ◽  
John Spafford ◽  
Matthew Siemon ◽  
...  
Keyword(s):  
New York ◽  
New England ◽  
Fire Blight ◽  
Management Practices ◽  
Erwinia Amylovora ◽  
Resistance Management ◽  
Strain Differences ◽  
Streptomycin Resistance ◽  
Management Recommendations

Fire blight, caused by the bacterium Erwinia amylovora, is one of the most important diseases of apple. The antibiotic streptomycin is routinely used in the commercial apple industries of New York and New England to manage the disease. In 2002, and again from 2011 to 2014, outbreaks of streptomycin resistance (SmR) were reported and investigated in NY. Motivated by new grower reports of control failures, we conducted a follow-up investigation of the distribution of SmR and E. amylovora strains for major apple production regions of NY over the last six years (2015-2020). Characterization of clustered regularly interspaced short palindromic repeat (CRISPR) profiles revealed that a few ‘cosmopolitan’ strains were widely prevalent across regions, while many other ‘resident’ strains were confined to one location. In addition, we uncovered novel CRISPR profile diversity in all investigated regions. SmR E. amylovora was detected only in a small area spanning two counties from 2017 to 2020, and always associated with one CRISPR profile (41:23:38), which matched the profile of SmR E. amylovora discovered in 2002. This suggests the original SmR E. amylovora was never fully eradicated and went undetected due to several seasons of low disease pressure in this region. Investigation of several representative isolates under controlled greenhouse conditions indicated significant differences in aggressiveness on ‘Gala’ apples. Potential implications of strain differences include the propensity of strains to become distributed across wide geographic regions and associated resistance management practices. Results from this work will directly influence sustainable fire blight management recommendations for commercial apple industries in NY State and other regions.

scholarly journals Prevalence of Streptomycin-Resistant Erwinia amylovora in New York Apple Orchards

Plant Disease ◽  
2016 ◽  
Vol 100 (4) ◽  
pp. 802-809 ◽  
Author(s):  
K. A. Tancos ◽  
S. Villani ◽  
S. Kuehne ◽  
E. Borejsza-Wysocka ◽  
D. Breth ◽  
...  
Keyword(s):  
United States ◽  
New York ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
The United States ◽  
Streptomycin Resistance ◽  
Apple Orchards ◽  
Wayne County ◽  
The Past ◽  
Shoot Blight

Resistance to streptomycin in Erwinia amylovora was first observed in the United States in the 1970s but was not found in New York until 2002, when streptomycin-resistant (SmR) E. amylovora was isolated from orchards in Wayne County. From 2011 to 2014, in total, 591 fire blight samples representing shoot blight, blossom blight, and rootstock blight were collected from 80 apple orchards in New York. From these samples, 1,280 isolates of E. amylovora were obtained and assessed for streptomycin resistance. In all, 34 SmR E. amylovora isolates were obtained from 19 individual commercial orchards. The majority of the resistant isolates were collected from orchards in Wayne County, and the remaining were from other counties in western New York. Of the 34 resistant isolates, 32 contained the streptomycin resistance gene pair strA/strB in the transposon Tn5393 on the nonconjugative plasmid pEA29. This determinant of streptomycin resistance has only been found in SmR E. amylovora isolates from Michigan and the SmR E. amylovora isolates discovered in Wayne County, NY in 2002. Currently, our data indicate that SmR E. amylovora is restricted to counties in western New York and is concentrated in the county with the original outbreak. Because the resistance is primarily present on the nonconjugative plasmid, it is possible that SmR has been present in Wayne County since the introduction in 2002, and has spread within and out of Wayne County to additional commercial growers over the past decade. However, research is still needed to provide in-depth understanding of the origin and spread of the newly discovered SmR E. amylovora to reduce the spread of streptomycin resistance into other apple-growing regions, and address the sustainability of streptomycin use for fire blight management in New York.

scholarly journals Effects of Consecutive Streptomycin and Kasugamycin Applications on Epiphytic Bacteria in the Apple Phyllosphere

Plant Disease ◽  
2017 ◽  
Vol 101 (1) ◽  
pp. 158-164 ◽  
Author(s):  
K. A. Tancos ◽  
K. D. Cox
Keyword(s):  
New York ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Streptomycin Resistance ◽  
Epiphytic Bacteria ◽  
Eastern United States ◽  
Pseudomonas Spp ◽  
Fluorescent Pseudomonas ◽  
Epiphyte Community

Antibiotic applications are essential for fire blight management in the eastern United States. Recently, streptomycin-resistant Erwinia amylovora strains were found in New York. There are growing concerns that streptomycin resistance may develop from postbloom streptomycin applications in local orchards. Our goal was to investigate the impacts of increasing streptomycin and kasugamycin applications on bacterial epiphyte community composition and antibiotic resistance in the phyllosphere of ‘Idared’ apple plantings in 2014 and 2015. Rinsate samples from leaves treated with 0, 3, 5, and 10 applications of streptomycin and kasugamycin were collected to isolate, enumerate, and identify epiphytic bacterial species. The majority of isolated epiphytic bacteria were identified as Pantoea agglomerans and fluorescent Pseudomonas spp., whereas E. amylovora was rarely found. Overall, postbloom streptomycin use did not result in an increased recovery of streptomycin-resistant E. amylovora. However, other streptomycin-resistant epiphytes (P. agglomerans and Pseudomonas spp.) did increase with increasing streptomycin applications. Increasing kasugamycin applications reduced the overall number and percentage of streptomycin-resistant epiphytes in the phyllosphere, which has important implications regarding the use of kasugamycin in orchards where streptomycin resistance is a concern.

scholarly journals Isolation of Streptomycin-Resistant Isolates of Erwinia amylovora in New York

Plant Disease ◽  
2008 ◽  
Vol 92 (5) ◽  
pp. 714-718 ◽  
Author(s):  
Nicole L. Russo ◽  
Thomas J. Burr ◽  
Deborah I. Breth ◽  
Herb S. Aldwinckle
Keyword(s):  
New York ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
New York State ◽  
The United States ◽  
Streptomycin Resistance ◽  
Antibiotic Resistant ◽  
Wayne County ◽  
Unintentional Movement ◽  
Growing Region

Streptomycin is currently the only antibiotic registered for the control of fire blight, a devastating disease of apple (Malus), pear (Pyrus), and other rosaceous plants caused by the bacterium Erwinia amylovora. Resistance of E. amylovora to streptomycin was first identified in California pear orchards in 1971 and is currently endemic in many parts of the United States. The Northeast remains the only major U.S. apple-growing region without streptomycin-resistant isolates of E. amylovora. In 2002, during a routine survey for streptomycin resistance, isolates from two neighboring orchards in Wayne County, NY were found to be highly resistant to streptomycin at a concentration of 100 μg/ml. This constitutes the first authenticated report of streptomycin resistance in New York State. Infected trees were shipped at the same time from a single nursery in Michigan. Resistance was caused by the acquisition of the strA-strB gene pair, inserted into the ubiquitous nontransmissible E. amylovora plasmid pEA29. Previously, streptomycin-resistant E. amylovora populations from Michigan were described with a similar mechanism of resistance, although the strA-strB genes are not unique to Michigan. These findings illustrate how unintentional movement of nursery material could undermine efforts to prevent the spread of antibiotic-resistant E. amylovora.

scholarly journals Fire Blight Symptomatic Shoots and the Presence of Erwinia amylovora in Asymptomatic Apple Budwood

Plant Disease ◽  
2017 ◽  
Vol 101 (1) ◽  
pp. 186-191 ◽  
Author(s):  
K. A. Tancos ◽  
E. Borejsza-Wysocka ◽  
S. Kuehne ◽  
D. Breth ◽  
Kerik D. Cox
Keyword(s):  
New York ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Causal Agent ◽  
Economic Losses ◽  
Apple Trees ◽  
The Mean ◽  
Collection Practices ◽  
Time Of Collection ◽  
Young Apple

Erwinia amylovora, the causal agent of fire blight, causes considerable economic losses in young apple plantings in New York on a yearly basis. Nurseries make efforts to only use clean budwood for propagation, which is essential, but E. amylovora may be present in trees that appear to have no apparent fire blight symptoms at the time of collection. We hypothesized that the use of infected budwood, especially by commercial nursery operations, could be the cause, in part, of fire blight outbreaks that often occur in young apple plantings in New York. Our goal was to investigate the presence of E. amylovora in asymptomatic budwood from nursery source plantings as it relates to trees with fire blight symptoms. From 2012 to 2015, apple budwood was collected from two commercial budwood source plantings of ‘Gala’ and ‘Topaz’ at increasing distances from visually symptomatic trees. From these collections, internal contents of apple buds were analyzed for the presence of E. amylovora. E. amylovora was detected in asymptomatic budwood in trees more than 20 m from trees with fire blight symptoms. In some seasons, there were significant (P ≤ 0.05) differences in the incidence of E. amylovora in asymptomatic budwood collected from symptomatic trees and those up to 20 m from them. In 2014 and 2015, the mean E. amylovora CFU per gram recovered from budwood in both the Gala and Topaz plantings were significantly lower in budwood collected 20 m from symptomatic trees. Further investigation of individual bud dissections revealed that E. amylovora was within the tissue beneath the bud scales containing the meristem. Results from the study highlight the shortcomings of current budwood collection practices and the need to better understand the factors that lead to the presence of E. amylovora in bud tissues to ensure the production of pathogen-free apple trees.

STREPTOMYCIN RESISTANCE OF ERWINIA AMYLOVORA IN ISRAEL AND OCCURRENCE OF FIRE BLIGHT IN PEAR ORCHARDS IN THE AUTUMN

1999 ◽  
pp. 85-92 ◽  
Author(s):  
S. Manulis ◽  
D. Zutra ◽  
F. Kleitman ◽  
O. Dror ◽  
E. Shabi ◽  
...  
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Streptomycin Resistance

scholarly journals Evaluation of Loop-Mediated Isothermal Amplification for Rapid Detection of Erwinia amylovora on Pear and Apple Fruit Flowers

Plant Disease ◽  
2011 ◽  
Vol 95 (4) ◽  
pp. 423-430 ◽  
Author(s):  
Todd N. Temple ◽  
Kenneth B. Johnson
Keyword(s):  
Rapid Detection ◽  
Pathogen Detection ◽  
Fire Blight ◽  
Management Practices ◽  
Erwinia Amylovora ◽  
Lamp Assay ◽  
Apple Fruit ◽  
Isothermal Amplification ◽  
Loop Mediated Isothermal Amplification ◽  
Forecasting Models

Fire blight of pear and apple is frequently an inoculum-limited disease but weather-based forecasting models commonly assume that the pathogen is omnipresent. To improve fire blight risk assessment during flowering, we developed a rapid pathogen detection protocol that uses loop-mediated isothermal amplification (LAMP) to detect DNA of epiphytic Erwinia amylovora on samples of pear and apple flowers. LAMP detected a single flower colonized epiphytically by E. amylovora in a sample of 100 flower clusters (approximately 600 flowers). Samples of 100 flower clusters from orchards (approximately one sample per hectare) were washed and subjected to LAMP, which was completed in 2 h. In three experimental orchards inoculated with E. amylovora, positive LAMP reactions were attained from nine of nine 100-flower cluster samples; pathogen populations in the floral washes averaged 5.2 × 103 CFU per flower as determined by dilution plating. Samples of pear and apple flowers obtained from 60 commercial orchards located in Oregon, Washington, California, and Utah resulted in detection of E. amylovora by LAMP assay from 34 sites, 20 of which developed fire blight. Of samples at early bloom, 10% were positive for epiphytic E. amylovora compared with 28% at petal fall; pathogen density in washes of positive samples averaged 3.2 × 102 CFU per flower. In another 26 orchards, all floral washes were negative for E. amylovora by LAMP and by dilution plating; a light severity of fire blight was observed in 8 of these orchards. Overall, positive detection of epiphytic E. amylovora in commercial orchards by LAMP-based scouting generally occurred at later stages of bloom after heat (risk) units had begun to accumulate, an indication that weather-based forecasting models may be an adequate measure of fire blight risk for many orchardists. Nonetheless, several orchardists communicated that information from the LAMP-based rapid detection protocol resulted in modification of their fire blight management practices.

scholarly journals Comparison of fire blight resistance screening methodologies

2014 ◽  
Vol 67 ◽  
pp. 145-150
Author(s):  
M.B. Horner ◽  
E.G. Hough ◽  
D.I. Hedderley ◽  
N.M. How ◽  
V.G.M. Bus
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Resistance Management ◽  
Breeding Programme ◽  
Bacterial Disease ◽  
Resistance Screening ◽  
Major Goal ◽  
Main Mode ◽  
Commercial Cultivars ◽  
Two Measures

Fire blight a bacterial disease caused by Erwinia amylovora is an ongoing problem for pipfruit growers with few control options available Most commercial cultivars and rootstocks are highly susceptible to the disease Breeding of fire blightresistant scions and rootstocks to manage the disease is a major goal of the New Zealand apple breeding programme The main mode of disease establishment is through flowers However the breeding programme currently evaluates disease resistance through shoot inoculations This study compared the degree of resistance in 109 progeny from a Royal Gala times; Malus robusta Robusta 5 family assessed by shoot inoculation and by floral inoculations Results indicate that the two measures of resistance do not correlate well and that different quantitative trait loci may be involved in flower and shoot resistance Management of fire blight through the implementation of resistant cultivars will require resistance screening on both shoot and flower assessments

scholarly journals Evaluation of Kasugamycin for Fire Blight Management, Effect on Nontarget Bacteria, and Assessment of Kasugamycin Resistance Potential in Erwinia amylovora

2011 ◽  
Vol 101 (2) ◽  
pp. 192-204 ◽  
Author(s):  
Gayle C. McGhee ◽  
George W. Sundin
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Management Strategies ◽  
Resistance Management ◽  
Aminoglycoside Antibiotic ◽  
Relative Fitness ◽  
Industry Standard ◽  
High Concentrations ◽  
New Compounds

The emergence and spread of streptomycin-resistant strains of Erwinia amylovora in Michigan has necessitated the evaluation of new compounds effective for fire blight control. The aminoglycoside antibiotic kasugamycin (Ks) targets the bacterial ribosome and is particularly active against E. amylovora. The efficacy of Ks formulated as Kasumin 2L for control of fire blight was evaluated in six experiments conducted over four field seasons in our experimental orchards in East Lansing, MI. Blossom blight control was statistically equivalent to the industry standard streptomycin in all experiments. E. amylovora populations remained constant on apple flower stigmas pretreated with Kasumin and were ≈100-fold lower than on stigmas treated with water. Kasumin applied to apple trees in the field also resulted in a 100-fold reduced total culturable bacterial population compared with trees treated with water. We performed a prospective analysis of the potential for kasugamycin resistance (KsR) development in E. amylovora which focused on spontaneous resistance development and acquisition of a transferrable KsR gene. In replicated lab experiments, the development of spontaneous resistance in E. amylovora to Ks at 250 or 500 ppm was not observed when cells were directly plated on medium containing high concentrations of the antibiotic. However, exposure to increasing concentrations of Ks in media (initial concentration 25 μg ml–1) resulted in the selection of Ks resistance (at 150 μg ml–1) in the E. amylovora strains Ea110, Ea273, and Ea1189. Analysis of mutants indicated that they harbored mutations in the kasugamycin target ksgA gene and that all mutants were impacted in relative fitness observable through a reduced growth rate in vitro and decreased virulence in immature pear fruit. The possible occurrence of a reservoir of KsR genes in orchard environments was also examined. Culturable gram-negative bacteria were surveyed from six experimental apple orchards that had received at least one Kasumin application. In total, 401 KsR isolates (42 different species) were recovered from apple flowers and leaves and orchard soil samples. Although we have not established the presence of a transferrable KsR gene in orchard bacteria, the frequency, number of species, and presence of KsR enterobacterial species in orchard samples suggests the possible role of nontarget bacteria in the future transfer of a KsR gene to E. amylovora. Our data confirm the importance of kasugamycin as an alternate antibiotic for fire blight management and lay the groundwork for the development and incorporation of resistance management strategies.

Examining spatial distribution and spread of fire blight in apple orchards: two case studies

2021 ◽  
Author(s):  
Anna Wallis ◽  
Kerik Cox
Keyword(s):  
Spatial Distribution ◽  
Case Studies ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Spatial Analyses ◽  
Focal Points ◽  
Planting Material ◽  
Apple Production ◽  
Management Recommendations ◽  
Different Sources

Fire blight, caused by the bacteria Erwinia amylovora, is an incredibly destructive disease of apples, capable of spreading rapidly through an orchard block. The pathogen is endemic to many apple production regions worldwide, but it is often introduced into newly planted sites on infested host material, while locally it is typically vectored by wind driven rain, hail, and insects. Here we present two case studies of orchard blocks infected with fire blight at the Cornell AgriTech Research orchards in which CRISPR profile characterization was used to identify strains present in the blocks and spatial analyses were used to describe the distribution and spread of the disease over the course of two years. Results indicated two very different sources of introduction (a nearby block or planting material) and patterns of spread (from a corner of the field or from focal points within the block). Describing the distribution and spread of fire blight within and between orchard blocks has the potential to improve our understanding of the disease movement, inform appropriate management recommendations, and facilitate traceback efforts.

scholarly journals Non-conventional possibilities of protection of apple and pear against fire blight (Erwinia amylovora)

2013 ◽  
Vol 55 (1) ◽  
pp. 299-310
Author(s):  
Piotr Sobiczewski ◽  
Grzegorz Krupiński ◽  
Joanna Puławska
Keyword(s):  
Plant Extracts ◽  
Fire Blight ◽  
Management Practices ◽  
Erwinia Amylovora ◽  
Control Method ◽  
Plant Protection ◽  
T4 Lysozyme ◽  
Resistance Inducers ◽  
Promising Perspective ◽  
Thymbra Spicata

Standard program of plant protection against fire blight consists of use of management practices and chemical control method. Recently a new, non-conventional possibilities based on application of biocontrol agents (two biopreparations have been already introduced into practice: Bliteban A506 (<i>Pseudomonas fluorescens</i>) and BlossomBless (<i>Pantoea agglomerans</i>), plant extracts active against <i>Erwinia amylovora</i> (AkseBio containing extracts from <i>Thymbra spicata</i> and Biomit Plussz with extracts from various plant species and microelements) and resistance inducers (Regalis, Bion and plant extracts) are of great interest. Also plant transformation with resistance genes such as: hrpN (harpin), <i>dpo</i> (EPS depolymerase) and lytic protein genes (attacin E, cecropin SB-37, T4 lysozyme) is a promising perspective.

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