Resistance to fludioxonil in Botrytis cinerea isolates from blackberry and strawberry

The HOG-pathway related AaOS1 leads to dicarboximide-resistance in field strains of Alternaria alternata and contributes, together with the Aafhk1, to mycotoxin production and virulence

BACKGROUND

Garlic leaf spot (GLS) caused by Alternaria alternata is one of the main diseases in the garlic production areas, and its management heavily relies on dicarboximide fungicides. However, the efficacy of dicarboximides against the GLS disease has decreased year on year.

RESULTS

In the present study, 10 of 148 A. alternata strains separated from Jiangsu Province were moderately resistant (MR) to a dicarboximide fungicide procymidone (ProMR). Positive cross-resistance was observed between Pro and iprodione (Ipro) or fludioxonil (Fld), but not between Pro and fluazinam or azoxystrobin. Mutations at AaOS1, but not Aafhk1, were confirmed to confer the Pro resistance by constructing replacement mutants, whereas mutations at both AaOS1 and Aafhk1 decreased the gene expression level of AapksI, as well as the ability to produce mycotoxin AOH (polyketide-derived alternariol) and virulence. Additionally, more genes (AaOS1 and Aafhk1) harboring the mutations experienced a larger biological fitness penalty.

CONCLUSION

To our knowledge, this is the first report on Pro resistance selected in garlic fields, and mutations at AaOS1 of A. alternata causing a decreased ability to produce the mycotoxin AOH. © 2024 Society of Chemical Industry.

Chilean Botrytis cinerea Isolates with Reduced Sensitivity to Fludioxonil Exhibit Low to Null Fitness Penalties

The main phytosanitary problem for table grape production in Chile is gray mold caused by the fungus Botrytis cinerea. To manage this issue, the primary method utilized is chemical control. Fludioxonil, a phenylpyrrole, is highly effective in controlling B. cinerea and other plant pathogens. Consistently, there have been no field reports of reduced efficacy of fludioxonil; however, subpopulations with reduced sensitivity to fludioxonil are on the rise globally, as per increasing reports. Our study involved a large-scale evaluation of B. cinerea's sensitivity to fludioxonil in the Central Valley of Chile's primary table grape production area during the growing seasons from 2015 to 2018. Out of 2,207 isolates, only 1.04% of the isolates (n = 23) exceeded the sensitivity threshold value of 1 μg/ml. Remarkably, 95.7% are concentrated in a geographic region (Valparaíso Region). Isolates with reduced sensitivity to fludioxonil showed growth comparable with sensitive isolates and even more robust growth under nutritional deficit, temperature, or osmotic stress, suggesting greater environmental adaptation. When table grape detached berries were stored at 0°C, isolates less sensitive to fludioxonil caused larger lesions than sensitive isolates (2.82 mm compared with 1.48 mm). However, the lesions generated by both types of isolates were equivalent at room temperature. This study found no cross-resistance between fludioxonil and fenhexamid, an essential fungicide integrated with fludioxonil in Chilean B. cinerea control programs. All the Chilean isolates with reduced sensitivity to fludioxonil were controlled by the fludioxonil/cyprodinil mixture, a commonly employed form of fludioxonil. The cyprodinil sensitivity in the isolates with reduced sensitivity to fludioxonil explains their low field frequency despite their null fitness penalties. However, the emergence of fludioxonil-resistant isolates inside the Chilean B. cinerea population demands a comprehensive analysis of their genetic bases, accompanied by monitoring tools that allow the permanence of field fludioxonil efficacy.

A Conservative Mutant Version of the Mrr1 Transcription Factor Correlates with Reduced Sensitivity to Fludioxonil in Botrytis cinerea

Fludioxonil is a highly effective phenylpyrrole fungicide for controlling Botrytis cinerea. Although the field efficacy of fludioxonil remains high, Botrytis cinerea isolates with reduced sensitivity have been reported globally. The molecular target of fludioxonil still remains unknown; however, a mechanism of reduced sensitivity to fludioxonil underlies the overexpression of the ATP binding cassette (ABC) transporter AtrB in a dependent pathway of the Mrr1 transcription factor. Fludioxonil is a key player in controlling B. cinerea infection in table grapes in Chile. However, some isolates with a reduced sensitivity to fludioxonil were detected. This study observed endogenous atrB overexpression in Chilean isolates with reduced sensitivity to fludioxonil (n = 22) compared to the sensitive isolates (n = 10). All isolates increased the expression of atrB in a growth medium supplemented with fludioxonil (0.05 μg/mL). However, sensitive isolates showed lower atrB expression than those with reduced fludioxonil sensitivity. Remarkably, a mutant version of the transcription factor Mrr1 carrying 21 amino acid modifications was identified in all isolates with reduced sensitivity to fludioxonil. These changes alter the protein's transcription factor domain and the C-terminal portion of the protein but not the Zn (2)-C6 fungal-type DNA-binding domain. These results suggest a direct relationship between the conserved and divergent mutant version of mrr1 and sensitivity to fludioxonil. This study provides a new target for developing molecular diagnostic strategies to monitor B. cinerea's sensitivity to fludioxonil in the field.

Procymidone Application Contributes to Multidrug Resistance of Botrytis cinerea

The necrotrophic pathogen Botrytis cinerea infects a broad range of plant hosts and causes substantial economic losses to many crops. Although resistance to procymidone has been observed in the field, it remains uncertain why procymidone is usually involved in multidrug resistance (MDR) together with other fungicides. Nine mutants derived from the B. cinerea strain B05.10 through procymidone domestication exhibited high resistance factors (RFs) against both procymidone and fludioxonil. However, the fitness of the mutants was reduced compared to their parental strain, showing non-sporulation and moderate virulence. Furthermore, the RFs of these mutants to other fungicides, such as azoxystrobin, fluazinam, difenoconazole, and pyrimethanil, ranged from 10 to 151, indicating the occurrence of MDR. Transcriptive expression analysis using the quantitative polymerase chain reaction (qPCR) revealed that the mutants overexpressed ABC transporter genes, ranging from 2 to 93.7-fold. These mutants carried single-point mutations W647X, R96X, and Q751X within BcBos1 by DNA sequencing. These alterations in BcBos1 conferred resistance to procymidone and other fungicides in the mutants. Molecular docking analysis suggested distinct interactions between procymidone and Bos1 in the B. cinerea standard strain B05.10 or the resistant mutants, suggesting a higher affinity of the former towards binding with the fungicide. This study provides a comprehensive understanding of the biological characteristics of the resistant mutants and conducts an initial investigation into its fungicide resistance traits, providing a reference for understanding the causes of multidrug resistance of B. cinerea in the field.

Resistance to Seven Site-Specific Fungicides in Botrytis cinerea from Greenhouse-Grown Ornamentals

The fungal pathogen Botrytis cinerea is a notorious problem on many floriculture greenhouse hosts including petunia, geranium, and poinsettia; these key crops contribute to the $6.43 billion U.S. ornamental industry. While growers use cultural strategies to reduce relative humidity and free moisture to limit Botrytis blight, fungicides remain a primary component of control programs. Isolates (n = 386) of B. cinerea sampled from symptomatic petunia, geranium, and poinsettia in Michigan greenhouses from 2018 to 2021 were screened for resistance to eight fungicides belonging to seven Fungicide Resistance Action Committee (FRAC) groups. Single-spored isolates were subjected to a germination-based assay using previously defined discriminatory doses of each fungicide. Resistance was detected to thiophanate-methyl (FRAC 1; 94%), pyraclostrobin (FRAC 11; 80%), boscalid (FRAC 7; 67%), iprodione (FRAC 2; 65%), fenhexamid (FRAC 17; 38%), cyprodinil (FRAC 9; 38%), fludioxonil (FRAC 12; 21%), and fluopyram (FRAC 7; 13%). Most isolates (63.5%) were resistant to at least four FRAC groups, with 8.7% of all isolates demonstrating resistance to all seven FRAC groups tested. Resistance frequencies for each fungicide were similar among crops, production regions, and growing cycles but varied significantly for each greenhouse. Phenotypic diversity was high, as indicated by the 48 different fungicide resistance profiles observed. High frequencies of resistance to multiple fungicides in B. cinerea populations from floriculture hosts highlight the importance of sustainable and alternative disease management practices for greenhouse growers.

Fungicide-Resistant Botrytis in Forest Nurseries May Impact Disease Control in Norway Spruce

Gray mold, caused by Botrytis spp., is a serious problem in Norway spruce seedling production in forest nurseries. From 2013 to 2019, 125 isolates of Botrytis were obtained from eight forest nurseries in Norway: 53 from Norway spruce seedlings, 16 from indoor air, 52 from indoor surfaces, and four from weeds growing close to seedlings. The majority of isolates were identified as B. cinerea, and over 60% of these were characterized as Botrytis group S. B. pseudocinerea isolates were obtained along with isolates with DNA sequence similarities to B. prunorum. Fungicide resistance was assessed with a mycelial growth assay, and resistance was found for the following: boscalid (8.8%), fenhexamid (33.6%), fludioxonil (17.6%), pyraclostrobin (36.0%), pyrimethanil (13.6%), and thiophanate-methyl (50.4%). Many isolates (38.4%) were resistant to two to six different fungicides. A selection of isolates was analyzed for the presence of known resistance-conferring mutations in the cytb, erg27, mrr1, sdhB, and tubA genes, and mutations leading to G143A, F412S, ΔL497, H272R, and E198A/F200Y were detected, respectively. Detection of fungicide resistance in Botrytis from Norway spruce and forest nursery facilities reinforces the necessity of employing resistance management strategies to improve control and delay development of fungicide resistance in the gray mold pathogens.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Identification of Fusarium Basal Rot Pathogens of Onion and Evaluation of Fungicides against the Pathogens

Onion (Allium cepa L.) is an economically important vegetable crop worldwide. However, various fungal diseases, including Fusarium basal rot (FBR), neck rot, and white rot, reduce onion production or bulb storage life. FBR caused by Fusarium species is among the most destructive onion diseases. In this study, we identified Fusarium species associated with FBR in Jeolla and Gyeongsang Provinces in South Korea and evaluated fungicides against the pathogens. Our morphological and molecular analyses showed that FBR in onions is associated with Fusarium commune, Fusarium oxysporum, and Fusarium proliferatum. We selected seven fungicides (fludioxonil, hexaconazole, mandestrobin, penthiopyrad, prochloraz-manganese, pydiflumetofen, and tebuconazole) and evaluated their inhibitory effects on mycelial growth of the pathogens at three different concentrations (0.01, 0.1, and 1 mg/mL). We found that prochloraz-manganese was highly effective, inhibiting 100% of the mycelial growth of the pathogens at all concentrations, followed by tebuconazole. Fludioxonil showed < 50% inhibition at 1 mg/mL for the tested isolates.

Transcriptomic Analysis of Resistant and Wild-Type Botrytis cinerea Isolates Revealed Fludioxonil-Resistance Mechanisms

Botrytis cinerea, the causal agent of gray mold, is one of the most destructive pathogens of cherry tomatoes, causing fruit decay and economic loss. Fludioxonil is an effective fungicide widely used for crop protection and is effective against tomato gray mold. The emergence of fungicide-resistant strains has made the control of B. cinerea more difficult. While the genome of B. cinerea is available, there are few reports regarding the large-scale functional annotation of the genome using expressed genes derived from transcriptomes, and the mechanism(s) underlying such fludioxonil resistance remain unclear. The present study prepared RNA-sequencing (RNA-seq) libraries for three B. cinerea strains (two highly resistant (LR and FR) versus one highly sensitive (S) to fludioxonil), with and without fludioxonil treatment, to identify fludioxonil responsive genes that associated to fungicide resistance. Functional enrichment analysis identified nine resistance related DEGs in the fludioxonil-induced LR and FR transcriptome that were simultaneously up-regulated, and seven resistance related DEGs down-regulated. These included adenosine triphosphate (ATP)-binding cassette (ABC) transporter-encoding genes, major facilitator superfamily (MFS) transporter-encoding genes, and the high-osmolarity glycerol (HOG) pathway homologues or related genes. The expression patterns of twelve out of the sixteen fludioxonil-responsive genes, obtained from the RNA-sequence data sets, were validated using quantitative real-time PCR (qRT-PCR). Based on RNA-sequence analysis, it was found that hybrid histidine kinase, fungal HHKs, such as BOS1, BcHHK2, and BcHHK17, probably involved in the fludioxonil resistance of B. cinerea, in addition, a number of ABC and MFS transporter genes that were not reported before, such as BcATRO, BMR1, BMR3, BcNMT1, BcAMF1, BcTOP1, BcVBA2, and BcYHK8, were differentially expressed in the fludioxonil-resistant strains, indicating that overexpression of these efflux transporters located in the plasma membranes may associate with the fludioxonil resistance mechanism of B. cinerea. All together, these lines of evidence allowed us to draw a general portrait of the anti-fludioxonil mechanisms for B. cinerea, and the assembled and annotated transcriptome data provide valuable genomic resources for further study of the molecular mechanisms of B. cinerea resistance to fludioxonil.

Under Pressure: A Comparative Study of Botrytis cinerea Populations from Conventional and Organic Farms in Cyprus and Greece

The highly heterogeneous nature of Botrytis cinerea provides adaptive benefits to variable environmental regimes. Disentangling pathogen population structure in anthropogenic agroecosystems is crucial to designing more effective management schemes. Herein, we studied how evolutionary forces exerted in different farming systems, in terms of agrochemicals-input, shape B. cinerea populations. In total, 360 B. cinerea isolates were collected from conventional and organic, strawberry and tomato farms in Cyprus and Greece. The occurrence and frequency of sensitivities to seven botryticides were estimated. Results highlighted widespread fungicide resistance in conventional farms since only 15.5% of the isolates were sensitive. A considerable frequency of fungicide-resistant isolates was also detected in the organic farms (14.9%). High resistance frequencies were observed for boscalid (67.7%), pyraclostrobin (67.3%), cyprodinil (65.9%), and thiophanate-methyl (61.4%) in conventional farms, while high levels of multiple fungicide resistance were also evident. Furthermore, B. cinerea isolates were genotyped using a set of seven microsatellite markers (simple sequence repeat [SSR] markers). Index of association analyses (Ia and rBarD) suggest asexual reproduction of the populations, even though the mating-type idiomorphs were equally distributed, indicating frequency-dependent selection. Fungicide resistance was correlated with farming systems across countries and crops, while SSRs were able to detect population structure associated with resistance to thiophanate-methyl, pyraclostrobin, boscalid, and cyprodinil. The expected heterozygosity in organic farms was significantly higher than in conventional, suggesting the absence of selective pressure that may change the allelic abundance in organic farms. However, genetic variance among strawberry and tomato populations was high, ranking host specificity higher than other selection forces studied.

Comparison of the Biological Characteristics and Molecular Mechanisms of Fludioxonil-Resistant Isolates of Botrytis cinerea from Tomato in Liaoning Province of China

Botrytis cinerea is a common filamentous phytopathogen that causes serious pre- and postharvest losses worldwide. The phenylpyrrole fungicide fludioxonil has been reported to have high activity against B. cinerea and has been applied to control gray mold in tomato. A total of 206 B. cinerea isolates were collected from tomato greenhouses in Liaoning Province, China, in 2016 and 2017, and sensitivity to fludioxonil was demonstrated by discriminatory concentrations. One highly fludioxonil-resistant isolate, 5 medium-fludioxonil-resistance isolates, and 23 low-fludioxonil-resistance isolates were detected in the field. The fludioxonil-resistant isolates were less fit than the sensitive isolates and presented reduced sporulation, pathogenicity, and mycelial growth and hypersensitivity to osmotic stress, even though sclerotium production had no connection with resistance. Positive cross-resistance was observed between fludioxonil and the dicarboximide fungicides procymidone and iprodione but not between fludioxonil and the fungicides boscalid, fluopyram, fluazinam, and pyrimethanil. Sequence alignment of the BcOS1 gene indicated that the observed sensitivity was identical to that of B05.10 and the low-resistance mutant had two types of mutations, F127S+I365N and A1259T. The medium-resistance mutants had only one type of mutation linked with the 3-aa mutant Q369P+N373S+A1259T, and the highly resistant mutant had a 3-aa mutation with I365S+N373S+A1259T. Molecular docking illustrated that all the resistant isolates showed less affinity than the sensitive isolates with fludioxonil.

De novo assembly provides new insights into the evolution of Elaeagnus angustifolia L

BACKGROUND

Elaeagnus angustifolia L. is a deciduous tree in the family Elaeagnaceae. It is widely used to study abiotic stress tolerance in plants and to improve desertification-affected land because of its ability to withstand diverse types of environmental stress, such as drought, salt, cold, and wind. However, no studies have examined the mechanisms underlying the resistance of E. angustifolia to environmental stress and its adaptive evolution.

METHODS

Here, we used PacBio, Hi-C, resequencing, and RNA-seq to construct the genome and transcriptome of E. angustifolia and explore its adaptive evolution.

RESULTS

The reconstructed genome of E. angustifolia was 526.80 Mb, with a contig N50 of 12.60 Mb and estimated divergence time of 84.24 Mya. Gene family expansion and resequencing analyses showed that the evolution of E. angustifolia was closely related to environmental conditions. After exposure to salt stress, GO pathway analysis showed that new genes identified from the transcriptome were related to ATP-binding, metal ion binding, and nucleic acid binding.

CONCLUSION

The genome sequence of E. angustifolia could be used for comparative genomic analyses of Elaeagnaceae family members and could help elucidate the mechanisms underlying the response of E. angustifolia to drought, salt, cold, and wind stress. Generally, these results provide new insights that could be used to improve desertification-affected land.

Biological and molecular characterizations of field fludioxonil-resistant isolates of Fusarium graminearum

Fusarium head blight (FHB) predominately caused by F. graminearum, is an economical devastating disease for grain cereal crops especially on wheat. The phenylpyrrole fungicide fludioxonil exhibits excellent activity against F. graminearum and has been registered to control FHB in China. In this study, 6 fludioxonil-resistant (FludR) isolates of F. graminearum were identified from 2910 isolates collected from wheat cultivated field in Jiang Su, An Hui and Henan province of China in 2020. The sensitivity assay showed that resistance factor (RF) of FludR isolates ranges from 170.73 to >1000. In comparison with fludioxonil-sensitive (FludS) isolates, all of FludR isolates showed fitness defects in terms of mycelial growth, conidiation and virulence. Under fludioxonil treatment condition, the glycerol accumulation was obviously increased in FludS isolates, but was slightly increased in FludR isolates. Four FludR isolates exhibited increased sensitivity to osmotic stresses. Moreover, there is no positive cross-resistance between fludioxonil and other fungicides including phenamacril, carbendazim and tebuconazole. When treated with fludioxonil, the phosphorylation level of Hog1 was significantly decreased in the four FludR isolates, which was in contrast to the observation in the FludS and two FludR isolates where phosphorylation level of Hog1 was increased. Sequencing assay showed that the mutations were identified in different domains in FgOS1, FgOS2 or FgOS4 in FludR isolates. This was first reported that biological and molecular characterizations of field isolates of F. graminearum resistant to fludioxonil. The results can provide scientific directions for controlling FHB using fludioxonil.

Fungicide resistance characterized across seven modes of action in Botrytis cinerea isolated from Australian vineyards

BACKGROUND

Botrytis bunch rot, caused by Botrytis cinerea, is an economically important disease of grapes in Australia and across grape-growing regions worldwide. Control of this disease relies on canopy management and the application of fungicides. Fungicide application can lead to the selection of resistant B. cinerea populations, which has an adverse effect on the management of the disease. Characterizing the distribution and severity of resistant B. cinerea populations is needed to inform resistance management strategies.

RESULTS

In this study, 724 isolates were sampled from 76 Australian vineyards during 2013-2016 and were screened against seven fungicides with different modes of action (MOAs). The resistance frequencies for azoxystrobin, boscalid, fenhexamid, fludioxonil, iprodione, pyrimethanil and tebuconazole were 5%, 2.8%, 2.1%, 6.2%, 11.6%, 7.7% and 2.9%, respectively. Nearly half of the resistant isolates (43.8%) were resistant to more than one of the fungicides tested. The frequency of vineyards with at least one isolate simultaneously resistant to one, two, three, four or five fungicides was 19.7%, 7.9%, 6.6%, 10.5% and 2.6%. Resistance was associated with previously published genotypes in CytB (G143A), SdhB (H272R/Y), Erg27 (F412S), Mrr1 (D354Y), Bos1 (I365S, N373S + Q369P, I365S + D757N) and Pos5 (V273I, P319A, L412F/V). Novel genotypes were also described in Mrr1 (S611N, D616G), Pos5 (V273L) and Cyp51 (P347S). Expression analysis was used to characterize fludioxonil-resistant isolates exhibiting overexpression (6.3-9.6-fold) of the ABC transporter gene AtrB (MDR1 phenotype).

CONCLUSION

Resistance frequencies were lower when compared to most previously published surveys of B. cinerea resistance in grape and other crops. Nevertheless, continued monitoring of critical MOAs used in Australian vineyards is recommended. © 2021 Society of Chemical Industry.

Sensitivity of Colletotrichum nymphaeae to Six Fungicides and Characterization of Fludioxonil-Resistant Isolates in China

Colletotrichum nymphaeae is the dominant species causing anthracnose disease of peach in China. In this study, 140 isolates of C. nymphaeae were assessed for their sensitivity to six fungicides. It was found that C. nymphaeae was highly resistant to carbendazim, procymidone, and boscalid but sensitive to pyraclostrobin and prochloraz. For fludioxonil, the fungus exhibited differential sensitivities (i.e., approximately 14% of isolates were resistant to fludioxonil and the resistance was stable). Fludioxonil-resistant isolates had a mean EC₅₀ value of 2.2380 µg/ml, whereas the mean EC₅₀ value was 0.0194 µg/ml in fludioxonil-sensitive isolates. The mean EC₅₀ values of C. nymphaeae for pyraclostrobin and prochloraz were 0.0083 µg/ml and 0.002 µg/ml, respectively. No cross-resistance was observed between fungicides from different groups. Mycelial growth rate, control efficacy, and osmotic stress responses were significantly different (P < 0.05) between fludioxonil-sensitive (Flu^S) and -resistant (Flu^R) isolates, but no significant difference was observed (P > 0.05) in virulence and sporulation between Flu^S and Flu^R isolates. No mutation was detected in coding regions of the CnOs-1, Cal, Hk1, Hog1, TPI, and Mrr1 genes. Interestingly, with fludioxonil treatment, the expression of ABC transporter gene atrB was significantly overexpressed in some resistant isolates. However, overexpression of the atrB gene was not detected in one moderately and one highly resistant isolate, indicating that other unknown mechanisms may be involved. Current findings uncovered several effective chemicals and provided the foundation for designing management strategies to practically control peach anthracnose with the most effective demethylation inhibitor fungicides and quinone outside inhibitor fungicides.

Sensitivity of Colletotrichum fructicola and Colletotrichum siamense of Peach in China to Multiple Classes of Fungicides and Characterization of Pyraclostrobin-Resistant Isolates

Anthracnose, mainly caused by Colletotrichum gloeosporioides species complex including Colletotrichum fructicola and Colletotrichum siamense, is a devastating disease of peach. Chemical control has been widely used for years, but management failures have increased with the commonly used fungicides. Therefore, screening of sensitivity of Colletotrichum spp. to fungicides with different modes of action is needed to make proper management strategies for peach anthracnose. In this study, the sensitivity of 80 isolates of C. fructicola and C. siamense was screened for pyraclostrobin, procymidone, prochloraz, and fludioxonil based on mycelial growth inhibition at discriminatory doses. Results showed that C. fructicola and C. siamense isolates were highly resistant to procymidone and fludioxonil with 100% resistance frequencies to both fungicides, but sensitive to prochloraz, i.e., no resistant isolates were found. For pyraclostrobin, 74% of C. fructicola isolates showed high resistance, 26% showed low resistance, and all of the C. siamense isolates showed low resistance. No positive cross-resistance was observed between pyraclostrobin and azoxystrobin even when they are members of the same quinone outside inhibitor (QoI) fungicide group or between pyraclostrobin and non-QoIs. Resistant isolates to QoI fungicides were evaluated for the fitness penalty. Results showed that no significant differences except for the mycelial growth rates that were detected between high- and low-resistance isolates of C. fructicola. Molecular characterization of the Cyt b gene revealed that the G143A point mutation was the determinant of the high resistance in C. fructicola. This study demonstrated the resistance status of C. fructicola and C. siamense to different fungicides and briefly discussed implications of that resistance. Demethylation inhibitor fungicides were found to be the best option among the different chemicals studied here, to control peach anthracnose in China.

Biological Characteristics and Molecular Mechanism of Procymidone Resistance in Stemphylium eturmiunum From Garlic

Garlic leaf blight caused by Stemphylium eturmiunum was first reported in Jiangsu Province in China. The dicarboximide fungicide (DCF) procymidone is reported to possess broad-spectrum action in inhibiting filamentous fungi and is widely used to control leaf disease of various plants. Of 41 Stemphylium eturmiunum isolates collected in this study from commercial garlic farms in Pizhou and Dafeng counties of Jiangsu Province, eight isolates were resistant to procymidone. The following three phenotypes were categorized according to in vitro responses to DCFs: sensitive, low resistance to iprodione and procymidone, and high resistance to all iprodione and procymidone. The fitness of all resistant isolates was decreased in accordance with data on mycelial growth, conidiation, and virulence. After treatment with 10 µg/ml of procymidone for 4 h, mycelial intracellular glycerol concentrations of resistant isolates were significantly lower than those of sensitive isolates. Positive cross-resistance was observed between dicarboximides and phenylpyrroles, but there was no cross-resistance between dicarboximides and fluazinam or difenoconazole in the two resistant phenotypes. Nucleotide sequence alignment of two-component histidine kinase genes from sensitive and resistant isolates indicated that amino acid mutations were located at the histidine kinase, adenylyl cyclase, methyl-accepting chemotaxis protein and at the phosphatase domain of the N-terminal region and the response regulator domain of the C-terminal region. To our knowledge, this is the first report of DCF resistance in Stemphylium eturmiunum, and these findings will help establish a rational strategy to manage DCF-resistant populations of Stemphylium eturmiunum in the field.

Tank-mixing adjuvants enhanced the efficacy of fludioxonil on cucumber anthracnose by ameliorating the penetration ability of active ingredients on target interface

In this study, pot and field experiments showed that S903, Hasten and Gemini-31511 can significantly enhanced the control efficacy of fludioxonil on cucumber anthracnose. Then by studying the deposition and penetration interaction between active ingredients and cucumber leaves to revealed how the adjuvants influence the interaction process between pesticide active ingredients and target plants to improve the control efficacy. By analysis the effect of fludioxonil deposition to synergism of adjuvants, indicated that fludioxonil active ingredient deposition caused by adjuvants was not the main factor for the adjuvants synergistic effect. Fludioxonil + S903 yielded the lowest surface tension and contact angle, which also implying the best wetting ability. The mean diameters in Hasten + fludioxonil group were much smaller than those in only fludioxonil group (5.39 μm-90 g a.i. ha^-1, 5.50 μm-180 g a.i. ha^-1), the average particle size only had 3.45 μm (90 g a.i. ha^-1) and 3.94 μm (180 g a.i. ha^-1). And the result of spray droplets was consistent with the particles of fludioxonil crystals observed on glass slides and cucumber leaves. Therefore, S903 improved the penetrability of fludioxonil in the target plants by improving the wetting and dispersion of active ingredients on the target interface. Meantime, Hasten improved the penetrability of fludioxonil in the target plants by decreasing the particle size of active ingredients.

Characterization of High Fludioxonil Resistance in Botrytis cinerea Isolates from Calibrachoa Flowers

The fungicide fludioxonil is one of the most effective single-site fungicides available for managing flower blight caused by Botrytis cinerea on fruit and ornamental crops. Although low and moderate levels of resistance to fludioxonil have been reported in the pathogen across the United States and Europe, high resistance has been reported only from greenhouses in China. In this study, two B. cinerea isolates with high resistance (half maximal effective concentration >100 µg/ml) to fludioxonil were detected on ornamental calibrachoa flowers grown in a greenhouse. These isolates exhibited stable resistance for >20 generations, produced symptoms on calibrachoa flowers sprayed with label rates of fludioxonil, and displayed in vitro fitness penalties with decreased mycelial growth (P < 0.0001) and sporulation (P < 0.0001) compared with sensitive isolates. Highly resistant isolates were identified as MDR1h, containing the ΔL/V497 deletion in mrr1. However, resistance levels and in vitro fitness parameter characteristics were not consistent with this phenotype. One isolate contained the mutation L267V between HAMP domains 1 and 2 of the Bos-1 gene, and both isolates exhibited high osmotic sensitivity and reduced glycerol accumulation in the presence of fludioxonil, indicating that high resistance of these isolates may be associated with the high-osmolarity glycerol mitogen-activated protein kinase pathway.

Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review

The rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.

Fungicide Resistance Profiles of Botrytis cinerea Isolates From Michigan Vineyards and Development of a TaqMan Assay for Detection of Fenhexamid Resistance

Botrytis cinerea on grapes causes bunch rot at both pre- and postharvest stages, in which losses can reach up to 100%. Chemical control primarily relies on the prophylactic use of site-specific fungicides. Repeated applications of these products raise the risk of fungicide resistance development in B. cinerea populations, which can result in disease control failures. To determine the extent of resistance, B. cinerea isolates were collected from grape clusters in the northwest and southwest grape growing regions of Michigan in 2014 and 2018 (n = 115 and 125, respectively). These isolates were phenotyped using discriminatory doses of eight fungicides to determine the levels of resistance. Fungicide resistance increased from 2014 to 2018, mostly affecting the active ingredients fenhexamid, fluopyram, and iprodione. B. cinerea isolates resistant to multiple fungicides were detected in 2014 and 2018, with a higher frequency of resistance in 2018. TaqMan real-time PCR has been developed to detect B. cinerea fungicide resistance to fenhexamid and to differentiate the erg27 F412S/I/V alleles. The TaqMan assay was tested for sensitivity, specificity, and reproducibility on purified DNA and infected grape tissue samples. Our data provide essential information to growers about the efficacy for B. cinerea control using the available botryticides. Furthermore, the developed fenhexamid markers will be transferred to diagnostic clinics to assist growers in the management of bunch rot before resistance-related control failures occur.

Engineering Plant Synthetic Pathways for the Biosynthesis of Novel Antifungals

Plants produce a wealth of biologically active compounds, many of which are used to defend themselves from various pests and pathogens. We explore the possibility of expanding upon the natural chemical diversity of plants and create molecules that have enhanced properties, by engineering metabolic pathways new to nature. We rationally broaden the set of primary metabolites that can be utilized by the core biosynthetic pathway of the natural biopesticide, brassinin, producing in planta a novel class of compounds that we call crucifalexins. Two of our new-to-nature crucifalexins are more potent antifungals than brassinin and, in some instances, comparable to commercially used fungicides. Our findings highlight the potential to push the boundaries of plant metabolism for the biosynthesis of new biopesticides.

Reduced sensitivity of azoxystrobin and thiophanate-methyl resistance in Lasiodiplodia theobromae from papaya

Stem-end rot caused by Lasiodiplodia theobromae is one of the most devastating diseases of papaya in northeastern Brazil. It is most effectively controlled by applications of fungicides, including site-specific fungicides at risk for resistance development. This study investigated the molecular mechanisms of reduced sensitivity to the QoI fungicide azoxystrobin and resistance to the MBC fungicide thiophanate-methyl in L. theobromae from Brazilian orchards. The EC₅₀ values for azoxystrobin in sixty-four isolates ranged from 0.36 μg/ml to 364.24 μg/ml and the frequency distribution of EC₅₀ values formed a multimodal curve, indicating reduced sensitivity to azoxystrobin. In detached fruit assays reduced sensitive isolates were not controlled as effectively as sensitive isolates at lowest label rate. Partial fragments were obtained from target genes β-tubulin (751 bp) and Cytb (687 bp) of isolates resistant to thiophanate-methyl and reduced sensitivity to azoxystrobin. Sequence analysis of the β-tubulin fragment revealed a mutation corresponding to E198K in all thiophanate-methyl-resistant isolates, while reduced sensitivity to axoxystrobin was not attributable to Cytb gene alterations. The target gene-based mechanism conferring resistance to thiophanate-methyl will likely be stable even if selection pressure subsides. However, the mechanism conferring reduced sensitivity to azoxystrobin is not based on target gene modifications and thus may not be as stable as other genotypes with mutations in Cytb gene.

atrB-Associated Fludioxonil Resistance in Botrytis fragariae Not Linked to Mutations in Transcription Factor mrr1

Resistance to fludioxonil in Botrytis cinerea and B. fragariae was previously found to be linked to either overexpression of the drug efflux pump atrB activated by mutations in transcription factor mrr1 or to mutations in the osmoregulation gene os1. In the present study, isolates of B. cinerea, Botrytis group S, or B. fragariae collected from strawberry fields in the United States were resistant to fludioxonil with half-maximal effective concentration values ranging from 0.04 to 0.43 µg/ml for B. cinerea, 0.03 to 1.03 µg/ml for Botrytis group S, and 0.28 to 3.48 µg/ml for B. fragariae. Analyses of mrr1 sequences revealed various mutations linked to fludioxonil resistance in B. cinerea and Botrytis group S isolates. However, no mutations in mrr1 correlated with atrB overexpression-mediated resistance in B. fragariae isolates. Neither nucleotide variations in the 1,370-bp upstream region of atrB nor increased atrB copy numbers could explain the atrB overexpression in these B. fragariae isolates. Mutations in os1 conferred resistance to iprodione in B. cinerea and Botrytis group S isolates; none correlated with resistance to fludioxonil in B. fragariae. In contrast to European isolates, U.S. B. fragariae isolates contained a 3-bp insertion in the coding region of os1. These isolates were more sensitive to osmotic stress but it is unclear whether the insertion is responsible for this phenotype. Our findings suggest that atrB overexpression-associated fludioxonil resistance is an across-species mechanism of resistance to fludioxonil that can be induced by mutations in mrr1 and other, still-unknown mechanisms.

Paecilomyces niveus: Pathogenicity in the Orchard and Sensitivity to Three Fungicides

Paecilomyces rot of apples is a postharvest disease caused by the thermotolerant fungus Paecilomyces niveus (Byssochlamys nivea). The etiology of disease and the activity of fungicides against P. niveus are not yet well understood. This study evaluated the ability of P. niveus to infect 'Gala' apples growing in a conventionally managed orchard. In addition, the sensitivity of P. niveus isolates to postharvest fungicides difenoconazole, fludioxonil, and pyrimethanil was characterized for isolates from both agricultural and nonagricultural environments. Apples were wounded and mock-inoculated or inoculated with P. niveus in early July. At the time of harvest, 8 weeks after wounding, the inoculated apples had significantly larger lesions than mock-inoculated apples (P < 0.005). The average diameter of lesions on wound-inoculated apples was 11.17 mm ± 6.82 SD, while the average diameter of mock-inoculated lesions was 3.34 mm ± 1.85 SD. Disease symptoms in the orchard were similar to postharvest symptoms of Paecilomyces rot. Symptoms included a brown, flattened, circular lesion with faint concentric rings. The necrosis of mesocarp was firm and roughly U-shaped. Baseline isolates of P. niveus, from nonagricultural environments, were used to determine the effective fungicide dose at which growth was inhibited by 50% (EC₅₀). Furthermore, fungicide sensitivity of P. niveus isolates was examined using relative growth assays at the mean baseline EC₅₀ values to compare baseline isolates with isolates obtained from commercial apple orchards where they were likely exposed to fungicides. Among the exposed isolates, reduced sensitivity to all fungicides was observed, but significant differences between baseline and exposed isolates were only observed with fludioxonil (P < 0.0001). This is the first report demonstrating that P. niveus can infect apples that are wound-inoculated in the orchard and that isolates from agricultural environments are less sensitive to common fungicides, especially fludioxonil. This finding may have implications for the control of this postharvest diseases. Whether natural infections of apples by P. niveus is initiated in the orchard or during postharvest has yet to be determined.

Sensitivity of Botrytis cinerea From Nectarine/Cherry in China to Six Fungicides and Characterization of Resistant Isolates

Botrytis cinerea, the causal agent of gray mold, can result in considerable preharvest and postharvest losses in many economically valuable plant species. Fungicides were widely used to minimize such losses, but fungicide resistances were detected frequently. In the present study, we collected 164 isolates from nectarine and cherry in China and tested the sensitivity to six fungicides. Among the tested isolates, 71 (43.3%) were resistant to azoxystrobin, 14 (8.5%) to cyprodinil, 7 (4.3%) to boscalid, 4 (2.4%) to carbendazim, 1 (0.6%) to iprodione, and no isolates were found to be resistant to fludioxonil. The EC₅₀ value and resistance factor (RF) of resistant isolates were determined. Fitness analysis showed that there were no significant differences between sensitive and resistant isolates for osmotic stress and pathogenicity, while more conidia production was observed for some resistant isolates. Control efficacy of fungicides showed that the resistant isolates could not be controlled efficiently by using corresponding fungicides. The point mutation G143A was detected in the Cyt b gene of the isolates resistant to azoxystrobin, while the point mutation H272R of SdhB gene was confirmed in boscalid-resistant isolates, and mutations E198V/A of TUB2 gene and mutation I365S of BcOs1 occurred in carbendazim-resistant and iprodione-resistant isolates, respectively. These results indicate that the occurrence of fungicide resistance greatly threatens the management of gray mold on stone fruits nectarine and cherry.

Uncertainty surrounding the mechanism and safety of the post-harvest fungicide fludioxonil

Fludioxonil is a phenylpyrrole pesticide that is applied to fruit and vegetable crops post-harvest to minimize losses to mold, both during transport and at point of sale. Its effectiveness is reflected in the dramatic increase in its production/usage since its introduction in 1994, an increase that has peaked in recent years as it became licenced for use abroad. Recently, doubts as to the nature of its mechanism of action have been raised. Given that the pesticide has long been known to induce stress intermediates in target and non-target organisms alike, the lack of a firmly established mechanism might be cause for concern. Troubling reports further delineate a capacity to disrupt hepatic, endocrine and neurological systems, indicating that fludioxonil may represent a health threat to consumers. In the absence of a clear, safe mechanism of action, fludioxonil should be re-evaluated for its potential to impact human health.

Potential Impact of Populations Drift on Botrytis Occurrence and Resistance to Multi- and Single-Site Fungicides in Florida Southern Highbush Blueberry Fields

Incidence of blossom blight and Botrytis fruit rot (BFR), caused by Botrytis cinerea, on two southern highbush blueberry cultivars was evaluated in several blueberry fields grown in the vicinity (BB-Str⁽⁺⁾) or not (BB-Str^(-)) of strawberry fields in central Florida. Blossom blight and BFR incidence were higher in BB-Str⁽⁺⁾ fields in 2014 and significantly higher in 2015 compared to BB-Str^(-) fields. In total, 613 B. cinerea isolates (i.e., 181 and 432 isolates from BB-Str^(-) and BB-Str⁽⁺⁾ fields, respectively) were collected. The isolates were evaluated for sensitivity to eight single-site and one multisite fungicides using a spore germination and a germ tube elongation assay. Overall, 5, 15, 24, 28, 54, and 93% of isolates collected from BB-Str^(-) were resistant to penthiopyrad, cyprodinil, boscalid, fenhexamid, pyraclostrobin, and thiophanate-methyl, respectively. Respective resistance frequencies in BB-Str⁽⁺⁾ isolates were 10, 30, 65, 66, 89, and 99%. Resistance frequencies for all fungicides were always higher in BB-Str⁽⁺⁾ fields compared to BB-Str^(-) fields. Isolates exhibiting resistance to six or five fungicides simultaneously were predominant (50 to 70%) in blueberry fields regardless if they were grown in the vicinity of strawberry fields or not. Among 308 and 305 B. cinerea isolates tested in 2014 and 2015, 41.8 and 47.1%, respectively, showed reduced sensitivity to the multisite fungicide captan. The lower label rate of captan applied preventively did not control isolates with reduced sensitivity on detached blueberry fruit. These findings suggest a potential population flow between strawberry and blueberry fields that may impact blossom blight and gray mold development in blueberry fields. The relatively lower fungicide input applied to blueberry fields compared with strawberry fields seems to be sufficient to select for resistance and multiple-resistant phenotypes in B. cinerea populations in blueberry.

Evaluating the Sensitivity and Efficacy of Fungicides with Different Modes of Action Against Botryosphaeria dothidea

Botryosphaeria dothidea, the causal agent of apple ring rot, is an important fungal plant pathogen that can cause serious reductions in crop yield, and fungicides still play a crucial role in management. In the present study, the sensitivity of B. dothidea to fludioxonil, fluazinam, and pyrisoxazole was assessed in 162 isolates. Moreover, the protective and curative activity of the three fungicides on detached apple fruit as well as the control efficacy in the field were determined. The results showed that the mean 50% effective concentration (EC₅₀) values (± standard deviation) were 0.01 ± 0.008, 0.04 ± 0.03, and 0.02 ± 0.01 μg ml^-1, with individual EC₅₀ values of 0.002 to 0.05, 0.003 to 0.19, and 0.005 to 0.26 μg ml^-1 for fludioxonil, fluazinam, and pyrisoxazole, respectively. In addition, the frequency distributions of EC₅₀ values were both unimodal curves. However, significant correlations (P < 0.05) were found between fludioxonil and iprodione, between fluazinam and iprodione, as well as between pyrisoxazole and difenoconazole. In field trials conducted during 2016 and 2017, the control efficacy ranged from 75.91 to 87.41% when fludioxonil was applied at 100 to 150 mg active ingredient (a.i.) kg^-1, 81.90 to 85.13% when fluazinam was applied at 400 mg a.i. kg^-1, and 77.43 to 80.97% when pyrisoxazole was applied at 400 mg a.i. kg^-1. The control efficacy of the fungicides in storage was higher than 60%, with the exception of fluazinam. These results demonstrated that fludioxonil, fluazinam, and pyrisoxazole have considerable potential to control apple ring rot.

Molecular Characterization, Fitness, and Mycotoxin Production of Fusarium asiaticum Strains Resistant to Fludioxonil

Fludioxonil is used in seedborne disease management of various fungal pathogens, including Fusarium asiaticum, the predominant causal agent of Fusarium head blight in China. In this study, we screened resistant strains from a large number of F. asiaticum strains collected from 2012 to 2016 and found that 4 of 1,000 field strains were highly resistant to fludioxonil. The 50% effective concentration values of the resistant strains and induced mutants ranged from 80 to >400 μg/ml. Compared with field-sensitive strains, all field-collected and laboratory-induced resistant strains exhibited fitness defects in traits including mycelial growth, conidial production, pathogenicity, and sensitivity to osmotic conditions. In the presence of fludioxonil, significantly higher glycerol accumulation was found in sensitive strains but not in resistant individuals. The fludioxonil-resistant strains produced lower amounts of glycerol in liquid culture and lower amounts of trichothecene mycotoxins in rice culture and inoculated wheat spikelets than the fludioxonil-sensitive strains. Sequence analyses of the key genes of the two-component histidine kinase signaling pathway showed various amino acid substitutions in the Os1, Os4, and Os5 genes between field-sensitive and resistant strains or mutants. The results of this study suggest a potential risk of fludioxonil resistance development and a possible influence of resistance mutations on fitness parameters and toxin production in F. asiaticum.

Prevalence of Botrytis Cryptic Species in Strawberry Nursery Transplants and Strawberry and Blueberry Commercial Fields in the Eastern United States

Botrytis isolates from strawberry transplants originating from Canada and the northern United States as well as isolates collected from strawberry and blueberry commercial fields in the southeastern United States were investigated for the frequency of Botrytis cinerea, other cryptic Botrytis spp. reported recently, and the transposable elements (TE) using six genetic markers. B. cinerea sensu stricto was predominant (94%) in strawberry and blueberry in all surveyed regions. Botrytis group S, a newly reported clade on strawberry from Germany, was found at low frequencies (6%) in strawberry in the United States and Canada and on blueberry isolates from Florida. Neither B. caroliniana nor B. pseudocinerea were detected in the U.S. or Canadian populations. Transposa isolates containing the TE boty and flipper accounted for 74% of 410 isolates studied herein. Isolates containing boty only or flipper only elements were found at 21 and 2%, respectively. However, boty isolates were predominant in the blueberry population with more than 50%. The TE were found in B. cinerea and Botrytis group S at similar frequencies, except that flipper was more frequent (10.7%) in Botrytis group S, compared with 1.6% in B. cinerea. The sensitivity of 256 Botrytis isolates from the different genetic groups described above was evaluated to seven fungicides registered to control gray mold in commercial fields. Results indicate that B. cinerea and transposa isolates have higher resistance frequencies to almost all fungicides tested compared with the other Botrytis genotypes or species, whereas the TE flipper may be related to resistance to fludioxonil. Similarities observed between nursery and commercial field populations and their impact on gray mold development and management are discussed.

Botrytis fragariae, a New Species Causing Gray Mold on Strawberries, Shows High Frequencies of Specific and Efflux-Based Fungicide Resistance

Botrytis cinerea causes pre- and postharvest decay of many fruit and vegetable crops. A survey of German strawberry fields revealed Botrytis strains that differed from B. cinerea in diagnostic PCR markers and growth appearance. Phylogenetic analyses showed that these strains belong to an undescribed species in Botrytis clade 2, named Botrytisfragariae sp. nov. Isolates of Bfragariae were detected in strawberry fields throughout Germany, sometimes at frequencies similar to those of B. cinerea, and in the southeastern United States. Bfragariae was isolated from overwintering strawberry tissue but not from freshly infected fruit. Bfragariae invaded strawberry tissues with an efficiency similar to or lower than that of B. cinerea but showed poor colonization of inoculated nonhost plant tissues. These data and the exclusive occurrence of this fungus on strawberry plants indicate that Bfragariae is host specific and has a tissue preference different from that of B. cinerea Various fungicide resistance patterns were observed in Bfragariae populations. Many Bfragariae strains showed resistance to one or several chemical classes of fungicides and an efflux-based multidrug resistance (MDR1) phenotype previously described in B. cinerea Resistance-related mutations in Bfragariae were identical or similar to those of B. cinerea for carbendazim (E198A mutation in tubA), azoxystrobin (G143A in cytB), iprodione (G367A+V368F in bos1), and MDR1 (gain-of-function mutations in the transcription factor mrr1 gene and overexpression of the drug efflux transporter gene atrB). The widespread occurrence of Bfragariae indicates that this species is adapted to fungicide-treated strawberry fields and may be of local importance as a gray mold pathogen alongside B. cinereaIMPORTANCE Gray mold is the most important fruit rot on strawberries worldwide and requires fungicide treatments for control. For a long time, it was believed to be caused only by Botrytis cinerea, a ubiquitous pathogen with a broad host range that quickly develops fungicide resistance. We report the discovery and description of a new species, named Botrytisfragariae, that is widely distributed in commercial strawberry fields in Germany and the southeastern United States. It was observed on overwintering tissue but not on freshly infected fruit and seems host specific on the basis of its occurrence and artificial infection tests. Bfragariae has also developed resistance to several fungicides that is caused by mutations similar to those known in B. cinerea, including an efflux-based multidrug resistance. Our data indicate that Bfragariae could be of practical importance as a strawberry pathogen in some regions where its abundance is similar to that of B. cinerea.

Multiple Fungicide Resistance in Botrytis cinerea from Greenhouse Strawberries in Hubei Province, China

Two hundred and forty isolates of Botrytis cinerea were collected during the early summer of 2012 and 2013 from strawberry greenhouses in 10 locations in Hubei Province and examined for sensitivity to five fungicides, most of which were commonly used to control this fungus. High frequency of resistance to carbendazim (Car, 63.63%) and cyprodinil (Cyp, 42.42%) was detected. Boscalid-resistant (Bos^R) isolates were detected for the first time in China, whereas no fludioxonil-resistant isolates were identified. Dual resistance to carbendazim and diethofencarb (Die) was also detected. There were six phenotypes of resistance profile (i.e., Car^RDie^SBos^SCyp^S, Car^RDie^RBos^SCyp^S, Car^RDie^SBos^SCyp^R, Car^RDie^SBos^RCyp^S, Car^RDie^RBos^SCyp^R, and Car^RDie^SBos^RCyp^R). Car^RDie^SBos^SCyp^S and Car^RDie^SBos^SCyp^R were the most common phenotypes, occurring at eight and seven locations, respectively. After 10 successive transfers on fungicide-free potato dextrose agar, tested resistant isolates retained levels of resistance similar to or comparative with the initial generation, indicating the stability of these resistances. Fitness evaluations based on investigation of mycelial growth, osmotic sensitivity, sporulation in vitro and in vivo, and virulence revealed the uncompromising fitness in resistant isolates, except that decreased virulence was observed in Bos^R isolates. The molecular basis of carbendazim, diethofencarb, and boscalid resistance was investigated. Results showed that all 13 sequenced carbendazim-resistant isolates harbored the mutation E198V or E198A in the β-tubulin gene and the five isolates with dual resistance to carbendazim and diethofencarb showed the mutation E198K in the same gene. Bos^R isolates possessed the H272R mutation in succinate dehydrogenase subunit B gene. The results achieved in this study challenge the current management strategies for B. cinerea, which largely depend on applications of these fungicides.

Characterization of Postharvest Fungicide-Resistant Botrytis cinerea Isolates From Commercially Stored Apple Fruit

Botrytis cinerea causes gray mold and is an economically important postharvest pathogen of fruit, vegetables, and ornamentals. Fludioxonil-sensitive B. cinerea isolates were collected in 2011 and 2013 from commercial storage in Pennsylvania. Eight isolates had values for effective concentrations for inhibiting 50% of mycelial growth of 0.0004 to 0.0038 μg/ml for fludioxonil and were dual resistant to pyrimethanil and thiabendazole. Resistance was generated in vitro, following exposure to a sublethal dose of fludioxonil, in seven of eight dual-resistant B. cinerea isolates. Three vigorously growing B. cinerea isolates with multiresistance to postharvest fungicides were further characterized and found to be osmosensitive and retained resistance in the absence of selection pressure. A representative multiresistant B. cinerea strain caused decay on apple fruit treated with postharvest fungicides, which confirmed the in vitro results. The R632I mutation in the Mrr1 gene, associated with fludioxonil resistance in B. cinerea, was not detected in multipostharvest fungicide-resistant B. cinerea isolates, suggesting that the fungus may be using additional mechanisms to mediate resistance. Results from this study show for the first time that B. cinerea with dual resistance to pyrimethanil and thiabendazole can also rapidly develop resistance to fludioxonil, which may pose control challenges in the packinghouse environment and during long-term storage.

Resistance to Increasing Chemical Classes of Fungicides by Virtue of "Selection by Association" in Botrytis cinerea

Previous research has shown that Botrytis cinerea isolates with resistance to multiple chemical classes of fungicides exist in eastern strawberry fields. In this study, the fungicide resistance profiles of 2,130 isolates from flowers of commercial strawberry fields located in multiple states was determined over four consecutive strawberry production seasons. Producers were asked to alternate single-site fungicides that were considered low risk in their specific location based on resistance monitoring results in their fields. This recommendation led to an increase of chemical class diversity used in the spray programs. Results indicated that simultaneous resistance in individual isolates to two, three, four, five, six, and seven classes of fungicides increased over time. The increase in chemical class resistances within isolates was likely due to a process we termed "selection by association", where fungicide resistance traits were often linked to the trait being selected rather than the selectable trait itself. Data analysis also indicated that the odds were highest for isolates resistant to one chemical class (1CCR) to be resistant to thiophanate-methyl; for 2CCR isolates to be resistant to thiophanate-methyl and pyraclostrobin; and for 3CCR isolates to be resistant to thiophanate-methyl, pyraclostrobin, and either cyprodinil or fenhexamid. We hypothesize that the more chemical classes are used in a spray program, the faster isolates will be selected with increasing numbers of chemical class resistances by virtue of selection by association if such isolates preexist in the population.

Occurrence of Fungicide Resistance in Botrytis cinerea from Greenhouse Tomato in Hubei Province, China

During the early summer of 2012 and 2013, samples of gray mold were collected from greenhouse tomato at eight locations in Hubei Province, and 221 isolates of Botrytis cinerea were obtained and evaluated for the sensitivity to fungicides carbendazim, diethofencarb, boscalid, fludioxonil, and cyprodinil. Results showed that isolates with resistance to carbendazim and cyprodinil were widespread, whereas isolates with resistance to carbendazim and diethofencarb were found at only two locations. No isolates with resistance to boscalid or fludioxonil were detected. Altogether, four resistant phenotypes were determined (i.e., Car^RDie^SCyp^S, Car^RDie^RCyp^S, Car^RDie^SCyp^R, and Car^RDie^RCyp^R). Among them, Car^RDie^SCyp^S and Car^RDie^SCyp^R were widely distributed, and there was a dominant resistant phenotype at each location. Interestingly, isolates resistant only to cyprodinil were not obtained because the resistance to cyprodinil was always associated with the resistance to carbendazim, demonstrating that a phenotype of multiple fungicide resistance of B. cinerea was more likely to have evolved from previously resistant subpopulations. Stability of resistance to carbendazim, diethofencarb, and cyprodinil was assessed, and the resistance was stable. Fitness tests showed that, as a group, the carbendazim-resistant isolates were not significantly different from sensitive isolates. However, the mycelial growth and virulence of the carbendazim, diethofencarb, and cyprodinil triple-resistant group were significantly lower than the sensitive group, indicating that the triple-resistant isolates suffered from the disability of colonizing the hosts. It should be noted that there was no significant difference for other fitness components (e.g., sporulation or osmotic sensitivity to NaCl), suggesting that the triple-resistant isolates were still competitive in these traits. To investigate the mechanisms of resistance to carbendazim and diethofencarb, partial β-tubulin genes of 10 carbendazim-resistant isolates and 5 isolates resistant to carbendazim and diethofencarb were sequenced, and all 10 carbendazim-resistant isolates harbored the mutation E198V or E198A. For the 5 isolates resistant to carbendazim and diethofencarb, all of them possessed the mutation E198K, and no other mutations were detected. The location-specific resistance profiles found in this study are crucial in designing proper gray mold management strategies in these areas.

Characterization of Botrytis cinerea Isolates from Strawberry with Reduced Sensitivity to Polyoxin D Zinc Salt

Polyoxin D is a Fungicide Resistance Action Committee (FRAC) code 19 fungicide that was recently registered for gray mold control of strawberry in the United States. In this study, we determined the sensitivity to polyoxin D zinc salt (hereafter, polyoxin D) of Botrytis cinerea isolates from 41 commercial strawberry farms in South Carolina, North Carolina, Maryland, Virginia, and Ohio and investigated the fitness of sensitive (S) and reduced sensitive (RS) isolates. Relative mycelial growth ranged between 0 and over 100% on malt extract agar amended with a discriminatory dose of polyoxin D at 5 μg/ml. Isolates that grew more than 70% at that dose were designated RS and were found in three of the five states. The 50% effective dose (EC₅₀) values of three S and three RS isolates ranged from 0.59 to 2.27 and 4.6 to 5.8 μg/ml, respectively. The three RS isolates grew faster on detached tomato fruit treated with Ph-D WDG at recommended label dosage than S isolates (P < 0.008). In all, 25 randomly selected RS isolates exhibited reduced sporulation ability (P < 0.0001) and growth rate (P < 0.0001) but increased production of sclerotia (P < 0.0386) compared with 25 S isolates. Of 10 isolates tested per phenotype, the number of RS isolates producing sporulating lesions on apple, tomato, and strawberry was significantly lower compared with S isolates (P < 0.0001 for each fruit type). The results of this study indicate that resistance management is necessary for fungicides containing polyoxin D. To our knowledge, this is the first study demonstrating reduced sensitivity to FRAC 19 fungicides in B. cinerea isolates from the United States.

Fitness and Competitive Ability of Botrytis cinerea Isolates with Resistance to Multiple Chemical Classes of Fungicides

Resistance to multiple chemical classes of fungicides in Botrytis cinerea isolates from eastern United States strawberry fields is common and strategies to control them are needed. In this study, we compared fitness and competitive ability of eight sensitive isolates (S), eight isolates resistant to five or six chemical classes of fungicides but not to phenylpyrroles (5CCR), and eight isolates resistant to six or seven chemical classes including phenylpyrroles (6CCR/MDR1h). The latter included the MDR1h phenotype due to overexpression of atrB based on Δ497V/L in mrr1. The 6CCR/MDR1h isolates grew more slowly at 4°C on potato dextrose agar, and both 5CCR and 6CCR/MDR1h isolates were hypersensitive to osmotic stress compared with S isolates. In contrast, no differences were found in oxidative sensitivity, aggressiveness, and spore production in vivo, and sclerotia production and viability in vitro. In competition experiments, the 5CCR and 6CCR/MDR1h isolates were both outcompeted by S isolates and 6CCR/MDR1h isolates were outcompeted by 5CCR isolates in the absence of fungicide pressure. Under selective pressure of a fludioxonil/pyraclostrobin rotation, the 6CCR/MDR1h isolates dominated after coinoculation with 5CCR and S isolates. The competitive disadvantage of 5CCR and especially 6CCR/MDR1h isolates suggest that, in the absence of fungicide selection pressure, S isolates may reduce inoculum potential of multifungicide-resistant isolates under field conditions.

Molecular and Biochemical Characterization of Laboratory and Field Mutants of Botrytis cinerea Resistant to Fludioxonil

Botrytis cinerea is a filamentous phytopathogen with a high risk of developing resistance to fungicides. The phenylpyrrole fungicide fludioxonil has been reported to have excellent activity against B. cinerea and increasingly has been applied to control gray mold in China. In this study, molecular and biochemical characteristics of laboratory and field mutants of B. cinerea resistant to fludioxonil has been investigated. During 2012 to 2014, B. cinerea isolates collected from Jiangsu and Shandong Provinces in China were tested in vitro for sensitivity to fungicides commonly used to suppress gray mold of cucumber and tomato. Among the 75 isolates collected from cucumber in 2013, two were highly resistant (HR) to fludioxonil. Of the 308 isolates collected from tomato in 2014, four were fludioxonil-HR. This was the first time that B. cinerea isolates HR to fludioxonil had been detected in the field. Six fludioxonil-resistant mutants were obtained in the laboratory by selection on fungicide-amended media. These mutants exhibited stable resistance to fludioxonil, as indicated by resistance factor values that ranged from 34.38 to >10,000. In comparison with fludioxonil-sensitive isolates of B. cinerea, all field and laboratory mutants showed reduced fitness, as defined by mycelial growth, sporulation, virulence, and sensitivity to osmotic stress. When treated with fludioxonil at 1 μg/ml, sensitive isolates showed increased glycerol contents in mycelium and expression levels of Bchog1, while levels in field and laboratory HR mutants increased only slightly. Sequences of the Bos1 gene of field and laboratory fludioxonil-HR mutants showed that mutations in field mutants were located in the histidine kinase, adenylyl cyclase, methyl-accepting chemotaxis protein, and phosphatase (HAMP) domains of the N-terminal region, whereas mutations in the laboratory mutants were distributed in HAMP domains or in the HATPase_c domain of the C-terminal region. These results will enhance our understanding of the resistance mechanism of B. cinerea to fludioxonil.

Monitoring Resistance to SDHI Fungicides in Botrytis cinerea From Strawberry Fields

Succinate dehydrogenase inhibitor (SDHI) fungicides have been used to control gray mold of strawberry for more than a decade, and selection for resistance in the causal agent Botrytis cinerea has become a threat to producers. In total, 2,570 B. cinerea isolates were collected from strawberry fields in the eastern United States across three seasons and their sensitivity to the SDHI materials boscalid, fluopyram, fluxapyroxad, and penthiopyrad was assessed. Assays were based on visual assessment of presence or absence of mycelial growth on media amended with discriminatory fungicide doses to distinguish sensitive from resistant isolates, respectively. Overall frequencies of isolates resistant to boscalid, fluopyram, fluxapyroxad, and penthiopyrad increased over the 3 years to 30.0, 1.0, 5.5, and 7.4%, respectively. Four resistance patterns, designated A, B, C, or D, were found. Pattern A isolates were resistant to boscalid with the allele H272R at locus sdhB; pattern B isolates were resistant to boscalid and penthiopyrad with the allele H272R or H272Y at locus sdhB; pattern C isolates were resistant to boscalid, fluxapyroxad, and penthiopyrad with the allele H272Y at locus sdhB; and pattern D isolates were resistant to boscalid, fluopyram, fluxapyroxad, and penthiopyrad with alleles P225F or N230I at locus sdhB. Isolates with alleles H272Y, N230I, or P225F were sensitive to a new SDHI, benzovindiflupyr, with mean effective dose that inhibits 50% of mycelial growth values of less than 0.5 μg/ml for each genotype, suggesting that this fungicide may be useful for resistance management. Our data show an increase of B. cinerea isolates resistant to SDHI fungicides over three consecutive production seasons. Resistance management practices must be implemented for the sustained efficacy of SDHI fungicides against gray mold of strawberry.

A Botrytis cinerea Population from a Single Strawberry Field in Germany has a Complex Fungicide Resistance Pattern

Gray mold, caused by the fungus Botrytis cinerea, is one of the most important diseases of strawberry in Germany. The application of site-specific fungicides remains the main strategy to reduce disease incidence and severity in the field. Isolates (n = 199) were collected from fungicide-treated strawberry fruit at a German research site with a long history of fungicide efficacy trials against gray mold. Sensitivities to the six site-specific botryticides registered in Germany were determined using microtiter assays. Values for the concentration of a fungicide at which fungal development is inhibited by 50% (EC₅₀) ranged from 0.03 to ≥30 ppm for the succinate dehydrogenase inhibitor boscalid, 0.015 to ≥10 ppm for the hydroxyanilide fenhexamid, 0.009 to 0.739 ppm for the phenylpyrrole fludioxonil, 0.55 to 43.45 ppm for the dicarboximide iprodione, 0.021 to ≥3 ppm for the quinone outside inhibitor pyraclostrobin, and 0.106 to ≥30 ppm for the anilinopyrimidine pyrimethanil. Pyrosequencing revealed that amino acid substitutions in the target proteins Bos1 (I365S/N, V368F + Q369H), CytB (G143A), Erg27 (F412S), and SdhB (P225F, N230I, and H272R/Y) were associated with reduced sensitivity levels to the corresponding fungicide classes. In most cases, isolates with a decreased sensitivity to fludioxonil showed a reduced sensitivity to tolnaftate. This reduction is considered to be an indication of multidrug efflux pump activity. The amino acid change I365S, I365N, or V368F + Q369H in Bos1 and H272R in SdhB by itself showed EC₅₀ values of 3.99 to 14.73 ppm, 3.87 to 5.37 ppm, 4.81 to 15.63 ppm, and 2.071 to ≥30 ppm, respectively. When isolates that contained one of these mutations were also multidrug resistant, the ranges of EC₅₀ values shifted to 6.47 to 43.45 ppm for I365S, 7.28 to 29.84 ppm for I365N, 6.89 to 26.67 ppm for V368F + Q369H, and ≥30 ppm for H272R. The reported data suggest that the combination of multidrug resistance and an amino acid change in the target site may result in a lower sensitivity to the fungicides than one resistance mechanism by itself. Although 20% of the population analyzed was sensitive to all six different chemical classes, the majority showed reduced sensitivity to one (6%), two (13%), three (23%), four (17%), five (11%), and six (11%) different fungicides.

Antibiotic-resistant bacteria: prevalence in food and inactivation by food-compatible compounds and plant extracts

Foodborne antibiotic-resistant pathogenic bacteria such as Campylobacter jejuni, Bacillus cereus, Clostridium perfringens, Escherichia coli, Salmonella enterica, Staphylococcus aureus, Vibrio cholerae, and Vibrio parahemolyticus can adversely affect animal and human health, but a better understanding of the factors involved in their pathogenesis is needed. To help meet this need, this overview surveys and interprets much of our current knowledge of antibiotic (multidrug)-resistant bacteria in the food chain and the implications for microbial food safety and animal and human health. Topics covered include the origin and prevalence of resistant bacteria in the food chain (dairy, meat, poultry, seafood, and herbal products, produce, and eggs), their inactivation by different classes of compounds and plant extracts and by the use of chlorine and physicochemical methods (heat, UV light, pulsed electric fields, and high pressure), the synergistic antimicrobial effects of combinations of natural antimicrobials with medicinal antibiotics, and mechanisms of antimicrobial activities and resistant effects. Possible areas for future research are suggested. Plant-derived and other safe natural antimicrobial compounds have the potential to control the prevalence of both susceptible and resistant pathogens in various environments. The collated information and suggested research will hopefully contribute to a better understanding of approaches that could be used to minimize the presence of resistant pathogens in animal feed and human food, thus reducing adverse effects, improving microbial food safety, and helping to prevent or treat animal and human infections.

Independent Emergence of Resistance to Seven Chemical Classes of Fungicides in Botrytis cinerea

Gray mold, caused by the fungal pathogen Botrytis cinerea, is one of the most destructive diseases of small fruit crops and control is largely dependent on the application of fungicides. As part of a region-wide resistance-monitoring program that investigated 1,890 B. cinerea isolates from 189 fields in 10 states of the United States, we identified seven isolates (0.4%) from five locations in four different states with unprecedented resistance to all seven Fungicide Resistance Action Committee (FRAC) codes with single-site modes of action including FRAC 1, 2, 7, 9, 11, 12, and 17 registered in the United States for gray mold control. Resistance to thiophanate-methyl, iprodione, boscalid, pyraclostrobin, and fenhexamid was based on target gene mutations that conferred E198A and F200Y in β-tubulin, I365N/S in Bos1, H272R/Y in SdhB, G143A in Cytb, and T63I and F412S in Erg27. Isolates were grouped into MDR1 and MDR1h phenotypes based on sensitivity to fludioxonil and variations in transcription factor mrr1. MDR1h isolates had a previously described 3-bp deletion at position 497 in mrr1. Expression of ABC transporter atrB was increased in MDR1 isolates but highest in MDR1h isolates. None of the isolates with seven single resistances (SR) had identical nucleotide variations in target genes, indicating that they emerged independently. Multifungicide resistance phenotypes did not exhibit significant fitness penalties for the parameters used in this study, but MDR1h isolates produced more sclerotia at low temperatures and exhibited increased sensitivity to salt stress. In this study we show that current resistance management strategies have not been able to prevent the geographically independent development of resistance to all seven site-specific fungicides currently registered for gray mold control in the United States and document the presence of MDR1h in North America.

Population Structure, Fungicide Resistance Profile, and sdhB Mutation Frequency of Botrytis cinerea from Strawberry and Greenhouse-Grown Tomato in Greece

Botrytis cinerea is a pathogen with high genetic variability that has also shown high risk for fungicide resistance development. In total, 1,169 isolates obtained from strawberry (n = 297) and tomato (n = 872) in five geographic regions of Greece were tested for their sensitivity to several botryticides. A high frequency of isolates with multiple resistance to carbendazim, cyprodinil, pyraclostrobin, and boscalid was found in isolates from strawberry. In the isolates from tomato, the predominant phenotype was that of dual resistance to carbendazim and cyprodinil in the Crete island, of single resistance to carbendazim in the region of Preveza, and of sensitive isolates in the region of Kyparissia. None of the tested isolates was found to be fludioxonil resistant. High frequencies of boscalid-resistant phenotypes were observed in the strawberry isolates, while boscalid-resistance frequency in the tomato isolates was lower. H272R was the predominant sdhB mutation, associated with resistance to boscalid, in all the sampled isolates, while other sdhB mutations were found at low frequencies. B. cinerea group S, identified by the presence of a 21-bp insertion in the transcription factor mrr1 gene, was predominant within the tomato isolates obtained from all three sampled regions, with frequencies ranging from 62 to 75% of the isolates; whereas, within strawberry isolates, B. cinerea was predominant, with frequencies of 75 to 95%. Correlations of isolate genotype and fungicide resistance profile showed that B. cinerea sensu stricto isolates were more prone to the development of resistance to boscalid compared with the Botrytis group S isolates, which may explain the observed predominance of B. cinerea sensu stricto in strawberry fields.