Fire blight’s causal agent, the bacterium Erwinia amylora, has shown resistance to the antibiotic streptomycin, which is one of three antibiotics utilized to control this destructive pathogen. While most commonly known as a pest of apple trees, fire blight also effects pears and other plants in the Rosaceae family.

The lab of Dr. Kerik Cox, Ph.D., of Cornell University’s School of Integrative Plant Science, has been focusing on managing fire blight in apple orchards as well as researching the genetics behind streptomycin-resistant strains of the pathogen. A recent webinar provided growers with background and updates on the latest in best management practices to keep streptomycin-resistant E. amylora (SmR Ea) out of the orchard, and the advances made in understanding how the pathogen gains resistance.

The greater the number of E. amylora, the more likely a mutation is to occur which would cause SmR Ea. When there are larger microbe populations, there are more opportunities for resistance to develop. In small populations, any E. amylora that might become resistant to streptomycin would readily be eradicated by an alternate antibiotic – oxytetracycline or kasugamycin – and prevent the selection of resistant strains. Mutations causing resistance can also occur randomly without prior antibiotic exposure, and it would also be much less likely for such a mutation to appear within a low population.

Paths to Resistance

In 2002, two neighboring orchards in western New York were found to have the first detected streptomycin-resistant fire blight infections detected in the state. The disease was eradicated, and no other instances of SmR Ea were found until 2011, when a handful of nursery blocks used for budwood were infected and died.

From 2012-2020, the Cox lab collected 3,000 isolates from 182 commercial sites, and numerous strains of SmR Ea were found. Those strains were 99.9% homologous.

Those small genetic differences seen in E. amylora were found to occur within a plasmid – a small, circular DNA molecule which is physically separate from chromosomal DNA, and which replicates separately from chromosomal DNA.

The “fingerprint” of E. amylora plasmid DNA has three distinct sections, or spacers, which can evolve, gaining or losing DNA. The original strain in New York has been identified as 41:23:38. Other strains have been isolated, including some with both sensitive and resistant E. amylora present, and which share the exact same profile. This phenomenon has led researchers to hypothesize that such strains may be indigenous to the farms on which they are found.

From 2015-2018, Cornell researchers examined 72 SmR Ea samples from 11 farms. These samples contained 27 distinct profiles.

When the season’s weather provided the optimal conditions for E. amylora to thrive, the number of strains seen increased. All of the strains must compete against one another for dominance, so having a mix of strains is actually beneficial, Cox said.

When fire blight pressure is low, and growers didn’t need to spray antibiotics as frequently, the SmR Ea can’t gain a foothold, and bacteria lacking the resistant gene are not selected out. In conditions ripe for fire blight, however, growers spray more, which can eradicate the competition and leave SmR Ea to survive and thrive.

Two genes, known as strA and strB, have been identified as causing resistance to streptomycin. Both work by making a protein which has the ability to inactivate the streptomycin molecule. But it isn’t a single mutation which causes the bacteria to become resistant to streptomycin. The mutation involves large pieces of genetic material, with hundreds of base pairs.

Researchers in other regions have also uncovered a “jumping gene” which codes for streptomycin resistance and can move directly from bacterium to bacterium via certain types of plasmids. In Michigan, physical movement of bacteria themselves, rather than a gene fragment being transferred from one bacterium to another, was found to be the cause of widespread fire blight outbreaks.

A jumping gene which moves from plasmid to plasmid within a bacterial cell, but cannot be transferred from bacterium to bacterium, is the culprit. Similar to citrus canker, some strains of SmR Ea can be dispersed by strong winds or rains.

A plasmid which is able to jump from host to host is prevalent in New York now. The original strain 41:23:38 is passed through budwood and trees and is not spread via jumping genes. Thus far it remains confined to a few western New York counties, and it’s being monitored to see if it eventually spreads.

In addition, a strain with a particular mutation found to have an “incredibly high level of resistance”’ to streptomycin has been identified, Cox said. So far, this strain has only been found once in New York, but it is prevalent in Utah, Idaho, Wisconsin and Oregon.

Stopping Resistance

“What do we do to beat this thing?” is the question researchers are hoping to answer, Cox said.

The exact answers will vary farm to farm, but general guidelines include pruning out cankers; applying copper several times from late silver to one-half inch green; appropriate use of antibiotics and/or biologics into bloom; and perhaps preventative applications of prohexadione-calcium growth regulator for blossom blight and early shoot blight at the “early pink” stage, particularly in young and high-vigor orchards.

At bloom, forecasting models local to your orchard should be utilized. In high risk conditions – and combined with strong fire blight pressures on the farm – antibiotic applications should be considered.

“You really just need one well-timed application,” Cox said. But knowing just when that optimal time is can be tricky. “If something doesn’t look right, don’t make an application. Ask for verification.”

Post-petal fall applications appear to help select for SmR Ea, Cox said.

Monitoring and managing the orchard, both to prevent and contain fire blight, is the first step in protection. For farms without any SmR Ea, mixing streptomycin and oxytetracycline at the full rate and applying at bloom only if high risk conditions exist is recommended. Alternate applications with kasugamycin. Another option is alternating oxytetracycline with biologicals and copper.

Organic orchards are able to have good control with Blossom Protect™ in many trials across several different states.

What’s Ahead For New York Research?

The Cox lab is focused on collecting samples for the 2023 season. Since 2020, when 189 samples from 15 counties found that SmR Ea was present only in two counties, resistant strains of E. amylora showed up in samples from 10 of 12 counties in 2022.

The lab is offering farm history reports which will help track the status of sensitive and resistant strains in each orchard, allowing growers to adapt best management practices to control their specific situation.

“Knowing when and in which block can really help to optimize management” of sensitive and resistant strains, Isabella Yannuzzi, graduate student in the Cox lab, said. “The more consistently an orchard is sampled, the more likely we are to catch the resistance before it is widespread.”

Tissue samples or fresh ooze samples can be mailed to the lab. The lesion where the healthy and infected tissues meet is where bacteria are most active, and wrapping samples in damp paper towels before mailing is recommended.

More detailed fire blight information from the Cox lab can be found at