BMC Microbiology最新文献

{"title":"Investigation of the in vitro antimicrobial activity of eravacycline alone and in combination with various antibiotics against MDR Acinetobacter baumanni strains.","authors":"Merve Ataman, Berna Özbek Çelik","doi":"10.1186/s12866-025-03914-8","DOIUrl":"https://doi.org/10.1186/s12866-025-03914-8","url":null,"abstract":"<p><strong>Background: </strong>Acinetobacter baumannii is an obligately aerobic, non-motile, non-fermenting, gram-negative, opportunistic pathogen. The fact that this pathogen, which is the leading cause of nosocomial infections, is naturally resistant to many antibiotics and quickly acquires new resistance mechanisms gradually limits the antibiotic options that can be used in treatment. So, our study aims to investigate the in vitro antibacterial effects of eravacycline, a new tetracycline-class antibiotic, and compare this antibiotic with the antibiotics used in the clinic to treat the infection caused by A. baumannii. Also, eravacycline was tested in combination with meropenem or colistin against A. baumannii strains, which are resistant to colistin and meropenem. The antibiotic susceptibility of strains was determined by the microbroth dilution method. In addition, the agar dilution method determined the mutant inhibition concentration (MPC) values of the studied antibiotics. To investigate the effects of the antibiotics mentioned in our study on biofilm formation, the biofilm-forming abilities of the strains were evaluated by the crystal violet staining method. The bactericidal and synergistic effects of the studied antibiotics alone or in combination were determined by the time-dependent killing curve (TKC) method.</p><p><strong>Results: </strong>The present antibacterial susceptibility experiments showed that 98% of the strains were multi-drug resistant (MDR). Our results in mutant inhibition studies showed that eravacycline is an antibiotic with the potential to prevent the emergence of resistant mutants with its low MPC value. When the effects of antibiotics on biofilm formation were investigated in our thesis study, it was determined that 95% of our strains formed biofilm. In biofilm inhibition experiments, it was observed that eravacycline at minimum inhibitory concentration (MIC) inhibited biofilm formation by 84% alone, 86% combined with colistin, and 85% combined with meropenem. Our combination experiments showed that 1×MIC eravacycline-meropenem and 4×MIC eravacycline-colistin combinations were synergistic against A. baumannii strains. In addition, the combination of 4×MIC eravacycline-meropenem also showed bactericidal activity at the 24th hour. No antagonist effects were detected in our combination studies.</p><p><strong>Conclusion: </strong>Present results reveal essential pharmacodynamic data on eravacycline, a new antibiotic for treating A. baumannii infections, which poses a global threat.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"167"},"PeriodicalIF":4.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The change of long tail fibers expanded the host range of a T5-like Salmonella phage and its application in milk.","authors":"Xiaofeng Zheng, Xin Wang, Pei Li, Yu Zhou, Xihui Zhu, Zimeng Hu, Hui Wang, Mianmian Chen, Xiang Huo, Yingyu Liu, Wei Zhang","doi":"10.1186/s12866-025-03895-8","DOIUrl":"https://doi.org/10.1186/s12866-025-03895-8","url":null,"abstract":"<p><p>We engineered novel T5-like bacteriophage (phage) with extended host ranges by editing the long-tail fibers (PB3 and PB4) to combat Salmonella Enteritidis. By replacing the long-tail fibers PB3 and PB4 regions of phage PH204 with those from phage SP76, we created phages RPA_1 - 3 and RPB_1 - 3, which exhibited expanded host ranges, lysing 54 strains compared to the original 30 strains. These phages retained the biological characteristics of PH204, including temperature, pH stability and adsorption rate. In milk, RPA_1 - 3 and RPB_1 - 3 inhibited Salmonella ZWSA605 growth, reducing bacterial counts to 1.51 log10 CFU/mL and 2.18 log10 CFU/mL after 8 h, respectively. Although the bacteriolytic activity of recombinant phages is lower than that of the parent phage, our findings suggest that these phages hold promise as candidates for future phage biocontrol applications in food.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"169"},"PeriodicalIF":4.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of metagenomic next-generation sequencing in treatment guidance for deep neck space abscess.","authors":"Han Lei, Jiarui Liao, Yu Lin, Tianrun Liu, Wenbin Lei, Wenxiang Gao","doi":"10.1186/s12866-025-03890-z","DOIUrl":"https://doi.org/10.1186/s12866-025-03890-z","url":null,"abstract":"<p><strong>Background: </strong>Infectious etiologies of deep neck space abscess (DNSA) by conventional culture tests can be challenging, which also leads to frequent irrational antibiotic usage. Metagenomic next-generation sequencing (mNGS), as a novel method for analyzing the complex microbial ecosystem from clinical samples, has been utilized in clinical research and practice of various infectious diseases but deep neck space abscess. We here aimed to explore the clinical value of mNGS for pathogen detection and treatment guidance in DNSA patients compared with conventional culture tests.</p><p><strong>Methods: </strong>One hundred six patients diagnosed with DNSA were retrospectively enrolled and allocated into mNGS group and culture group according to whether mNGS was conducted. The pathogen detection effectiveness was of mNGS was compared with conventional culture. Effectiveness of mNGS-modified antimicrobial therapy was evaluated by comparing the treatment outcomes between two groups.</p><p><strong>Results: </strong>mNGS showed a significantly higher detection rate than conventional culture (p < 0.05) with faster result acquisition. Treatment success rate of patients in the mNGS group was significantly higher than in the culture group (RR: 1.22, 95%CI: 1.07-1.82, p = 0.033). Besides, patients in the mNGS group had shorter duration of irrational antimicrobial therapy, shorter hospital stay and less medical costs (p < 0.05).</p><p><strong>Conclusions: </strong>mNGS is an effective technology for facilitating pathogen detection and improving treatment outcomes of DNSA patients.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"166"},"PeriodicalIF":4.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unravelling the complex relationship between Suillus bovinus and Gomphidius roseus through investigation of their sporocarps in Pinus massoniana forests.","authors":"Deng Li, Guiyun Yuan, Xueguang Sun","doi":"10.1186/s12866-025-03881-0","DOIUrl":"https://doi.org/10.1186/s12866-025-03881-0","url":null,"abstract":"<p><strong>Background: </strong>The co-occurrence of sporocarps has revealed many intimate associations between different ectomycorrhizal (ECM) fungi species. The co-occurrence of sporocarps of Suillus bovinus and Gomphidius roseus, two edible ECM fungi, is well recognized; however, the interactions between them remain largely unknown. This study investigated the relationship between these two fungi occurring in Pinus massoniana forests through phenological, microbiome, and metabolome analyses.</p><p><strong>Results: </strong>Gomphidius roseus sporocarps were always found alongside sporocarps of S. bovinus, but not vice versa. The ECM associated with S. bovinus sporocarps exhibited a long-distance exploration type, whereas the ECM associated with G. roseus sporocarps formed a contact exploration type. Both S. bovinus and G. roseus sporocarps and ECM contained the mycelia of both fungi. In contrast, different fungal sporocarps and ECM were dominated by distinct bacterial species. Suillus bovinus sporocarps were recorded in all ages investigated, ranging from 1 to 5 years old to over 30 years old. In contrast, G. roseus sporocarps were mainly found in forests older than 10 years. Previous studies suggested that G. roseus parasitizes S. bovinus; however, the occurrence of G. roseus sporocarps did not significantly affect S. bovinus sporocarp production or P. massoniana growth, challenging this assumption. Despite their intimate interactions, the metabolic profiles of S. bovinus sporocarps more closely resembled those of S. luteus, not G. roseus.</p><p><strong>Conclusion: </strong>Overall, our analyses showed both similarities and dissimilarities in phenology, microbiome, and metabolome features between the two fungi, and the genesis of G. roseus sporocarps is highly dependent on S. bovinus. These results further indicate that while the formation of ECM between G. roseus and the host may rely on ECM formed by S. bovinus and the same host, it is not parasitic.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"170"},"PeriodicalIF":4.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lacticaseibacillus rhamnosus G7 alleviates DSS-induced ulcerative colitis by regulating the intestinal microbiota.","authors":"Jianlong Lao, Man Chen, Shuping Yan, Han Gong, Zhaohai Wen, Yanhong Yong, Dan Jia, Shuting Lv, Wenli Zou, Junmei Li, Huiming Tan, Hong Yin, Xiangying Kong, Zengyuan Liu, Fucheng Guo, Xianghong Ju, Youquan Li","doi":"10.1186/s12866-025-03904-w","DOIUrl":"https://doi.org/10.1186/s12866-025-03904-w","url":null,"abstract":"<p><p>Ulcerative colitis (UC) is an intestinal disease caused by many factors that seriously harms the health of humans and animals. Probiotics are currently widely used to treat intestinal inflammation; however, different strains are specific, and the functions and effects of different strains are still unclear. In this study, Lacticaseibacillus rhamnosus G7 isolated from herdsmen yogurt was used. The results of the in vitro evaluation revealed that it had good tolerance and safety. In mice with colitis, G7 alleviated weight loss and colon shortening and reduced the DAI score. After G7 treatment, the levels of proinflammatory factors (IL-1β, IL-6 and TNF-α) and histopathological scores decreased, whereas the level of IL-10 increased. In addition, G7 rebalanced the intestinal microbial composition of colitis model mice by increasing the abundance of Faecalibaculum and decreasing the abundance of Bacteroides and Escherichia_Shigella. In summary, G7 has great potential in the prevention of colitis.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"168"},"PeriodicalIF":4.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A one-pot method for universal Dengue virus detection by combining RT-RPA amplification and CRISPR/Cas12a assay.","authors":"Yunkai Zhang, Yan Xiang, Dengyong Hou, Liben Fang, Shuqi Cai, Jianping Zhang, Yujia Wang, Yuyu Jiang, Bin Liu, Jie Bai, Yue Ding, Jingjing Fang, Shuanghong Chen, Xingguang Liu, Xiaomeng Ren","doi":"10.1186/s12866-025-03882-z","DOIUrl":"10.1186/s12866-025-03882-z","url":null,"abstract":"<p><p>Dengue Virus (DENV) is a life-threatening pathogen leading to dengue fever, which brings about huge public health challenges globally. However, traditional detection methods currently fail to meet the increasing demands of clinic practice in terms of speed, simplicity, and accuracy. To address these limitations, we developed a novel, rapid, and highly sensitive diagnostic method for universal DENV detection by integrating recombinase polymerase amplification (RPA) assay and the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and associated (Cas) protein 12a (CRISPR/Cas12a) system into one-pot. This approach achieves exceptional sensitivity and specificity for DENV detection, with the entire process completed within 40 min, without the need for sophisticated equipment. The limit of detection (LOD) was determined to be 91.7 copies/test. Using this one-pot RT-RPA CRISPR/Cas12a detection system, all four serotypes of DENV (1 to 4) were successfully identified. In terms of specificity, the assay accurately detected DENV-infected positive samples without cross-reactivity with four other interfering viruses-infected samples (VSV, SeV, HSV-1 and IAV). Furthermore, we established a universal DENV RT-RPA-CRISPR/Cas12a-lateral flow dipstick (LFD) platform, which successfully identified all four serotypes of DENV with a sensitivity of approximately 250 copies/test. Collectively, our method not only provides a robust alternative for universal DENV detection but also offers valuable insights for the identification of other viruses.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"163"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wolbachia elevates host methyltransferase expression and alters the m⁶A methylation landscape in Aedes aegypti mosquito cells.","authors":"Michael Leitner, Valentine Murigneux, Kayvan Etebari, Sassan Asgari","doi":"10.1186/s12866-025-03898-5","DOIUrl":"10.1186/s12866-025-03898-5","url":null,"abstract":"<p><p>Wolbachia pipientis is an intracellular endosymbiotic bacterium that blocks the replication of several arboviruses in transinfected Aedes aegypti mosquitoes, yet its antiviral mechanism remains unknown. For the first time, we employed Nanopore direct RNA sequencing technology to investigate the impact of wAlbB strain of Wolbachia on the host's N⁶-methyladenosine (m⁶A) machinery and post-transcriptional modification landscape. Our study revealed that Wolbachia infection elevates the expression of genes involved in the mosquito's m⁶A methyltransferase complex. However, knocking down these m⁶A-related genes did not affect Wolbachia density. Nanopore sequencing identified 1,392 differentially modified m⁶A DRACH motifs on mosquito transcripts, with 776 showing increased and 616 showing decreased m⁶A levels due to Wolbachia. These m⁶A sites were predominantly enriched in coding sequences and 3'-untranslated regions. Gene Ontology analysis revealed that genes with reduced m⁶A levels were over-represented in functional GO terms associated with purine nucleotide binding functions critical in the post-transcriptional modification process of m⁶A. Differential gene expression analysis of the Nanopore data uncovered that a total of 643 protein-coding genes were significantly differentially expressed, 427 were downregulated, and 216 were upregulated. Several classical and non-classical immune-related genes were amongst the downregulated DEGs. Notably, it revealed a critical host factor, transmembrane protein 41B (TMEM41B), which is required for flavivirus infection, was upregulated and methylated in the presence of Wolbachia. Indeed, there is a strong correlation between gene expression being upregulated in genes with both increased and decreased levels of m⁶A modification, respectively. Our findings underscore Wolbachia's ability to modulate many intracellular aspects of its mosquito host by influencing post-transcriptional m⁶A modifications and gene expression, and it unveils a potential link behind its antiviral properties.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"164"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.","authors":"Ning Sun, Jiaxun Zhang, Wentao Guo, Jin Cao, Yong Chen, Deyu Gao, Xinyi Xia","doi":"10.1186/s12866-025-03887-8","DOIUrl":"10.1186/s12866-025-03887-8","url":null,"abstract":"<p><strong>Objectives: </strong>This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS.</p><p><strong>Methods: </strong>A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records.</p><p><strong>Results: </strong>In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84%, significantly lower than the 95% observed in cfDNA mNGS (p < 0.05). Using culture results as a reference, concordance rates were 63.33% (19/30) for wcDNA mNGS and 46.67% (14/30) for cfDNA mNGS. Additionally, wcDNA mNGS showed greater consistency in bacterial detection with culture results, achieving a rate of 70.7% (29/41) compared to 58.54% (24/41) for 16S rRNA NGS. The sensitivity and specificity of wcDNA mNGS for pathogen detection in body fluid samples were 74.07% and 56.34%, respectively, when compared to culture results.</p><p><strong>Conclusion: </strong>Whole-cell DNA mNGS demonstrates significantly higher sensitivity for pathogen detection and identification compared to both cfDNA mNGS and 16S rRNA NGS in clinical body fluid samples, particularly those associated with abdominal infections. However, the compromised specificity of wcDNA mNGS highlights the necessity for careful interpretation in clinical practice.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"165"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple antimicrobial resistance indices of Staphylococcus aureus from the nares of goats and slaughterhouse attendants in Kampala city, Uganda- a cross sectional study.","authors":"Kizito M Muwonge, Hellen Ndagire, Julius Mulindwa, Charles Kakuhikire Twesigye","doi":"10.1186/s12866-025-03891-y","DOIUrl":"https://doi.org/10.1186/s12866-025-03891-y","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The emergence of antimicrobial resistance (AMR) is a global menace to both public and animal health sectors with devastating effects in developing countries. Indiscriminate use of antibiotics in human health and livestock management contributes to development and rapid spread of AMR. Staphylococcus aureus is a major opportunistic zoonotic pathogen that colonises the skin and nostrils of human beings and animals and continues to develop antimicrobial resistance against different agents. The study aimed to determine multiple antibiotic resistance indices of S. aureus isolates from healthy domestic goats and slaughterhouse attendants in Kampala, Uganda.Demographic characteristics of consenting slaughterhouse attendants and goat keepers were recorded through a questionnaire. Antibiotics use among slaughterhouse workers and domestic goats and skin infections in the past twelve months were recorded. Nasal swabs were collected from healthy domestic goats at household level (n = 378) and slaughterhouse attendants (n = 131). Isolates were obtained on mannitol salt agar (MSA) upon incubation at 35°C for 24 h. The Kirby-Bauer disc diffusion method was used to determine antimicrobial susceptibility to penicillin, gentamycin, erythromycin, tetracycline, ciprofloxacin, clindamycin, trimethoprim-sulfamethoxazole, linezolid, amoxicillin, ceftriaxone and cefoxitin. In this study, the participating slaughterhouse workers were predominantly male (79%) while does (90%) were the majority of the goats sampled. S. aureus carriage was 32% and 43% among slaughterhouse workers and goats, respectively. Methicillin resistant S. aureus carriage was 12% and 11% among slaughterhouse attendants and goats, respectively. There was a high level of exposure to antibiotics among S. aureus carriers (62%) and goats (41%) in the past one year, including use of critically important antimicrobials in human medicine for livestock disease management. Amoxicillin (17%) and ciprofloxacin (12%) were the most used antibiotics among the S. aureus carriers. Oxytetracycline (33%) and Penicillin-streptomycin combination (21%) were the most used antimicrobials in goat keeping. Close to a quarter of the human participants reported having suffered probable staphylococcal related infections like pustules in the previous months. With the exception of gentamycin and linezolid, all the S. aureus isolates from human nasal swabs were resistant to at least one of the antibiotics used. S. aureus isolates from goats' nasal swabs were resistant to at least one of the antibiotics studied. The multiple antibiotic resistance (MAR) index of 41% of S. aureus isolates from slaughterhouse attendants was greater than 0.2 (mean = 0.2 ± 0.2, range 0.1 to 0.7). The MAR index of 22% of S. aureus isolates from goats was greater than 0.2 (mean = 0.2 ± 0.1, range = 0 to 0.7). The most frequent multidrug resistance (MDR) pattern was FOX, CIP, E, TE, SXT, CRO, and CD among S. aureus isolates from slaughterhouse attendant","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"162"},"PeriodicalIF":4.0,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MPSeqM, a tool combining multiplex PCR and high-throughput sequencing to study the polymorphism of eight Leptosphaeria maculans avirulence genes and its application to field surveys in France.","authors":"Angélique Gautier, Valérie Laval, Marie-Hélène Balesdent","doi":"10.1186/s12866-025-03855-2","DOIUrl":"10.1186/s12866-025-03855-2","url":null,"abstract":"<p><strong>Context: </strong>Leptosphaeria maculans is a fungal pathogen causing stem canker of oilseed rape (Brassica napus). The disease is mainly controlled by the deployment of varieties with major resistance genes (Rlm). Rlm genes can rapidly become ineffective following the selection of virulent isolates of the fungus, i.e. with mutations, including deletions, in the corresponding avirulence genes (AvrLm). Reasoned and durable management of Rlm genes relies on the detection and monitoring of virulent isolates in field populations. Based on previous knowledge of AvrLm gene polymorphism, we developed a tool combining multiplex PCR and Illumina sequencing to characterize allelic variants for eight AvrLm genes in field L. maculans populations.</p><p><strong>Results: </strong>We tested the method on DNA pools of 71 characterised L. maculans isolates and of leaf spots from 32 L. maculans isolates. After multiplex-PCR and sequencing with MiSeq technology, reads were mapped on an AvrLm sequence database. Data were filtered using thresholds defined from control samples included in each sequencing run. Proportions of each allelic variant per gene, including deletions, perfectly correlated with expected ones. The method was then applied to around 1300 symptoms (42 pools of mainly 32 leaf spots) from nine B. napus fields. The proportions of virulent isolates estimated by sequencing leaf spot pools perfectly correlated with those estimated by pathotyping single isolates. In addition, the proportions of allelic variants determined at the national scale also correlated with those previously determined following individual sequencing of AvrLm genes in a representative collection of isolates. Finally, the method also allowed us to detect still undescribed and rare allelic variants.</p><p><strong>Conclusions: </strong>Despite the diversity of mechanisms generating virulent isolates and the gene-dependent diversity of AvrLm gene polymorphism, the method proved suitable for large-scale and regular monitoring of L. maculans populations, which will facilitate the deployment of effective Rlm genes and the early detection of resistance breakdowns.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"25 1","pages":"159"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143676839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}