Pub Date : 2026-01-24DOI: 10.1016/j.diagmicrobio.2026.117285
Ali Abdul Hussein S Al-Janabi
Background: Yeasts are one of the important fungi in food production. Some of them can be used as food. Pathogenic Candida is not known to be food for other organisms. This study aims to evaluate the use of pathogenic Candida as a supplement for dermatophyte growth.
Methods: Standard fungal media, Sabouraud's dextrose agar (SDA), were supplied with dead cells of three pathogenic Candida species, C. albicans, C. glabrata, and C. tropicalis, for culturing of 14 isolates of dermatophytes. Dry weight was measured to determine the biomass of growing dermatophytes.
Results: Candida-containing media significantly enhanced dermatophytic growth. C. tropicalis dead cells promoted the growth of Microsporum species, while Trichophyton species preferred growing on media of all Candida spp. with less variability among them. In contrast to C. tropicalis, media with C. albicans and C. glabrata were less effective at supporting Microsporum canis growth (0.150 g of biomass, 95% CI: 0.0482-0.252, and 0.165 g of biomass, 95% CI: 0.157-0.173, respectively).
Conclusions: Candida cells have a promotional impact on the growth of dermatophytes. Pathogenic Candida can be used by dermatophytes as an enhancement growth factor when they are in a dead state.
{"title":"Pathogenic Candida as a supplementary nutrient for dermatophytes.","authors":"Ali Abdul Hussein S Al-Janabi","doi":"10.1016/j.diagmicrobio.2026.117285","DOIUrl":"https://doi.org/10.1016/j.diagmicrobio.2026.117285","url":null,"abstract":"<p><strong>Background: </strong>Yeasts are one of the important fungi in food production. Some of them can be used as food. Pathogenic Candida is not known to be food for other organisms. This study aims to evaluate the use of pathogenic Candida as a supplement for dermatophyte growth.</p><p><strong>Methods: </strong>Standard fungal media, Sabouraud's dextrose agar (SDA), were supplied with dead cells of three pathogenic Candida species, C. albicans, C. glabrata, and C. tropicalis, for culturing of 14 isolates of dermatophytes. Dry weight was measured to determine the biomass of growing dermatophytes.</p><p><strong>Results: </strong>Candida-containing media significantly enhanced dermatophytic growth. C. tropicalis dead cells promoted the growth of Microsporum species, while Trichophyton species preferred growing on media of all Candida spp. with less variability among them. In contrast to C. tropicalis, media with C. albicans and C. glabrata were less effective at supporting Microsporum canis growth (0.150 g of biomass, 95% CI: 0.0482-0.252, and 0.165 g of biomass, 95% CI: 0.157-0.173, respectively).</p><p><strong>Conclusions: </strong>Candida cells have a promotional impact on the growth of dermatophytes. Pathogenic Candida can be used by dermatophytes as an enhancement growth factor when they are in a dead state.</p>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"115 1","pages":"117285"},"PeriodicalIF":1.8,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146131304","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}
Pub Date : 2026-01-24DOI: 10.1016/j.diagmicrobio.2026.117284
Ilkay Bozkurt
This study aimed to evaluate the Galactomannan (GM) correlation with radiologic findings, treatment decisions and financial impact of over-testing. In this cohort, GM testing yielded a low diagnostic return, requiring 53 tests to obtain one positive result and 103 tests to identify a probable invasive aspergillosis (IA) case, generating a considerable avoidable financial burden. These findings highlight the need to rationalize GM utilization and align testing with IA risk to reduce hospital costs.
{"title":"Over-testing Galactomannan in patients with hematological malignancies: A retrospective analysis from a tertiary care university hospital in Türkiye","authors":"Ilkay Bozkurt","doi":"10.1016/j.diagmicrobio.2026.117284","DOIUrl":"10.1016/j.diagmicrobio.2026.117284","url":null,"abstract":"<div><div>This study aimed to evaluate the Galactomannan (GM) correlation with radiologic findings, treatment decisions and financial impact of over-testing. In this cohort, GM testing yielded a low diagnostic return, requiring 53 tests to obtain one positive result and 103 tests to identify a probable invasive aspergillosis (IA) case, generating a considerable avoidable financial burden. These findings highlight the need to rationalize GM utilization and align testing with IA risk to reduce hospital costs.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"115 1","pages":"Article 117284"},"PeriodicalIF":1.8,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146076032","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}
Pub Date : 2026-01-23DOI: 10.1016/j.diagmicrobio.2026.117282
Lisa Nkatha Micheni, Sammy Wambua, Karani Magutah, Jimmy Nkaiwuatei, Joel Bazira, Charles Sande
Introduction: Tuberculosis (TB) remains a major global health concern, particularly in low-income countries where the impact is greater. The lack of proper surveillance tools in these countries is a big impediment to effective TB control. Whole-genome sequencing (WGS) has successfully been integrated into routine TB programs in high-income countries and transformed disease surveillance by providing rapid, high-resolution transmission insights, drug resistance profiling, and outbreak detection. However, its uptake in resource-limited settings where TB burden is most prevalent remains limited.
Methods: This review examines how WGS is currently being utilised for TB surveillance and highlights the main obstacles to its adoption in limited-resource settings as well as the strategies that could improve its uptake. A literature search was conducted in PubMed, Google Scholar, and the World Health Organisation (WHO) databases with keywords "whole genome sequencing," "tuberculosis," "surveillance," "transmission," and "drug resistance." Studies published between 2015 and 2025 were prioritised, with a focus on applications in high-burden settings.
Results: Key challenges identified include infrastructural issues whereby 78% of high-burden countries lack adequate sequencing facilities according to WHO 2023 data; financial barriers, with recurring costs surpassing $150 per sample in low-resource settings as compared to $80 in high-income countries, and a shortage of trained personnel with only 2.3 bioinformaticians being available per African country. Other hurdles involve concerns over data sovereignty, weak regulatory frameworks, and ethical dilemmas surrounding privacy and equitable data usage, with only 31% of low-resource countries having genomic data policies. Nevertheless, promising innovations like portable sequencing devices which have a sensitivity of up to 92% and cloud-based platforms that reduce computational needs by 70% offer scalable opportunities for equitable integration. We also highlight partnership models that blend WHO technical guidance, Global Fund financing, and South-South collaborations that could enhance sustainability.
Conclusion: To realise the full potential of WGS in TB-endemic regions, a coordinated approach that combines technical advancements with policy changes, ethical data governance, and sustained investment is needed. Tackling these challenges is essential in achieving equitable, genomics-informed TB control that aligns with global TB elimination goals.
{"title":"Bridging the implementation gap: Challenges and opportunities for integrating whole genome sequencing in tuberculosis surveillance in low-resource settings.","authors":"Lisa Nkatha Micheni, Sammy Wambua, Karani Magutah, Jimmy Nkaiwuatei, Joel Bazira, Charles Sande","doi":"10.1016/j.diagmicrobio.2026.117282","DOIUrl":"https://doi.org/10.1016/j.diagmicrobio.2026.117282","url":null,"abstract":"<p><strong>Introduction: </strong>Tuberculosis (TB) remains a major global health concern, particularly in low-income countries where the impact is greater. The lack of proper surveillance tools in these countries is a big impediment to effective TB control. Whole-genome sequencing (WGS) has successfully been integrated into routine TB programs in high-income countries and transformed disease surveillance by providing rapid, high-resolution transmission insights, drug resistance profiling, and outbreak detection. However, its uptake in resource-limited settings where TB burden is most prevalent remains limited.</p><p><strong>Methods: </strong>This review examines how WGS is currently being utilised for TB surveillance and highlights the main obstacles to its adoption in limited-resource settings as well as the strategies that could improve its uptake. A literature search was conducted in PubMed, Google Scholar, and the World Health Organisation (WHO) databases with keywords \"whole genome sequencing,\" \"tuberculosis,\" \"surveillance,\" \"transmission,\" and \"drug resistance.\" Studies published between 2015 and 2025 were prioritised, with a focus on applications in high-burden settings.</p><p><strong>Results: </strong>Key challenges identified include infrastructural issues whereby 78% of high-burden countries lack adequate sequencing facilities according to WHO 2023 data; financial barriers, with recurring costs surpassing $150 per sample in low-resource settings as compared to $80 in high-income countries, and a shortage of trained personnel with only 2.3 bioinformaticians being available per African country. Other hurdles involve concerns over data sovereignty, weak regulatory frameworks, and ethical dilemmas surrounding privacy and equitable data usage, with only 31% of low-resource countries having genomic data policies. Nevertheless, promising innovations like portable sequencing devices which have a sensitivity of up to 92% and cloud-based platforms that reduce computational needs by 70% offer scalable opportunities for equitable integration. We also highlight partnership models that blend WHO technical guidance, Global Fund financing, and South-South collaborations that could enhance sustainability.</p><p><strong>Conclusion: </strong>To realise the full potential of WGS in TB-endemic regions, a coordinated approach that combines technical advancements with policy changes, ethical data governance, and sustained investment is needed. Tackling these challenges is essential in achieving equitable, genomics-informed TB control that aligns with global TB elimination goals.</p>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"115 1","pages":"117282"},"PeriodicalIF":1.8,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146117903","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}
Malaria is an infectious disease that severely affects people worldwide. The detection of its causative organism, Plasmodium, is mainly based on microscopy, polymerase chain reaction, and rapid diagnostic tests, all relying on blood samples. Obtaining blood samples causes pain, poses a risk of infections, and leads to poor compliance in cases of repeated sampling. This highlights the need for non-invasive diagnostic alternatives. Several studies have explored the potential use of non-blood samples, such as saliva, urine, stool, and skin to detect Plasmodium. Urine accumulates changes from the body and thus is an appropriate source for biomarker discovery. A biomarker is a measurable change in the body that is associated with a disease or condition. In this study, the urine samples of Plasmodium vivax infected patients were analyzed through mass spectrometry. A comparison of the infected and control samples revealed several proteins present in one group but absent in the other, with some proteins showing altered levels. A total of 252 human proteins were found in the infected samples only. Gene ontology analysis and functional annotation revealed that these proteins are involved in key biological pathways and processes in both the human host and the parasite, and their presence in urine samples could aid in a deeper understanding of malaria biology. Twenty-eight P. vivax proteins were found in the mass spectrometric analysis of urine samples, including rifin-like protein, single-stranded DNA-binding protein, and profilin. These might serve as potential biomarkers for the non-invasive detection of Plasmodium infection.
{"title":"Discovery of parasite proteins in the urine of vivax malaria patients through mass spectrometry","authors":"Himani Tripathi , Prajna Parimita Kar , Araveti Prasanna Babu , Anand Srivastava , Geeta Pachori , Tarun Kumar Bhatt","doi":"10.1016/j.diagmicrobio.2026.117281","DOIUrl":"10.1016/j.diagmicrobio.2026.117281","url":null,"abstract":"<div><div>Malaria is an infectious disease that severely affects people worldwide. The detection of its causative organism, <em>Plasmodium</em>, is mainly based on microscopy, polymerase chain reaction, and rapid diagnostic tests, all relying on blood samples. Obtaining blood samples causes pain, poses a risk of infections, and leads to poor compliance in cases of repeated sampling. This highlights the need for non-invasive diagnostic alternatives. Several studies have explored the potential use of non-blood samples, such as saliva, urine, stool, and skin to detect <em>Plasmodium</em>. Urine accumulates changes from the body and thus is an appropriate source for biomarker discovery. A biomarker is a measurable change in the body that is associated with a disease or condition. In this study, the urine samples of <em>Plasmodium vivax</em> infected patients were analyzed through mass spectrometry. A comparison of the infected and control samples revealed several proteins present in one group but absent in the other, with some proteins showing altered levels. A total of 252 human proteins were found in the infected samples only. Gene ontology analysis and functional annotation revealed that these proteins are involved in key biological pathways and processes in both the human host and the parasite, and their presence in urine samples could aid in a deeper understanding of malaria biology. Twenty-eight <em>P. vivax</em> proteins were found in the mass spectrometric analysis of urine samples, including rifin-like protein, single-stranded DNA-binding protein, and profilin. These might serve as potential biomarkers for the non-invasive detection of <em>Plasmodium</em> infection.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"115 1","pages":"Article 117281"},"PeriodicalIF":1.8,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146046303","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}
Pub Date : 2026-01-17DOI: 10.1016/j.diagmicrobio.2026.117280
Zhixiong Duan , Shaohong Yu , Honglin Wang , Chunyan Yang , Xuelian Peng , Shan Shi , Jin Li
The emergence of hypervirulent Klebsiella pneumoniae (hvKP), particularly the K1 and K2 serotypes, presents a significant public health threat due to their increased virulence and resistance. Rapid and accurate detection of hvKP is crucial for effective clinical management. This study developed and evaluated a duplex real-time multienzyme isothermal rapid amplification (MIRA) assay for the simultaneous detection of hvKP K1 and K2 serotypes in spiked blood samples. The assay employed optimized primers and probes targeting specific capsular genes. Sensitivity and specificity were assessed using spiked blood specimens and compared to real-time PCR. The detection limit was 1 × 10³ CFU per reaction for both serotypes, with no cross-reactivity with non-hvKP K1/K2 strains. The assay demonstrated superior reproducibility and stability, offering faster detection and simplified infrastructure requirements compared to real-time PCR. These features make the duplex real-time MIRA assay a promising tool for clinical diagnostics and outbreak surveillance.
{"title":"Development and evaluation of a duplex real-time multienzyme isothermal rapid amplification assay for simultaneous detection of hypervirulent Klebsiella pneumoniae K1 and K2 serotypes in spiked blood samples","authors":"Zhixiong Duan , Shaohong Yu , Honglin Wang , Chunyan Yang , Xuelian Peng , Shan Shi , Jin Li","doi":"10.1016/j.diagmicrobio.2026.117280","DOIUrl":"10.1016/j.diagmicrobio.2026.117280","url":null,"abstract":"<div><div>The emergence of hypervirulent <em>Klebsiella pneumoniae</em> (hvKP), particularly the K1 and K2 serotypes, presents a significant public health threat due to their increased virulence and resistance. Rapid and accurate detection of hvKP is crucial for effective clinical management. This study developed and evaluated a duplex real-time multienzyme isothermal rapid amplification (MIRA) assay for the simultaneous detection of hvKP K1 and K2 serotypes in spiked blood samples. The assay employed optimized primers and probes targeting specific capsular genes. Sensitivity and specificity were assessed using spiked blood specimens and compared to real-time PCR. The detection limit was 1 × 10³ CFU per reaction for both serotypes, with no cross-reactivity with non-hvKP K1/K2 strains. The assay demonstrated superior reproducibility and stability, offering faster detection and simplified infrastructure requirements compared to real-time PCR. These features make the duplex real-time MIRA assay a promising tool for clinical diagnostics and outbreak surveillance.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117280"},"PeriodicalIF":1.8,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017828","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}
Pub Date : 2026-01-16DOI: 10.1016/j.diagmicrobio.2026.117279
Patrick M. McDaneld , Theresa Okeyo Owuor , Shivaramu Keelara , Carrie E. Lasky , Andrea M. Prinzi
Timely and effective antimicrobial therapy is essential for managing bacteremia and reducing associated morbidity and mortality. Fast phenotypic antimicrobial susceptibility testing (fAST) technologies offer the potential to accelerate optimal therapy by providing fast, actionable results. However, real-world adoption of fAST is influenced by laboratory infrastructure, antimicrobial stewardship practices, and the adaptability of new diagnostic platforms. We conducted an Early Evaluation Program (EEP) of the VITEK® REVEAL™ system at 13 U.S. hospital-based microbiology laboratories to assess performance and user experience related to the assay and fAST in general. A survey was performed as a component of the EEP to qualitatively assess barriers and facilitators to fAST implementation. Survey responses highlighted that ease of use, improved turnaround time, and clinical impact were the most valued features of fAST. Willingness to adopt fAST was high, but hesitations centered on evidence gaps, resource constraints, and the need for robust performance data. Key determinants of adoption included patient complexity, laboratory staffing, and workflow integration. Mapping responses to the Consolidated Framework for Implementation Research (CFIR) identified critical domains such as evidence base, adaptability, cost, and communication pathways. Successful implementation strategies included stakeholder education and engagement, consensus-building, and tailoring software to local needs. These findings highlight that while fAST can transform bacteremia management, its impact depends on addressing local barriers, fostering multidisciplinary collaboration, and ensuring ongoing evaluation of clinical and operational outcomes.
{"title":"Real-world laboratory functionality requirements and implementation considerations for fast phenotypic antimicrobial susceptibility testing","authors":"Patrick M. McDaneld , Theresa Okeyo Owuor , Shivaramu Keelara , Carrie E. Lasky , Andrea M. Prinzi","doi":"10.1016/j.diagmicrobio.2026.117279","DOIUrl":"10.1016/j.diagmicrobio.2026.117279","url":null,"abstract":"<div><div>Timely and effective antimicrobial therapy is essential for managing bacteremia and reducing associated morbidity and mortality. Fast phenotypic antimicrobial susceptibility testing (fAST) technologies offer the potential to accelerate optimal therapy by providing fast, actionable results. However, real-world adoption of fAST is influenced by laboratory infrastructure, antimicrobial stewardship practices, and the adaptability of new diagnostic platforms. We conducted an Early Evaluation Program (EEP) of the VITEK® REVEAL™ system at 13 U.S. hospital-based microbiology laboratories to assess performance and user experience related to the assay and fAST in general. A survey was performed as a component of the EEP to qualitatively assess barriers and facilitators to fAST implementation. Survey responses highlighted that ease of use, improved turnaround time, and clinical impact were the most valued features of fAST. Willingness to adopt fAST was high, but hesitations centered on evidence gaps, resource constraints, and the need for robust performance data. Key determinants of adoption included patient complexity, laboratory staffing, and workflow integration. Mapping responses to the Consolidated Framework for Implementation Research (CFIR) identified critical domains such as evidence base, adaptability, cost, and communication pathways. Successful implementation strategies included stakeholder education and engagement, consensus-building, and tailoring software to local needs. These findings highlight that while fAST can transform bacteremia management, its impact depends on addressing local barriers, fostering multidisciplinary collaboration, and ensuring ongoing evaluation of clinical and operational outcomes.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117279"},"PeriodicalIF":1.8,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146009304","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}
High-risk human papillomavirus (HR-HPV) infection is the primary cause of cervical cancer. However, conventional PCR-based assays provide limited HPV genotyping, and cytology alone has low sensitivity for detecting subclinical infections. Comprehensive molecular approaches are needed to better characterize HPV genotypes and co-infections in community screening settings.
Methods
This study evaluated the analytical performance of a next-generation sequencing (NGS)–based HPV–STI assay in comparison with the clinically validated Roche CobasⓇ 4800 platform in a community screening cohort from South India. Cervical exfoliated cell samples from 96 asymptomatic, married women previously tested by CobasⓇ 4800 with partial HR-HPV genotyping (HPV16, HPV18, and a pooled group of 12 other high-risk types) were analyzed using NGS. The NGS assay enabled comprehensive detection of 28 HPV genotypes and 13 sexually transmitted infections (STIs) on the Illumina NextSeq 550 platform. Liquid-based cytology with RAPID-Pap staining was performed for all sequenced samples.
Results
The NGS assay showed high agreement with the CobasⓇ 4800 platform, with an overall concordance of 95.8% (92/96). Concordance was 94.4% (17/18) for HPV16 detection, 100% (3/3) for HPV18, 96.7% (58/60) for pooled other high-risk HPV types (non-HPV16/18), and 85.7% (7/8) for mixed infections, including co-infections of HPV16 or HPV18 with non-HPV16/18 high-risk types as well as HPV16/18 dual infections. Among women with abnormal cytology (ASCUS and HSIL), non-HPV16/18 infections were identified in 58.3% (7/12) of cases. Concurrent non-HPV STIs were detected in 52.1% (50/96) of participants, with Ureaplasma parvum and Mycoplasma hominis being the most prevalent.
Conclusion
A substantial proportion of women with abnormal cytology in this community cohort harboured non-HPV16 and HPV18 high-risk infections, highlighting the importance of extended HPV genotyping. NGS-based HPV genotyping was concordant with the comparator assay used and had simultaneous STI identification, supporting its potential utility as a comprehensive tool for community-based cervical cancer screening and risk stratification.
{"title":"High throughput HPV genotyping by next generation sequencing for detection of 28 HPV types and 13 sexually transmitted infections: A first community-based cervical cancer screening study from India","authors":"Yasasve Madhavan, Vasanthkumar Muthukumar, Srinidhi Ramasubramanian, Vijayalakshmi Ramshankar","doi":"10.1016/j.diagmicrobio.2026.117278","DOIUrl":"10.1016/j.diagmicrobio.2026.117278","url":null,"abstract":"<div><h3>Background</h3><div>High-risk human papillomavirus (HR-HPV) infection is the primary cause of cervical cancer. However, conventional PCR-based assays provide limited HPV genotyping, and cytology alone has low sensitivity for detecting subclinical infections. Comprehensive molecular approaches are needed to better characterize HPV genotypes and co-infections in community screening settings.</div></div><div><h3>Methods</h3><div>This study evaluated the analytical performance of a next-generation sequencing (NGS)–based HPV–STI assay in comparison with the clinically validated Roche Cobas<sup>Ⓡ</sup> 4800 platform in a community screening cohort from South India. Cervical exfoliated cell samples from 96 asymptomatic, married women previously tested by Cobas<sup>Ⓡ</sup> 4800 with partial HR-HPV genotyping (HPV16, HPV18, and a pooled group of 12 other high-risk types) were analyzed using NGS. The NGS assay enabled comprehensive detection of 28 HPV genotypes and 13 sexually transmitted infections (STIs) on the Illumina NextSeq 550 platform. Liquid-based cytology with RAPID-Pap staining was performed for all sequenced samples.</div></div><div><h3>Results</h3><div>The NGS assay showed high agreement with the Cobas<sup>Ⓡ</sup> 4800 platform, with an overall concordance of 95.8% (92/96). Concordance was 94.4% (17/18) for HPV16 detection, 100% (3/3) for HPV18, 96.7% (58/60) for pooled other high-risk HPV types (non-HPV16/18), and 85.7% (7/8) for mixed infections, including co-infections of HPV16 or HPV18 with non-HPV16/18 high-risk types as well as HPV16/18 dual infections. Among women with abnormal cytology (ASCUS and HSIL), non-HPV16/18 infections were identified in 58.3% (7/12) of cases. Concurrent non-HPV STIs were detected in 52.1% (50/96) of participants, with <em>Ureaplasma parvum</em> and <em>Mycoplasma hominis</em> being the most prevalent.</div></div><div><h3>Conclusion</h3><div>A substantial proportion of women with abnormal cytology in this community cohort harboured non-HPV16 and HPV18 high-risk infections, highlighting the importance of extended HPV genotyping. NGS-based HPV genotyping was concordant with the comparator assay used and had simultaneous STI identification, supporting its potential utility as a comprehensive tool for community-based cervical cancer screening and risk stratification.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117278"},"PeriodicalIF":1.8,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146035254","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}
Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human–animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across viral, bacterial, fungal, and parasitic threats to characterize how diverse pathogens emerge and spread. Foundational events such as the 1918 influenza pandemic, mid-century influenza pandemics, the emergence of HIV/AIDS, and the eradication of smallpox provide context for understanding modern disease dynamics. In recent decades, coronaviruses including SARS, MERS, and SARS-CoV-2, pandemic H1N1, avian influenza subtypes, and major arboviruses such as dengue, chikungunya, Zika, West Nile virus, and yellow fever have demonstrated the rapidity with which zoonotic pathogens can disseminate globally. Viral hemorrhagic fevers including Ebola, Marburg, Lassa, and Crimean–Congo hemorrhagic fever remain critical threats, especially in regions with limited health-care capacity. Concurrently, antimicrobial resistance, the emergence of Candida auris, and the climate-driven expansion of endemic mycoses involving Histoplasma, Coccidioides, and Blastomyces highlight the increasing importance of fungal pathogens. Parasitic diseases such as artemisinin-resistant malaria, zoonotic trypanosomiasis, and expanding Leishmania transmission reflect shifting ecological conditions. These patterns are shaped by intersecting drivers including deforestation, wildlife trade, agricultural intensification, urban crowding, conflict, and rapid microbial evolution that enable spillover and sustained transmission. Although advances in genomic surveillance, metagenomic diagnostics, mRNA vaccines, monoclonal antibodies, and broad-spectrum antivirals have strengthened global response capacity, substantial gaps persist in equity, surveillance, and access to countermeasures. Strengthening One Health systems and resilient public health infrastructures is essential to anticipate and mitigate emerging infectious threats.
{"title":"From pandemic influenza to novel coronaviruses: emerging infectious diseases of the 21st century","authors":"Sijo Asokan , Isiaka Ismaila Damilare , Sunil Kumar , Rohan Kumar Pandey , Gaurav Verma , Nilotpal Banerjee , Guhanraj Radhamanalan , Smitha Vijayan , Teena Jacob , Divya Rajeswary","doi":"10.1016/j.diagmicrobio.2026.117277","DOIUrl":"10.1016/j.diagmicrobio.2026.117277","url":null,"abstract":"<div><div>Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human–animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across viral, bacterial, fungal, and parasitic threats to characterize how diverse pathogens emerge and spread. Foundational events such as the 1918 influenza pandemic, mid-century influenza pandemics, the emergence of HIV/AIDS, and the eradication of smallpox provide context for understanding modern disease dynamics. In recent decades, coronaviruses including SARS, MERS, and SARS-CoV-2, pandemic H1N1, avian influenza subtypes, and major arboviruses such as dengue, chikungunya, Zika, West Nile virus, and yellow fever have demonstrated the rapidity with which zoonotic pathogens can disseminate globally. Viral hemorrhagic fevers including Ebola, Marburg, Lassa, and Crimean–Congo hemorrhagic fever remain critical threats, especially in regions with limited health-care capacity. Concurrently, antimicrobial resistance, the emergence of <em>Candida auris</em>, and the climate-driven expansion of endemic mycoses involving <em>Histoplasma, Coccidioides</em>, and <em>Blastomyces</em> highlight the increasing importance of fungal pathogens. Parasitic diseases such as artemisinin-resistant malaria, zoonotic trypanosomiasis, and expanding Leishmania transmission reflect shifting ecological conditions. These patterns are shaped by intersecting drivers including deforestation, wildlife trade, agricultural intensification, urban crowding, conflict, and rapid microbial evolution that enable spillover and sustained transmission. Although advances in genomic surveillance, metagenomic diagnostics, mRNA vaccines, monoclonal antibodies, and broad-spectrum antivirals have strengthened global response capacity, substantial gaps persist in equity, surveillance, and access to countermeasures. Strengthening One Health systems and resilient public health infrastructures is essential to anticipate and mitigate emerging infectious threats.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117277"},"PeriodicalIF":1.8,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146017815","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}
Pub Date : 2026-01-15DOI: 10.1016/j.diagmicrobio.2026.117275
Alana Mazzetti , Helena R.S. D’Espindula , Debora O. Kulek , Karen L. Jones , Leticia Kraft , Theo H.M. Smits , Fabio Rezzonico , Marcelo T. Mira , Marcelo Pillonetto
Background
Members of the genus Phytobacter, part of the Enterobacteriaceae, represent an emerging clinical threat. Standard identification methodologies often fail to accurately identify members of this genus because they are absent from current clinical databases. Molecular techniques are thus pivotal for differentiating Phytobacter from similar genera such as Pantoea, Kluyvera, and Kosakonia. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) provides a rapid, reliable, and cost-effective method for identification.
Methods
A Phytobacter-specific SuperSpectrum was constructed from 18 well-characterized isolates using standardized culture conditions, protein extraction, and triplicate MALDI-TOF MS acquisition. Only conserved, high-quality peaks were retained in the final model. Its performance was evaluated using 282 retrospective isolates and 23 prospective Phytobacter-suspect isolates. All Phytobacter identifications, along with 154 non-Phytobacter identifications, were benchmarked against API 20E biochemical testing, VITEK-2 automated identification, MALDI-TOF MS current database for in vitro diagnostic analysis, 16S rRNA gene sequencing, and whole-genome sequencing (WGS).
Results
Spectral clustering showed consistent separation of Phytobacter at the genus level. Integration of the new SuperSpectrum into the MALDI-TOF MS SARAMIS database enabled accurate identification, leading to the identification of two retrospective Phytobacter out of 282 Enterobacterales isolates. Finally, prospective testing of 23 contemporary isolates suspected to belong to Phytobacter confirmed their identification against the new reference spectra, achieving 100% concordance with WGS identification, demonstrating the reliability of the updated database for genus-level identification.
Conclusion
Phytobacter identification by MALDI-TOF MS provides a rapid alternative method for molecular identification of this emerging pathogen.
植物杆菌属的成员，肠杆菌科的一部分，代表了一个新兴的临床威胁。标准的鉴定方法往往不能准确地识别这一属的成员，因为他们不存在于目前的临床数据库。因此，分子技术是区分植物杆菌与类似属（如Pantoea， Kluyvera和Kosakonia）的关键。基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS）提供了一种快速、可靠、经济的鉴定方法。方法采用标准化培养条件、蛋白提取、三次MALDI-TOF MS采集等方法，对18株植物细菌进行超谱分析。最终模型中只保留了守恒的、高质量的峰。利用282株回顾性分离株和23株疑似植物杆菌的前瞻性分离株对其性能进行了评价。所有Phytobacter鉴定以及154个非Phytobacter鉴定均以API 20E生化测试、vittek -2自动鉴定、MALDI-TOF MS当前体外诊断分析数据库、16S rRNA基因测序和全基因组测序（WGS）为基准。结果光谱聚类显示植物杆菌在属水平上的分离一致。将新的SuperSpectrum整合到MALDI-TOF MS SARAMIS数据库中可以实现准确的鉴定，从而在282株肠杆菌中鉴定出2株回顾性植物杆菌。最后，对23株疑似属于Phytobacter的当代分离物进行前瞻性测试，证实了它们与新的参考光谱的鉴定，与WGS鉴定的一致性达到100%，证明了更新后的数据库用于属水平鉴定的可靠性。结论利用MALDI-TOF质谱法对植物病原菌进行鉴定是一种快速的分子鉴定方法。
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Pub Date : 2026-01-15DOI: 10.1016/j.diagmicrobio.2026.117273
Majie C. Foster, Kailee Cummings, Mohammad Y. Khan, Janine Bodnar, Christine Jacobsen, Kara Miller, Nicola Faraci, Shannon Morris, Catharine Prussing, Elizabeth Nazarian, Kimberlee A. Musser
Carbapenemase-producing organisms, including carbapenem-resistant Enterobacterales, Acinetobacter and Pseudomonas species, contribute to over 49,000 infections and >4,000 deaths annually in the United States. The Centers for Disease Control and Prevention recommends surveillance using dual swab testing.
While a culture-first approach is routinely utilized for carbapenemase-producing organism screening, results require 3 workdays or more. In contrast, Wadsworth Center employs a molecular-first algorithm, combining the Cepheid Xpert Carba-R assay with laboratory developed test multiplex PCR. Using shared reagents for efficiency and specimen preservation, this method detects the most prevalent carbapenemase genes, blaKPC, blaNDM, blaVIM, blaOXA-48-like, and blaIMP, as well as Acinetobacter baumannii-associated genes, blaOXA-23-like, blaOXA-24/40-like, and blaOXA-58-like, and produces actionable results in less than one workday. Wadsworth Center’s rapid carbapenemase-producing organism colonization screening algorithm supports prompt healthcare protocol initiation and epidemiological response.
{"title":"Achieving 24-hour reporting turnaround for clinical surveillance detection of eight carbapenemase genes using combined multiplex molecular assays","authors":"Majie C. Foster, Kailee Cummings, Mohammad Y. Khan, Janine Bodnar, Christine Jacobsen, Kara Miller, Nicola Faraci, Shannon Morris, Catharine Prussing, Elizabeth Nazarian, Kimberlee A. Musser","doi":"10.1016/j.diagmicrobio.2026.117273","DOIUrl":"10.1016/j.diagmicrobio.2026.117273","url":null,"abstract":"<div><div>Carbapenemase-producing organisms, including carbapenem-resistant Enterobacterales, <em>Acinetobacter</em> and <em>Pseudomonas</em> species, contribute to over 49,000 infections and >4,000 deaths annually in the United States. The Centers for Disease Control and Prevention recommends surveillance using dual swab testing.</div><div>While a culture-first approach is routinely utilized for carbapenemase-producing organism screening, results require 3 workdays or more. In contrast, Wadsworth Center employs a molecular-first algorithm, combining the Cepheid Xpert Carba-R assay with laboratory developed test multiplex PCR. Using shared reagents for efficiency and specimen preservation, this method detects the most prevalent carbapenemase genes, <em>bla</em><sub>KPC</sub>, <em>bla</em><sub>NDM</sub>, <em>bla</em><sub>VIM</sub>, <em>bla</em><sub>OXA-48-like</sub>, and <em>bla</em><sub>IMP</sub>, as well as <em>Acinetobacter baumannii</em>-associated genes, <em>bla</em><sub>OXA-23-like</sub>, <em>bla</em><sub>OXA-24/40-like</sub>, and <em>bla</em><sub>OXA-58-like</sub>, and produces actionable results in less than one workday. Wadsworth Center’s rapid carbapenemase-producing organism colonization screening algorithm supports prompt healthcare protocol initiation and epidemiological response.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117273"},"PeriodicalIF":1.8,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145974570","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}
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