Introduction to fungicide and bactericide resistance

Updated October 2023, R.M. Beresford

The apple black spot (apple scab) fungus
(Venturia inaequalis) has developed resistance
to multiple fungicide groups used in New Zealand

On behalf of the New Zealand Committee on Pesticide Resistance (NZCPR), a sub-committee of the New Zealand Plant Protection Society (NZPPS)

Modes of action of fungicides and bactericides

Chemicals at risk from resistance are mainly the modern synthetic ones developed since the 1960s that have a mode of action (MOA) targeting a specific biochemical pathway in a plant pathogen (single-site inhibitors). Many older therapeutants, such as captan, thiram, mancozeb, metiram, copper and sulphur, which have a non-specific MOA (multi-site inhibitors), are active against a broad spectrum of plant pathogens and are not generally considered to be at risk from resistance development. Having said that, copper resistance has been recorded in the peach leaf curl fungus (Taphrinia deformans) and can occur in some bacterial pathogens, e.g. bacterial blast (Pseudomonas syringae) and fire blight of apples and pears (Erwinia amylovora).

See the Glossary section for an explanation of fungicide and bactericide resistance related terms

How resistance develops

Resistance arises when repeated use of an at-risk fungicide or bactericide selects pathogen genetic types (strains) that are less sensitive (more resistant) to the therapeutant chemical. These strains have acquired a genetic mutation that reduces the inhibitory effect of the therapeutant on their metabolism. Continued use of the at-risk chemical selects out the less sensitive part of the population until the overall population becomes more resistant than it was previously. In other words, resistant strains survive the fungicide and go on to multiply while the non-resistant (sensitive) strains are killed off. Resistance can develop in two ways, either as directional selection or disruptive selection.

Directional selection: When the more resistant strains in the population encounter sub-lethal doses of a given therapeutant, they can survive when the more sensitive strains are killed. Repeated use of the therapeutant causes the overall sensitivity of the population to shift over time (often many years) until it becomes predominantly resistant. Sub-lethal doses in the field can result from patchy spray deposition, weathering of spray deposit over time or product applications below the recommended label rate.

Disruptive selection: This usually occurs with single-site inhibitor fungicides when a single gene in the fungal pathogen mutates to provide a different biochemical pathway that is less inhibited by the fungicide. The mutated strains can then survive in the presence of the chemical. This type of selection can give rise to a high degree of resistance quite rapidly (e.g., 3-5 years for some fungicides). Pathogen populations undergoing disruptive selection often show two distinct peaks in sensitivity to the fungicide, one that is highly sensitive for the non-mutated strains and another that is highly resistant for the mutated strains. The population resistance following disruptive selection is often stable and persists even when use of the affected fungicide is discontinued.

Detecting resistance

The presence of resistant strains in a pathogen population is detected by laboratory methods. The first step is to isolate into pure culture representative samples of the pathogen (typically 20-30) from a given population (e.g., a field, orchard or region). Each isolate must represent a single genetic type (genotype) and this is achieved from a single spore for fungi or from a single colony growing on a Petri dish for bacteria. Two approaches are used for detecting resistant isolates:

Growth inhibition: A range of fungicide or bactericide doses is used to determine the concentration which, for fungi, inhibits growth by 50% (EC50 value) or, for bacteria, is the lowest dose that inhibits growth (minimum inhibitory concentration; MIC). Growth inhibition methods reveal phenotype information on the overall sensitivity/resistance characteristic of each individual isolate but they do not reveal information about the genetic mechanism controlling resistance.
Resistance gene mutation detection: Molecular DNA-based methods are used to detect the presence of gene mutations in the pathogen isolates that are known from previous research to be associated with resistance to a fungicide or bactericide. The biochemical mode of action of the fungicide or bactericide must be understood as well as the genes controlling resistance. Genetic detection can allow the frequency of a resistance mutation in the population to be determined and can provide insights into the mechanisms that control resistance. This is important for interpreting whether directional or disruptive selection is occurring and for developing resistance management strategies.

Information from both growth inhibition studies and detection of gene mutations is valuable for detecting and understanding the nature of a resistance problem, and helps the development of appropriate and robust resistance management strategies.

Practical resistance

Laboratory studies may detect pathogen isolates with gene mutations that confer a degree of resistance in the laboratory (in vitro) but these may not be associated with ‘practical resistance’ in the field environment (i.e., they do not cause a loss of disease control). It is crucial to determine, using in-planta studies, whether the resistant isolates detected either by growth inhibition or gene detection can actually cause a loss of disease control compared with sensitive isolates. These tests require plants to be treated with an appropriate dose of fungicide or bactericide, then inoculated with putative resistant isolates to determine whether a significant decrease in disease control occurs.

Fitness cost associated with resistance

Sometimes the mutation and biochemical change that allows a resistant strain of the pathogen to survive in the presence of a fungicide or bactericide also decreases its ability to survive when that chemical is not used any more. In other words, the biochemical pathway associated with resistance is less efficient, so when use of the therapeutant stops, the pathogen cannot survive as well as non-resistant strains. Such a ‘fitness cost’ caused by resistance can allow the sensitivity in the pathogen population to increase when use of the chemical is reduced or stopped altogether. In some cases this can be used to manage resistance and can allow the useful life of a chemical to be prolonged. An example of this is use of the fungicide dodine in apples for control of Venturia inaequalis (apple black spot or scab), where reducing the number of applications per season has allowed the population sensitivity to increase.

Resistance management principles

When resistance develops, either by directional selection or disruptive selection, resistance can be delayed by the following means:

Limiting numbers of applications of the at-risk fungicide or bactericide.
Mixing the at-risk chemical with one from a different MOA (cross-resistance) group. This helps to ensure that no part of the pathogen population survives when the at-risk fungicide is applied.
Alternating each application of an at-risk fungicide or bactericide with ones from a different cross-resistance groups. This reduces exposure of the population to the at-risk therapeutant.
Avoiding exposure to sub-lethal doses that would favour directional selection. Some argue that the total amount of exposure of the pathogen to an at-risk MOA group is what selects resistance. This may be true for disruptive selection and is a point of contention among researchers.
Using non-chemical disease management practices, including crop hygiene to minimise pathogen carry-over and crop canopy management to make the crop environment less suitable for disease development.
Using recommended chemical application rates and ensuring uniform spray coverage from the use of appropriate spraying equipment that is correctly calibrated.

Glossary of fungicide and bactericide resistance related terms

Active ingredient (active constituent). The component(s) in a formulated fungicide or bactericide product that specifically inhibit the target pathogen. Products also contain other chemicals to achieve effective delivery of the active ingredient to the plant. The active ingredient name is the common name of the fungicide (e.g., triadimenol).

Disease control: Demonstrable prevention or inhibition of disease development.

Cross-resistance: When resistance that has developed to one fungicide or bactericide chemical also affects resistance to a different chemical. Cross-resistance can be positive if resistance to one chemical is associated with increased resistance to the other, or negative if it is associated with decreased resistance (increased sensitivity) to the other. Positive cross-resistance is what defines the chemicals belonging to a given mode of action (MOA) group.

Curative (systemic). A fungicide active ingredient that is absorbed into the plant and inhibits the pathogen within the plant tissues after infection has occurred. Such fungicides generally have a limited time after infection to ‘cure’ the infection (e.g., 1-3 days). This is often referred to as the ‘reach-back’ or ‘kick-back’ interval or period. ‘Systemic’ means within the plant tissue and is often used synonymously with ‘curative’. Curatives may also be effective protectants.

Efficacy: The intrinsic ability of a fungicide to prevent infection or inhibit the pathogen and thereby control disease, determined under controlled conditions.

Effectiveness: The disease control outcome from using fungicide(s) in the real world where factors in addition to efficacy affect control, e.g., application rate and mixing with other agents.

Effective dose: The amount of a fungicide with efficacy against a pathogen that must be applied to plants to achieve disease control.

Eradicant. A fungicide that kills existing fungal lesions on the plant. Eradicant is sometimes used synonymously with curative, but eradicants are not necessarily absorbed into the plant. Eradicants may be older multi-site inhibitor fungicides.

Mode of action (MOA). The biochemical pathway(s) within fungal cells inhibited by a particular fungicide. The Fungicide Resistance Action Committee (FRAC) assigns a code number to each MOA Group (frac-code-list-2022—final.pdf). The product label displays all the active ingredient groups in the product and their group code numbers. When fungicide resistance develops in a pathogen to a particular fungicide, then all the active ingredients within the same MOA group are expected to be affected by that resistance (positive cross-resistance). However, in practice different active ingredients within a group are often affected by resistance slightly differently.

Multi-site inhibitors. Usually older fungicides or bactericides that inhibit many metabolic pathways in the target pathogen (also known as broad-spectrum fungicides). These are generally not at risk from resistance development in the pathogen, although instances of copper resistance sometimes occur, particularly in bacterial pathogens.

Protectant. A fungicide or bactericide that is present only on the plant surface (not absorbed into the plant) and inhibits the pathogen by preventing infection.

Single-site inhibitors. Modern synthetic fungicides that inhibit a specific metabolic pathway in the target pathogen. These are often at risk of development of resistance in the pathogen.