Major Resistance Genes Research Articles

Phosphorus Supply Does Not Affect Fusarium Crown Rot of Winter Wheat

Fusarium crown rot (FCR) is a major limitation to the wheat (Triticum aestivum L.) industry in the inland Pacific Northwest, United States. Genetic resistance to FCR is poorly understood and major gene resistance is not available in adapted cultivars. Chemical control is ineffective and crop rotations, which disrupt cycles of the disease, are not feasible in the region’s precipitation-limited climate. Cultural control methods are the only realistic option for farmers who struggle to minimize the impact of this disease. It is well established that FCR is favored by moisture-limited environments and an oversupply of plant-available nitrogen in soil. Effects of the supply of phosphorus in soil have not been clearly delineated. We conducted a 2-year FCR experiment at two locations in the low-precipitation zone (<30 cm) of north-central Oregon. Phosphorus fertilizer was applied in-furrow with phosphorus (P) at rates of 0, 5, and 15 kg ha−1, to plots planted with either a hard red or soft white winter wheat cultivar. The P at 15 kg ha−1 application rate increased tissue phosphorus concentration, early-season dry matter, and phosphorus uptake at both locations and both years of this study. Phosphorus treatment had no effect on grain yield, protein, or test weight. Phosphorus had no effect on the severity of FCR. This research improved our knowledge of cultural management boundaries as they relate to the control of FCR. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Nitrogenous Fertilizer Reduces Resistance but Enhances Tolerance to the Brown Planthopper in Fast-Growing, Moderately Resistant Rice.

Simple SummaryThe brown planthopper is a major rice pest in Asia that causes extensive damage where farmers apply large amounts of nitrogenous fertilizers. Over the last 50 years, host-plant resistance, i.e., a plant’s ability to deter planthoppers or reduce their survival and reproduction, has been the main focus of public research into planthopper management. However, there have been calls for increased attention to issues of rice tolerance against the planthopper, i.e., a plant’s ability to withstand attack and compensate for damage. We examined the interactions between planthoppers and 16 varieties of rice under varying levels of soil nitrogen. The varieties included susceptible, resistant and tolerant lines. We found that nitrogen generally increased planthopper fitness across the varieties; however, relative resistance was maintained in varieties with major resistance genes. Functional plant loss was found to be greatest in susceptible varieties after planthopper attack, and generally declined in resistant and tolerant varieties under increasing nitrogen levels. This increase in tolerance was most apparent among resistant and moderately resistant, large-sized, fast-growing varieties that were capable of overcoming relatively high weight and growth rate reductions.The brown planthopper, Nilaparvata lugens (Stål), is a key challenge to rice production in Asia. Outbreaks of planthoppers are associated with excessive fertilizer applications; consequently, we examined planthopper interactions with susceptible, tolerant and resistant varieties of rice under varying levels of soil nitrogen in a greenhouse experiment. We compared planthopper fitness (survival × reproduction) and plant tolerance (functional plant loss index) for 16 varieties at 0, 80 and 150 Kg added nitrogen ha−1. The planthoppers grew larger, developed more quickly and laid more eggs on susceptible varieties, compared with the resistant and tolerant varieties. Moreover, soil nitrogen generally increased planthopper fitness on resistant varieties, but relative resistance was maintained. Functional plant loss was highest among the susceptible varieties, but weight and growth rate reductions per mg of planthopper were often highest in the tolerant varieties. Tolerance was associated with large, fast-growing plants, with at least moderate resistance to the planthopper. Susceptibility was associated with a small size and/or an absence of resistance genes. Our results suggested that early-tillering rice plants can be both resistant and tolerant to the brown planthopper, but cannot be both susceptible and tolerant of planthoppers at high densities. This indicates that at least moderate resistance is required for tolerance against this herbivore. Furthermore, although dwarf varieties had a low tolerance of planthoppers, they could express resistance through functioning resistance genes.

In silico molecular and morphological analysis of rice blast resistant gene Pi-ta in Sri Lankan rice germplasm

BackgroundPi-ta is a major blast resistant gene, introgressed from indica rice varieties. In this study, diversity of the Pi-ta gene of 47 Sri Lankan rice accessions was studied by bioinformatics, and the results were validated with molecular and disease reaction assays. Sequences of rice accessions at the locus Os12g0281300 were retrieved from Rice SNP-Seek Database, and the coding sequence of reference Pi-ta gene of cultivar Tetep (accession no. GQ918486.1) was obtained from GenBank. Comparisons were made at nucleotide, amino acid, and protein structure level, and the 3D models predicted using Phyre2 software were superimposed using TM-align software. ResultsIn silico analysis revealed that 10 accessions possessed resistant allele of the Pi-ta gene. The remaining accessions recorded high polymorphism in the leucine-rich domain resulting in 9 allele types, leading to single–amino acid substitutions at 27 different positions including a functional mutation of alanine to serine at the 918th amino acid position. None of the genotypes led to truncations in the amino acid sequence. The in silico analysis results were validated on 23 accessions comprising resistant and susceptible genotypes and another 25 cultivars from Northern Sri Lanka, by molecular assay using YL183/YL87 and YL155/YL87 resistant and susceptible allele-specific markers. Resistance of Pi-ta gene for the causal fungus, Magnaporthe oryzae, was further validated through pathogenicity assay. ConclusionThe Pi-ta gene, especially the LRD region, revealed significant variations within Sri Lankan rice cultivars leading to high levels of resistance against blast. This information would be highly useful in breeding programmes for resistance against rice blast.

Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa.

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Registration of ‘CP 12‐1753’ sugarcane

Abstract‘CP 12‐1753’ (Reg. no. CV‐203, PI 698657) sugarcane (complex hybrid of Saccharum spp.) cultivar was developed through a cooperative research between USDA‐ARS, the Florida Sugar Cane League, Inc., and the University of Florida. It was derived from a polycross made at Canal Point, FL, on 8 Dec. 2010 between a female parent CP 08‐2409 and several male parents. CP 12‐1753 had 11 harvests in Stage 4: plant cane and first ratoon at four locations and second ratoon at three locations. Harvest data showed that CP 12‐1753 had significantly (P ≤ .05) higher cane yield and economic index than the reference cultivars ‘CL 88‐4730’ and ‘CPCL 97‐2730’, respectively, but had significantly lower cane yield in plant cane and lower economic index than the reference cultivar ‘CP 96‐1252’. Freeze tolerance of CP 12‐1753 was lower than the reference cultivars. CP 12‐1753 possesses Bru1, a major gene for brown rust resistance, and showed resistance to brown rust. At the time of release, it was resistant to orange rust, mosaic, and smut. It was moderately resistant to leaf scald and ratoon stunting disease. Considering the agronomic, yield, and disease traits, CP 12‐1753 was released by the Florida Sugarcane Variety Committee in June 2020 to growers for commercial use on mineral (sand) soils.

Experimental evaluation of genomic selection prediction for rust resistance in sugarcane

The total sugarcane (SaccharumL.) production has increased worldwide; however, the rate of growth is lower compared with other major crops, mainly due to a plateauing of genetic gain. Genomic selection (GS) has proven to substantially increase the rate of genetic gain in many crops. To investigate the utility of GS in future sugarcane breeding, a field trial was conducted using 432 sugarcane clones using an augmented design with two replications. Two major diseases in sugarcane, brown and orange rust (BR and OR), were screened artificially using whorl inoculation method in the field over two crop cycles. The genotypic data were generated through target enrichment sequencing technologies. After filtering, a set of 8,825 single nucleotide polymorphic markers were used to assess the prediction accuracy of multiple GS models. Using fivefold cross-validation, we observed GS prediction accuracies for BR and OR that ranged from 0.28 to 0.43 and 0.13 to 0.29, respectively, across two crop cycles and combined cycles. The prediction ability further improved by including a known major gene for resistance to BR as a fixed effect in the GS model. It also substantially reduced the minimum number of markers and training population size required for GS. The nonparametric GS models outperformed the parametric GS suggesting that nonadditive genetic effects could contribute genomic sources underlying BR and OR. This study demonstrated that GS could potentially predict the genomic estimated breeding value for selecting the desired germplasm for sugarcane breeding for disease resistance.

Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking quality. However, the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast disease. The genetic improvement of Varalu was done by introgressing a major yield QTL, qDTY12.1, along with two major blast resistance genes i.e. Pi54 and Pi1 through marker-assisted backcross breeding. Both traits were transferred till BC2 generation and intercrossing was followed to pyramid the two traits. Stringent foreground selection was carried out using linked markers as well as peak markers (RM28099, RM28130, RM511 and RM28163) for the targeted QTL (qDTY12.1), RM206 for Pi54 and RM224 for Pi1. Extensive background selection was done using genome-wide SSR markers. Six best lines (MSM-36, MSM-49, MSM-53, MSM-57, MSM-60 and MSM-63) having qDTY12.1 and two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%-96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were identified. These lines showed yield advantage under drought stress as well as irrigated conditions. MSM-36 showed better performance in the national coordinated trials conducted across India, which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice production. The present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.

Breeding With Major and Minor Genes: Genomic Selection for Quantitative Disease Resistance.

Disease resistance in plants is mostly quantitative, with both major and minor genes controlling resistance. This research aimed to optimize genomic selection (GS) models for use in breeding programs that are needed to select both major and minor genes for resistance. In this study, stripe rust (Puccinia striiformis Westend. f. sp. tritici Erikss.) of wheat (Triticum aestivum L.) was used as a model for quantitative disease resistance. The quantitative nature of stripe rust is usually phenotyped with two disease traits, infection type (IT) and disease severity (SEV). We compared two types of training populations composed of 2,630 breeding lines (BLs) phenotyped in single-plot trials from 4 years (2016–2020) and 475 diversity panel (DP) lines from 4 years (2013–2016), both across two locations. We also compared the accuracy of models using four different major gene markers and genome-wide association study (GWAS) markers as fixed effects. The prediction models used 31,975 markers that are replicated 50 times using a 5-fold cross-validation. We then compared GS models using a marker-assisted selection (MAS) to compare the prediction accuracy of the markers alone and in combination. GS models had higher accuracies than MAS and reached an accuracy of 0.72 for disease SEV. The major gene and GWAS markers had only a small to nil increase in the prediction accuracy more than the base GS model, with the highest accuracy increase of 0.03 for the major markers and 0.06 for the GWAS markers. There was a statistical increase in the accuracy using the disease SEV trait, BLs, population type, and combining years. There was also a statistical increase in the accuracy using the major markers in the validation sets as the mean accuracy decreased. The inclusion of fixed effects in low prediction scenarios increased the accuracy up to 0.06 for GS models using significant GWAS markers. Our results indicate that GS can accurately predict quantitative disease resistance in the presence of major and minor genes.

Genotypes and phenotypes of methicillin‐resistant staphylococci isolated from shrimp aquaculture farms

The population of methicillin-resistant (MR) staphylococci in aquatic environment is rarely investigated. Here, we characterized a collection of MR staphylococci recovered from shrimp aquaculture farms (n= 37) in Kerala, India. A total of 261 samples yielded 47 MR isolates (16 S. aureus, 13 S. haemolyticus, 11 S. epidermidis, 3 S. saprophytics and 2 each of S.intermedius and S. kloosii). Multi-drug resistance was evident in 72.3% of the isolates, with resistance mainly towards erythromycin (78.7%), norfloxacin and trimethoprim-sulfamethoxazole (53.2%), and gentamicin (34%). Major resistance genes identified included mecA (100%), ermC (38.3%), aacA-aphD (21.3%), tetK (14.9%) and tetM (21.3%). Almost 60% of the isolates carried type V SCCmec (Staphylococcal Cassette Chromosome mec), and the remaining harboured untypeable SCCmec elements. Comprehensive genotyping of the methicillin-resistant Staphylococcus aureus isolates revealed high prevalence of ST772-t345-V (sequence type-spa type-SCCmec type) (75%), followed by minor representations of ST6657-t345-V and ST3190-t12353. The isolates of S. haemolyticus and S. epidermidis were genotypically diverse as shown by their pulsed-field gel electrophoresis (PFGE) profiles. Genes encoding staphylococcal enterotoxins were observed in 53.2% of the isolates. Various genes involved in adhesion and biofilm formation were also identified. In conclusion, our findings provide evidence that shrimp aquaculture settings can act as reservoirs of methicillin-resistant staphylococci.

Metagenomics reveals the taxonomy and resistance mechanism of antibiotic resistance genes in bacterial communities of an aquaculture pond

In order to reveal the distribution characteristics of antibiotic resistance genes (ARGs) in freshwater aquaculture ponds, the microbial composition and antibiotic resistance gene types in the aquaculture environment were analyzed by using high-throughput and metagenomics sequencing technology. Our results showed that there were significant differences in the dominant bacteria composition in the water and sediment of aquaculture ponds. The dominant phylum in aquaculture water was Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes, while the phylum Actinobacteria, Chloroflexi and Proteobacteria were enriched in sediment. Compared with the comprehensive antibiotic research database (CARD), a total of 187 ARGs were identified, which were mainly multidrug, MLS and Tetracycline antibiotic resistance genes. There were 5 resistance mechanisms in the aquaculture environment, of which antibiotic efflux was the main resistance mechanism. Correlation analysis between ARGs and microbes showed that the abundance of Bacteroidetes, Cyanobacteria and Chloroflexi significantly affected the abundance of major resistance genes. This study is of great significance to protect the micro-environment of aquaculture ponds and control the pollution and spread of ARGs.

Registration of twoOryza sativatropicaljaponicagermplasm lines selected for panicle architecture and grain size traits

AbstractTwo rice (Oryza sativaL.) germplasm lines, SC14_166 (Reg. no. GP‐148, PI 698103) and SC14_072 (Reg. no. GP‐147, PI 698102), containing alleles for increased panicle branching, seeds per panicle, and grain length were developed by the USDA‐ARS. They are recombinant inbred lines selected from a cross of ‘Estrela’ (GSOR 301227) and NSFTV199 (GSOR 301190), both of tropicaljaponicaorigin. SC14_166 is a medium grain cultivar and contains alleles for two major genes,SPIKELET NUMBERon chromosome (chr.) 4 andFRIZZY PANICLEon chr. 7, which result in a greater number of primary branches, seeds per panicle, and panicle weight compared with the parents. SC14_072 is an extra‐long grain cultivar and contains alleles for two major genes on chr. 3,GRAIN SIZE 3andGRAIN LENGTH 3.2, resulting in greater grain length, width, thickness, and kernel weight. The germplasm lines possessPi‐ks, whereas SC_072 also hasPi‐z, both of which are major genes for resistance to rice blast disease. These germplasm lines are well adapted to growing conditions in the southern United States and will benefit long‐grain and medium‐grain breeding programs that desire to increase grain dimensions and panicle architecture traits. Because they are derived from the tropicaljaponicasubpopulation like most U.S. cultivars, they will be highly compatible for making breeding crosses and will contribute novel alleles to the gene pool.

Capturing Multiple Disease Resistance in Wheat through Intergeneric Hybridization.

Simple SummaryProviding disease resistance in our crop plants is our ongoing exercise for plant pathologists/breeders/geneticists. Pathogens are continually evolving and releasing new variants. The variants arise through mutations or through sexual cycles on their respective alternate hosts. Thus, the search continues for unique genes for resistance. Another newer concept is the “pyramiding” of resistance genes. It has been shown that a cultivar may last only 3 years or so before being overcome by a new variant of the pathogen. The release of new cultivars with up to four resistance genes will delay their breakdown. In our ongoing work we have also produced pyramids containing a combination of resistance genes, including SrCad for resistance to new races of stem rust, Lr34, which is a major gene for resistance to leaf rust, and Fhb1, which is a common FHB QTL. This required the production of a series of doubled haploids (DH) to produce lines containing all four genes in reasonable-sized populations. A complex series of four-way crosses were required to generate the various gene combinations. In the studies reported here, the essential tools for marker-assisted-selection are produced, i.e., mapping populations containing the resistance genes and molecular makers assigned to each gene. It should be possible to simultaneously manipulate several resistance genes from existing genetic stocks without requiring complex cross combinations. Derivatives from 4 species from the secondary gene pool of wheat—1 diploid (T. monococcum), 2 tetraploid (T. carthlicum; T. timopheevi), and 1 hexaploid (T. miguschovae)—were screened for resistance to Fusarium head blight, leaf rust, stem rust, and stripe rust. Where screening, genetic studies, and mapping were completed it was shown that all species carried resistance to multiple plant diseases. Some derived lines carried resistance to up to four different diseases. Where mapping was completed, it was shown that different diseases mapped to different chromosomes within any one accession.

Molecular typing, virulence traits and risk factors of pandrug-resistant Acinetobacter baumannii spread in intensive care unit centers of Baghdad city, Iraq

Objective: The virulence traits of pandrug-resistant (PDR) Acinetobacter baumannii strains have not been fully disclosed. Our aim was the assessment of PDR-A. baumannii (PDR-AB) virulence traits and risk factors in the intensive care unit (ICU), Baghdad, Iraq. Methods: Among 689 samples, 200 of them were identified as A. baumannii. In the disk diffusion test, 150 of them were PDR-AB. The virulence factors and antibiotic resistance genes were screened using the polymerase chain reaction (PCR) technique. Pulsed-field gel electrophoresis (PFGE) was performed for genetic typing of strains. Results: The age range >55 years (141/150, P < 0.0001), previous hospitalization (133/150, P < 0.001) and consumption of antibiotics (149/150, P < 0.0001), diabetes (122/150, P < 0.001) and prior contact to domestic animals (111/150, P = 0.00109) were significant risk factors associated with isolation of PDR-AB. PDR-AB from wound infections harbored the fimH, afa/draBC, csgA,cnf2, ibeA, cvaC, iutA, papC, traT, PAI, kpsMII, PapGII and papGIII. PFGE results outlined no clonal spread. Major drug resistance genes included blaOXA-23-like (100%), blaOXA-24-like (98%), tetA (98%), tetB (96%), dfrA (91%), sul1(75%), blaOXA-58-like (76%), blaOXA-51-like (76%) and aadA1 (76%). The fyuA gene was significantly (P = 0.039) higher in non-PDR-AB. Conclusion: A. baumannii with a high rate of virulence factors were detected among wound infections in ICU. In addition, the strains exhibited no genetic relation in the PFGE method. Risk factors of the high incidence of PDR-AB in Baghdad prior hospitalization and consumption of antibiotics, diabetes and contact with domestic animals. Therefore, there is a demand for control of PDR and virulent strains spread in healthcare settings.

DRR Dhan 53 (RP-6113-Patho-BB9; IET 27294) – a high yielding, bacterial blight resistant, fine grain type rice variety

DRR Dhan 53 was released for commercial cultivation in Samba Mahsuri/Improved Samba Mahsuri growing regions of Telangana, Andhra Pradesh, Tamilnadu, Karnataka, Chhattisgarh, Orissa, Jharkhand, Bihar, Gujarat and Maharashtra by Central Sub-committee on Crop Standards, Notification and Release of Varieties in 2020. It is a cross between Improved Samba Mahsuri*3/PAU 3554. DRR Dhan 53 (IET 27294) is a marker assisted selection (MAS) derived product in the genetic background of Improved Samba Mahsuri. DRR Dhan 53 is a durable bacterial blight resistant, high-yielding, fine-grain type rice variety having the major bacterial blight resistance genes, Xa21+xa13+xa5+Xa38 with seed to seed maturity of 130-135 days and average yield of 5.5- 6 t/ ha.

R-BPMV-Mediated Resistance to Bean pod mottle virus in Phaseolus vulgaris L. Is Heat-Stable but Elevated Temperatures Boost Viral Infection in Susceptible Genotypes.

In the context of climate change, elevated temperature is a major concern due to the impact on plant–pathogen interactions. Although atmospheric temperature is predicted to increase in the next century, heat waves during summer seasons have already become a current problem. Elevated temperatures strongly influence plant–virus interactions, the most drastic effect being a breakdown of plant viral resistance conferred by some major resistance genes. In this work, we focused on the R-BPMV gene, a major resistance gene against Bean pod mottle virus in Phaseolus vulgaris. We inoculated different BPMV constructs in order to study the behavior of the R-BPMV-mediated resistance at normal (20 °C) and elevated temperatures (constant 25, 30, and 35 °C). Our results show that R-BPMV mediates a temperature-dependent phenotype of resistance from hypersensitive reaction at 20 °C to chlorotic lesions at 35 °C in the resistant genotype BAT93. BPMV is detected in inoculated leaves but not in systemic ones, suggesting that the resistance remains heat-stable up to 35 °C. R-BPMV segregates as an incompletely dominant gene in an F2 population. We also investigated the impact of elevated temperature on BPMV infection in susceptible genotypes, and our results reveal that elevated temperatures boost BPMV infection both locally and systemically in susceptible genotypes.

Genome-wide association mapping of seedling and adult plant response to stem rust in a durum wheat panel.

Many of the major stem rust resistance genes deployed in commercial wheat (Triticum spp.) cultivars and breeding lines become ineffective over time because of the continuous emergence of virulent races. A genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers and 280 durum wheat [Triticum turgidum L. subsp. Durum (Desf.) Husnot] lines from CIMMYT to identify genomic regions associated with seedling resistance to races TTKSK, TKTTF, JRCQC, and TTRTF and field resistance to TKTTF and JRCQC. The phenotypic data analysis across environments revealed 61-91 and 59-77% of phenotypic variation was explained by the genotypic component for seedling and adult plant response of lines, respectively. For seedling resistance, mixed linear model (MLM) identified eight novel and nine previously reported quantitative trait loci (QTL) while a fixed and random model circulating probability unification (FarmCPU) detected 12 novel and eight previously reported QTL. For field resistance, MLM identified 12 novel and seven previously reported loci while FarmCPU identified seven novel and nine previously reported loci. The regions of Sr7a, Sr8155B1, Sr11, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. Novel loci on chromosomes 3B, 4A, 6A, 6B, 7A, and 7B could be used as sources of resistance to the races virulent on durum wheat. Two large-effect markers on chromosome 6A could potentially be used to differentiate resistant haplotypes of Sr13 (R1 and R3). Allelism tests for Sr13, breaking the deleterious effect associated with Sr22/Sr25 and retaining the resistance allele at the Sr49 locus, are needed to protect future varieties from emerging races.

The population structure, antimicrobial resistance, and pathogenicity of Streptococcus suis cps31

Streptococcus suis is a zoonotic pathogen that can cause invasive infections in humans and pigs. The S. suis cps31 strains (SS31) were frequently isolated from healthy or diseased pigs and one human infection case caused by SS31 was reported in Thailand in 2015. However, except for a few epidemiologic studies, little information is available for SS31. To characterize SS31, a total of 75 SS31 strains were analyzed, including 52 strains that were isolated from healthy or diseased pigs and 23 strains whose information was accessed from NCBI. The MLST analysis showed that SS31 exhibited high heterogeneity. The phylogenetic analysis and minimum core-genome (MCG) classification revealed that 75 strains were clustered into 3 lineages. Strains from NCBI mainly at Lineage 2 belong to MCG7-3, and most of strains from China at Lineage 3 belong to MCG7-2. This finding indicated that their evolutionary path was different. All SS31 strains were resistant to more than three classes of antimicrobial agents, and major antimicrobial resistance genes for strains from Lineage 3 were carried by prophages. This observation is different from the previous observation that integrative conjugative elements and integrative and mobilizable elements are major vehicles of antimicrobial resistance genes for S. suis. In addition to strains isolated from diseased pigs, seven of 47 strains isolated from clinically healthy pigs were also pathogenic in a zebrafish infection model. These findings reveal unique characteristics of SS31 and contribute to establishing public health surveillance for SS31 and clarifying the diversity of S. suis.

Validating the Strategic Deployment of Blackleg Resistance Gene Groups in Commercial Canola Fields on the Canadian Prairies.

Blackleg, caused by the fungal pathogen Leptosphaeria maculans, is a serious threat to canola (Brassica napus L.) production in western Canada. Crop scouting and extended crop rotation, along with the use of effective genetic resistance, have been key management practices available to mitigate the impact of the disease. In recent years, new pathogen races have reduced the effectiveness of some of the resistant cultivars deployed. Strategic deployment and rotation of major resistance (R) genes in cultivars have been used in France and Australia to help increase the longevity of blackleg resistance. Canada also introduced a grouping system in 2017 to identify blackleg R genes in canola cultivars. The main objective of this study was to examine and validate the concept of R gene deployment through monitoring the avirulence (Avr) profile of L. maculans population and disease levels in commercial canola fields within the Canadian prairies. Blackleg disease incidence and severity was collected from 146 cultivars from 53 sites across Manitoba, Saskatchewan, and Alberta in 2018 and 2019, and the results varied significantly between gene groups, which is likely influenced by the pathogen population. Isolates collected from spring and fall stubble residues were examined for the presence of Avr alleles AvrLm1, AvrLm2, AvrLm3, AvrLm4, AvrLm5, AvrLm6, AvrLm7, AvrLm9, AvrLm10, AvrLm11, AvrLepR1, AvrLepR2, AvrLep3, and AvrLmS using a set of differential host genotypes carrying known resistance genes or PCR-based markers. The Simpson’s evenness index was very low, due to two dominant L. maculans races (AvrLm2-4-5-6-7-10-11 and AvrLm2-5-6-7-10-11) representing 49% of the population, but diversity of the population was high from the 35 L. maculans races isolated in Manitoba. AvrLm6 and AvrLm11 were found in all 254 L. maculans isolates collected in Manitoba. Knowledge of the blackleg disease levels in relation to the R genes deployed, along with the L. maculans Avr profile, helps to measure the effectiveness of genetic resistance.

Quantitative resistance linked to late effectors.

Quantitative resistance linked to late effectors.

Recent advances in rapid antimicrobial susceptibility testing systems

Introduction Until recently antimicrobial susceptibility testing (AST) methods based on demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged. Areas covered Advances in rapid phenotypic and molecular-based AST systems. Expert opinion AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use has allowed many laboratories to be able to use many of these systems. Continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.