Pub Date : 2026-01-02DOI: 10.1016/j.diagmicrobio.2025.117250
Hengfang Shi , Haiyong Wang , Huiling Cao , Junyao Sha , Xiaofei Zhu
Objective
To investigate the feasibility of utilizing neural network algorithm to analyze parameters from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of methicillin-resistant Staphylococcus aureus (MRSA).
Methods
Strain identification was performed using MALDI-TOF MS, and antimicrobial susceptibility testing was conducted with the VITEK 2 Compact AST-GP639 card. Mass spectrometry parameters were collected from 41 Staphylococcus aureus strains isolated from different patients and anatomical sites, including 20 MRSA and 21 methicillin-susceptible Staphylococcus aureus (MSSA) isolates. Twenty characteristic mass spectral features were screened using LASSO regression analysis. A neural network model was established using these 20 mass spectrometry parameters to rapidly discriminate MRSA.
Results
LASSO identified 20 discriminatory m/z features, with individual AUCs ranging from 0.825 to 0.982. The ANN model, evaluated by leave-one-out cross-validation, achieved an overall accuracy of 97.56%, with 95% sensitivity and 100% specificity. Compared to single characteristic mass spectral features, the discrimination efficiency of the ANN model was significantly improved, while demonstrating high consistency with classical methods. In addition, SHapley Additive explanations analysis revealed that characteristic features e.g. m/z 147.7004 and 39,767.2735 played major roles in model predictions.
Conclusion
The neural network model based on MALDI-TOF MS parameters enables accurate discrimination between MRSA and MSSA. This approach offers rapid identification and cost-effectiveness, providing a novel strategy for clinical differentiation of MRSA and MSSA.
{"title":"Neural network-enabled MALDI-TOF MS for rapid clinical identification of methicillin-resistant Staphylococcus aureus","authors":"Hengfang Shi , Haiyong Wang , Huiling Cao , Junyao Sha , Xiaofei Zhu","doi":"10.1016/j.diagmicrobio.2025.117250","DOIUrl":"10.1016/j.diagmicrobio.2025.117250","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the feasibility of utilizing neural network algorithm to analyze parameters from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of methicillin-resistant <em>Staphylococcus aureus</em> (MRSA).</div></div><div><h3>Methods</h3><div>Strain identification was performed using MALDI-TOF MS, and antimicrobial susceptibility testing was conducted with the VITEK 2 Compact AST-GP639 card. Mass spectrometry parameters were collected from 41 <em>Staphylococcus aureus</em> strains isolated from different patients and anatomical sites, including 20 MRSA and 21 methicillin-susceptible <em>Staphylococcus aureus</em> (MSSA) isolates. Twenty characteristic mass spectral features were screened using LASSO regression analysis. A neural network model was established using these 20 mass spectrometry parameters to rapidly discriminate MRSA.</div></div><div><h3>Results</h3><div>LASSO identified 20 discriminatory m/z features, with individual AUCs ranging from 0.825 to 0.982. The ANN model, evaluated by leave-one-out cross-validation, achieved an overall accuracy of 97.56%, with 95% sensitivity and 100% specificity. Compared to single characteristic mass spectral features, the discrimination efficiency of the ANN model was significantly improved, while demonstrating high consistency with classical methods. In addition, SHapley Additive explanations analysis revealed that characteristic features e.g. m/z 147.7004 and 39,767.2735 played major roles in model predictions.</div></div><div><h3>Conclusion</h3><div>The neural network model based on MALDI-TOF MS parameters enables accurate discrimination between MRSA and MSSA. This approach offers rapid identification and cost-effectiveness, providing a novel strategy for clinical differentiation of MRSA and MSSA.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117250"},"PeriodicalIF":1.8,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145898006","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 : 2025-12-30DOI: 10.1016/j.diagmicrobio.2025.117248
Maria Celidonio Gutfreund , Gustavo Yano Callado , Isabele Pardo , Mariana Kim Hsieh , Patrícia Deffune Celeghini , Gabriel O.V. Lopes , Pedro S. Marra , Yan Runa Cheng , Takaaki Kobayashi , João Renato Rebello Pinho , José Roberto Generoso Jr , Lucas Bulgarelli , Eneida A Mendonça , Rodrigo Octávio Deliberato , Deyvid Emanuel Amgarten , Fernanda de Mello Malta , Michael B Edmond , Alexandre R. Marra
Background
Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.
Methods
This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.
Results
Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82–0.86) and 0.71 (95% CI: 0.66–0.75), respectively, compared with 0.40 (95% CI: 0.37–0.43) and 0.82 (95% CI: 0.78–0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.
Conclusions
mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.
{"title":"Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis","authors":"Maria Celidonio Gutfreund , Gustavo Yano Callado , Isabele Pardo , Mariana Kim Hsieh , Patrícia Deffune Celeghini , Gabriel O.V. Lopes , Pedro S. Marra , Yan Runa Cheng , Takaaki Kobayashi , João Renato Rebello Pinho , José Roberto Generoso Jr , Lucas Bulgarelli , Eneida A Mendonça , Rodrigo Octávio Deliberato , Deyvid Emanuel Amgarten , Fernanda de Mello Malta , Michael B Edmond , Alexandre R. Marra","doi":"10.1016/j.diagmicrobio.2025.117248","DOIUrl":"10.1016/j.diagmicrobio.2025.117248","url":null,"abstract":"<div><h3>Background</h3><div>Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.</div></div><div><h3>Methods</h3><div>This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.</div></div><div><h3>Results</h3><div>Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82–0.86) and 0.71 (95% CI: 0.66–0.75), respectively, compared with 0.40 (95% CI: 0.37–0.43) and 0.82 (95% CI: 0.78–0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.</div></div><div><h3>Conclusions</h3><div>mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 4","pages":"Article 117248"},"PeriodicalIF":1.8,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145898005","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}
The etiological role of human papillomavirus (HPV) in prostate carcinogenesis remains controversial, despite its well-established causal association with cervical and oropharyngeal cancers. Exosomes, recognized as key mediators of intercellular communication, are increasingly implicated in viral dissemination and tumor progression, and have been proposed as minimally invasive diagnostic tools.
In this study, we investigated the prevalence of HPV DNA in prostate tissue, plasma-derived exosomes, and urine-derived exosomes, and examined its correlation with clinicopathological parameters in patients with histologically confirmed prostate cancer. Fifty patients were prospectively included. HPV DNA was detected in 32% of prostate tissue samples, 24% of plasma-derived exosomes, and 28% of urine-derived exosomes. Statistically significant associations were observed between HPV positivity and higher Gleason scores (p = 0.017), advanced T stage (p = 0.003), and alcohol consumption (p = 0.035). In contrast, only 2% of control samples were HPV DNA positive.
Notably, detection of HPV DNA in exosomal fractions mirrored tissue-based positivity, highlighting the potential of exosome-based liquid biopsies as noninvasive diagnostic approaches. While our findings support a possible association between HPV and prostate cancer, causality remains unresolved. Nevertheless, the study underscores the promise of exosome-based detection methods for future applications in noninvasive diagnosis, disease monitoring, and development of targeted therapeutic strategies—approaches that are already clinically relevant in HPV-driven cancers such as cervical cancer.
{"title":"Comparative analysis of human papillomavirus detection in tissue and urinary/plasmatic exosomes in prostatic adenocarcinoma: Links with clinicopathological parameters","authors":"Khaoula Elghazali , Zineb Sakhi , Youssef Ennaji , Abdelilah Laraqui , Anouar Elghazzaly , Abdessamad Amine , Moulay Mustapha Ennaji","doi":"10.1016/j.diagmicrobio.2025.117249","DOIUrl":"10.1016/j.diagmicrobio.2025.117249","url":null,"abstract":"<div><div>The etiological role of human papillomavirus (HPV) in prostate carcinogenesis remains controversial, despite its well-established causal association with cervical and oropharyngeal cancers. Exosomes, recognized as key mediators of intercellular communication, are increasingly implicated in viral dissemination and tumor progression, and have been proposed as minimally invasive diagnostic tools.</div><div>In this study, we investigated the prevalence of HPV DNA in prostate tissue, plasma-derived exosomes, and urine-derived exosomes, and examined its correlation with clinicopathological parameters in patients with histologically confirmed prostate cancer. Fifty patients were prospectively included. HPV DNA was detected in 32% of prostate tissue samples, 24% of plasma-derived exosomes, and 28% of urine-derived exosomes. Statistically significant associations were observed between HPV positivity and higher Gleason scores (<em>p</em> = 0.017), advanced T stage (<em>p</em> = 0.003), and alcohol consumption (<em>p</em> = 0.035). In contrast, only 2% of control samples were HPV DNA positive.</div><div>Notably, detection of HPV DNA in exosomal fractions mirrored tissue-based positivity, highlighting the potential of exosome-based liquid biopsies as noninvasive diagnostic approaches. While our findings support a possible association between HPV and prostate cancer, causality remains unresolved. Nevertheless, the study underscores the promise of exosome-based detection methods for future applications in noninvasive diagnosis, disease monitoring, and development of targeted therapeutic strategies—approaches that are already clinically relevant in HPV-driven cancers such as cervical cancer.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117249"},"PeriodicalIF":1.8,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880406","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 : 2025-12-29DOI: 10.1016/j.diagmicrobio.2025.117244
Yuanzhu Liu , Haokun Mei , Chang Gao , Yingqi Yang
Aims
Respiratory syncytial virus (RSV) is the most significant pathogen causing acute lower respiratory tract infections in children. Early detection of RSV can help control disease progression and reduce complications. However, RT-qPCR-based detection methods cannot provide accurate results within one hour and are not suitable for use in resource-limited settings. Therefore, there is a pressing need to develop a rapid and precise bedside RSV detection assay to meet clinical demands.
Methods and results
Firstly, we developed a RT-LAMP-assisted CRISPR/Cas12b method for detecting RSV M gene, capable of identifying target RNA with a limit of detection as low as 100 copies/μL within 40 min. Secondly, we created and tested a sampling lysis reagent, demonstrating its effectiveness in enabling direct detection without the need for nucleic acid extraction, thus improving bedside detection efficiency. Lastly, to facilitate use in resource-limited areas, we designed and developed a gravity-driven microfluidic chip that simplifies the stepwise process of RT-LAMP amplification and CRISPR/Cas12b detection. This chip allows for visual recognition of results without the need for an external power source when used in point-of-care (POC) settings. This assay showed 99% agreement with RT-qPCR, highlighting its potential for practical application. Additionally, no cross-reactivity was observed with other respiratory pathogens infection, demonstrating good clinical specificity.
Conclusions
In summary, the platform we developed is faster and more user-friendly than RT-qPCR, while achieving comparable sensitivity.
Impact statement
Our finding fills the gap in the inability to detect RSV in POC setting, safeguarding the health of children, and offers new insights for the innovation of CRISPR diagnostics.
{"title":"Rapid detection of respiratory syncytial virus using RT-LAMP-CRISPR/Cas12b on a gravity-driven microfluidic chip","authors":"Yuanzhu Liu , Haokun Mei , Chang Gao , Yingqi Yang","doi":"10.1016/j.diagmicrobio.2025.117244","DOIUrl":"10.1016/j.diagmicrobio.2025.117244","url":null,"abstract":"<div><h3>Aims</h3><div>Respiratory syncytial virus (RSV) is the most significant pathogen causing acute lower respiratory tract infections in children. Early detection of RSV can help control disease progression and reduce complications. However, RT-qPCR-based detection methods cannot provide accurate results within one hour and are not suitable for use in resource-limited settings. Therefore, there is a pressing need to develop a rapid and precise bedside RSV detection assay to meet clinical demands.</div></div><div><h3>Methods and results</h3><div>Firstly, we developed a RT-LAMP-assisted CRISPR/Cas12b method for detecting RSV M gene, capable of identifying target RNA with a limit of detection as low as 100 copies/μL within 40 min. Secondly, we created and tested a sampling lysis reagent, demonstrating its effectiveness in enabling direct detection without the need for nucleic acid extraction, thus improving bedside detection efficiency. Lastly, to facilitate use in resource-limited areas, we designed and developed a gravity-driven microfluidic chip that simplifies the stepwise process of RT-LAMP amplification and CRISPR/Cas12b detection. This chip allows for visual recognition of results without the need for an external power source when used in point-of-care (POC) settings. This assay showed 99% agreement with RT-qPCR, highlighting its potential for practical application. Additionally, no cross-reactivity was observed with other respiratory pathogens infection, demonstrating good clinical specificity.</div></div><div><h3>Conclusions</h3><div>In summary, the platform we developed is faster and more user-friendly than RT-qPCR, while achieving comparable sensitivity.</div></div><div><h3>Impact statement</h3><div>Our finding fills the gap in the inability to detect RSV in POC setting, safeguarding the health of children, and offers new insights for the innovation of CRISPR diagnostics.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117244"},"PeriodicalIF":1.8,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880495","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 : 2025-12-26DOI: 10.1016/j.diagmicrobio.2025.117245
Yan Zhang , Dian Yuan , Hua-Li Wang , Chao-Qiong Zhou , Yan-Qun Liu , Ye-Hong Xie , Li-Rui Kong
Tuberculosis (TB) remains a major global public health challenge, and its control efforts are increasingly complicated by the rising prevalence of drug-resistant TB (DR-TB). Rifampicin (RIF), a cornerstone of first-line anti-TB treatment regimens, plays a pivotal role in TB therapy. The emergence of rifampicin resistance (RR) necessitates significant adjustments in treatment strategies. Therefore, determining Mycobacterium tuberculosis (MTB) resistance to RIF is crucial for optimizing clinical decision-making and improving patient outcomes. This article systematically analyzes current epidemiological trends in rifampicin-resistant TB (RR-TB), explores its molecular mechanisms of resistance in depth, and comprehensively reviews the clinical utility of existing drug-susceptibility testing methods. The aim is to provide a reference for the accurate diagnosis, treatment, and control of RR-TB.
{"title":"A review of rifampicin resistance in mycobacterium tuberculosis: from molecular mechanism to laboratory diagnosis","authors":"Yan Zhang , Dian Yuan , Hua-Li Wang , Chao-Qiong Zhou , Yan-Qun Liu , Ye-Hong Xie , Li-Rui Kong","doi":"10.1016/j.diagmicrobio.2025.117245","DOIUrl":"10.1016/j.diagmicrobio.2025.117245","url":null,"abstract":"<div><div>Tuberculosis (TB) remains a major global public health challenge, and its control efforts are increasingly complicated by the rising prevalence of drug-resistant TB (DR-TB). Rifampicin (RIF), a cornerstone of first-line anti-TB treatment regimens, plays a pivotal role in TB therapy. The emergence of rifampicin resistance (RR) necessitates significant adjustments in treatment strategies. Therefore, determining Mycobacterium tuberculosis (MTB) resistance to RIF is crucial for optimizing clinical decision-making and improving patient outcomes. This article systematically analyzes current epidemiological trends in rifampicin-resistant TB (RR-TB), explores its molecular mechanisms of resistance in depth, and comprehensively reviews the clinical utility of existing drug-susceptibility testing methods. The aim is to provide a reference for the accurate diagnosis, treatment, and control of RR-TB.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117245"},"PeriodicalIF":1.8,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877430","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}
Human Papillomavirus (HPV) 16 and HPV18 strains cause approximately 70% of all cervical cancer cases. Understanding the predominant strains is critical for HPV vaccination programmes. We identified the HPV strains prevalent among women in Southern Nigeria to generate evidence to guide the national HPV vaccination programme.
Methods
HPV genotypes were identified in three geopolitical zones of Nigeria among asymptomatic women using two molecular methods. The BGI workflow was a PCR-NGS method utilising samples collected with cards. The Sansure workflow involves two real-time PCR assays: the first to identify OHR from HPV16/18, and the second to genotype the OHR. Both Sansure assays had different detection limits of 1000 DNA copies/mL and 400 DNA copies/mL, respectively. We further collected self-reported data on HPV vaccination.
Results
985 women were recruited and tested. Twelve and fourteen women had HPV genotypes 16 and 18, respectively, while 188 had other high-risk genotypes. Women had infections with one (69.8%), two (18.1%) or multiple (10.9%) HPV strains, while a few were unresolved (1.3%). The detection frequencies for the OHR strains (n) were HPV45 (29), HPV35(28), HPV51(22), HPV66(20), HPV58(19), HPV52(18), HPV59(18), HPV68(17), HPV31(15), HPV56(15), HPV39(11), HPV53(11) and HPV33(4). HPV 16/18 strains were detected more frequently in the unvaccinated group, although the difference was not statistically significant.
Conclusion
HPV infection among women in southern Nigeria shows other high-risk HPV predominant, often as a co-infection with multiple strains. Further studies are needed to evaluate their oncogenic association, guide the national vaccination and implement a risk-based screening programme to focus treatment resources on the highest-risk patients.
{"title":"Epidemiology of human papillomavirus strains in Southern Nigeria: A cross-sectional analysis","authors":"Chika Kingsley Onwuamah , Grace Deborah Vincent , Abidemi Esther Amoo , Jane Okwuzu , Mary Adesina , Chinenye Angela Ogbu , Temiloluwa Ore , Mabel Uwandu , Rahaman Ademolu Ahmed , Bowofoluwa Sharon Abimbola , Ifeoma Idigbe , Nkem Okonkwo , Judith Sokei , Chika Leona Okoli , Priscilla Ngozi Ezemelue , Olaoniye Habeebat Ajigbewu , Joseph Ojonugwa Shaibu , Kofoworola Abifarin , Gregory Aigbe Ohihoin , Emily Nzeribe , Oliver Chukwujekwu Ezechi","doi":"10.1016/j.diagmicrobio.2025.117240","DOIUrl":"10.1016/j.diagmicrobio.2025.117240","url":null,"abstract":"<div><h3>Background</h3><div>Human Papillomavirus (HPV) 16 and HPV18 strains cause approximately 70% of all cervical cancer cases. Understanding the predominant strains is critical for HPV vaccination programmes. We identified the HPV strains prevalent among women in Southern Nigeria to generate evidence to guide the national HPV vaccination programme.</div></div><div><h3>Methods</h3><div>HPV genotypes were identified in three geopolitical zones of Nigeria among asymptomatic women using two molecular methods. The BGI workflow was a PCR-NGS method utilising samples collected with cards. The Sansure workflow involves two real-time PCR assays: the first to identify OHR from HPV16/18, and the second to genotype the OHR. Both Sansure assays had different detection limits of 1000 DNA copies/mL and 400 DNA copies/mL, respectively. We further collected self-reported data on HPV vaccination.</div></div><div><h3>Results</h3><div>985 women were recruited and tested. Twelve and fourteen women had HPV genotypes 16 and 18, respectively, while 188 had other high-risk genotypes. Women had infections with one (69.8%), two (18.1%) or multiple (10.9%) HPV strains, while a few were unresolved (1.3%). The detection frequencies for the OHR strains (n) were HPV45 (29), HPV35(28), HPV51(22), HPV66(20), HPV58(19), HPV52(18), HPV59(18), HPV68(17), HPV31(15), HPV56(15), HPV39(11), HPV53(11) and HPV33(4). HPV 16/18 strains were detected more frequently in the unvaccinated group, although the difference was not statistically significant.</div></div><div><h3>Conclusion</h3><div>HPV infection among women in southern Nigeria shows other high-risk HPV predominant, often as a co-infection with multiple strains. Further studies are needed to evaluate their oncogenic association, guide the national vaccination and implement a risk-based screening programme to focus treatment resources on the highest-risk patients.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117240"},"PeriodicalIF":1.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877524","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 : 2025-12-24DOI: 10.1016/j.diagmicrobio.2025.117243
Sonali Padhy , Malay Prithwiraj Sahoo , Arpita Nibedita Rout , Diptanu Paul , Madhucchanda Das , Vinaykumar Hallur
Nannizzia gypsea (formerly Microsporum gypseum) is a geophilic dermatophyte that rarely causes human infection. We report an 8-year-old boy presenting with a tender, edematous scalp lesion with pustules and alopecia for six weeks. Initially misdiagnosed as a bacterial furuncle, mycological examination of plucked hairs revealed hyaline septate hyphae, and culture on Sabouraud’s agar showed powdery buff colonies with brown reverse pigmentation. Lactophenol cotton blue mount demonstrated fusiform, thin-walled macroconidia with 4–6 septa. Molecular identification (ITS sequencing) confirmed Nannizzia gypsea with 100% homology. The patient was treated with oral terbinafine for four weeks, resulting in complete resolution without recurrence. This case is notable for the absence of soil or pet exposure, highlighting the diagnostic challenges of kerion due to geophilic species. Early mycological confirmation enables targeted therapy, prevents mismanagement, and supports antifungal stewardship.
{"title":"Beyond soil and pets: Nannizzia gypsea causing kerion in a child","authors":"Sonali Padhy , Malay Prithwiraj Sahoo , Arpita Nibedita Rout , Diptanu Paul , Madhucchanda Das , Vinaykumar Hallur","doi":"10.1016/j.diagmicrobio.2025.117243","DOIUrl":"10.1016/j.diagmicrobio.2025.117243","url":null,"abstract":"<div><div><em>Nannizzia gypsea</em> (formerly <em>Microsporum gypseum</em>) is a geophilic dermatophyte that rarely causes human infection. We report an 8-year-old boy presenting with a tender, edematous scalp lesion with pustules and alopecia for six weeks. Initially misdiagnosed as a bacterial furuncle, mycological examination of plucked hairs revealed hyaline septate hyphae, and culture on Sabouraud’s agar showed powdery buff colonies with brown reverse pigmentation. Lactophenol cotton blue mount demonstrated fusiform, thin-walled macroconidia with 4–6 septa. Molecular identification (ITS sequencing) confirmed <em>Nannizzia gypsea</em> with 100% homology. The patient was treated with oral terbinafine for four weeks, resulting in complete resolution without recurrence. This case is notable for the absence of soil or pet exposure, highlighting the diagnostic challenges of kerion due to geophilic species. Early mycological confirmation enables targeted therapy, prevents mismanagement, and supports antifungal stewardship.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117243"},"PeriodicalIF":1.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880492","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 : 2025-12-24DOI: 10.1016/j.diagmicrobio.2025.117242
Yueshan Liang , Liangcai Xu , Song Liu , Zheng Liang , Biyu Lin , Jiaqi Ye , Shuping Nie
Background
Neisseria meningitidis serogroup Y (NmY), first reported in China in 2015, remains rare, with only a few cases reported to date. Previously documented NmY invasive meningococcal disease (IMD) cases in China predominantly occurred among adolescents or children. This study reports the first confirmed adult IMD case caused by NmY in China.
Methods
A 22-year-old male in Guangdong Province presented with IMD symptoms. The causative agent (NmY20231109) was isolated from blood culture. Antimicrobial susceptibility testing was performed. Whole-genome sequencing (WGS) was conducted for molecular characterization and phylogenetic analysis against global NmY strains.
Results
The isolate (NmY20231109) was susceptible to most tested antibiotics but resistant to sulfamethoxazole/trimethoprim. WGS identified the strain as Y: P1.5-1,10-1: F4-1: ST-1655 (CC23). Phylogenetic analysis revealed that NmY20231109 clustered closely with ST-1655 strains from the UK and Germany. It showed genetic distance from the four ST-1655 strains previously reported in China. Virulence gene profiling identified 52 associated genes, including key factors such as fHbp and porB.
Conclusion
This report describes the first adult IMD case caused by NmY in China. The identification of NmY20231109 as ST-1655 (CC23), closely related to European strains, suggests a potential imported origin and highlights the ongoing risk of NmY transmission in China.
{"title":"Clinical and molecular characterization of a fulminant meningococcemia case in an adult caused by Neisseria meningitidis serogroup Y clonal complex 23 strain in China","authors":"Yueshan Liang , Liangcai Xu , Song Liu , Zheng Liang , Biyu Lin , Jiaqi Ye , Shuping Nie","doi":"10.1016/j.diagmicrobio.2025.117242","DOIUrl":"10.1016/j.diagmicrobio.2025.117242","url":null,"abstract":"<div><h3>Background</h3><div><em>Neisseria meningitidis serogroup Y</em> (NmY), first reported in China in 2015, remains rare, with only a few cases reported to date. Previously documented NmY invasive meningococcal disease (IMD) cases in China predominantly occurred among adolescents or children. This study reports the first confirmed adult IMD case caused by NmY in China.</div></div><div><h3>Methods</h3><div>A 22-year-old male in Guangdong Province presented with IMD symptoms. The causative agent (NmY20231109) was isolated from blood culture. Antimicrobial susceptibility testing was performed. Whole-genome sequencing (WGS) was conducted for molecular characterization and phylogenetic analysis against global NmY strains.</div></div><div><h3>Results</h3><div>The isolate (NmY20231109) was susceptible to most tested antibiotics but resistant to sulfamethoxazole/trimethoprim. WGS identified the strain as Y: P1.5-1,10-1: F4-1: ST-1655 (CC23). Phylogenetic analysis revealed that NmY20231109 clustered closely with ST-1655 strains from the UK and Germany. It showed genetic distance from the four ST-1655 strains previously reported in China. Virulence gene profiling identified 52 associated genes, including key factors such as fHbp and porB.</div></div><div><h3>Conclusion</h3><div>This report describes the first adult IMD case caused by NmY in China. The identification of NmY20231109 as ST-1655 (CC23), closely related to European strains, suggests a potential imported origin and highlights the ongoing risk of NmY transmission in China.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117242"},"PeriodicalIF":1.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145880493","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 : 2025-12-24DOI: 10.1016/j.diagmicrobio.2025.117241
Wanxian Hong , Weihua Luo , Lijia Mao , Zihuan Lu , Wenbo Wang , Xinqiang Zhang , Yanhui Wu , Genquan Yin , Lihong Sun
Nucleic acid extraction represents a critical preanalytical step in clinical molecular diagnostics. This study evaluated a novel viral nucleic acid extraction kit (HeSheng) against three commercial kits (Qiagen QIAamp, Daan, and Yocon) using 170 clinical samples across five specimen types. Performance was assessed through plaque-based serial dilution combined with RT-qPCR to determine the limit of detection (LOD), alongside measurements of nucleic acid concentration, OD260/280 ratio, and Ct values. While all kits demonstrated equivalent LODs (10 PFU/mL), the HeSheng kit consistently yielded lower Ct values, indicating enhanced sensitivity. It also produced nucleic acids with superior concentration, purity, and amplification efficiency. Clinical sample RT-qPCR results showed high concordance with diagnoses (sensitivity 98.6%; specificity 97.4%). The protocol combines viral lysis with rapid column-based adsorption and completes extraction within 10 minutes using standard equipment. These findings demonstrate that the HeSheng kit provides a simplified, cost-effective, and broadly applicable method suitable for molecular diagnostics in resource-limited or high-throughput settings.
{"title":"Evaluation of a novel viral nucleic acid extraction kit from a variety of clinical specimens","authors":"Wanxian Hong , Weihua Luo , Lijia Mao , Zihuan Lu , Wenbo Wang , Xinqiang Zhang , Yanhui Wu , Genquan Yin , Lihong Sun","doi":"10.1016/j.diagmicrobio.2025.117241","DOIUrl":"10.1016/j.diagmicrobio.2025.117241","url":null,"abstract":"<div><div>Nucleic acid extraction represents a critical preanalytical step in clinical molecular diagnostics. This study evaluated a novel viral nucleic acid extraction kit (HeSheng) against three commercial kits (Qiagen QIAamp, Daan, and Yocon) using 170 clinical samples across five specimen types. Performance was assessed through plaque-based serial dilution combined with RT-qPCR to determine the limit of detection (LOD), alongside measurements of nucleic acid concentration, OD260/280 ratio, and Ct values. While all kits demonstrated equivalent LODs (10 PFU/mL), the HeSheng kit consistently yielded lower Ct values, indicating enhanced sensitivity. It also produced nucleic acids with superior concentration, purity, and amplification efficiency. Clinical sample RT-qPCR results showed high concordance with diagnoses (sensitivity 98.6%; specificity 97.4%). The protocol combines viral lysis with rapid column-based adsorption and completes extraction within 10 minutes using standard equipment. These findings demonstrate that the HeSheng kit provides a simplified, cost-effective, and broadly applicable method suitable for molecular diagnostics in resource-limited or high-throughput settings.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117241"},"PeriodicalIF":1.8,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145854675","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 : 2025-12-22DOI: 10.1016/j.diagmicrobio.2025.117238
Blanca Lopez-Villalba , Fernando Tortosa , Javier Castrodeza-Sanz , Camino Prada , Omar Sued
Background
Respiratory virus infections are a major cause of morbidity and mortality globally, particularly among people living with HIV.
Objectives
To evaluate the impact of respiratory virus infections on clinical outcomes in HIV-positive individuals compared with HIV-negative individuals.
Study design
We conducted a systematic review and meta-analysis of 19 studies comparing HIV-positive and HIV-negative individuals infected with common respiratory viruses (excluding SARS-CoV-2).
Results
HIV-positive individuals had significantly higher odds of in-hospital mortality, prolonged hospitalization, and antibiotic use at admission. No significant differences were observed in intensive care unit admission, initial hospitalization, mechanical ventilation, or oxygen therapy. The most severe outcomes were associated with adenovirus, respiratory syncytial virus, and influenza. The certainty of evidence was moderate but limited by study heterogeneity and risk of bias.
Conclusions
These findings underscore the need for improved diagnostic tools, infection control strategies, and tailored clinical management for HIV-positive populations. Further prospective, multicenter studies are essential to inform evidence-based guidelines in both high- and low-resource settings.
{"title":"Systematic review and meta-analysis of respiratory virus infections in HIV-positive and HIV-negative patients","authors":"Blanca Lopez-Villalba , Fernando Tortosa , Javier Castrodeza-Sanz , Camino Prada , Omar Sued","doi":"10.1016/j.diagmicrobio.2025.117238","DOIUrl":"10.1016/j.diagmicrobio.2025.117238","url":null,"abstract":"<div><h3>Background</h3><div>Respiratory virus infections are a major cause of morbidity and mortality globally, particularly among people living with HIV.</div></div><div><h3>Objectives</h3><div>To evaluate the impact of respiratory virus infections on clinical outcomes in HIV-positive individuals compared with HIV-negative individuals.</div></div><div><h3>Study design</h3><div>We conducted a systematic review and meta-analysis of 19 studies comparing HIV-positive and HIV-negative individuals infected with common respiratory viruses (excluding SARS-CoV-2).</div></div><div><h3>Results</h3><div>HIV-positive individuals had significantly higher odds of in-hospital mortality, prolonged hospitalization, and antibiotic use at admission. No significant differences were observed in intensive care unit admission, initial hospitalization, mechanical ventilation, or oxygen therapy. The most severe outcomes were associated with adenovirus, respiratory syncytial virus, and influenza. The certainty of evidence was moderate but limited by study heterogeneity and risk of bias.</div></div><div><h3>Conclusions</h3><div>These findings underscore the need for improved diagnostic tools, infection control strategies, and tailored clinical management for HIV-positive populations. Further prospective, multicenter studies are essential to inform evidence-based guidelines in both high- and low-resource settings.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"114 3","pages":"Article 117238"},"PeriodicalIF":1.8,"publicationDate":"2025-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145849007","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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