First detection of extended-spectrum cephalosporin- and fluoroquinolone-resistant Escherichia coli in Australian food-producing animals

This study aimed to define the frequency of resistance to critically important antimicrobials (CIAs) [i.e. extended-spectrum cephalosporins (ESCs), fluoroquinolones (FQs) and carbapenems] among Escherichia coli isolates causing clinical disease in Australian food-producing animals. Clinical E. coli isolates (n = 324) from Australian food-producing animals [cattle (n = 169), porcine (n = 114), poultry (n = 32) and sheep (n = 9)] were compiled from all veterinary diagnostic laboratories across Australia over a 1-year period. Isolates underwent antimicrobial susceptibility testing to 18 antimicrobials using the Clinical and Laboratory Standards Institute disc diffusion method. Isolates resistant to CIAs underwent minimum inhibitory concentration determination, multilocus sequence typing (MLST), phylogenetic analysis, plasmid replicon typing, plasmid identification, and virulence and antimicrobial resistance gene typing. The 324 E. coli isolates from different sources exhibited a variable frequency of resistance to tetracycline (29.0–88.6%), ampicillin (9.4–71.1%), trimethoprim/sulfamethoxazole (11.1–67.5%) and streptomycin (21.9–69.3%), whereas none were resistant to imipenem or amikacin. Resistance was detected, albeit at low frequency, to ESCs (bovine isolates, 1%; porcine isolates, 3%) and FQs (porcine isolates, 1%). Most ESC- and FQ-resistant isolates represented globally disseminated E. coli lineages (ST117, ST744, ST10 and ST1). Only a single porcine E. coli isolate (ST100) was identified as a classic porcine enterotoxigenic E. coli strain (non-zoonotic animal pathogen) that exhibited ESC resistance via acquisition of blaCMY-2. This study uniquely establishes the presence of resistance to CIAs among clinical E. coli isolates from Australian food-producing animals, largely attributed to globally disseminated FQ- and ESC-resistant E. coli lineages.

Strategies to limit the impact of nematode pressure on sugarcane productivity in the Isis

Two trials were done in this project. One was a continuation of work started under a previous GRDC/SRDC-funded activity, 'Strategies to improve the integration of legumes into cane based farming systems'. This trial aimed to assess the impact of trash and tillage management options and nematicide application on nematodes and crop performance. Methods and results are contained in the following publication: Halpin NV, Stirling GR, Rehbein WE, Quinn B, Jakins A, Ginns SP. The impact of trash and tillage management options and nematicide application on crop performance and plant-parasitic nematode populations in a sugarcane/peanut farming system. Proc. Aust. Soc. Sugar Cane Technol. 37, 192-203. Nematicide application in the plant crop significantly reduced total numbers of plant parasitic nematodes (PPN) but there was no impact on yield. Application of nematicide to the ratoon crop significantly reduced sugar yield. The study confirmed other work demonstrating that implementation of strategies like reduced tillage reduced populations of total PPN, suggesting that the soil was more suppressive to PPN in those treatments. The second trial, a variety trial, demonstrated the limited value of nematicide application in sugarcane farming systems. This study has highlighted that growers shouldn’t view nematicides as a ‘cure all’ for paddocks that have historically had high PPN numbers. Nematicides have high mammalian toxicity, have the potential to contaminate ground water (Kookana et al. 1995) and are costly. The cost of nematicide used in R1 was approx. $320 - $350/ha, adding $3.50/t of cane in a 100 t/ha crop. Also, our study demonstrated that a single nematicide treatment at the application rate registered for sugarcane is not very effective in reducing populations of nematode pests. There appears to be some levels of resistance to nematodes within the current suite of varieties available to the southern canelands. For example the soil in plots that were growing Q183 had 560% more root knot nematodes / 200mL soil compared to plots that grew Q245. The authors see great value in investment into a nematode screening program that could rate varieties into groups of susceptibility to both major sugarcane nematode pests. Such a rating could then be built into a decision support ‘tree’ or tool to better enable producers to select varieties on a paddock by paddock basis.

The grand challenge of food security - general lessons from a comprehensive approach to protecting stored grain from insect pests in Australia and India

We outline a philosophical approach to Grand Challenge projects, with particular reference to our experience in our food security project involving the protection of stored grain from insect attack in two countries on different continents. A key consideration throughout has been the management of resistance in these pests to the valuable fumigant phosphine. Emphasis is given to the chain of research issues that required solution and the assembly of a well-integrated team, overlapping in skills for effective communication, in each country to solve the problems identified along that chain. A crucial aspect to maintaining direction is the inclusion of key end users in all deliberations, as well as the establishment and maintenance of effective outlets for the dissemination of practical recommendations. We finish with a summary of our achievements with respect to our approach to this food security Grand Challenge.

Use of sulfuryl fluoride in the management of strongly phosphine-resistant insect pest populations in bulk grain storages in Australia

Sulfuryl fluoride (SF), an effective structural fumigant, is registered recently as Profume™ for controlling insect pests of stored grains and processed commodities. Information on its effectiveness in disinfestation of bulk grain, however, is limited. The ongoing problem with the strong level of resistance to phosphine has been addressed recently through deployment of SF as a ‘resistance breaker’ in bulk storages in Australia. This paper discusses important results on the efficacy of SF against key phosphine- resistant insect pests, lesser grain borer, Rhyzopertha dominca, red flour beetle, Tribolium castaneum, rice weevil, Sitophilus oryzae and the rusty grain beetle, Cryptolestes ferrugineus. We have established CT (g-hm3) profiles for SF against these insect pests at two temperature regimes 25 and 30°C, that showed that both temperature and exposure period (t) has significant influence on the effectiveness of SF than the concentration. Over a seven days fumigation period, CTs of 800 and 400 g-hm3 achieved complete control of all the target pests, including the most strongly phosphine - resistant species, C. ferrugineus at 25 and 30°C, respectively. Results from four industry scale field trials involving currently registered rate of SF (1500 g-hm3) over 2–14 d exposure period, confirmed its effectiveness in achieving complete control of the target pest species. The assessment of postfumigation grain samples across all the test storages indicated that the reinfestation occurs after three months. Monitoring resistance to phosphine in C. ferrugineus over a six year period (2009–2015), showed a significant reduction in resistant populations after the introduction of SF into the fumigation strategy at problematic storage sites. Overall our research concludes that SF is a good candidate to be used as a ‘resistance breaker’ where phosphine resistance is prevalent.

Research into crown rot and wilt diseases of strawberries in Queensland

Plant losses due to fungal diseases in strawberry (Fragaria × ananassa Duch.) can potentially cause total loss of production. Three fungal pathogens, Fusarium oxysporum f. sp. fragariae, Colletotrichum gloeosporioides and Macrophomina phaseolina, cause similar crown rot and wilt symptoms in strawberries in Queensland. Since the withdrawal of methyl bromide in 2005, no effective chemical control of any of the three pathogens has been available. This study aims at identifying sources of plant genetic resistance that can be used in the breeding program to develop resistant cultivars for use as part of an integrated disease management plan in commercial strawberry production. Results from glasshouse pathogenicity and screening trials on the three pathogens showed that when breeding for resistance against a pathogen, resistance to other pathogens also needs to be considered, e.g., cultivar 'Festival' is resistant to F. oxysporum f. sp. fragariae, but is highly susceptible to C. gloeosporioides. The cultivars 'Earlisweet', 'Kabarla' and 'Phenomenal', two seedling clones and four DAFF breeding lines were resistant to C. gloeosporioides. Cultivar 'Suncoast Delight' showed the most promising level of resistance to M. phaseolina. These cultivars, breeding lines and seedling selections have been made available for incorporation into the crossing program to support the Queensland strawberry breeding program.

Effect of diet on phosphine toxicity, rate of development and reproduction of the rice weevil Sitophilus oryzae (Linnaeus)

One of the loci responsible for strong phosphine resistance encodes dihydrolipoamide dehydrogenase (DLD). The strong co-incidence of enzyme complexes that contain DLD, and enzymes that require thiamine as a cofactor, motivated us to test whether the thiamine deficiency of polished white rice could influence the efficacy of phosphine fumigation against insect pests of stored grain. Three strains of Sitophilus oryzae (susceptible, weak and strong resistance) were cultured on white rice (thiamine deficient), brown rice or whole wheat. As thiamine is an essential nutrient, we firstly evaluated the effect of white rice on developmental rate and fecundity and found that both were detrimentally affected by this diet. The mean time to reach adult stage for the three strains ranged from 40 to 43 days on brown rice and 50–52 days on white rice. The mean number of offspring for the three strains ranged from 7.7 to 10.3 per female over a three day period on brown rice and 2.1 to 2.6 on white rice. Growth and reproduction on wheat was similar to that on brown rice except that the strongly resistant strain showed a tendency toward reduced fecundity on wheat. The susceptible strain exhibited a modest increase in tolerance to phosphine on white rice as expected if thiamine deficiency could mimic the effect of the dld resistance mutation at the rph2 locus. The strongly resistant strain did not respond to thiamine deficiency, but this was expected as these insects are already strongly resistant. We failed, however, to observe the expected synergistic increase in resistance due to combining thiamine deficiency with the weakly resistant strain. The lack of interaction between thiamine content of the diet and the resistance genotype in determining the phosphine resistance phenotype suggests that the mode of inhibition of the complexes is a critical determinant of resistance.

Control of grey mould and stem-end rot in strawberry plants growing in a subtropical environment

The effect of different fungicide programs on grey mould (caused by Botrytis cinerea) and stem-end rot (caused by Gnomoniopsis fructicola) affecting strawberry plants (Fragaria ×ananassa cv. Festival) was studied in subtropical Australia over three years. The treatments involved a range of different synthetic multi- and single-site fungicides with different modes of action, a plant-defence promoter, plant extracts (lupin and rhubarb), organic acids, fatty acids, a salt, two strains of Bacillus subtilis, and single strains of B. amyloliquefaciens, Streptomyces lydicus and Trichoderma harzianum. Standard programs based on captan and thiram alternated, and applied with iprodione, fenhexamid, cyprodinil + fludioxonil, and penthiopyrad resulted in 3–4 % of unmarketable fruit compared with 25–38 % in the water-treated controls. There was no difference in the level of disease suppression when five or thirteen applications of single-site fungicides were rotated with the two multi-site fungicides. The incidence of unmarketable fruit was similar to the standard programs using isopyrazam (in 1 year out of 2), or penthiopyrad, fluazinam, chlorothalonil or thiram alone (in 1 year out of 1). The other fungicide programs were generally less effective. There were strong relationships between marketable yield and the incidence of unmarketable fruit over the three years (R2s = 0.82–0.93). A strategy based on thiram and captan applied alternately, with reduced applications of single-site fungicides is recommended and should reduce the chance of resistance to single-site fungicides becoming widespread in populations of the grey mould fungus. Although the program based on thiram alone had a similar incidence of unmarketable fruit as the standard program, repeated weekly applications of thiram are not recommended as they may cause unacceptable residues in the fruit. There were issues with some of the other fungicides due to phytotoxicity, residues, or difficulties with registering new fungicides that are in the same chemical group as currently registered products.