Resistance Genes Research Articles

Unravelling the role of key genes involved coffee leaf rust resistance

The biotrophic fungus Hemileia vastatrix is the pathogen responsible for coffee leaf rust, a devastating disease in several coffee-producing countries. Despite the importance of studying the interaction between Coffea and H. vastatrix, a more comprehensive understanding of the mechanisms involved in this pathosystem is necessary. The role of eight candidate genes was analyzed aiming at identifying and validating new important coffee resistance genes and understanding their interaction with H. vastatrix. These genes were identified in the most important sources of coffee resistance, the Híbrido de Timor CIFC 832/2 and CIFC 832/1. Previous works found six resistance genes and, in our research, other two new genes were identified in BAC clones and validated by RT-qPCR during compatible and incompatible interactions between Coffea and H. vastatrix. An interactome approach was performed using Coffea-H. vastatrix and Coffea-Coffea proteins to better understand the biological process and the interaction of the host-pathogen. Two networks of interactions from the compiled data were built focused on candidate genes associated with pre-haustorial resistance (12 and 24h.a.i) in coffee plants against the pathogen. The results showed, for the first time, differentially expressed proteins (DEPs) positively regulated in the incompatible interaction Coffea-H. vastatrix. These coffee proteins interact with each other and with secreted and/or transmembrane pathogen proteins. The obtained results also show that DEPs found are involved in important plant defense pathways such as pathways associated with the response to wounds, signaling, regulation of the innate immune response and the transmembrane receptor protein serine/threonine kinase pathway. The present work shows the involvement of genes in both pathogen recognition and signaling cascades, which act in pre-haustorial defense mechanisms of HdT coffee. Therefore, the candidate genes analyzed, together with the biological processes elucidated, have the potential to contribute to the development of new control strategies against the fungus H. vastatrix within coffee breeding programs aiming to develop cultivars with durable resistance.

Zoonotic bacterial and parasitic intestinal pathogens in foxes, raccoons and other predators from eastern Germany.

In this study, we investigated faecal specimens from legally hunted and road-killed red foxes, raccoons, raccoon dogs, badgers and martens in Germany for parasites and selected zoonotic bacteria. We found that Baylisascaris procyonis, a zoonotic parasite of raccoons, had spread to northeastern Germany, an area previously presumed to be free of this parasite. We detected various pathogenic bacterial species from the genera Listeria, Clostridium (including baratii), Yersinia and Salmonella, which were analysed using whole-genome sequencing. One isolate of Yersinia enterocolitica contained a virulence plasmid. The Salmonella Cholerasuis isolate encoded an aminoglycoside resistance gene and a parC point mutation, conferring resistance to ciprofloxacin. We also found tetracycline resistance genes in Paeniclostridium sordellii and Clostridium baratii. Phylogenetic analyses revealed that the isolates were polyclonal, indicating the absence of specific wildlife-adapted clones. Predators, which scavenge from various sources including human settlements, acquire and spread zoonotic pathogens. Therefore, their role should not be overlooked in the One Health context.

Improving the detection of integrative conjugative elements in bovine nasopharyngeal swabs using multiplex recombinase polymerase amplification

Bovine respiratory disease (BRD) is an important health and economic burden to the cattle industry worldwide. Three bacterial pathogens frequently associated with BRD (Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) can possess integrative and conjugative elements (ICEs), a diverse group of mobile genetic elements that acquire antimicrobial resistance (AMR) genes (ARGs) and decrease the therapeutic efficacy of antimicrobial drugs. We developed a duplex recombinase polymerase amplification (RPA) assay to detect up to two variants of ICEs in these Pasteurellaceae. Whole genome sequence analysis of M. haemolytica, P. multocida, and H. somni isolates harbouring ICEs revealed the presence of tnpA or ebrB next to tet(H), a conserved ARG that is frequently detected in ICEs within BRD-associated bacteria. This real-time multiplex RPA assay targeted both ICE variants simultaneously, denoted as tetH_tnpA and tetH_ebrB, with a limit of detection (LOD) of 29 (95% CI [23, 46]) and 38 genome copies (95% CI [30, 59]), respectively.DNA was extracted from 100 deep nasopharyngeal swabs collected from feedlot cattle on arrival. Samples were tested for ICEs using a real-time multiplex RPA assay, and for M. haemolytica, P. multocida, H. somni, and Mycoplasma bovis using both culture methods and RPA. The assay provided sensitive and accurate identification of ICEs in extracted DNA, providing a useful molecular tool for timely detection of potential risk factors associated with the development of antimicrobial-resistant BRD in feedlot cattle.

Evolution of invasive pneumococcal disease by serotype 3 in adults: a Spanish three-decade retrospective study

Invasive pneumococcal disease due to serotype 3 (S3-IPD) is associated with high mortality rates and long-term adverse effects. The introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into the Spanish paediatric immunisation programme has not led to a decrease in the adult S3-IPD. We aimed to analyse the incidence, clinical characteristics and genomics of S3-IPD in adults in Spain. Adult IPD episodes hospitalized in a Southern Barcelona hospital were prospectively collected (1994-2020). For genomic comparison, S3-IPD isolates from six Spanish hospitals (2008-2020) and historical isolates (1989-1993) were analysed by WGS (Illumina and/or MinION). From 1994 to 2020, 270 S3-IPD episodes were detected. When comparing pre-PCV (1994-2001) and late-PCV13 (2016-2020) periods, only modest changes in S3-IPD were observed (from 1.58 to 1.28 episodes per 100,000 inhabitants year). In this period, the incidence of the two main lineages shifted from 0.38 to 0.67 (CC180-GPSC12) and from 1.18 to 0.55 (CC260-GPSC83). The overall 30-day mortality remained high (24.1%), though a decrease was observed between the pre-PCV (32.4%; 95.0% CI, 22.0-45.0) and the late-PCV13 period (16.7%; 95.0% CI, 7.5-32.0) (p=0.06). At the same time, comorbidities increased from 77.3% (95.0% CI, 65.0-86.0) to 85.7% (95.0% CI, 71.0-94.0) (p=0.69). There were no differences in clinical characteristics or 30-day mortality between the two S3 lineages. Although both lineages were genetically homogeneous, the CC180-GPSC12 lineage presented a higher SNP density, a more open pan-genome, and a major presence of prophages and mobile genetic elements carrying resistance genes. Adult S3-IPD remained stable in our area over the study period despite PCV13 introduction in children. However, a clonal shift was observed. The decrease in mortality rates and the increase in comorbidities suggest a change in clinical management and overall population characteristics. The low genetic variability and absence of clinical differences between lineages highlight the role of the S3 capsule in the disease severity. This study has been funded by Instituto de Salud Carlos III (ISCIII) "PI18/00339", "PI21/01000", "INT22/00096", "FI22/00279", CIBER "CIBERES-CB06/06/0037", "CIBERINFEC-CB21/13/00009" and MSD grant "IISP 60168".

Advancements in water purification: A defective MPN-based light-responsive self-cleaning membrane for superior bacteria and resistance gene removal, biofouling mitigation, and mechanistic insights

Advancements in water purification: A defective MPN-based light-responsive self-cleaning membrane for superior bacteria and resistance gene removal, biofouling mitigation, and mechanistic insights

Bioinformatics analysis of clinical isolates of Escherichia coli from Nigeria and other countries for quinolone and fluoroquinolone resistance

Quinolones were the drugs of choice for the treatment of bacterial infections, especially, infections caused by Gram negative bacteria. Unfortunately, these drugs have been resisted by the microbial agents including Escherichia coli, known to be the leading cause of Urinary Tract Infection (UTI) globally. This study therefore was aimed at detecting all the genes involved in Quinolone resistance by the E. coli pathogen isolated from Nigeria and from other geographical regions, using robust techniques. Twenty-three sequence data files of Escherichia coli from various countries of the world were retrieved from the National Centre for biotechnology Information (NCBI) database and sent for genome assembly for processing of the short reads into long reads. The outcome was config. fasta files which were comprehensively annotated and characterized for genetic functions and mechanisms. A total of 208 antibiotic resistance genes were detected, out of which 27(13.0%) were linked to quinolone resistance and 14(6.7%) to multi- drug resistance. The result of this study significantly implicated many genes in quinolone resistance; notably were the efflux pump genes and their high percentage abundance. We recommend in-depth study of the genes for their expression capabilities, also the structure and features of the efflux pump genes to enable proper redesigning of drugs by integrating anti efflux pump substances that will selectively prevent the expression of the genes for antibiotic resistance, without any harm to the host, or that can destabilize the positive regulation of the operon for antibiotic resistance.

Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital.

The availability of rapid diagnostic platforms for positive blood cultures has accelerated the speed at which the clinical microbiology laboratory can identify the causative organism and facilitate early appropriate antimicrobial therapy. There is a paucity of data regarding the clinical utility of the blood culture identification 2 (BCID2) panel test and its correlation with phenotypic drug susceptibility testing (DST) in flagged blood culture bottles from intensive care units (ICUs) in countries such as India, which have high rates of multidrug-resistant gram-negative bacteria (MDR-GNB). We conducted a retrospective observational study in a tertiary care ICU on 200 patients above 18 years of age in whom a BCID2 test was ordered when blood cultures flagged positive. We found 99% concordance between BCID2 and cultures in the identification of bacteria and yeasts and 96.5% concordance between phenotypic and genotypic DST. Furthermore, BCID2 was available about 1.5 days earlier than conventional ID and DST and played a key role in tailoring antimicrobials in 82.5% of the patients. Polymyxin-based therapy was discontinued earlier after an empiric dose in 138 patients (69%) based on BCID2 reports. In critically ill patients with monomicrobial bacteremia, BCID2 rapidly identifies bacteria and antimicrobial resistance (AMR) genes and is significantly faster than conventional culture and sensitivity testing. Antibiotics were escalated in more than a third of patients and de-escalated in almost a fifth on the same day. We recommend that all ICUs routinely incorporate the test in their antibiotic decision-making process and in antimicrobial stewardship. Vineeth VK, Nambi PS, Gopalakrishnan R, Sethuraman N, Ramanathan Y, Chandran C, et al. Clinical Utility of Blood Culture Identification 2 Panel in Flagged Blood Culture Samples from the Intensive Care Unit of a Tertiary Care Hospital. Indian J Crit Care Med 2024;28(5):461-466.

Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat.

Fusarium head blight (FHB) stands out as one of the most devastating wheat diseases and leads to significantly grain yield losses and quality reductions in epidemic years. Exploring quantitative trait loci (QTL) for FHB resistance is a critical step for developing new FHB-resistant varieties. We previously constructed a genetic map of unigenes (UG-Map) according to the physical positions using a set of recombinant-inbred lines (RILs) derived from the cross of 'TN18 × LM6' (TL-RILs). Here, the number of diseased spikelets (NDS) and relative disease index (RDI) for FHB resistance were investigated under four environments using TL-RILs, which were distributed across 13 chromosomes. A number of 36 candidate genes for NDS and RDI from of 19 stable QTLs were identified. The average number of candidate genes per QTL was 1.89, with 14 (73.7%), two (10.5%), and three (15.8%) QTLs including one, two, and 3-10 candidate genes, respectively. Among the 24 candidate genes annotated in the reference genome RefSeq v1.1, the homologous genes of seven candidate genes, including TraesCS4B02G227300 for QNds/Rdi-4BL-4553, TraesCS5B02G303200, TraesCS5B02G303300, TraesCS5B02G303700, TraesCS5B02G303800 and TraesCS5B02G304000 for QNds/Rdi-5BL-9509, and TraesCS7A02G568400 for QNds/Rdi-7AL-14499, were previously reported to be related to FHB resistance in wheat, barely or Brachypodium distachyon. These genes should be closely associated with FHB resistance in wheat. In addition, the homologous genes of five genes, including TraesCS1A02G037600LC for QNds-1AS-2225, TraesCS1D02G017800 and TraesCS1D02G017900 for QNds-1DS-527, TraesCS1D02G018000 for QRdi-1DS-575, and TraesCS4B02G227400 for QNds/Rdi-4BL-4553, were involved in plant defense responses against pathogens. These genes should be likely associated with FHB resistance in wheat.

Optimized Antibiotic Resistance Genes Monitoring Scenarios Promote Sustainability of Urban Water Cycle.

Dissemination of antibiotic resistance genes (ARGs) in urban water bodies has become a significant environmental and health concern. Many approaches based on real-time quantitative PCR (qPCR) have been developed to offer rapid and highly specific detection of ARGs in water environments, but the complicated and time-consuming procedures have hindered their widespread use. Herein, we developed a facile one-step approach for rapid detection of ARGs by leveraging the trans-cleavage activity of Cas12a and recombinase polymerase amplification (RPA). This efficient method matches the sensitivity and specificity of qPCR and requires no complex equipment. The results show a strong correlation between the prevalence of four ARG markers (ARGs: sul1, qnrA-1, mcr-1, and class 1 integrons: intl1) in tap water, human urine, farm wastewater, hospital wastewater, municipal wastewater treatment plants (WWTPs), and proximate natural aquatic ecosystems, indicating the circulation of ARGs within the urban water cycle. Through monitoring the ARG markers in 18 WWTPs in 9 cities across China during both peak and declining stages of the COVID epidemic, we found an increased detection frequency of mcr-1 and qnrA-1 in wastewater during peak periods. The ARG detection method developed in this work may offer a useful tool for promoting a sustainable urban water cycle.

Lipid A modification of colistin-resistant Klebsiella pneumoniae does not alter innate immune response in a mouse model of pneumonia.

Polymyxin resistance in carbapenem-resistant Klebsiella pneumoniae bacteria is associated with high morbidity and mortality in vulnerable populations throughout the world. Ineffective antimicrobial activity by these last resort therapeutics can occur by transfer of mcr-1, a plasmid-mediated resistance gene, causing modification of the lipid A portion of lipopolysaccharide (LPS) and disruption of the interactions between polymyxins and lipid A. Whether this modification alters the innate host immune response or carries a high fitness cost in the bacteria is not well established. To investigate this, we studied infection with K. pneumoniae (KP) ATCC 13883 harboring either the mcr-1 plasmid (pmcr-1) or the vector control (pBCSK) ATCC 13883. Bacterial fitness characteristics of mcr-1 acquisition were evaluated. Differentiated human monocytes (THP-1s) were stimulated with KP bacterial strains or purified LPS from both parent isolates and isolates harboring mcr-1. Cell culture supernatants were analyzed for cytokine production. A bacterial pneumonia model in WT C57/BL6J mice was used to monitor immune cell recruitment, cytokine induction, and bacterial clearance in the bronchoalveolar lavage fluid (BALF). Isolates harboring mcr-1 had increased colistin MIC compared to the parent isolates but did not alter bacterial fitness. Few differences in cytokines were observed with purified LPS from mcr-1 expressing bacteria in vitro. However, in a mouse pneumonia model, no bacterial clearance defect was observed between pmcr-1-harboring KP and parent isolates. Consistently, no differences in cytokine production or immune cell recruitment in the BALF were observed, suggesting that other mechanisms outweigh the effect of these lipid A mutations in LPS.

Genetic assessment of diverse rice germplasm for yield-related and stress tolerance traits

AbstractThe development of stress-resistant crops without compromising their yield and nutritional quality is one of the major challenges in plant biology. Plant breeders have made considerable effort in developing cultivars with high yield and tolerance to biotic and abiotic stresses. This research aimed to evaluate pre-breeding resources for favorable genes conferring good yield and resistance to biotic and abiotic stresses for rice varietal improvement. Two hundred forty diverse rice cultivars from top countries with which the United States imports and exports rice were selected from the Germplasm Resource Information Network (GRIN) collection, and these were characterized using molecular markers for various desirable traits. Among the cultivars, 16 were used as checks. The genes of various traits evaluated were grain number (Gn1a), panicle weight (WFP), cold stress tolerance (qSCT-11 and qCTS-12), anaerobic germination (AG1 and AG2), rice blast disease resistance (PiB, Pi-ta, Ptr, and Piz), wide compatibility (S5-n), and restoring ability (Rf4). Out of these 240 accessions, 192 have the Gn1a gene, 168 possess the qSCT-11 cold tolerance gene, 139 carry the Rf4 gene, 152 have the qCTS12 cold tolerance gene, 87 have blast resistance genes, and 44 possess the WC gene. None of the 240 accessions possess the WFP (Wealthy Farmer’s Panicle) gene. The selections with favorable genes can be used by breeders as potential donor parents for varietal improvement programs to produce new and promising cultivars with desired specific traits that may contribute towards alleviating global issues related to food security.

Genome analyses of colistin-resistant high-risk blaNDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings

BackgroundColistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT).ResultsThis study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32–128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357).ConclusionThe global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.

Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia

A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding.

KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes.

Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.

Complete genome sequence of the linezolid-resistant clinical Enterococcus faecalis N23-3408 linked to a livestock lineage in Switzerland.

Here, we report the complete genome of human clinical linezolid-resistant Enterococcus faecalis N23-3408. N23-3408 harbored a 59.5 kb plasmid with antimicrobial resistance genes cat, erm(B), fexA, optrA, tet(L), and tet(M). Closely related E. faecalis harboring this plasmid was previously obtained from livestock animals and pet food in Switzerland.

Antibiotic resistance of heterotrophic bacteria from the sediments of adjoining high Arctic fjords, Svalbard.

Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are now considered major global threats. The Kongsfjorden and Krossfjorden are the interlinked fjords in the Arctic that are currently experiencing the effects of climate change and receiving input of pollutants from distant and regional sources. The present study focused on understanding the prevalence of antibiotic resistance of retrievable heterotrophic bacteria from the sediments of adjacent Arctic fjords Kongsfjorden and Krossfjorden. A total of 237 bacterial isolates were tested against 16 different antibiotics. The higher resistance observed towards Extended Spectrum β-lactam antibiotic (ESBL) includes ceftazidime (45.56%) followed by trimethoprim (27%) and sulphamethizole (24.05%). The extent of resistance was meagre against tetracycline (2.53%) and gentamycin (2.95%). The 16S rRNA sequencing analysis identified that Proteobacteria (56%) were the dominant antibiotic resistant phyla, followed by Firmicutes (35%), Actinobacteria (8%) and Bacteroidetes. The dominant resistant bacterial isolates are Bacillus cereus (10%), followed by Alcaligenes faecalis (6.47%), Cytobacillus firmus (5.75%) Salinibacterium sp. (5%) and Marinobacter antarcticus (5%). Our study reveals the prevalence of antibiotic resistance showed significant differences in both the inner and outer fjords of Kongsfjorden and Krossfjorden (p < 0.05). This may be the input of antibiotic resistance bacteria released into the fjords from the preserved permafrost due to the melting of glaciers, horizontal gene transfer, and human influence in the Arctic region act as a selection pressure for the development and dissemination of more antibiotic resistant bacteria in Arctic fjords.

Anthracnose and bean common mosaic necrosis virus resistance in wild and landrace Phaseolus vulgaris (L.) genetic stocks

AbstractWild crop germplasm and landrace varieties have long been considered as a source of novel genetic variation for improving domesticated crops. Due to genetic bottlenecks that occurred during domestication, dissemination, and subsequent crop improvement, many beneficial genes are absent from commercial varieties and elite breeding germplasm, yet are still present in wild populations. To catalog potential novel disease resistance genes useful for breeding more resilient dry beans, we screened wild and landrace Phaseolus vulgaris L. accessions archived in the USDA GRIN seed bank for untapped resistance to anthracnose (Colletotrichum lindemuthianum) and bean common mosaic necrosis virus (BCMNV). A population of 194 wild and 55 landrace accessions were screened for resistance to two highly virulent races of anthracnose (race 2047 and race 3481) and for resistance to the BCMNV strain NL‐3. Thirteen accessions, all wild, were resistant to both anthracnose races, with MX‐QT‐3 and PI 661812 displaying complete resistance with no disease symptoms across all replications. Surprisingly, no natural resistance to BCMNV strain NL‐3 was detected in the wild germplasm. PI 442541, PI 661891, and W6 10164 were the only three accessions that expressed the I‐gene phenotype and all three have some history of cultivation. This study provides a resource for introgression of genetic diversity for anthracnose resistance into cultivated beans and reveals that innate resistance to BCMNV may not exist in wild populations of P. vulgaris.

Virulence phenotypes of Puccinia graminis on barley, wheat and oat in Canada from 2020 to 2022

Stem rust of barley and wheat is caused by the obligate pathogen Puccinia graminis f. sp. tritici (Pgt) and stem rust of oat is caused by P. graminis f. sp. avenae (Pga). Stem rust can be a very destructive disease of cereal crops and, until the development of resistant host varieties, was responsible for millions of dollars of losses to producers. Genetic host resistance is the most common and effective method to control stem rust on cereals. Knowledge of the virulence genes and races present in the pathogen population is important to identify effective host resistance genes for use by cereal plant breeders. The objectives of this study were to determine the incidence and severity of P. graminis in wheat, barley and oat in Manitoba, Canada, and assess the virulence frequencies and races of isolates collected from Manitoba, Saskatchewan and Ontario, Canada during 2020 to 2022. Stem rust incidence and severity was very light in Manitoba in 2020, 2021 and 2022. Virulence was not observed on resistance genes Sr30, Sr24 and Sr31 from Canadian collections of Pgt isolates made during 2020 to 2022. Race QFCSC was the most common race of Pgt in Canada, and races MCCFC and TPMKC were also common in Manitoba in 2022. Virulence to resistance genes Pg6, Pg10 and Pg16 was not observed among Pga isolates. The most common race of Pga from Manitoba and Saskatchewan was TGN, followed by SGB and TJS. The most frequent Pga races were TDJ, TDD and TGN in Ontario.

Fulvic acid and fermentation agent optimize in situ composting by reducing antibiotic resistance genes abundances and altering succession of bacterial communities

The use of biostimulants to enhance microbial activity has been extensively reported. However, their regulatory properties on the ecological security of in situ composting have not yet been fully elucidated. Here, the effects of two biostimulants (fermentation agent [FM] and fulvic acid [FA]) on in situ composting were investigated under field conditions. The abundances of antibiotic resistance genes (ARGs), as well as those of the microbial communities and the activities of enzymes, were comprehensively investigated. The addition of biostimulants significantly reduced the abundances of streptomycin and sulfonamide resistance genes by 79%–97% and decreased the abundance of Gammaproteobacteria. This was particularly true for species that are members of the Enterobacteriaceae and contain many ARGs. The addition of biostimulants promoted the succession of bacterial communities toward enhancing the solubility of phosphorus, promoting the degradation of aromatic compounds, and reducing the emissions of NOx gas. The application of FA and FM resulted in distinct bacterial network structures, and many negative correlations were associated with ARGs in the temperature subnetwork in the FM treatment. This study provides an effective strategy for the in situ treatment of agricultural waste and underscores the significance of biostimulants in improving the biological safety of medium-temperature in-situ composting.

Comparative microbiome analysis in cystic fibrosis and non-cystic fibrosis bronchiectasis.

Bronchiectasis is a condition characterized by abnormal and irreversible bronchial dilation resulting from lung tissue damage and can be categorized into two main groups: cystic fibrosis (CF) and non-CF bronchiectasis (NCFB). Both diseases are marked by recurrent infections, inflammatory exacerbations, and lung damage. Given that infections are the primary drivers of disease progression, characterization of the respiratory microbiome can shed light on compositional alterations and susceptibility to antimicrobial drugs in these cases compared to healthy individuals. To assess the microbiota in the two studied diseases, 35 subjects were recruited, comprising 10 NCFB and 13 CF patients and 12 healthy individuals. Nasopharyngeal swabs and induced sputum were collected, and total DNA was extracted. The DNA was then sequenced by the shotgun method and evaluated using the SqueezeMeta pipeline and R. We observed reduced species diversity in both disease cohorts, along with distinct microbial compositions and profiles of antimicrobial resistance genes, compared to healthy individuals. The nasopharynx exhibited a consistent microbiota composition across all cohorts. Enrichment of members of theBurkholderiaceaefamily and an increased Firmicutes/Bacteroidetes ratio in the CF cohort emerged as key distinguishing factors compared to NCFB group.Staphylococcus aureusand Prevotella shahii also presented differential abundance in the CF and NCFB cohorts, respectively, in the lower respiratory tract. Considering antimicrobial resistance, a high number of genes related to antibiotic efflux were detected in both disease groups, which correlated with the patient's clinical data. Bronchiectasis is associated with reduced microbial diversity and a shift in microbial and resistome composition compared to healthy subjects. Despite some similarities, CF and NCFB present significant differences in microbiome composition and antimicrobial resistance profiles, suggesting the need for customized management strategies for each disease.