Diagnostic microbiology and infectious disease最新文献_第3页

Decoding omicron: Genetic insight into its transmission dynamics, severity spectrum and ever-evolving strategies of immune escape in comparison with other SARS-CoV-2 variants

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-23 DOI: 10.1016/j.diagmicrobio.2025.116705

Kundan Tandel , Divya Niveditha , Sanjay Pratap Singh , Kavita Bala Anand , Vaishnavi Shinde , Mayank Ghedia , Ashwini Sondakar , Mahesh Reddy

{"title":"Decoding omicron: Genetic insight into its transmission dynamics, severity spectrum and ever-evolving strategies of immune escape in comparison with other SARS-CoV-2 variants","authors":"Kundan Tandel , Divya Niveditha , Sanjay Pratap Singh , Kavita Bala Anand , Vaishnavi Shinde , Mayank Ghedia , Ashwini Sondakar , Mahesh Reddy","doi":"10.1016/j.diagmicrobio.2025.116705","DOIUrl":"10.1016/j.diagmicrobio.2025.116705","url":null,"abstract":"<div><h3>Background</h3><div>The coronavirus disease 2019 (COVID-19) pandemic, driven by the rapid evolution of the SARS-CoV-2 virus, has led to the emergence of multiple variants with significant impacts on global health. This study aims to analyze the evolutionary trends and mutational landscape of SARS-CoV-2 variants circulating in Pune, Maharashtra, India, from August 2022 to April 2024. Using comprehensive genomic surveillance data, we identified the predominance of variants such as BA.2.75, XBB.x, and the newly emerged subvariants JN.1, KP.1, and KP.2. These subvariants, belonging to the BA.2.86 lineage, have raised concerns owing to their potential for increased transmissibility and immune evasion.</div></div><div><h3>Results</h3><div>Phylogenetic analysis of 84 sequenced samples from Pune revealed 18 distinct lineages, with JN.1 and KP.2 forming a novel branch compared with their ancestral lineage, BA.2. Detailed mutational analysis highlighted key mutations in the N-terminal domain (NTD) and receptor-binding domain (RBD) of the spike protein, affecting viral stability, ACE2 binding affinity, and neutralizing antibody escape. Our findings, along with the predictions of SpikePro, suggest that the combination of these mutations enhances the viral fitness of JN.1 and KP.2, contributing to their rapid emergence and spread.</div></div><div><h3>Conclusion</h3><div>This study underscores the importance of continuous genomic surveillance and advanced computational modeling to track and predict the evolutionary trajectories of SARS-CoV-2 variants. The insights gained from this research are crucial for informing public health strategies, vaccine updates, and therapeutic interventions to mitigate the impact of current and future SARS-CoV-2 variants.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116705"},"PeriodicalIF":2.1,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073187","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

Diagnostic utility of next-generation sequencing in neurological infections: Two cases in point

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-23 DOI: 10.1016/j.diagmicrobio.2025.116713

Ravi Teja Kandikuppa , Vidya Krishna , Nandini Sethuraman , Anuradha Sridhar , Srinivasan Paramasivam

引用次数: 0

Corrigendum to "Clinical utility of PCR compared to conventional culture & sensitivity testing for the management of complicated urinary tract infections in adults:Part I. Assessment of clinical outcomes,investigator satisfaction scores & turnaround times" [Diagnostic Microbiology & Infectious Disease 111 (2025) 116601].

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-22 DOI: 10.1016/j.diagmicrobio.2025.116695

Frank L Spangler, Cheau Williams, Michael E Aberger, Bradley A Wilson, Khaled Ajib, Shahram S Gholami, Henry N Goodwin, Lauren Y Park, Moustafa Kardjadj, DeAndre Derrick, Thomas K Huard

引用次数: 0

Evaluating the accuracy of multiple rapid diagnostic tests for HIV detection in serum samples analysed during point-of-care proficiency testing assessments

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-21 DOI: 10.1016/j.diagmicrobio.2025.116706

Nozuko P. Blasich , Jerom Okot , Artur Ramos , Mduduzi B. Buthelezi , Dumisani F. Shabangu , Mahlatse M. Maleka , Sarvashni Moodliar , Nqobile Ngoma , Tendesayi Kufa

{"title":"Evaluating the accuracy of multiple rapid diagnostic tests for HIV detection in serum samples analysed during point-of-care proficiency testing assessments","authors":"Nozuko P. Blasich , Jerom Okot , Artur Ramos , Mduduzi B. Buthelezi , Dumisani F. Shabangu , Mahlatse M. Maleka , Sarvashni Moodliar , Nqobile Ngoma , Tendesayi Kufa","doi":"10.1016/j.diagmicrobio.2025.116706","DOIUrl":"10.1016/j.diagmicrobio.2025.116706","url":null,"abstract":"<div><h3>Background</h3><div>HIV rapid diagnostic tests are crucial for timely diagnosis, especially in resource-limited settings. The World Health Organization recommends sensitivity ≥99 % and specificity ≥98 %. This study assessed RDT performance across South Africa's provinces using a proficiency testing program.</div></div><div><h3>Methods</h3><div>From April to June 2023, 25,458 blinded serum samples were sent to testing facilities for screening and confirmatory testing. Sensitivity, specificity, predictive values, and concordance (Cohen's Kappa) were evaluated.</div></div><div><h3>Results</h3><div>The response rate was 98.25 %. Sensitivity and specificity were both 98.7 %, with agreement at 98.7 % (kappa 0.97, <em>p</em> < 0.001). Northern Cape showed the lowest sensitivity (91.8 %) and specificity (92.0 %), while Gauteng, KwaZulu-Natal, and Mpumalanga exceeded 99 %.</div></div><div><h3>Conclusion</h3><div>Although national RDT performance met WHO standards, Northern Cape's results reveal the need for improved training, quality assurance, and proficiency testing to strengthen diagnostic accuracy.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116706"},"PeriodicalIF":2.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037452","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

Exploring the dynamics of SARS-CoV-2 and HIV Co-infection: Mutation risks, therapeutic efficacy, and future variant prevention

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-21 DOI: 10.1016/j.diagmicrobio.2025.116707

Sumaiya Tasnim Maliha , Rabeya Fatemi , Marjana Akter , Qingcong Zheng , Yusha Araf , Tahani Tabassum , Mohammad Raguib Munif , Sukumar Saha , Mengzhou Xue , Huiqing Wang , Chunfu Zheng , Md. Golzar Hossain

{"title":"Exploring the dynamics of SARS-CoV-2 and HIV Co-infection: Mutation risks, therapeutic efficacy, and future variant prevention","authors":"Sumaiya Tasnim Maliha , Rabeya Fatemi , Marjana Akter , Qingcong Zheng , Yusha Araf , Tahani Tabassum , Mohammad Raguib Munif , Sukumar Saha , Mengzhou Xue , Huiqing Wang , Chunfu Zheng , Md. Golzar Hossain","doi":"10.1016/j.diagmicrobio.2025.116707","DOIUrl":"10.1016/j.diagmicrobio.2025.116707","url":null,"abstract":"<div><div>High mutation rates in SARS-CoV-2, particularly among immunocompromised patients living with HIV, continue to complicate the current COVID-19 pandemic. The threshold for severe COVID-19 and a greater risk of mortality have increased in many immunocompromised individuals due to a weakened immune system. Low CD4+ <em>T</em>-cell counts in people living with both HIV and COVID-19 lead to prolonged disease duration and, therefore, an increased likelihood of viral infection with SARS-CoV-2 mutations in such individuals. These mutations could decrease the efficiency of ongoing vaccines and cause new outbreaks. Recently, the rise of new mutations in this patient population has created increasing concern; however, few data are currently available on the direct association of HIV infection with SARS-CoV-2 mutations. This review highlights the implications of SARS-CoV-2 and HIV co-infection, highlighting the need for extra caution and monitoring of the immune-compromised population during a pandemic. Access to HIV care and COVID-19 treatments, careful surveillance, and adapted health strategies are key to reducing risks and protecting these populations. Further research is required to elucidate the dynamics of mutations and develop intervention methods to manage COVID-19 among immunocompromised patients.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116707"},"PeriodicalIF":2.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037455","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

Immunoblot evaluation of rubella humoral immunity in Portuguese women with negative or low-positive rubella IgG

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-21 DOI: 10.1016/j.diagmicrobio.2025.116690

Maria Chasqueira , Sara Costa , Margarida Paixão , Margarida Albuquerque , Maria José Sousa Rego , Paulo Paixão

{"title":"Immunoblot evaluation of rubella humoral immunity in Portuguese women with negative or low-positive rubella IgG","authors":"Maria Chasqueira , Sara Costa , Margarida Paixão , Margarida Albuquerque , Maria José Sousa Rego , Paulo Paixão","doi":"10.1016/j.diagmicrobio.2025.116690","DOIUrl":"10.1016/j.diagmicrobio.2025.116690","url":null,"abstract":"<div><div>Despite its low incidence in Europe, rubella's immune status is still routinely assessed using commercial immunoassays. However, some discrepancies have been observed between these tests and the Immunoblot.</div><div>The main objective of this study is to evaluate, by a commercial immunoblot, the immune status of a female population that had previously presented negative, low-positive, or equivocal rubella IgG with a commercial immunoassay. In total, 146 serum samples were reevaluated.</div><div>The results demonstrated that 81 % and 73 % of the samples, were positive by Immunoblot (Immunoblot interpretation criterion 1 and criterion 2, respectively).</div><div>Our results confirm previous studies, showing that Immunoblot can significantly reduce the false negatives for rubella in the female population. This application by avoiding unnecessary revaccinations represents a potential gain for health. However, it is pertinent to conduct an extended multidisciplinary discussion to analyse the pros and cons of this algorithm.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116690"},"PeriodicalIF":2.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037573","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

Searching for sexually transmitted infections by midstream urine pooling after exclusion of urinary tract infection: A cost-effectiveness analysis

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-20 DOI: 10.1016/j.diagmicrobio.2025.116700

María Jesús Castaño , Javier Guillem , Juan José Ripoll , David Navarro , Eliseo Albert

{"title":"Searching for sexually transmitted infections by midstream urine pooling after exclusion of urinary tract infection: A cost-effectiveness analysis","authors":"María Jesús Castaño , Javier Guillem , Juan José Ripoll , David Navarro , Eliseo Albert","doi":"10.1016/j.diagmicrobio.2025.116700","DOIUrl":"10.1016/j.diagmicrobio.2025.116700","url":null,"abstract":"<div><div>We aimed to evaluate the cost-effectiveness of screening for sexually transmitted infections (STI), <em>Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium,</em> and <em>Trichomonas vaginalis</em> in patients with suspected urinary tract infection (UTI) but negative urine cultures, using a pooled sampling method. A cohort of 200 patients was analyzed. A decision tree model based on cost-effectiveness was used to evaluate the following five diagnostic strategies: (A) no screening;(B) screening only men;(C) screening only women;(D) screening men and women with high leukocyte counts (>70cells/µL);(E) screening all men and women. The pooling method reduced reagent testing costs by 75 %. The most cost-effective strategy was screening men and women with high leukocyte counts, yielding an incremental cost-effectiveness ratio of 489.05euros. STI screening using pooled midstream urine samples in patients with suspected UTI and negative urine cultures is cost-effective, particularly when targeting individuals with high leukocyte counts. This approach optimizes resource use and improves early STI detection.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116700"},"PeriodicalIF":2.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058199","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

Utility of anaerobic blood cultures in the clinical management of infectious patients

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-20 DOI: 10.1016/j.diagmicrobio.2025.116702

K. Diallo , A. Belkacem , A. Raffetin , F. Medina , D. Jaafar , C. Corlouer , P. Caraux-Paz (b)

{"title":"Utility of anaerobic blood cultures in the clinical management of infectious patients","authors":"K. Diallo , A. Belkacem , A. Raffetin , F. Medina , D. Jaafar , C. Corlouer , P. Caraux-Paz (b)","doi":"10.1016/j.diagmicrobio.2025.116702","DOIUrl":"10.1016/j.diagmicrobio.2025.116702","url":null,"abstract":"<div><div>Paired aerobic/anaerobic cultures are routinely performed for the diagnosis of bacteraemia. This study aimed to assess the utility of anaerobic cultures in the management of infectious patients. All positive blood cultures taken from adult patients in a French hospital between November 2018 and March 2020 were evaluated. Clinical and microbiological data were collected for all patients with a positive anaerobic culture. Among the 17,272 positive pairs, 1402 included an anaerobic culture (8 %). In the 487 patients with anaerobic bacteraemia, the most commonly detected microorganisms were Enterobacterales (45 %), <em>Staphylococcus aureus</em> (16 %) and obligate anaerobes (6 %). In the 30 patients with obligate anaerobic bacteraemia, the most commonly detected bacterial species were <em>Bacteroides</em> spp. (30 %). When the bacteraemia-causing microorganism grew in both cultures (76 %), the anaerobic culture became positive prior to the aerobic culture in 54 % of cases—mainly for Enterobacterales and <em>S. aureus</em>. Our findings support the utility of performing anaerobic cultures.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116702"},"PeriodicalIF":2.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037553","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

Potential therapeutics and vaccines: Current progress and challenges in developing antiviral treatments or vaccines for Oropouche virus

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-20 DOI: 10.1016/j.diagmicrobio.2025.116699

Abhishek Vijukumar, Aryan Kumar, Hardik Kumar

引用次数: 0

Whole genome sequencing characterization of Clostridioides difficile from Bulgaria during the COVID-19 pandemic

IF 2.1 4区医学

Diagnostic microbiology and infectious disease Pub Date : 2025-01-18 DOI: 10.1016/j.diagmicrobio.2025.116703

Elina Dobreva , Deyan Donchev , Ivan Stoikov , Deana Teneva , Rumyana Hristova , Marianna Murdjeva , Rossitza Vatcheva-Dobrevska , Ivan N. Ivanov

{"title":"Whole genome sequencing characterization of Clostridioides difficile from Bulgaria during the COVID-19 pandemic","authors":"Elina Dobreva , Deyan Donchev , Ivan Stoikov , Deana Teneva , Rumyana Hristova , Marianna Murdjeva , Rossitza Vatcheva-Dobrevska , Ivan N. Ivanov","doi":"10.1016/j.diagmicrobio.2025.116703","DOIUrl":"10.1016/j.diagmicrobio.2025.116703","url":null,"abstract":"<div><div>Increased incidence of <em>Clostridioides difficile</em> infections were documented in Bulgarian hospitals during COVID-19. WGS was performed on 39 isolates from seven hospitals during 2015-2022. Antimicrobial resistance and toxin genes were inferred from genomes. MLST profiles, cgMLST, and wgMLST phylogeny analyses were performed. Isolates were grouped into eight MLST types as predominant were ST3 (46.15%) and ST1/RT027 (33.33%). ST3 was detected in a single hospital (16/18) and characterized by two toxin variants: <em>tcdA+/tcdB+</em> (14) and <em>tcdA-/tcdB+</em> (4). Twelve ST3 strains belonged to the country-specific cgMLST HC2_6485 cluster and ten were identified as a putative outbreak in the infectious disease ward. All the ST1/RT027 isolates were distributed in six hospitals and clustered in an HC2_4711 with strains from neighbouring countries. All <em>C. difficile</em> were susceptible to vancomycin despite the Thr349Ile mutation in <em>van</em>S in three isolates. We report the first insights into the <em>C. difficile</em> genotype hospital prevalence during the pandemic.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116703"},"PeriodicalIF":2.1,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037555","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