Journal of Microbiology Immunology and Infection最新文献

{"title":"Complete response to front-line therapies is associated with long-term survival in HIV-related lymphomas in Taiwan","authors":"Wei-Li Ma ,&nbsp;Wang-Da Liu ,&nbsp;Hsin-Yun Sun ,&nbsp;Wang-Huei Sheng ,&nbsp;Szu-Min Hsieh ,&nbsp;Shang-Ju Wu ,&nbsp;Chien-Ching Hung","doi":"10.1016/j.jmii.2024.04.001","DOIUrl":"10.1016/j.jmii.2024.04.001","url":null,"abstract":"<div><h3>Background</h3><p>The prognosis for people living with HIV (PLWH) who develop lymphomas has been greatly improved by combination antiretroviral therapy (cART) and anti-CD20 monoclonal antibodies. However, real-world clinical data on this patient group in Asia are limited.</p></div><div><h3>Methods</h3><p>Treatment outcomes were retrospectively examined for 104 PLWH with lymphomas between 2000 and 2019. The cohort comprised five PLWH with Hodgkin lymphoma (HL) and 99 with non-Hodgkin lymphomas, including 61 with diffuse large B-cell lymphoma (DLBCL), 19 with Burkitt lymphoma (BL), nine with primary central nervous system lymphoma (PCNSL) and ten with other subtypes.</p></div><div><h3>Results</h3><p>The 5-year overall survival (OS) rates were as follows: HL (100%), PCNSL (76.2%), other subtypes (60.0%), BL (57.4%), and DLBCL (55.6%). Individuals who achieved complete response (CR) to front-line therapies had a significantly better 5-year OS rate than those without (96.2% vs. 17.8%, p &lt; 0.001). PLWH who received cART for ≤6 months had significantly lower CD4+ T-cell counts at lymphoma diagnosis than those who received cART for longer periods (<em>p</em> = 0.048). Additionally, the 5-year OS rate was better for PLWH who received cART for ≤6 months before lymphomas diagnosis than those who received cART for longer periods (64.5% vs. 51.9%, <em>p</em> = 0.114).</p></div><div><h3>Conclusions</h3><p>PLWH with DLBCL or BL had OS rates compatible to patients without HIV infection. Better outcomes for patients achieving CR to front-line therapy and those with shorter cART duration before lymphoma diagnosis suggest an underlying biological distinction in the lymphomas and the involvement of immunity, which warrants further studies.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 426-436"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000707/pdfft?md5=bfcae08a560f15344eea91ee92ffb38d&pid=1-s2.0-S1684118224000707-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stool microbiota analysis for abundance of genus Klebsiella among adults and children in endemic area for community Klebsiella pneumoniae infection","authors":"Chun-Hsing Liao ,&nbsp;Kai-Liang Kao ,&nbsp;Shu-I Wu ,&nbsp;Chia-Jui Yang","doi":"10.1016/j.jmii.2024.02.001","DOIUrl":"10.1016/j.jmii.2024.02.001","url":null,"abstract":"<div><h3>Background</h3><p>Invasive <em>Klebsiella pneumoniae</em> syndrome is a significant endemic disease in Taiwan. Intestinal colonization of virulent clones that cause this phenomenon has been demonstrated in asymptomatic adults. Comparisons of healthy adults and children with stool <em>K. pneumoniae</em> colonization have rarely been reported. We aimed to evaluate the frequency and abundance of <em>K. pneumoniae</em> in the stool of adults and children by stool microbiota analysis.</p></div><div><h3>Methods</h3><p>Healthy volunteers and their children without antibiotic exposure within 3 months were recruited in a Taiwanese medical center. Stool samples were sent for gut microbiota analysis, using amplification of V3–V4 hypervariable regions of 16sRNA followed by high-throughput sequence. Rectal/stool swabs were sent for <em>K. pneumoniae</em> culture and identification by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS).</p></div><div><h3>Results</h3><p>Fifty-five adults with a mean age of 46.9 years (range, 23.1–72.1 years) and 20 children with a mean age of 2.3 years (range, 0.9–5.8) were enrolled, and 29 adults and 6 children had positive <em>K. pneumoniae</em> swabs. Children had lower microbiota diversity than adults, including higher abundance of phylum <em>Actinobacteria</em> and <em>Proteobacteria</em>, and lower <em>Bacteriodetes</em>. For genus comparison, higher abundance of <em>Escherichia</em>, <em>Streptococcus, Enterococcus</em> and <em>Bifidobacterium</em> were found in children, but the composite abundance of <em>Klebsiella</em> in adults (median: 0.0156, range: 0–0.031) and in children (median: 0.0067, range: 0–0.043) were similar. <em>Klebsiella</em> abundance was significantly higher in participants with positive swabs (p &lt; 0.0001). <em>Klebsiella-</em>positive swabs were strongly negatively correlated with <em>Enterobacter</em> spp. (p &lt; 0.0001), but no known demographic factors correlated with <em>Klebsiella</em>-positive swabs.</p></div><div><h3>Conclusion</h3><p><em>Klebsiella</em> species are present in young children, and the abundance is similar in adults and children. Positive swabs correlate strongly with higher abundance in microbiota analysis.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 470-479"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000380/pdfft?md5=f4fdd732a89b1c5f4c57be5f810f9fb7&pid=1-s2.0-S1684118224000380-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139919382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molnupiravir for the treatment of COVID-19 outpatients: An updated meta-analysis","authors":"Huzaifa Ahmad Cheema ,&nbsp;Saleha Abdul Rab ,&nbsp;Momina Butt ,&nbsp;Uzair Jafar ,&nbsp;Abia Shahid ,&nbsp;Aqeeb Ur Rehman ,&nbsp;Ka Yiu Lee ,&nbsp;Syeda Sahra ,&nbsp;Ranjit Sah","doi":"10.1016/j.jmii.2024.03.002","DOIUrl":"10.1016/j.jmii.2024.03.002","url":null,"abstract":"<div><h3>Background</h3><p>The majority of available data on molnupiravir come from an unvaccinated COVID-19 population. Therefore, we conducted this meta-analysis to integrate evidence from recent randomized controlled trials (RCTs) as well as observational studies stratified by vaccination status to determine the clinical efficacy and safety of molnupiravir in COVID-19 outpatients.</p></div><div><h3>Methods</h3><p>We searched PubMed, Embase, the Cochrane Library, medRxiv, and ClinicalTrials.gov from inception to November 2023. We conducted our meta-analysis using RevMan 5.4 with risk ratio (RR) as the effect measure.</p></div><div><h3>Results</h3><p>We included 8 RCTs and 5 observational studies in our meta-analysis. Molnupiravir reduced the risk of all-cause mortality (RR 0.28; 95% CI: 0.20–0.79, I² = 0%) but did not decrease the hospitalization rate (RR 0.67; 95% CI: 0.45–1.00, I² = 53%) in the overall population; in the immunized population, no benefits were observed. Molnupiravir lowered the rate of no recovery (RR 0.78; 95% CI: 0.76–0.81, I² = 0%) and increased virological clearance at day 5 (RR 2.68; 95% CI: 1.94–4.22, I² = 85%). There was no increase in the incidence of adverse events.</p></div><div><h3>Conclusions</h3><p>Molnupiravir does not decrease mortality and hospitalization rates in immunized patients with COVID-19. However, it does shorten the disease course and increases the recovery rate. The use of molnupiravir will need to be considered on a case-by-case basis in the context of the prevailing social circumstances, the resource setting, drug costs, and the healthcare burden.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 396-402"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000483/pdfft?md5=4b6955650f5b9b2cd94342d06166bf4f&pid=1-s2.0-S1684118224000483-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physical Activity and the incidence of sepsis: A 10-year observational study among 4 million adults","authors":"Kyoung Hwa Lee ,&nbsp;Eun Hwa Lee ,&nbsp;Kyu-na Lee ,&nbsp;Yebin Park ,&nbsp;Young Goo Song ,&nbsp;Kyung Do Han ,&nbsp;Sang Hoon Han","doi":"10.1016/j.jmii.2024.04.009","DOIUrl":"10.1016/j.jmii.2024.04.009","url":null,"abstract":"<div><h3>Background</h3><p>As the group at high risk for sepsis is increasing with the aging of the population, physical activity (PA), which has beneficial effects on various diseases, needs to be considered as a personalized prevention strategy for sepsis without direct anti-sepsis drug.</p></div><div><h3>Purpose</h3><p>To examine the association between the amount of PA (based on intensity, duration, and frequency) and the incidence rates of sepsis and mortality after sepsis.</p></div><div><h3>Methods</h3><p>This was a large-scale, retrospective, longitudinal cohort study using data from the Korean National Health Insurance Service and the biennial general health screening program. The amount of PA self-reported at the time of the health screening was categorized as non-PA, mild (&lt;500 metabolic equivalents [METs]-Min/Week), moderate (500–1000), severe (1000–1500), and extreme (≥1500). The multivariable regression model was adjusted for age, sex, income, body mass index, smoking, alcohol consumption, diabetes, hypertension, dyslipidemia, and chronic diseases.</p></div><div><h3>Results</h3><p>From 4,234,415 individuals who underwent a health screening in 2009, 3,929,165 subjects were selected after exclusion for wash-out period and a 1-year lag period, and then observed for the event of sepsis or all-cause death until December 2020. During a median 10.3 years of follow-up, 83,011 incidents of sepsis were detected. The moderate-PA group showed the lowest incidence (1.56/1000 person-years) and risk for sepsis, with an adjusted hazard ratio (aHR) of 0.73 (95% CI, 0.72–0.75, <em>P</em> &lt; 0.001) compared with the non-PA group. The occurrence of sepsis among people aged ≥65 years and ex-smokers were significantly lower in the moderate-PA group (aHR; 0.77, 95% CI; 0.74–0.79; and 0.68, 0.64–0.71, respectively, <em>P</em>s &lt; 0.001). The long-term all-cause mortality after sepsis was significantly lower in the PA group than in the non-PA group (overall <em>P</em> = 0.003).</p></div><div><h3>Conclusions</h3><p>Physical activity is associated with a lower risk of sepsis, especially in elderly people who have the highest incidence of sepsis. The protective effects of aerobic PA on sepsis might need to be incorporated with other interventions in sepsis guidelines through the accumulation of future studies.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 354-364"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S168411822400077X/pdfft?md5=323572f5921902f73e5598c4686e4ef4&pid=1-s2.0-S168411822400077X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ddPCR enables rapid detection of bloodstream infections in patients on home parenteral nutrition: A prospective cohort study","authors":"Veerle E.L.M. Gillis ,&nbsp;Daisy Dalloyaux ,&nbsp;Rene H.M. te Morsche ,&nbsp;Jakko van Ingen ,&nbsp;Özcan Sir ,&nbsp;Chantal P. Rovers ,&nbsp;Yannick Wouters ,&nbsp;Geert J.A. Wanten","doi":"10.1016/j.jmii.2024.03.003","DOIUrl":"10.1016/j.jmii.2024.03.003","url":null,"abstract":"<div><h3>Introduction</h3><p>Chronic intestinal failure patients (CIF) require a central venous access device (CVAD) to administer parenteral nutrition. Most serious complication related to a CVAD is a central line-associated bloodstream infection (CLABSI). The golden standard to diagnose a CLABSI are blood cultures, however, they may require 1–5 days before getting a result. Droplet digital polymerase chain reaction (ddPCR) for the detection of pathogen 16S/28S rRNA is a novel culture-independent molecular technique that has been developed to enhance and expedite infection diagnostics within two and a half hours. In this study, we prospectively compared ddPCR with blood cultures to detect pathogens in whole blood.</p></div><div><h3>Methods</h3><p>We included adult CIF patients with a clinical suspicion of CLABSI in this prospective single-blinded clinical study. Blood cultures were routinely collected and subsequently two central samples from the CVAD and two peripheral samples from a peripheral venous access point. Primary outcome was the sensitivity and specificity of ddPCR.</p></div><div><h3>Results</h3><p>In total, 75 patients with 126 suspected CLABSI episodes were included, with 80 blood samples from the CVAD and 114 from peripheral veins. The central ddPCR samples showed a sensitivity of 91% (95%CI 77–98), and specificity of 96% (95%CI 85–99). Peripheral ddPCR samples had a sensitivity of 63% (95%CI 46–77) and specificity of 99% (95%CI 93–100).</p></div><div><h3>Conclusion</h3><p>ddPCR showed a high sensitivity and specificity relative to blood cultures and enables rapid pathogen detection and characterization. Clinical studies should explore if integrated ddPCR and blood culture outcomes enables a more rapid pathogen guided CLABSI treatment and enhancing patient outcomes.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 375-384"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000495/pdfft?md5=bb494a380ddd49fe7d64903a92774782&pid=1-s2.0-S1684118224000495-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140278755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intestinal capillariasis: An indigenous case in Taiwan","authors":"Wei-Te Lee,&nbsp;Chih-Lin Huang,&nbsp;Rong-Jyh Lin,&nbsp;Chao-Ju Chen,&nbsp;Kuan-Li Wu,&nbsp;June-Der Lee,&nbsp;Yue-Chiu Su","doi":"10.1016/j.jmii.2024.04.007","DOIUrl":"10.1016/j.jmii.2024.04.007","url":null,"abstract":"","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 520-522"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000756/pdfft?md5=f4859888ce83d05350bc08e0c1306147&pid=1-s2.0-S1684118224000756-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140765597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combination of trimethoprim-sulfamethoxazole and clindamycin in the treatment of relapsing toxoplasmic encephalitis","authors":"Shih-Wen Ting,&nbsp;Jien-Wei Liu","doi":"10.1016/j.jmii.2024.02.008","DOIUrl":"10.1016/j.jmii.2024.02.008","url":null,"abstract":"","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 518-519"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000458/pdfft?md5=75af8bbc49ac367feb65c2f6de89046b&pid=1-s2.0-S1684118224000458-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140040998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting the association between vitamin D deficiency and active tuberculosis: A prospective case-control study in Taiwan","authors":"Meng-Shiuan Hsu ,&nbsp;Tzu-Chien Chung ,&nbsp;Ping-Huai Wang ,&nbsp;Shih-Lung Cheng ,&nbsp;Yen-Wen Wu ,&nbsp;Jung-Cheng Hsu ,&nbsp;Bing-Hsiean Tzeng ,&nbsp;Heng-Hsu Lin ,&nbsp;Chung-Ming Tu ,&nbsp;Fang-Yeh Chu ,&nbsp;Chi-Tai Fang","doi":"10.1016/j.jmii.2024.03.005","DOIUrl":"10.1016/j.jmii.2024.03.005","url":null,"abstract":"<div><h3>Background</h3><p>To revisit the association between vitamin D deficiency (VDD, defined as serum 25(OH)D &lt; 20 ng/ml) and incident active tuberculosis (TB), after two potentially underpowered randomized trials showed statistically non-significant 13%–22% decrease in TB incidence in vitamin D supplementation groups.</p></div><div><h3>Methods</h3><p>We prospectively conducted an age/sex-matched case–control study that accounting for body-mass index (BMI), smoking, and other confounding factors to examine the association between VDD and active TB among non-HIV people in Taiwan (latitude 24°N), a high-income society which continues to have moderate TB burden.</p></div><div><h3>Results</h3><p>We enrolled 62 people with incident active TB and 248 people in control group. The TB case patients had a significantly higher proportion of VDD compared to the control group (51.6% vs 29.8%, <em>p</em> = 0.001). The 25(OH)D level was also significantly lower in TB patients compared to control group (21.25 ± 8.93 ng/ml vs 24.45 ± 8.36 ng/ml, <em>p</em> = 0.008). In multivariable analysis, VDD (adjusted odds ratio [aOR]: 3.03, <em>p</em> = 0.002), lower BMI (aOR: 0.81, <em>p</em> &lt; 0.001), liver cirrhosis (aOR: 8.99, <em>p</em> = 0.042), and smoking (aOR: 4.52, <em>p</em> = 0.001) were independent risk factors for incident active TB.</p></div><div><h3>Conclusions</h3><p>VDD is an independent risk factor for incident active TB. Future randomized trials examining the effect of vitamin D supplementation on TB incidence should focus on people with a low BMI or other risk factors to maximize the statistical power.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 490-497"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000689/pdfft?md5=ed5b48cc6f1590009f8468b243daf469&pid=1-s2.0-S1684118224000689-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140402537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influenza and the risk of active tuberculosis occurrence among individuals with latent tuberculosis infection: A national cohort study in South Korea (2015–2020)","authors":"Jaehee Lee ,&nbsp;Hyewon Seo ,&nbsp;Dohyang Kim ,&nbsp;Jinseub Hwang ,&nbsp;Jin-Won Kwon","doi":"10.1016/j.jmii.2024.04.003","DOIUrl":"10.1016/j.jmii.2024.04.003","url":null,"abstract":"<div><h3>Background</h3><p>Influenza's potential impact on active tuberculosis (TB) development has been debated, with limited clinical evidence. To address this, we explored the association between influenza episodes and TB incidence in a national cohort of individuals with latent TB infection (LTBI).</p></div><div><h3>Methods</h3><p>We examined adults (≥20 years) diagnosed with LTBI between 2015 and 2020, using the Health Insurance Review and Assessment Service's national database in South Korea. We collected demographic data, comorbidities, and influenza episodes within 6 months before and after the initial LTBI diagnosis (prior vs. subsequent episode). We stratified the analysis into groups with and without TB preventive therapy (TPT).</p></div><div><h3>Results</h3><p>Among 220,483 LTBI subjects, 49% received TPT, while 51% did not. The average age was 48.4 years, with 52% having comorbidities. A prior and subsequent influenza episode was identified in 3221 and 4580 individuals, respectively. Of these, 1159 (0.53%) developed incident TB over an average follow-up of 1.86 years. The incidence rates of TB were comparable between individuals with and without prior and/or subsequent influenza episodes in the TPT group, but 1.4 times higher in the non-TPT group for those with such episodes. Cox proportional-hazards regression analysis indicated that influenza was not a risk factor for incident TB in the TPT group. However, a subsequent influenza episode significantly increased TB risk in the non-TPT group (hazard ratio: 1.648 [95% CI, 1.053–2.580]).</p></div><div><h3>Conclusions</h3><p>In individuals with LTBI not receiving TPT, experiencing an influenza episode may elevate the risk of developing active TB.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 437-445"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000719/pdfft?md5=fc1877d020ae9a07b41ecbfe251fe6e2&pid=1-s2.0-S1684118224000719-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ProFun: A web server for functional enrichment analysis of parasitic protozoan genes","authors":"Po-Jung Huang ,&nbsp;Yi-Chen Weng ,&nbsp;Kuo-Yang Huang ,&nbsp;Chi-Ching Lee ,&nbsp;Yuan-Ming Yeh ,&nbsp;Yu-Tong Chen ,&nbsp;Cheng-Hsun Chiu ,&nbsp;Petrus Tang","doi":"10.1016/j.jmii.2024.01.007","DOIUrl":"10.1016/j.jmii.2024.01.007","url":null,"abstract":"<div><h3>Background</h3><p>The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts from a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the most important pathogen in the tropics, no FEA package is available for protozoan functional (ProFun) enrichment analysis. To speed up comparative multi-omics research on parasitic protozoans, we constructed ProFun, a web-based, user-friendly platform for the research community.</p></div><div><h3>Methods</h3><p>ProFun utilizes the Docker container, ShinyProxy, and R Shiny to construct a scalable web service with load-balancing infrastructure. We have integrated a series of visual analytic functions, in-house scripts, and custom-made annotation packages to create three analytical modules for 40 protozoan species: (1) Gene Overlaps; (2) Over-representation Analysis (ORA); (3) Gene Set Enrichment Analysis (GSEA).</p></div><div><h3>Results</h3><p>We have established ProFun, a web server for functional enrichment analysis of differentially expressed genes. FEA becomes as simple as pasting a list of gene IDs into the textbox of our website. Users can customize enrichment parameters and results with just one click. The intuitive web interface and publication-ready charts enable users to reveal meaningful biological events and pinpoint potential targets for further studies.</p></div><div><h3>Conclusion</h3><p>ProFun is the first web application that enables gene functional enrichment analysis of parasitic protozoans. In addition to supporting FEA analysis, ProFun also allows the comparison of FEA results across complicated experimental designs. ProFun is freely available at <span>http://dalek.cgu.edu.tw:8080/app/profun</span><svg><path></path></svg>.</p></div>","PeriodicalId":56117,"journal":{"name":"Journal of Microbiology Immunology and Infection","volume":"57 3","pages":"Pages 509-517"},"PeriodicalIF":7.4,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1684118224000082/pdfft?md5=da2b1e7df910725f9a188a4ac4ea5200&pid=1-s2.0-S1684118224000082-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139679427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}