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Role of Ancillary Techniques in the Differential Diagnosis of Salivary Gland Carcinomas
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-19 DOI: 10.1111/apm.70008
António Paiva-Correia, Henrik Hellquist, Joana Apolónio, Pedro Castelo-Branco
{"title":"Role of Ancillary Techniques in the Differential Diagnosis of Salivary Gland Carcinomas","authors":"António Paiva-Correia,&nbsp;Henrik Hellquist,&nbsp;Joana Apolónio,&nbsp;Pedro Castelo-Branco","doi":"10.1111/apm.70008","DOIUrl":"https://doi.org/10.1111/apm.70008","url":null,"abstract":"<div>\u0000 \u0000 <p>Paiva-Correia A, Hellquist H, Apolónio J, Castelo-Branco P. Role of ancillary techniques in the differential diagnosis of salivary gland carcinomas. The diagnosis of salivary gland carcinomas (SGC) rests mainly on histology, but immunohistochemical and molecular investigations are often necessary for differential diagnosis. This review is primarily aimed as a tool for pathologists in non-specialised head and neck hospitals who encounter a limited number of SGC annually. The use of testing an initial antibody panel, which may comprise both positive and negative expression for a suspected entity, and examples of different panels are outlined. We also focused on acinic cell carcinoma (AcCC), which is positive for DOG1 and negative for mammaglobin, whilst secretory carcinoma (SC) is positive for mammaglobin and negative for DOG1. In addition, the exclusive expression of androgen and HER2 in salivary duct carcinoma (SDC) and its use for differential diagnosis are also addressed. This review also highlights the particularities of mucoepidermoid carcinoma (MEC) and its negativity for S100 and SOX10, which distinguishes it from some of its mimics. In laboratories with limited access to antibodies for SGC, we recommend inclusion of mammaglobin. The use of molecular techniques for the diagnosis of MEC (<i>MAML2</i>), SC (<i>ETV6</i>), adenoid cystic carcinoma (<i>MYB</i>), and AcCC (<i>NR4A3</i>) is discussed. We highlight the role of commonly available antibodies for the histological classification of SGC.</p>\u0000 </div>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How to Write a Pathology Research Paper—Basic Principles and Beyond—A Primer for Residents
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-19 DOI: 10.1111/apm.70007
Glen Kristiansen
{"title":"How to Write a Pathology Research Paper—Basic Principles and Beyond—A Primer for Residents","authors":"Glen Kristiansen","doi":"10.1111/apm.70007","DOIUrl":"https://doi.org/10.1111/apm.70007","url":null,"abstract":"<p>Medical writing is an art but still it is usually not in the curriculum of medical students. With the beginning of scientific activity during residency, many perceive this gap increasingly, and stay behind their own expectations in their scientific productivity. Many universities offer courses to teach scientific writing and many books and article address this void, but in real life the main work to carve a readable paper out of a pile of unsorted data remains often in the hands of the scientific supervisors. This little paper tries to address this issue with a focus on typical pathology related subjects by outlining the structure of a paper and explaining typical dos and don'ts of crafting a publishable scientific paper as a pathology resident.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/apm.70007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143438810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Prognostic Significance of PD-L1 Expression and Associated Tumor-Infiltrating Lymphocytes in Supraglottic Laryngeal Squamous Cell Carcinoma
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-17 DOI: 10.1111/apm.70005
Elvir Zvrko, Muhedin Kadic, Ljiljana Vuckovic
{"title":"The Prognostic Significance of PD-L1 Expression and Associated Tumor-Infiltrating Lymphocytes in Supraglottic Laryngeal Squamous Cell Carcinoma","authors":"Elvir Zvrko,&nbsp;Muhedin Kadic,&nbsp;Ljiljana Vuckovic","doi":"10.1111/apm.70005","DOIUrl":"https://doi.org/10.1111/apm.70005","url":null,"abstract":"<div>\u0000 \u0000 <p>Laryngeal squamous cell carcinoma (LSCC) is characterized by diverse profiles of tumor-infiltrating lymphocytes (TILs). We aimed to investigate the potential prognostic role of TILs and programmed death-ligand 1 (PD-L1) in patients with supraglottic LSCC. The expression of PD-L1 and TILs was assessed using immunohistochemistry in 39 patients with primary supraglottic LSCC and correlated with clinicopathological characteristics and disease-free survival (DFS). Survival curves were measured using the Kaplan–Meier method, and differences in survival between the groups were estimated using the log-rank test. TIL density was significantly higher in PD-L1-positive (combined positive score: CPS ≥ 1) than in PD-L1-negative (CPS &lt; 1) patients (<i>p</i> = 0.000). Lower PD-L1 expression was significantly associated with a locoregional recurrence (Fisher's exact test, <i>p</i> = 0.008). DFS was significantly longer in patients with CPS ≥ 1 than in those with CPS &lt; 1 (Log-rank test, <i>p</i> = 0.004). Multivariate Cox regression analysis showed that a low CPS (<i>p</i> = 0.003) and positive nodal status (<i>p</i> = 0.012) were statistically significant and independent predictors of malignancy recurrence. PD-L1 represents a valuable marker for predicting recurrence and shorter survival after definitive therapy.</p>\u0000 </div>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Helicobacter pylori Infection in Colombia: Phylogeny, Resistome, and Virulome
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-11 DOI: 10.1111/apm.70003
Angela B. Muñoz, Johanna Stepanian, Juan S. Solano-Gutierrez, Filipa F. Vale, Alba A. Trespalacios-Rangel
{"title":"Helicobacter pylori Infection in Colombia: Phylogeny, Resistome, and Virulome","authors":"Angela B. Muñoz,&nbsp;Johanna Stepanian,&nbsp;Juan S. Solano-Gutierrez,&nbsp;Filipa F. Vale,&nbsp;Alba A. Trespalacios-Rangel","doi":"10.1111/apm.70003","DOIUrl":"https://doi.org/10.1111/apm.70003","url":null,"abstract":"<p><i>Helicobacter pylori</i> is a successful etiologic gastric agent that reaches a prevalence around 80% in Colombia. This bacterium is extremely diverse and has shown a phylogeographic pattern. The objective of this study was to perform an analysis of genomic epidemiology of <i>H. pylori</i> in Colombia. We enriched our set of 29 newly sequenced Colombian <i>H. pylori</i> genomes with additional data from public databases, reaching a total of 221 genomes in our dataset. Phylogenetic characterization was carried out using MLST and whole genome SNP analysis. We also performed a characterized the diversity of virulence factors and mutations associated with antimicrobial resistance. Phylogenetic analyzes showed two new Colombian <i>H. pylori</i> clades. Furthermore, many virulence genotype combinations were found, mutations associated with resistance were found for all the studied antibiotics, highlighting 14.4% of the genomes presented profiles associated with resistance to more than one family of antibiotics. Our analyzes described the genomics of Colombian <i>H. pylori</i> and verify the presence of a population group formed exclusively by Colombian isolates. We demonstrated the great diversity among the isolates and that the analysis by comparative genomics of <i>H. pylori</i> are valuable tools to assess the diversity, virulence, and resistance of <i>H. pylori</i>.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/apm.70003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing of Oral Anaerobes
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-09 DOI: 10.1111/apm.70002
Anne Birkeholm Jensen, Ellen Frandsen Lau, Thomas Greve, Niels Nørskov-Lauritsen
{"title":"The EUCAST Disk Diffusion Method for Antimicrobial Susceptibility Testing of Oral Anaerobes","authors":"Anne Birkeholm Jensen,&nbsp;Ellen Frandsen Lau,&nbsp;Thomas Greve,&nbsp;Niels Nørskov-Lauritsen","doi":"10.1111/apm.70002","DOIUrl":"https://doi.org/10.1111/apm.70002","url":null,"abstract":"<p>There is a need for standardized methods for antimicrobial susceptibility testing (AST) of anaerobic bacteria involved in oral and extra-oral infections. We tested the recently published EUCAST disk diffusion method for rapidly growing anaerobes on selected oral anaerobes. AST of 20 strains of <i>Prevotella</i> spp., 11 strains of <i>Porphyromonas gingivalis, and</i> six <i>Fusobacterium nucleatum</i> complex strains was performed with amoxicillin and metronidazole disks using EUCAST guidelines. Plates were incubated anaerobically, and inhibition zones were evaluated after 20 h (EUCAST recommendations) and again after 44 h. The recommended agar supported the growth of all 38 strains. Twenty-hour incubation was sufficient for the assessment of inhibition zone diameters of <i>Fusobacterium</i> strains. Although approved for <i>Prevotella</i>, an extended study of <i>Prevotella</i> species showed inconsistent growth within the EUCAST time limit of 20 h for some strains. All <i>P. gingivalis</i> strains required 44 h of incubation for the evaluation of inhibition zones. The EUCAST disk diffusion method for AST of rapidly growing anaerobes is applicable to members of the <i>Fusobacterium nucleatum</i> complex. <i>P. gingivalis</i> and several oral strains of <i>Prevotella</i> needed 44 h of incubation to enable reading of diffusion diameter. Further studies are necessary to validate the prolonged incubation of slow-growing anaerobes.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/apm.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143380163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study
IF 2.2 4区 医学
Apmis Pub Date : 2025-02-03 DOI: 10.1111/apm.70001
Yitong Li, Yuhe Mai, Yao Jiao, Yali Yuan, Yingdi Qu, Ye Zhang, Muyuan Wang, Wenji Zhang, Xinyu Lu, Zhengdao Lin, Chengtao Liang, Junxiang Li, Tangyou Mao, Chune Xie
{"title":"Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study","authors":"Yitong Li,&nbsp;Yuhe Mai,&nbsp;Yao Jiao,&nbsp;Yali Yuan,&nbsp;Yingdi Qu,&nbsp;Ye Zhang,&nbsp;Muyuan Wang,&nbsp;Wenji Zhang,&nbsp;Xinyu Lu,&nbsp;Zhengdao Lin,&nbsp;Chengtao Liang,&nbsp;Junxiang Li,&nbsp;Tangyou Mao,&nbsp;Chune Xie","doi":"10.1111/apm.70001","DOIUrl":"10.1111/apm.70001","url":null,"abstract":"<div>\u0000 \u0000 <p>The gut microbiota plays a critical role in the occurrence and development of IBS-D, however, IBS-D-associated tongue coating microbiome dysbiosis has not yet been clearly defined. To address this, we analyzed the structure and composition of the tongue coating microbiome in 23 IBS-D patients and 12 healthy controls using 16S rRNA high-throughput sequencing analysis. The 16S rRNA sequencing results revealed that the overall observed OTUs of tongue coating microbiome in IBS-D patients exhibited a significant decrease compared with the healthy controls. Alpha diversity analysis showed that the diversity and community richness were significantly reduced in IBS-D patients, and PCoA revealed a distinct clustering of tongue coating microbiome between the IBS-D patients and healthy controls. Microbial comparisons at the genus level showed that the abundance of <i>Veillonella</i>, <i>Prevotella</i> in IBS-D patients was higher than those in healthy controls, while <i>Streptococcus</i>, <i>Haemophilus</i>, <i>Granulicatella</i>, and <i>Rothia</i> were significantly reduced compared with the healthy volunteers. Functional analysis results showed significant differences in 88 functional metabolic pathways between the IBS-D patients and the healthy controls, including fatty acid biosynthesis. These findings identified the structure, composition, functionality of tongue coating microbiome in IBS-D patients, and hold promise the potential for therapeutic targets during IBS-D management.</p>\u0000 </div>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Colonic Vitamin D Receptor and Inflammatory Bowel Disease: No Correlation to Histologic or Endoscopic Inflammation 结肠维生素D受体与炎症性肠病:与组织学或内镜炎症无关。
IF 2.2 4区 医学
Apmis Pub Date : 2025-01-20 DOI: 10.1111/apm.70000
Harald Bagger-Jörgensen, Christian Thomsen, Martine Borrisholt, Alkwin Wanders, Klas Sjöberg
{"title":"The Colonic Vitamin D Receptor and Inflammatory Bowel Disease: No Correlation to Histologic or Endoscopic Inflammation","authors":"Harald Bagger-Jörgensen,&nbsp;Christian Thomsen,&nbsp;Martine Borrisholt,&nbsp;Alkwin Wanders,&nbsp;Klas Sjöberg","doi":"10.1111/apm.70000","DOIUrl":"10.1111/apm.70000","url":null,"abstract":"<p>The role of the vitamin D receptor (VDR) in inflammatory bowel disease (IBD) is poorly described. The aim of this study was to examine the relationship between immunohistochemical VDR expression and IBD activity. The immunohistochemical expression of VDR was analysed in biopsies from active and inactive IBD in 28 patients (ulcerative colitis: 21, Crohn's disease: 7) and 12 non-IBD controls. VDR expression did not change in active compared to inactive disease (<i>p</i> = 0.40 in epithelium and <i>p</i> = 0.29 in stroma). There was a trend for higher VDR expression in controls compared to IBD patients. No relationship was found between VDR expression and histologic inflammation (<i>r</i> = −0.19, <i>p</i> = 0.89 for epithelium and <i>r</i> = 0.13, <i>p</i> = 0.35 for stroma), colonoscopic picture and clinical and laboratory measures including serum 25(OH) vitamin D status (<i>r</i> = −0.91, <i>p</i> = 0.82). IBD disease activity did not correlate to VDR immunohistochemical expression, nor did it differ compared to controls. These results partly conflict with prior studies, but these have only shown modest correlations. Prospective studies investigating VDR activity between IBD and controls should be contemplated.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
No Bacterial Biomass Detected in Tissue From Patients With Ovarian Cancer and Serous Tubal Intraepithelial Carcinomas Using 16S rDNA Sequencing 使用16S rDNA测序未检测到卵巢癌和浆液性输卵管上皮内癌患者组织中的细菌生物量。
IF 2.2 4区 医学
Apmis Pub Date : 2025-01-16 DOI: 10.1111/apm.13509
Kasper Ingerslev, Tim Svenstrup Poulsen, Mikael Lenz Strube, Wojciech Skovrider-Ruminski, Doris Schledermann, Tine Henrichsen Schnack, Claus Høgdall, Jan Blaakær, Estrid Høgdall
{"title":"No Bacterial Biomass Detected in Tissue From Patients With Ovarian Cancer and Serous Tubal Intraepithelial Carcinomas Using 16S rDNA Sequencing","authors":"Kasper Ingerslev,&nbsp;Tim Svenstrup Poulsen,&nbsp;Mikael Lenz Strube,&nbsp;Wojciech Skovrider-Ruminski,&nbsp;Doris Schledermann,&nbsp;Tine Henrichsen Schnack,&nbsp;Claus Høgdall,&nbsp;Jan Blaakær,&nbsp;Estrid Høgdall","doi":"10.1111/apm.13509","DOIUrl":"10.1111/apm.13509","url":null,"abstract":"<p>The ovarian oncobiome is subject to increasing scientific focus, but a potential link between bacterial dysbiosis and ovarian carcinogenesis remains controversial. Our primary aim was to characterize the bacterial microbiota in epithelial ovarian cancer samples. Secondarily, we aimed to compare results from the bacterial microbiota in formalin-fixed, paraffin-embedded ovarian tissue samples from 194 patients with epithelial ovarian cancer, fallopian tube tissue samples from 16 patients with serous tubal intraepithelial carcinomas and in benign fallopian tube tissue samples from 25 patients. Bacterial abundance was investigated by means of 16S rDNA Next Generation Sequencing. The 16S rDNA sequencing run produced a very low number of bacterial reads. Only seven samples displayed bacterial reads above 5000. Validation of detected bacterial reads by qPCR was negative and indicative of results being background amplification. Our results indicate no amount of bacterial biomass in the ovarian cancer, benign fallopian tube and in the samples with serous tubal intraepithelial carcinomas. The findings underline the importance of validating results from bacterial microbiota studies with additional technical assays before any conclusion may be drawn.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Antigen Specificity: A Fluctuating Aspect in the Development of Clinical Antibodies? 抗原特异性:临床抗体发展的波动方面?
IF 2.2 4区 医学
Apmis Pub Date : 2025-01-14 DOI: 10.1111/apm.13515
Sandeep, Suraj H. Shinde, Abhay H. Pande
{"title":"Antigen Specificity: A Fluctuating Aspect in the Development of Clinical Antibodies?","authors":"Sandeep,&nbsp;Suraj H. Shinde,&nbsp;Abhay H. Pande","doi":"10.1111/apm.13515","DOIUrl":"10.1111/apm.13515","url":null,"abstract":"<div>\u0000 \u0000 <p>Development of antibodies for clinical use is a complex process involving numerous aspects, with antigen specificity being the most important. Initially, polyclonal antibodies, that can recognize multiple specific and nonspecific antigens (polyreactive), were developed and were very effective in the treatments. Later on, the polyspecificity/polyreactivity of these polyclonal antibodies (binding to multiple antigens) raised concerns about therapeutic efficacy because of their nonspecific interactions and challenges, such as development of immune complexes, batch-to-batch variability. This highlighted the need for more targeted approaches. It was resolved by the marked invention of hybridoma technology in 1975 which resulted in the revolution in the antibody development field by offering monoclonal monospecific antibodies (bind single antigen). However, their limited application in complex pathologies sparked a paradigm shift, leading to the resurgence of polyspecific antibodies in the form of monoclonal polyspecific antibodies (Polybodies), which bind multiple antigens, but specifically. Till today, 14 Polybodies are approved for clinical use. This fluctuation in antigen specificity is directing the evolution of engineered antibodies that are going to drive the biopharmaceutical sector in the coming years. Through this write-up, we assert the fluctuating nature of antigen specificity during the antibody development and how it will be crucial for advancing biologics.</p>\u0000 </div>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142977282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing 使用纳米孔测序的基于散弹枪宏基因组学的血流感染诊断的关键步骤。
IF 2.2 4区 医学
Apmis Pub Date : 2025-01-14 DOI: 10.1111/apm.13511
Amelia Björnberg, David Nestor, Nilay Peker, Bhanu Sinha, Natacha Couto, John Rossen, Martin Sundqvist, Paula Mölling
{"title":"Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing","authors":"Amelia Björnberg,&nbsp;David Nestor,&nbsp;Nilay Peker,&nbsp;Bhanu Sinha,&nbsp;Natacha Couto,&nbsp;John Rossen,&nbsp;Martin Sundqvist,&nbsp;Paula Mölling","doi":"10.1111/apm.13511","DOIUrl":"10.1111/apm.13511","url":null,"abstract":"<p>Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for <i>Staphylococcus aureus</i> and <i>Streptococcus pneumoniae</i> were more pronounced compared to <i>Escherichia coli</i>. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.</p>","PeriodicalId":8167,"journal":{"name":"Apmis","volume":"133 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142977291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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