Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.

BACKGROUND: Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. RESULTS: Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. CONCLUSIONS: Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

Physiological Races and Virulence Dynamics of Setosphaeria turcica in Northeast China.

Northern corn leaf blight (NCLB), caused by Setosphaeria turcica, is an important foliar disease in corn. Since 2005, the damage from NCLB has increased in Northeast China, probably from the emergence of new physiological races. In this study, 883 single conidial isolates of S. turcica were obtained from 12 sites across three provinces of Northeast China between 2007 and 2017. The virulence of the isolates was evaluated in five corn lines (B37, B37Ht1, B37Ht2, B37Ht3, and B37HtN). Sixteen physiological races (0, 1, 2, 3, N, 12, 13, 1N, 23, 2N, 3N, 123, 12N, 13N, 23N, and 123N) were obtained, depending on their resistance or susceptibility. Three races (0, 1, and 2) were most prevalent, with frequencies of 40.5, 19.6, and 11.3% in all isolates, respectively. Races varied across provinces and years. Virulence to more than one Ht resistance genes occurred in 21.5% of isolates, with 8.5% virulent to three or more genes. Overall, 41% of isolates were avirulent to all Ht genes, 36% were virulent to Ht1, 28% to Ht2, 11% to Ht3, and 16% to HtN. Isolates from Heilongjiang had a greater frequency of virulence to Ht2 and Ht3, whereas isolates from Jilin and Liaoning were more frequently virulent to Ht1 and HtN, respectively. The frequency of isolate virulence to Ht2 ranged from 8% in 2009 to a maximum of 29% in 2015, and in 2015, isolates were more virulent to Ht2 than Ht1. This study will help growers to purposefully select commercial hybrids with multiple effective Ht resistance genes, and reduce the utilization of Ht1 and Ht2 genes in the process of corn production to strengthen NCLB control.

Catalase eliminates reactive oxygen species and influences the intestinal microbiota of shrimp.

Intestinal innate immune response is an important defense mechanism of animals and humans against external pathogens. The mechanism of microbiota homeostasis in host intestines has been well studied in mammals and Drosophila. The reactive oxygen species (ROS) and antimicrobial peptides have been reported to play important roles in homeostasis. However, how to maintain the microbiota homeostasis in crustacean intestine needs to be elucidated. In this study, we identified a novel catalase (MjCAT) involved in ROS elimination in kuruma shrimp, Marsupenaeus japonicus. MjCAT mRNA was widely distributed in hemocytes, heart, hepatopancreas, gills, stomach, and intestine. After the shrimp were challenged with pathogenic bacteria via oral infection, the expression level of MjCAT was upregulated, and the enzyme activity was increased in the intestine. ROS level was also increased in the intestine at early time after oral infection and recovered rapidly. When MjCAT was knocked down by RNA interference (RNAi), high ROS level maintained longer time, and the number of bacteria number was declined in the shrimp intestinal lumen than those in the control group, but the survival rate of the MjCAT-RNAi shrimp was declined. Further study demonstrated that the intestinal villi protruded from epithelial lining of the intestinal wall were damaged by the high ROS level in MjCAT-knockdown shrimp. These results suggested that MjCAT participated in the intestinal host-microbe homeostasis by regulating ROS level.

Genetic Diversity and Reproduction Trends of Phytophthora infestans in Estonia: EU_41_A2 Detected without an Indication of Clonal Reproduction.

This study explores the population dynamics of Phytophthora infestans in Estonia from 2005 to 2022, focusing on genetic diversity and potential shifts in reproductive strategies. In total, 153 P. infestans isolates were collected throughout Estonia over ten growing seasons. Genotyping revealed considerable genetic diversity, with most isolates not corresponding to known multilocus genotypes (MLGs). Still, instances of invasive clonal lineages were observed, notably EU_41_A2. The data indicate the likelihood of random mating rather than clonal reproduction in all the analyzed years. The principal coordinate analysis (PCoA) results revealed no distinct clustering among the sampling years. Statistical analysis and the minimum spanning network (MSN) indicated low genetic differentiation between years with minimal fluctuations in allele frequencies. The continuous monitoring of P. infestans populations is essential for detecting any changes from the current evolutionary trajectory and implement effective disease management strategies, especially considering the recent emergence of EU_41_A2 in the Nordics and the potential impacts of climate change.

Prevalence of Borrelia burgdorferi and diversity of its outer surface protein C (ospC) alleles in blacklegged ticks (Ixodes scapularis) in Delaware.

Characterizing the diversity of genes associated with virulence and transmission of a pathogen across the pathogen's distribution can inform our understanding of host infection risk. Borrelia burgdorferi is a vector-borne bacterium that causes Lyme disease in humans and is common in the United States. The outer surface protein C (ospC) gene of B. burgdorferi exhibits substantial genetic variation across the pathogen's distribution and plays a critical role in virulence and transmission in vertebrate hosts. In fact, B. burgdorferi infections that disseminate across host tissues in humans are associated with only a subset of ospC alleles. Delaware has a high incidence of Lyme disease, but the diversity of ospC in B. burgdorferi in the state has not been evaluated. We used PCR to amplify ospC in B. burgdorferi-infected blacklegged ticks (Ixodes scapularis) in sites statewide and used short-read sequencing to identify ospC alleles. B. burgdorferi prevalence in blacklegged ticks varied across sites, but not significantly so. We identified 15 previously characterized ospC alleles accounting for nearly all of the expected diversity of alleles across the sites as estimated using the Chao1 index. Nearly 40% of sequenced infections (23/58) had more than one ospC allele present suggesting mixed strain infections and the relative frequencies of alleles in single infections were positively correlated with their relative frequencies in mixed infections. Turnover of ospC alleles was positively related to distance between sites with closer sites having more similar allele compositions than more distant sites. This suggests a degree of B. burgdorferi dispersal limitation or habitat specialization. OspC alleles known to cause disseminated infections in humans were found at the highest frequencies across sites, corresponding to Delaware's high incidence of Lyme disease.

Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates.

The Dickeya and Pectobacterium bacterial species cause blackleg and soft-rot diseases on potato plants and tubers. Prophylactic actions are essential to conserve a high quality of seed potato tubers. Biocontrol approaches are emerging, but we need to know how efficient biocontrol agents are when facing the natural diversity of pathogens. In this work, we sampled 16 production fields, which were excluded from the seed tuber certification scheme, as well as seven experimental parcels, which were planted with seed tubers from those production fields. We collected and characterized 669 Dickeya and Pectobacterium isolates, all characterized using nucleotide sequence of the gapA gene. This deep sampling effort highlighted eleven Dickeya and Pectobacterium species, including four dominant species namely D. solani, D. dianthicola, P. atrosepticum and P. parmentieri. Variations in the relative abundance of pathogens revealed different diversity patterns at a field or parcel level. The Dickeya-enriched patterns were maintained in parcels planted with rejected seed tubers, suggesting a vertical transmission of the pathogen consortium. Then, we retained 41 isolates representing the observed species diversity of pathogens and we tested each of them against six biocontrol agents. From this work, we confirmed the importance of prophylactic actions to discard contaminated seed tubers. We also identified a couple of biocontrol agents of the Pseudomonas genus that were efficient against a wide range of pathogen species.

Fire blight resistance, irrigation and conducive wet weather improve Erwinia amylovora winter survival in cankers.

Erwinia amylovora causes fire blight, a disease responsible for enormous economic losses in the pome fruit-producing areas where it is present. Despite the abundant research on fire blight, information about E. amylovora population dynamics and survival in fire blight cankers and the plant defense responses to this pathogen in the infected bark are limited. In our study, we obtained fire blight cankers in apple, pear, and Asian pear cultivars showing differing resistance to the disease by shoot inoculation with E. amylovora. We collected cankers from irrigated and non-irrigated trees every 3 months in two independent field experiments and analyzed samples by viability digital PCR. We also assessed the expression of pathogenicity-related (PR) genes in the bark of selected apple and Asian pear cultivars. A logistic regression analysis revealed the impact of environmental and host factors on E. amylovora detection rates in cankers. The chances of detecting live E. amylovora cells in cankers increased significantly in those collected from irrigated trees, in July, and/or during an experiment performed in a year with an expected average rainfall when compared to samples from non-irrigated trees, collected in January, and/or during an experiment performed under environmental conditions dominated by drought. We found a positive correlation between the pathogen detection rates in cankers and the host resistance to fire blight that might be explained by lower E. amylovora survival rates in more damaged tissues of susceptible hosts. The genes PR-1, PR-2, PR-5, and PR-8 were induced in the bark surrounding apple and Asian pear fire blight cankers. Our study, involving the analysis of more than 800 canker samples, provides new knowledge about the fire blight disease cycle and lays the foundation for improved fire blight management and eradication strategies in pome fruit orchards.

Achieving broad-spectrum resistance against rice bacterial blight through targeted promoter editing and pathogen population monitoring.

Plant diseases severely reduce crop yields and threaten global food security. Broad-spectrum resistance (BSR) is a desirable trait because it confers resistance against more than one pathogen species or the majority of races/strains of the same pathogen. To control plant diseases, breeders have selected BSR to reduce disease occurrence and prolong the life-span of newly released cultivars in the last several decades (Mundt, Phytopathology 108(7):792-802, 2018). Although effective, breeding of BSR cultivars in crop plants is still time-consuming and technically challenging. Recently, new gene-editing technologies such as CRISPR/Cas9 have dramatically accelerated the process of plant breeding and provided an approach for rapidly creating new varieties with BSR and other beneficial traits (Borrelli et al., Front Plant Sci 9:1245, 2018). In addition, close surveillance of pathogen populations in the field can provide useful information for the deployment of appropriate resistance genes in the target regions. In this mini-review, we focus on the significance and application of the exciting results from two recent companion papers published in Nature Biotechnology that provide new strategies to develop crop plants with BSR against pathogens through targeted promoter editing of susceptibility genes in plants as well as pathogen population monitoring.

Multiple pairs of allelic MLA immune receptor-powdery mildew AVRA effectors argue for a direct recognition mechanism.

Nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins in plants and animals mediate intracellular pathogen sensing. Plant NLRs typically detect strain-specific pathogen effectors and trigger immune responses often linked to localized host cell death. The barley Mla disease resistance locus has undergone extensive functional diversification in the host population and encodes numerous allelic NLRs each detecting a matching isolate-specific avirulence effector (AVRA) of the fungal pathogen Blumeria graminis f. sp. hordei (Bgh). We report here the isolation of Bgh AVRa7, AVRa9, AVRa10, and AVRa22, which encode small secreted proteins recognized by allelic MLA7, MLA9, MLA10, and MLA22 receptors, respectively. These effectors are sequence-unrelated, except for allelic AVRa10 and AVRa22 that are co-maintained in pathogen populations in the form of a balanced polymorphism. Contrary to numerous examples of indirect recognition of bacterial effectors by plant NLRs, co-expression experiments with matching Mla-AVRa pairs indicate direct detection of the sequence-unrelated fungal effectors by MLA receptors.

Hydroxycoumarins: New, effective plant-derived compounds reduce Ralstonia pseudosolanacearum populations and control tobacco bacterial wilt.

Plant wilt disease caused by the soilborne bacterial pathogen Ralstonia pseudosolanacearum is one of the most devastating plant diseases; however, no effective protection against this disease has been developed. Coumarins are important natural plant-derived compounds with a wide range of bioactivities and extensive applications in medicine and agriculture. In the present study, three hydroxycoumarins (Hycs), umbelliferone (UM), esculetin (ES) and daphnetin (DA) significantly inhibited the growth of R. pseudosolanacearum on solid medium in a concentration-dependent manner, and the minimum inhibitory concentration (MICs) of these compounds was 325  mg L-1, 125 mg L-1 and 75 mg L-1, respectively. The percentage of live cells of R. pseudosolanacearum when supplemented with UM, ES, and DA was 63.61%, 17.81% and 7.23%, respectively, which were significantly lower than the DMSO treatment with 92%. Furthermore, irrigating roots with hydroxycoumarins (Hycs) 24 h before inoculation with R. pseudosolanacearum significantly delayed the occurrence of tobacco bacterial wilt, with the control efficiency of the DA treatment (the most efficient of Hycs treatment) 80.03%, 69.83%, 59.19%, 45.49%, 44.12%, 38.27% at 6, 8, 10, 12, 14, and 16 days after inoculation, respectively. Compared with the DMSO treatment, the pathogen populations of tobacco stems supplemented with 100 mg L-1 DA were the lowest, with population significantly reduced by 22.46%, 27.34%, and 18.06% at 4, 7, and 10 days after inoculation, respectively. Based on this study, these Hycs could be applied as potential protective agents in the management of tobacco bacterial wilt.