Pathogenic Isolates Research Articles

First report of Fusarium humuli causing stem spots in Nicotiana tabacum L in China.

Tobacco is one of the most important economic crops in China. Disease is one of the main factors affecting the quality of tobacco production (Cai et al. 2022). Stem spot disease of tobacco was observed in the Planting Demonstration Garden in Chang Ning (26°37N; 112° 31E), Hunan Province of China, from May to June 2023. The disease seriously retarded tobacco growth and the incidence rate was about 30-50% of the plants(Yun Yan 87). Most of infected tobacco had black spots on the stems, and the spots expanded and joined together quickly, while many stems turned black and withered. For pathogen isolation, symptomatic stem samples were collected and disinfected with 75% ethanol for 30 s and 2% sodium hypochlorite for 1 minute, followed by rinsing with sterile distilled water three times. Subsequently, small pieces (5 × 5 mm) of diseased tissues were placed on potato dextrose agar (PDA) and incubated in the dark at 25 °C for 24 h to 36 h. The emerging fungal hyphal tips were transferred to PDA and purified by the single-spore method(Yu et al. 2022). In total, 16 cultures with the same appearance were isolated from 30 disease spots on the stem. Strain coded as hnxryc2 was randomly selected for identification. After culturing in PDA for 7 days, white and dense colonies wereobserved with a mean radial growth rate of 6.4 mm/day. The strain cultured 10 days on SNA. Morphological observations were made on 10-day-old culture on SNA medium, and macroconidia were sickle-shaped and slightly curved, with 3-5 septa (2.32-7.00 µm × 0.53-1.17 µm, n = 50), neither microconidia nor chlamydospores were observed. These morphological characteristics were consistent with the description of Fusarium humuli (Wang et al. 2019, Li et al. 2023). Furthermore, primers ITS1/ITS4, EF728F/EF986R, RPB1-F5/RPB1-R8 and fRPB2-5F2/fRPB2-7cR(Xie et al. 2023) were used to amplify the ITS region, EF-1α, RPB1, and RPB2 from strain hnxryc2, respectively. The sequence alignment of hnxryc2 with the NCBI database and FUSARIOID-ID shows the following results: The sequence of ITS region(GenBank accession number PP543715) was 100% identical to these of Fusarium sp. (MN428026.1), the sequences of EF-1α, RPB1, and RPB2 of strain hnxryc2(GenBank accession numbersOR257586, OR326856 and OR257587 respectively) were 99% to 100% identical to these of F. humuli (GenBank accession numbers MK289578.1, MZ824672.1 and MZ824673.1, respectively). Then a phylogenetic tree based on ITS region, EF-1α, and RPB2 sequences was constructed (Kroon et al. 2004). The strain hnxryc2 was more closely related to F. humuli (CGMCC3.19374 GenBank accession nos. MK280845.1, MK289570.1 and MK289724.1, respectively), with bootstrap values 88%. Pathogenicity tests were performed on detached stems of tobacco and potted plants. Wounded stems were inoculated with conidial suspensions (100 μL, 1×107 spores/mL), and the controls were inoculated with sterile water (Xu et al. 2023). The inoculated detached stems were kept in humid chambers (Zhong et al., 2019), each treatment was given a 12h/12h light/dark cycle at 25°C. Deep black spots were observed for 3 days after inoculation. After 9 days, typical symptoms similar to the original diseased plants in the field were found on all inoculated stems, while the control stems did not exhibit any symptoms. Pathogenicity assays were repeated thrice. The pathogen F. humuli was successfully reisolated from the stem of inoculated samples showing symptoms. To our knowledge, this is the first report of F. humuli inducing stem spot on tobacco in China. Since F. humuli is a common pathogenic fungus that infects different plant species, more attention should be paid to its prevalence in tobacco, and the potential risk of a disease outbreak in other provinces of China.

Performance of blood enterovirus and parechovirus polymerase chain reaction testing in young febrile infants: a prospective multicentre observational study

ObjectivesTo analyse the performance of blood enterovirus and parechovirus PCR testing (ev-PCR) for invasive bacterial infection (IBI) (isolation of a single bacterial pathogen in a blood or cerebrospinal fluid culture)...

Comparison of the Results of BAL and ETA Culture in Intubated COVID-19 Patients.

The isolation of pathogens using bronchoalveolar lavage (BAL) culture or endotracheal aspirate (ETA) culture may enhance the treatment success for secondary pneumonia due to COVID-19, thereby reducing the risk of morbidity and mortality. This study aimed to retrospectively analyze the results of BAL and ETA cultures in intubated COVID-19 patients and to determine whether BAL has an advantage over ETA. We routinely perform BAL culture via bronchoscopy or ETA culture within the first 48 h after intubation. We retrospectively reviewed cases that underwent BAL and ETA. The patients were divided into two groups: Group B (BAL) and Group E (ETA). Various parameters were evaluated and compared between the two groups. The demographic data and blood test results were similar between the two groups. However, ICU stay, duration of intubation, and culture positivity were significantly higher in Group B. Although not statistically significant, the mortality rate was higher in Group E. The most commonly isolated microorganisms were Candida species. The observed mortality rates were consistent with the existing literature. Since the microorganism isolation rate is higher with BAL, leading to more effective antimicrobial treatment, early deaths were prevented, and ICU stay durations were prolonged. Conversely, these durations were shorter in the ETA group due to higher mortality. In intubated COVID-19 patients, a more effective treatment process can be achieved by clearing the airway with fiberoptic bronchoscopy and tailoring the treatment based on BAL culture results. This approach may positively impact prognosis and mortality rates.

First Report of Streptomyces brasiliscabiei Causing Common Scab on Potato in China.

Severe typical deep-pitted lesions of Potato Common Scab (PCS) disease were observed in two locations in China, Dingxi, Gansu Province, and Shuozhou, Shaanxi Province, in 2021. Potato farms in Dingxi growing cultivar Huangxin 226 (26 hectares) exhibited a scab disease incidence of 10%, while cultivar Jinshu 15# (4 hectares) in Shuozhou showed a disease incidence of 30% (Fig. 1). During harvest, tubers displaying PCS symptoms were collected for pathogen isolation. To obtain pathogen isolates, surface-sterilized tuber tissue with scab lesions was ground in sterile water, serially diluted, and plated onto ISP5 agar medium plates (Handique et al. 2022). Five pure colonies of Streptomyces isolate were obtained, designated as ZRIMU1503, ZRIMU1502, ZRIMU1320, ZRIMU1321and ZRIMU791. Genomic DNA was extracted and sequenced using Illumina technology. Sequencing data of the 5 isolates were uploaded to NCBI GenBank and annotated (Accession numbers: JBBAYL010000000, JBBAYM010000000, JBBAYN010000000, JBBAYO010000000 and JBBAYP010000000, respectively) using the PGAP pipeline (Tatusova et al. 2016). Average Nucleotide Identity (ANI) values (97.52 %, 97.53 %,97.54 %,97.57 % and 97.52 %, respectively) indicated the identity of the five isolates to the type strain S. brasiliscabiei IBSBF 2867T. Additionally, pairwise comparisons of Digital DNA Hybridization (DDH) value (76.2%, 76.3%, 76.4%, 76.4% and 76.2% respectively) of all the Streptomyces type strains show the highest identity to S. brasiliscabiei IBSBF 2867T. Twelve housekeeping genes (acnA, atpD, dnaN, gap, gyrA, gyrB , infB, mdh, recA, rplB, rpoB, and trpB) were extracted from the genome sequence of the five isolates to construct a multi-locus sequence analysis (MLSA) tree. The evolutionary distance of the five isolates was constructed using MEGAX software (Kumar et al., 1994), along with other Streptomyces strains that are known to cause PCS. The resulting cladogram demonstrated the isolated strains clustered together with S. brasiliscabiei IBSBF 2867T (Fig.2). Koch's postulates were fulfilled by inoculating a perlite potting mix with spore suspensions of each isolate (104 CFU/ml), planting tubers (cv. Favorita), and reproducing PCS symptoms at harvest after three months. Negative control received water treatment. The plants were kept in greenhouse with 12 h of light per day and irrigated regularly. The experiment was repeated twice, once in April 2022 and again in April 2023. On harvest, all five isolates exhibited development of severe symptoms of PCS (Fig.1), while the negative controls had no lesions. The pathogen was reisolated from the lesions and confirmed to be identical to the original isolate by 16S rRNA gene sequences. To our knowledge, this is the first report of S. brasiliscabiei causing PCS in China. S. brasiliscabiei was identified as a new species to cause PCS in Brazil and was identified based on morphology, pathogenicity, and genetic features (Corrêa et al. 2021). Multiple pathogen-causing PCS has been recognized in China and a surge of disease incidence in potato fields has been reported (Handique et al. 2022; Wu et al. 2023). S. brasiliscabiei causes severe symptoms which makes potatoes unmarketable. The disease epidemiology of this pathogen needs to be investigated.

Isolation and identification of mulberry fruit sclerotiniosis pathogen and laboratory screening of biological fungicides

Isolation and identification of mulberry fruit sclerotiniosis pathogen and laboratory screening of biological fungicides

Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models

Key messageIntegrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance.Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.

Characterization of Fungal Species Isolated from Cankered Apple Barks Demonstrates the Alternaria alternata Causing Apple Canker Disease.

Apple canker disease, also named as apple Valsa canker, is one of the most destructive diseases for apples (Malus domestica Borkh.). Cytospora/Valsa spp. are the dominant causal agent of this disease, but many studies have revealed that fungi from some other genus can also cause typical apple canker symptoms. In this study, we performed fungal pathogen isolation from cankered 'Fuji' apple barks. Six representative morphologically different fungi (Strain 1-6) were further subjected to ITS sequencing and evolutionary analysis. Molecular identification results revealed that Strains 1-6 are Cytospora mali, Fusarium cf. solani, Alternaria alternata, C. mali, Diplodia seriata and F. proliferatum, respectively. All these fungi have been reported to be causal agents of apple diseases. By inoculating fungal plugs onto trunks of 'Fuji' apple trees, the pathogenicity of the six fungi were accessed. Only the inoculations of the two C. mali strains (Strain 1 and Strain 4) and the A. alternata strain (Strain 3) resulted in typical apple canker symptoms in trunks. It is worth noting that Strain 1 caused much more severe canker symptoms and higher pathogenicity incidence than the other two fungi. A. alternata has been identified as a pathogen causing diseases on apple fruits and leaves. By further assessing its pathogenicity on apple fruits and leaves, we verified that it can also cause typical fruit rot and leaf spot symptoms. To the best of our knowledge, this is the first report on apple canker disease caused by A. alternata in China. Our present study can provide a theoretical foundation for the prevention and control of apple canker disease.

Seasonal Prevalence of Major Mastitis Pathogens Isolated from Crossbred Cow Milk Samples in Sub-tropical India

The dairy industry suffers significant financial losses due to mastitis. In order to control and prevent mastitis, it is imperative to continuously monitor the bacteriology, prevalence, and incidence of major mastitis pathogens. Thus, the objective of this research was to find out how often mastitis causing bacteria were isolated from milk samples of crossbred cows over various seasons in India's sub-tropical environment. 240 milk samples from 80 different cows were collected over the course of three seasons [Hot Dry (April to June), Hot Humid (July to September), and Autumn (October to November)] in order to correlate the prevalence of four main mastitis pathogens (Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, and Escherichia coli) with the season. The most prevalent isolate during all seasons was Staphylococcus aureus. Our findings demonstrated a discernible relationship between seasonal change and the isolation rate of the bacterium associated with bovine mastitis, with the hot-humid season having the greatest pathogen isolation rate.

PREVALENCE OF URINARY TRACT INFECTION AMONG OUT PATIENTS A JOS HOSPITAL PLATEAU STATE NIGERIA.

Infection of the urinary tract(called UTI) is caused by microbes thatinvade and inhabit the urinary system (urethra, bladder, ureters, andkidney). Because the urine is an excellent culture medium for the UTI pathogens,these pathogens ascend into the urinary system causing UTI varying from boils, cystitis, and prostitis which may even lead to sepsis if left untreated. This research was conducted to assess the preponderance of UTI among out-patients who attendedthe Plateau Specialist Hospital, Jos. We observed that of the 80 samples examined, 15 tested positive for UTI,suggesting a prevalence of 18.75%. According to age group, it was discovered that age group between 41 above has the highest prevalence of urinary tract infection with 12.5%. Based on gender, the female has the highest prevalence rate of 10(15.0%), though more in number than the males. the female were 60 out of 80 while the male were 20 in number. There was no positive sample obtained in children sample.It was discovered that Escherichia coli has the highest prevalence rate at 6(7.5%), followed by Staphylococcus aureus 4 (5.0%). The isolation of urinary tract pathogens from these patients though with a lower prevalence stresses the urgent need for public enlightenment campaigns by the appropriate authorities to educate the patients as well as the masses on the etiological agents, the possible risk factors, routes of transmission and health implication of urinary tract infection and ways of preventing the bacteria, as well as early diagnosis and treatment of infected ones.

Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat.

A total of 65 SNPs associated with resistance to tan spot and septoria nodorum blotch were identified in a panel of 180 cultivated emmer accessions through association mapping Tan spot and septoria nodorum blotch (SNB) are foliar diseases caused by the respective fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum that affect global wheat production. To find new sources of resistance, we evaluated a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for reactions to four P. tritici-repentis isolates Pti2, 86-124, 331-9 and DW5, two P. nodorum isolate, Sn4 and Sn2000, and four necrotrophic effectors (NEs) produced by the pathogens. About 8-36% of the accessions exhibited resistance to the four P. tritici-repentis isolates, with five accessions demonstrating resistance to all isolates. For SNB, 64% accessions showed resistance to Sn4, 43% to Sn2000 and 36% to both isolates, with Spain (11% accessions) as the most common origin of resistance. To understand the genetic basis of resistance, association mapping was performed using SNP (single nucleotide polymorphism) markers generated by genotype-by-sequencing and the 9K SNP Infinium array. A total of 46 SNPs were significantly associated with tan spot and 19 SNPs with SNB resistance or susceptibility. Six trait loci on chromosome arms 1BL, 3BL, 4AL (2), 6BL and 7AL conferred resistance to two or more isolates. Known NE sensitivity genes for disease development were undetected except Snn5 for Sn2000, suggesting novel genetic factors are controlling host-pathogen interaction in cultivated emmer. The emmer accessions with the highest levels of resistance to the six pathogen isolates (e.g., CItr 14133-1, PI 94634-1 and PI 377672) could serve as donors for tan spot and SNB resistance in wheat breeding programs.

Phylogenomic Analyses of Three Distinct Lineages Uniting Staphylococcus cohnii and Staphylococcus urealyticus from Diverse Hosts.

We sequenced and assembled genomes for 17 isolates of Staphylococcus cohnii isolated from osteomyelitis lesions in young broilers from two separate experiments where we induced lameness using a hybrid wire-litter flooring system. Whole genome comparisons using three different methods support a close relationship of genomes from both S. cohnii and Staphylococcus urealyticus. The data support three different lineages, which we designated as Lineage 1, Lineage 2, and Lineage 3, uniting these two species within an evolving complex. We present evidence for horizontal transfer between lineages of genomic regions from 50-440 kbp. The transfer of a 186 kbp region from Lineage 1 to Lineage 2 appears to have generated Lineage 3. Human-associated isolates appear to be limited to Lineages 2 and 3 but Lineage 2 appears to contain a higher number of human pathogenic isolates. The chicken isolates from our lameness trials included genomically diverse isolates from both Lineage 1 and 2, and isolates from both lineages were obtained from osteomyelitis lesions of individual birds. Our results expand the diversity of Staphylococci associated with osteomyelitis in poultry and suggest a high diversity in the microbiome of day-old chicks. Our data also support a reevaluation and unification of the taxonomic classifications of S. cohnii and S. urealyticus.

Isolation of Potential Antagonistic Rhizosphere Fungi against Alternaria alternata from Organic Carrot Productions

Rhizospheric fungi can have serve as biological agents against plant pathogens Alternaria alternata, which infects carrot plants. Rhizospheric fungi are more abundant in organic lands. This study aims to isolate fungi from organic carrot’s rhizosphere that are able to suppress A. alternata’s growth and determine isolate rhizospheric fungi ability to inhibit A. alternata to identify potential biological control agents against A. alternata. This research was conducted at the Laboratory of Biotechnology and Basic Biology, Diponegoro University, between January–June 2023. Research methods include survey location, soil sampling, rhizospheric fungi isolation, pathogenic fungi isolation, creating growth curve, pathogenicity tests, antagonism tests, and fungi identification. This study used a complete randomized design (CRD) and was analyzed using ANOVA at the 5% level of significance and Duncan's hoc-posttest. Fungi isolation from organic carrot plant’s rhizosphere resulted in 13 isolates consisting of six genera: Penicillium, Aspergillus, Paecilomyces, Myrothecium, Trichoderma, and Simplicillium. The antagonism test showed that eight antagonistic isolates, including the genus Penicillium (WO1, WO6, WO10), Paecilomyces (WO5), Myrothecium (WO7), Trichoderma (WO9), and Aspergillus (WO11, WO13), where WO1, WO6, WO10, and WO11 have a medium percentage of inhibition (44.12-57.84%), while WO5, WO7, WO9, and WO13 have a high percentage of inhibition (64.29-76.06%). The eight isolates showed antagonism mechanisms, including antibiosis (WO1, WO5, WO6, WO7, WO10, and WO11) and parasitism (WO9 and WO13).

Pestalotiopsis kenyana causes leaf spot disease on Rhododendron agastum in China

Rhododendron agastum, a well-known flower with significant aesthetic and medicinal value, belongs to the Rhododendron genus in the Ericaceae family. In April 2023, a leaf spot disease on R. agastum plants was found in the Baili Azalea Forest Area in Guizhou province, China. Approximately 400 plants were surveyed, and the incidence of leaf spot on R. agastum leaves was 20%. The damaged leaves had gray-white irregular diseased spots with black-brown margins and black conidiomata on the surface of the spots. When the disease is severe, the leaves fall. Leaf spot disease is a serious problem for rhododendrons, reducing their ornamental value and causing significant economic losses. To identify the pathogen, we conducted pathogen isolation and pathogenicity study. The pathogen was identified as Pestalotiopsis kenyana by morphological features and combined analysis of multiple genes (ITS, tef1-α, and Tub2). Koch's postulates was tested by isolating and reidentifying the pathogen from inoculated plants, showing that P. kenyana was the causative agent of the disease. To our knowledge, this is the first report of P. kenyana causing leaf spot in R. agastum. This study gives important information for the identification and control of the leaf spot disease caused by P. kenyana.

Impact of Trichoderma afroharzianum infection on fresh matter content and grain quality in maize.

Trichoderma afroharzianum, a ubiquitous soil-borne fungus found on plant roots and decaying residues, displays competitive traits and mycoparasitic behavior against diverse microorganisms. Selected strains of this fungus are known in agriculture for their beneficial effects on plant growth and as bio-fungicides. However, recent findings have pinpointed Trichoderma afroharzianum as the causal agent behind maize ear rot disease in Europe since 2018, notably impacting maize cobs in Germany, France, and Italy. This study aims to evaluate the severity of Trichoderma ear rot disease on maize fresh matter content and specific quality parameters under semi-field conditions. Two distinct maize varieties were artificially inoculated with a pathogenic Trichoderma isolate at the flowering stage using needle pin or silk channel methods. Disease severity was assessed visually at the time of harvest based on the percentage of infected kernels according to EPPO Guidelines (PP 1/285). Fresh matter content and quality parameters such as alpha-amylase activity, C/N ratio, water, and sugar content were analyzed. Results showed that needle pin inoculation led to higher disease severity (60%) compared to silk channel inoculation (39%). Cob weight decreased significantly at the highest disease severity level by up to 50% compared to control plants. In both varieties, alpha-amylase activity increased significantly with higher Trichoderma disease severity, resulting in starch degradation and increased glucose release. The germination rate was severely affected by the infection, with only 22% of grains germinating, and the seedlings showed shortened and deformed growth. This is the first report on Trichoderma ear rot infection and its effect on fresh matter content and quality parameters in maize after artificial inoculation under field conditions. The results address an important knowledge gap and provide valuable insights into the infection pathway and impact on maize quality.

Identification and Antimicrobial Susceptibility Patterns of Neisseria gonorrhoeae, Ureaplasma spp. and Mycoplasma spp. Isolated from Tribal Women

Sexually transmitted infections (STIs) are a major public health problem worldwide with significant social and economic implications. Effective control and prevention strategies necessitate a thorough understanding of the prevalence, isolation, and identification of STI pathogens. The present study aims to provide a comprehensive analysis of the isolation, identification, prevalence, and antimicrobial susceptibility pattern of STI pathogens based on culture method analysis. Endocervical /vaginal swab samples from female patients symptomatic for STI were cultured on different selective and differential media and pathogens were identified by colony morphology and biochemical tests. Antimicrobial Susceptibility Test (AST) of isolated and identified culture pathogen was performed by using Kirby-Bauer disc diffusion method. Among 209 endocervical/vaginal swab samples from symptomatic patients, 126 (60.28%) tested positive and 83 (39.71%) negative. Ureaplasma spp. (n = 100) was the most prevalent isolate, constituting 79.36% of culture-positive samples, followed by N. gonorrhoea (n = 99) at 78.57%, and Mycoplasma spp. (n = 41) at 32.54% individually and in combination. AST analysis revealed erythromycin (74%), ofloxacin (69%), and roxithromycin (64%) as the most resistant antibiotics for Ureaplasma spp. N. gonorrhoea showed the highest resistance to cefixime (78.79%), followed by ofloxacin (75.76%) and erythromycin (69.7%). Azithromycin and erythromycin exhibited 100% resistance against Mycoplasma spp. The study provides information on the prevalent bacterial pathogens involved in STIs among women in Anuppur and Shahdol districts, Madhya Pradesh. Understanding the diversity, distribution patterns and antibiotic sensitivity of these pathogens is crucial for developing targeted interventions and effective prevention strategies in such resource-limited areas.

Occurrence, isolation, and identification of emergent pathogens of taxon Vibrio from the Danube river in Bratislava city, Slovakia

The occurrence of Vibrio cholerae, Vibrio metschnikovii and Vibrio fluvialis, important aquatic human pathogens of genus Vibrio, were determined in the surface water of the Danube River in Bratislava. The isolates were identified by biochemical tests. Biochemical characteristics of environmental isolates could be slightly different from reference and clinical strains which is reflected in dissimilarity rate, which was in our case not sufficient. A molecular method called amplified ribosomal DNA restriction analysis was used for confirmation of phenotypic identification. The species identity of 19 out of 22 isolates was confirmed, in the case of 3 misidentified ones, the identity of the genus did not change. The identity of all V. cholerae isolates was confirmed by PCR using species-specific gene called ompW. Also, main virulence factors of these isolates were determined. None of the isolates possessed all three virulence factors necessary for the induction of cholera.

Allelic variations in the chpG effector gene within Clavibacter michiganensis populations determine pathogen host range.

Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here, we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the putative serine hydrolase chpG (chpGC), an effector that is recognized in eggplant. Introduction of chpGC into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic Cm isolate (C48), eliminated its pathogenicity on eggplant, and enabled C48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.

Early detection of gray blight in tea leaves and rapid screening of resistance varieties by hyperspectral imaging technology.

Gray blight (GB) is a significant disease of tea leaves, posing a severe threat to both the yield and quality. In this study, the process of leaf infection by a pathogenic isolate of the GB disease (DDZ-6) was simulated. Hyperspectral images of normal leaves, infected leaves without symptoms, and infected leaves with mild and moderate symptoms were collected. Combining convolution neural network (CNN), long short-term memory (LSTM), and support vector machine (SVM) algorithms, the early detection model of GB disease, and the rapid screening model of resistant varieties were established. The generality of this method was verified by collecting datasets under field conditions. The visible red-light band demonstrated a pronounced responsiveness to GB disease, with three sensitive bands identified through rigorous screening processes utilizing uninformative variable elimination (UVE), competitive adaptive reweighted sampling (CARS), and the successive projections algorithm (SPA). The 693, 727, and 766 nm bands emerged as highly sensitive indicators of GB. Under ideal conditions, the CARS-LSTM model excelled in early detection of GB, achieving an accuracy of 92.6%. However, under field conditions, the combination of 693 and 727 nm bands integrated with a CNN provided the most effective early detection model, attaining an accuracy of 87.8%. For screening tea varieties resistant to GB, the SPA-LSTM model excelled, achieving an accuracy of 82.9%. This study provides a core algorithm for a GB disease instrument with detection capabilities, which is of great importance for the early prevention of GB disease in tea plantations. © 2024 Society of Chemical Industry.

First Report of Xanthomonas euvesicatoria pv. sesami Causing Leaf Spot on Sesame (Sesamum indicum L.) in South Carolina, USA.

Sesame (Sesamum indicum L.) is an annual plant known as one of the first domesticated oilseed crops. It is cultivated worldwide, mostly in Asia, Africa, and the Americas (Singh, 2006). In August 2022 and September 2023, dark angular necrotic spots on leaves and stems (100% incidence), blights, and severe defoliation were observed in a 4-acre rainfed sesame field located in the Colleton County of South Carolina, USA (Fig. S1). Bacterial streaming from cut leaf lesions was observed from diseased plants in both years. Two plants were collected for pathogen isolation in 2023. Symptomatic leaves were surface sterilized with 70% ethanol for 1 min and dried in a laminar flow hood. For each isolate, four sterile toothpicks were used to poke lesion margins and stirred in 300 µl of sterile distilled water in a 2-ml sterile microcentrifuge tube and soaked at room temperature (c. 21 °C) for 10 min. Each bacterial suspension (10 µl) was streaked on nutrient agar (NA) in a Petri dish. Convex and mucoid yellow colonies formed after a 48-h incubation at 28°C in the dark. Two isolates (S813 and S814), one from each plant, were obtained by transferring single colonies to new NA plates. Both isolates were preliminarily identified as Xanthomonas [S813: X. campestris (P = 0.53); S814: X. campestris (P = 0.77)] using a Biolog Microbial Identification System (GEN III Microplate; Identification Database v.2.8.0.15G). PCR amplification of the atpD and dnaK genes was performed for both isolates using the conditions described in Félix-Gastélum et al. (2019). The sequences of both amplicons are 100% identical for each gene between the two isolates. PCR and sequencing of the gyrB gene was also done for S813 with the primers from Young et al. (2008). The atpD (S813/S814), dnaK (S813/S814), and gyrB (S813) sequences (GenBank accessions: PP507118 to PP507120) showed the best match with 100% identity to the corresponding gene sequences [GenBank accessions: KJ491167 (100% coverage), KJ491257 (99% coverage), EU285201 (100% coverage)] of the X. euvesicatoria pv. sesami (=X. campestris pv. sesami) type strain LMG865 (Constantin et al. 2015, Parkinson et al. 2009). A neighbor joining tree with the concatenated sequences of these three genes (2,210 nt) showed that S813 and LMG 865 had the closet relationship with X. euvesicatoria pv. alfalfae (CFBP3836, Fig. S2). To fulfill Koch's postulates, three healthy sesame plants (cultivar Shirogoma) were spray inoculated separately with each suspension of S813 and S814 in sterile tap water until runoff (approx. 5×108 CFU/ml). Two sesame plants were sprayed with sterile tap water and served as negative control. All plants were maintained in a greenhouse at approximately 28/20°C (day/night) with natural photoperiod. Dark leaf spots and leaf yellowing were observed on inoculated plants 7 to 14 days after inoculation. No disease symptom was observed on the control plants. Bacteria were reisolated from leaf spots of the inoculated plants and confirmed to be X. euvesicatoria pv. sesami based on atpD and dnaK sequences. The disease was first reported in Sudan (Sabet and Dowson, 1960), after which it was reported in USA (Isakeit et al., 2012) and Mexico (Félix-Gastélum et al. 2019). To the best of our knowledge, this is the first report of this disease in South Carolina, USA. Since the interest of sesame to the farmers is increasing in the southeastern USA, it is necessary to perform further research to examine the disease distribution and its economic impact.

Evolutionary genomic analyses of canine E. coli infections identify a relic capsular locus associated with resistance to multiple classes of antimicrobials.

Much of the human genomic epidemiology data available for E. coli mechanism discovery studies has been heavily biased toward shiga-toxin producing strains from humans and livestock. E. coli occupies many niches and produces a wide variety of other significant pathotypes, including some implicated in chronic disease. We hypothesized that since dogs tend to share similar strains with their owners and are treated with similar antibiotics, their pathogenic isolates will harbor unexplored AMR mechanisms of importance to humans as well as animals. By comparing over 1,000 genomes with in vitro antimicrobial susceptibility data from sick dogs across the US and Canada, we identified a strong multidrug resistance association with an operon that appears to have once conferred a type 1 capsule production system.