{"title":"Detection of pulmonary tuberculosis and drug resistance in sputum samples using targeted next-generation sequencing","authors":"Chang Song , Chun-Yan Zhao , Hang-Biao Qiang , Xue-Wen Huang, Ai-Chun Huang, Chun-Mei Zeng, Chun-Ming Gong, Qiu-Qing Tan, Zhen-Tao Huang, Xiao-Shi Lin, Qing-Dong Zhu, Zhou-Hua Xie","doi":"10.1016/j.jinf.2025.106621","DOIUrl":"10.1016/j.jinf.2025.106621","url":null,"abstract":"","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106621"},"PeriodicalIF":11.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-18DOI: 10.1016/j.jinf.2025.106615
Hermaleigh Townsley, Thomas E. Locke, Nicholas Laundy, Christopher Keil, Alexander J. Keeley, Jean Hamilton, Abdullah Pandor, Thomas C. Darton, Thushan I. de Silva
{"title":"A systematic review of asymptomatic colonisation with Group A Streptococcus in lower- and middle-income countries","authors":"Hermaleigh Townsley, Thomas E. Locke, Nicholas Laundy, Christopher Keil, Alexander J. Keeley, Jean Hamilton, Abdullah Pandor, Thomas C. Darton, Thushan I. de Silva","doi":"10.1016/j.jinf.2025.106615","DOIUrl":"10.1016/j.jinf.2025.106615","url":null,"abstract":"","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106615"},"PeriodicalIF":11.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-18DOI: 10.1016/j.jinf.2025.106617
Anubama Rajan , Divya Nagaraj , Carolyn Bomidi , Gina M. Aloisio , Ashley M. Murray , Emily M. Schultz , Amal Kambal , Mary K. Estes , Erin Nicholson , Vasanthi Avadhanula , Sarah E. Blutt , Pedro A. Piedra
Respiratory syncytial virus (RSV) is a leading cause of infant death across the globe. Age is a significant factor that contributes to the severity of infection in young children. RSV primarily infects the ciliated cells of the airway epithelium, induces mucus hypersecretion, and impaired mucociliary clearance. Better understanding of RSV infection at the cellular level is needed for the development of effective therapeutic interventions. To investigate the age difference and comprehensively understand gene signatures associated with RSV infection, we performed single-cell transcriptomic analysis of adult and pediatric human nose organoids (HNOs) infected with RSV. Our analysis revealed a significant difference in transcriptomic signature associated with cellular differentiation and proliferative pathways between the adult and pediatric HNOs. Moreover, we found a distinct innate immune response to RSV infection, with pediatric HNO revealing a lower and dysregulated response. Through sub-clustering analysis of the ciliated cell population, we identified the primary ciliary cell as a novel and prominent susceptible ciliary cell type to RSV infection. Intriguingly and unexpectedly, we found that in the pediatric more than in the adult, HNO RSV infects other novel airway cells, including basal cells, and ionocytes/tuft cells, as demonstrated by increased RSV-gene counts and induction of interferon-related pathways. Together, our study provides the first HNO cell atlas dissecting the heterogeneity of RSV infection in airway epithelium between adult versus pediatric HNOs and identifies novel cell types that are susceptible to RSV infection, which altogether provides a key resource for research on RSV pathogenesis, therapeutics and vaccines.
{"title":"Single cell sequencing analysis of respiratory syncytial virus–infected pediatric and adult human nose organoids reveals age differences, proliferative diversity and identifies novel cellular tropism","authors":"Anubama Rajan , Divya Nagaraj , Carolyn Bomidi , Gina M. Aloisio , Ashley M. Murray , Emily M. Schultz , Amal Kambal , Mary K. Estes , Erin Nicholson , Vasanthi Avadhanula , Sarah E. Blutt , Pedro A. Piedra","doi":"10.1016/j.jinf.2025.106617","DOIUrl":"10.1016/j.jinf.2025.106617","url":null,"abstract":"<div><div>Respiratory syncytial virus (RSV) is a leading cause of infant death across the globe. Age is a significant factor that contributes to the severity of infection in young children. RSV primarily infects the ciliated cells of the airway epithelium, induces mucus hypersecretion, and impaired mucociliary clearance. Better understanding of RSV infection at the cellular level is needed for the development of effective therapeutic interventions. To investigate the age difference and comprehensively understand gene signatures associated with RSV infection, we performed single-cell transcriptomic analysis of adult and pediatric human nose organoids (HNOs) infected with RSV. Our analysis revealed a significant difference in transcriptomic signature associated with cellular differentiation and proliferative pathways between the adult and pediatric HNOs. Moreover, we found a distinct innate immune response to RSV infection, with pediatric HNO revealing a lower and dysregulated response. Through sub-clustering analysis of the ciliated cell population, we identified the primary ciliary cell as a novel and prominent susceptible ciliary cell type to RSV infection. Intriguingly and unexpectedly, we found that in the pediatric more than in the adult, HNO RSV infects other novel airway cells, including basal cells, and ionocytes/tuft cells, as demonstrated by increased RSV-gene counts and induction of interferon-related pathways. Together, our study provides the first HNO cell atlas dissecting the heterogeneity of RSV infection in airway epithelium between adult versus pediatric HNOs and identifies novel cell types that are susceptible to RSV infection, which altogether provides a key resource for research on RSV pathogenesis, therapeutics and vaccines.</div></div>","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106617"},"PeriodicalIF":11.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-12DOI: 10.1016/j.jinf.2025.106613
Michael Mueller , Alice Blandino , Dominique Scherer , Inés Zulantay , Werner Apt , Nelson M. Varela , Marcelo Llancaqueo , Lineth Garcia , Lourdes Ortiz , Emanuele Nicastri , Maria Letizia Giancola , Andrea Angheben , Simona Gabrielli , Trine B. Rounge , Hilde Langseth , Melanie Waldenberger , Pamela Salinas-Alvarez , Justo Lorenzo Bermejo
Background
Chagas disease, caused by the parasite Trypanosoma cruzi (T. cruzi), affects around 6–7 million people in Latin America and hundreds of thousands in the United States and Europe. A main complication of chronic Chagas disease is cardiomyopathy, possibly manifesting as arrhythmias, heart failure, or sudden cardiac death. Understanding the link between T. cruzi infection and cardiomyopathy is essential for early diagnosis and adequate treatment.
Methods
We sequenced small RNAs in serum samples from 228 Chagas patients recruited in Chile, Bolivia and Italy. After bioinformatic processing of sequencing data to quantify serum miRNA expression, robust logistic regression was applied to identify miRNAs differentially expressed in Chagas patients with abnormalities in electrocardiography (ECG), bundle-branch block on ECG, and high Kuschnir scores. We also investigated the association between genotype-based miRNA expression and the risk of abnormal ECG findings.
Findings
As reported, the risk of abnormal ECG findings was higher in male patients and increased with age. Three miRNAs showed lower serum expression levels in patients with abnormal ECG: miRNA-101-3p, miRNA-576-3p and miRNA-629-5p (p < 0.0002), especially in patients with high Kuschnir scores. The expression of miRNA-629-5p was negatively correlated with the CCL5 expression (p = 3.7×10-8), a chemokine frequently reported in Chagas disease. Gene enrichment analyses indicated involvement of cytokine signalling in Chagas cardiomyopathy.
Interpretation
The findings demonstrate the potential of circulating miRNAs as diagnostic biomarkers for Chagas cardiomyopathy. The associations found with disease severity and immune response may help to improve our knowledge of complications’ development in Chagas disease.
{"title":"Small-RNA sequencing identifies serum microRNAs associated with abnormal electrocardiography findings in patients with Chagas disease","authors":"Michael Mueller , Alice Blandino , Dominique Scherer , Inés Zulantay , Werner Apt , Nelson M. Varela , Marcelo Llancaqueo , Lineth Garcia , Lourdes Ortiz , Emanuele Nicastri , Maria Letizia Giancola , Andrea Angheben , Simona Gabrielli , Trine B. Rounge , Hilde Langseth , Melanie Waldenberger , Pamela Salinas-Alvarez , Justo Lorenzo Bermejo","doi":"10.1016/j.jinf.2025.106613","DOIUrl":"10.1016/j.jinf.2025.106613","url":null,"abstract":"<div><h3>Background</h3><div>Chagas disease, caused by the parasite <em>Trypanosoma cruzi</em> (<em>T. cruzi</em>), affects around 6–7 million people in Latin America and hundreds of thousands in the United States and Europe. A main complication of chronic Chagas disease is cardiomyopathy, possibly manifesting as arrhythmias, heart failure, or sudden cardiac death. Understanding the link between <em>T. cruzi</em> infection and cardiomyopathy is essential for early diagnosis and adequate treatment.</div></div><div><h3>Methods</h3><div>We sequenced small RNAs in serum samples from 228 Chagas patients recruited in Chile, Bolivia and Italy. After bioinformatic processing of sequencing data to quantify serum miRNA expression, robust logistic regression was applied to identify miRNAs differentially expressed in Chagas patients with abnormalities in electrocardiography (ECG), bundle-branch block on ECG, and high Kuschnir scores. We also investigated the association between genotype-based miRNA expression and the risk of abnormal ECG findings.</div></div><div><h3>Findings</h3><div>As reported, the risk of abnormal ECG findings was higher in male patients and increased with age. Three miRNAs showed lower serum expression levels in patients with abnormal ECG: miRNA-101-3p, miRNA-576-3p and miRNA-629-5p (p < 0.0002), especially in patients with high Kuschnir scores. The expression of miRNA-629-5p was negatively correlated with the <em>CCL5</em> expression (p = 3.7×10<sup>-8</sup>), a chemokine frequently reported in Chagas disease. Gene enrichment analyses indicated involvement of cytokine signalling in Chagas cardiomyopathy.</div></div><div><h3>Interpretation</h3><div>The findings demonstrate the potential of circulating miRNAs as diagnostic biomarkers for Chagas cardiomyopathy. The associations found with disease severity and immune response may help to improve our knowledge of complications’ development in Chagas disease.</div></div>","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106613"},"PeriodicalIF":11.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
COVID-19 impacts physical and respiratory health, and the clinical presentation ranges from asymptomatic cases to severe infections requiring hospitalisation. While the long-term effects on lung function and physical capacity are well-documented in moderate to severe cases, the long-term outcome for individuals with mild COVID-19 remains poorly understood. This study investigates the long-term recovery of physical capacity and breathlessness among both hospitalised and non-hospitalised individuals.
Methods
This prospective cohort study enrolled individuals with confirmed SARS-CoV-2 infection between April 2020 and May 2021 through the CoVUm-study. Participants underwent assessments of lung function at 3–6 months after infection and attended follow-ups up to three years post-infection. Physical capacity was evaluated at follow-ups, using the one-minute sit-to-stand test and the modified Medical Research Council scale to assess breathlessness.
Results
The cohort included 291 participants, 35% of whom were hospitalised during SARS-CoV-2 infection. At the 3-year follow-up, 191 participants completed the physical capacity test and 179 had an assessment of breathlessness. Physical capacity improved significantly in the total cohort up to two years post-infection, where improvement plateaued. Hospitalisation and impaired diffusing capacity were significantly associated with reduced physical capacity (beta –6.4, p < 0.001; beta –8.9, p < 0.001, respectively) and breathlessness (beta 3.9, p < 0.001; beta 1.6, p = 0.012, respectively). While non-hospitalised participants demonstrated improvements in physical capacity for up to two years, improvement for hospitalised individuals plateaued by six months.
Conclusion
Hospitalisation and impaired diffusing capacity are strong independent predictors of reduced physical capacity and persistent breathlessness up to three years post-infection. Non-hospitalised individuals also experience long-term reductions in physical capacity, underscoring the need for targeted rehabilitation strategies.
目的：COVID-19影响身体和呼吸系统健康，临床表现从无症状病例到需要住院治疗的严重感染不等。虽然中度至重度病例对肺功能和体能的长期影响已有充分记录，但对轻度COVID-19患者的长期后果仍知之甚少。本研究调查住院和非住院个体的体能和呼吸困难的长期恢复情况。方法：本前瞻性队列研究通过covum研究招募了2020年4月至2021年5月期间确诊的SARS-CoV-2感染的个体。参与者在感染后3-6个月接受肺功能评估，并在感染后随访3年。在随访中评估身体能力，使用一分钟坐立测试和修改后的医学研究委员会量表来评估呼吸困难。结果：该队列包括291名参与者，其中35%在SARS-CoV-2感染期间住院。在3年的随访中，191名参与者完成了体能测试，179名参与者进行了呼吸困难评估。在整个队列中，身体能力在感染后两年内显著改善，改善趋于稳定。住院治疗和弥散能力受损与身体能力下降（β -6.4, p < 0.001; β -8.9, p < 0.001）和呼吸困难（β 3.9, p < 0.001; β 1.6, p = 0.012）显著相关。虽然未住院的参与者在长达两年的时间里表现出身体能力的改善，但住院个体的改善在六个月后停滞不前。结论：住院治疗和弥散能力受损是感染后3年内身体能力下降和持续呼吸困难的独立预测因素。未住院的个人也会经历身体能力的长期下降，这突出了有针对性的康复战略的必要性。
{"title":"Long-term physical capacity following COVID-19: A prospective, three-year study","authors":"Christoffer Granvik , Ida-Lisa Persson , Guilherme W.F. Barros , Clas Ahlm , Mattias N.E. Forsell , Staffan Tevell , Josefin Sundh , Anders Blomberg , Alicia Lind , Sara Cajander , Johan Normark","doi":"10.1016/j.jinf.2025.106614","DOIUrl":"10.1016/j.jinf.2025.106614","url":null,"abstract":"<div><h3>Objectives</h3><div>COVID-19 impacts physical and respiratory health, and the clinical presentation ranges from asymptomatic cases to severe infections requiring hospitalisation. While the long-term effects on lung function and physical capacity are well-documented in moderate to severe cases, the long-term outcome for individuals with mild COVID-19 remains poorly understood. This study investigates the long-term recovery of physical capacity and breathlessness among both hospitalised and non-hospitalised individuals.</div></div><div><h3>Methods</h3><div>This prospective cohort study enrolled individuals with confirmed SARS-CoV-2 infection between April 2020 and May 2021 through the CoVUm-study. Participants underwent assessments of lung function at 3–6 months after infection and attended follow-ups up to three years post-infection. Physical capacity was evaluated at follow-ups, using the one-minute sit-to-stand test and the modified Medical Research Council scale to assess breathlessness.</div></div><div><h3>Results</h3><div>The cohort included 291 participants, 35% of whom were hospitalised during SARS-CoV-2 infection. At the 3-year follow-up, 191 participants completed the physical capacity test and 179 had an assessment of breathlessness. Physical capacity improved significantly in the total cohort up to two years post-infection, where improvement plateaued. Hospitalisation and impaired diffusing capacity were significantly associated with reduced physical capacity (beta –6.4, p < 0.001; beta –8.9, p < 0.001, respectively) and breathlessness (beta 3.9, p < 0.001; beta 1.6, p = 0.012, respectively). While non-hospitalised participants demonstrated improvements in physical capacity for up to two years, improvement for hospitalised individuals plateaued by six months.</div></div><div><h3>Conclusion</h3><div>Hospitalisation and impaired diffusing capacity are strong independent predictors of reduced physical capacity and persistent breathlessness up to three years post-infection. Non-hospitalised individuals also experience long-term reductions in physical capacity, underscoring the need for targeted rehabilitation strategies.</div></div>","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106614"},"PeriodicalIF":11.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The aim of this work was to study the epidemiology of urogenital trichomoniasis in the setting of systematic screening of STIs, using a multiplex molecular assay. Besides, the specificity for T. vaginalis detection of the syndromic panel was assessed comparatively to an in-house PCR.
Methods
41,507 samples sent for STI screening between 2020 and 2024 were analysed using the Allplex® STI Essential molecular panel targeting T. vaginalis, C. trachomatis, N. gonorrhoeae, M. genitalium, M. hominis, Ureaplasma parvum, and U. urealyticum. Remaining samples positive for T. vaginalis were stored for confirmation using a simplex in-house qPCR assay targeting the beta-tubulin gene.
Results
337 (0.8%) samples (282 patients; 0.93%) were positive for T. vaginalis. The highest rate of positivity was observed in patients aged between 20 and 24 (1.6%), whereas the number of cases over 45 years was anecdotal (0.4%). Prevalence was ten times lower in men than in women. Twenty-four percent were co-infected with at least one pathogen, i.e., C. trachomatis (n=17%) and/or M. genitalium (9.2%) and/or N. gonorrhoeae (3.6%). More than half patients positive for T. vaginalis were asymptomatic, of whom 88% were treated. Symptomatic patients presented mostly with abnormal leucorrhea, pruritus and/or dysuria. Amplification of 160 samples by simplex PCRs showed an excellent concordance rate of 95% (n= 152/160) with the multiplex PCR.
Conclusions
Allplex® STI Essential multiplex PCR assay improves the detection of T. vaginalis with an excellent specificity and therefore represents an interesting tool to evaluate the prevalence of this neglected infection.
{"title":"Prevalence and bio-clinical characterisation of Trichomonas vaginalis infection in a large cohort of French patients screened using a molecular syndromic panel for sexually transmitted infections","authors":"Lya Hamet , Florence Robert-Gangneux , Clément Cazala , Gabriel Auger , Jean-Pierre Gangneux","doi":"10.1016/j.jinf.2025.106610","DOIUrl":"10.1016/j.jinf.2025.106610","url":null,"abstract":"<div><h3>Objectives</h3><div>The aim of this work was to study the epidemiology of urogenital trichomoniasis in the setting of systematic screening of STIs, using a multiplex molecular assay. Besides, the specificity for <em>T. vaginalis</em> detection of the syndromic panel was assessed comparatively to an in-house PCR.</div></div><div><h3>Methods</h3><div>41,507 samples sent for STI screening between 2020 and 2024 were analysed using the Allplex® STI Essential molecular panel targeting <em>T. vaginalis, C. trachomatis, N. gonorrhoeae, M. genitalium, M. hominis, Ureaplasma parvum,</em> and <em>U. urealyticum.</em> Remaining samples positive for <em>T. vaginalis</em> were stored for confirmation using a simplex in-house qPCR assay targeting the beta-tubulin gene.</div></div><div><h3>Results</h3><div>337 (0.8%) samples (282 patients; 0.93%) were positive for <em>T. vaginalis</em>. The highest rate of positivity was observed in patients aged between 20 and 24 (1.6%), whereas the number of cases over 45 years was anecdotal (0.4%). Prevalence was ten times lower in men than in women. Twenty-four percent were co-infected with at least one pathogen, i.e., <em>C. trachomatis</em> (n=17%) and/or <em>M. genitalium</em> (9.2%) and/or <em>N. gonorrhoeae</em> (3.6%). More than half patients positive for <em>T. vaginalis</em> were asymptomatic, of whom 88% were treated. Symptomatic patients presented mostly with abnormal leucorrhea, pruritus and/or dysuria. Amplification of 160 samples by simplex PCRs showed an excellent concordance rate of 95% (n= 152/160) with the multiplex PCR.</div></div><div><h3>Conclusions</h3><div>Allplex® STI Essential multiplex PCR assay improves the detection of <em>T. vaginalis</em> with an excellent specificity and therefore represents an interesting tool to evaluate the prevalence of this neglected infection.</div></div>","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106610"},"PeriodicalIF":11.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-03DOI: 10.1016/j.jinf.2025.106612
Emma Pritchard , Karina-Doris Vihta , Samuel Lipworth , Koen B. Pouwels , Nicole Stoesser , Russell Hope , Berit Muller-Pebody , T. Phuong Quan , Jack Cregan , Colin Brown , Susan Hopkins , David W. Eyre , A. Sarah Walker
Objectives
Escherichia coli bacteraemias have been under mandatory surveillance in the UK for fifteen years, but cases continue to rise. Systematic searches of all features present within electronic healthcare records (EHRs), described here as an EHR-wide association study (EHR-WAS), could potentially identify under-appreciated factors that could be targeted to reduce infections.
Methods
We used data from Oxfordshire, UK, and an EHR-WAS method developed for use with large-scale COVID-19 data to estimate associations between E. coli bacteraemia cases, hospital-exposed controls, and 377 potential risk factors using Poisson regression models adjusted for potential confounders for three two-year financial year (FY) periods.
Results
FY2022/23–2023/24 analysis included 757 (0.3%) cases and 276,758 (99.7%) controls. We identified six broad disease areas associated with increased or decreased E. coli bacteraemia risk. Renal/urological/urinary tract infection-related variables had the largest impact, with 47% of cases theoretically removed if these factors could be minimised. Cancer-related variables were associated with higher E. coli bacteraemia risk (1.20 times higher (95%CI 1.08–1.34) per three months closer to chemotherapy in the last year), as were gastrointestinal- and infectious disease-related variables. Cardiac/respiratory-related variables were associated with lower E. coli bacteraemia risk, whereas greater healthcare exposure showed no consistent effect. Associated factors varied across periods, but broad groups remained similar.
Conclusions
Applying an EHR-WAS approach, we show E. coli bacteraemias are largely driven by known risk factors and frailty, highlighting the importance of monitoring these factors and targeting modifiable risks where possible.
{"title":"An electronic health record-wide association study to identify populations at increased risk of E. coli bacteraemia","authors":"Emma Pritchard , Karina-Doris Vihta , Samuel Lipworth , Koen B. Pouwels , Nicole Stoesser , Russell Hope , Berit Muller-Pebody , T. Phuong Quan , Jack Cregan , Colin Brown , Susan Hopkins , David W. Eyre , A. Sarah Walker","doi":"10.1016/j.jinf.2025.106612","DOIUrl":"10.1016/j.jinf.2025.106612","url":null,"abstract":"<div><h3>Objectives</h3><div><em>Escherichia coli</em> bacteraemias have been under mandatory surveillance in the UK for fifteen years, but cases continue to rise. Systematic searches of all features present within electronic healthcare records (EHRs), described here as an EHR-wide association study (EHR-WAS), could potentially identify under-appreciated factors that could be targeted to reduce infections.</div></div><div><h3>Methods</h3><div>We used data from Oxfordshire, UK, and an EHR-WAS method developed for use with large-scale COVID-19 data to estimate associations between <em>E. coli</em> bacteraemia cases, hospital-exposed controls, and 377 potential risk factors using Poisson regression models adjusted for potential confounders for three two-year financial year (FY) periods.</div></div><div><h3>Results</h3><div>FY2022/23–2023/24 analysis included 757 (0.3%) cases and 276,758 (99.7%) controls. We identified six broad disease areas associated with increased or decreased <em>E. coli</em> bacteraemia risk. Renal/urological/urinary tract infection-related variables had the largest impact, with 47% of cases theoretically removed if these factors could be minimised. Cancer-related variables were associated with higher <em>E. coli</em> bacteraemia risk (1.20 times higher (95%CI 1.08–1.34) per three months closer to chemotherapy in the last year), as were gastrointestinal- and infectious disease-related variables. Cardiac/respiratory-related variables were associated with lower <em>E. coli</em> bacteraemia risk, whereas greater healthcare exposure showed no consistent effect. Associated factors varied across periods, but broad groups remained similar.</div></div><div><h3>Conclusions</h3><div>Applying an EHR-WAS approach, we show <em>E. coli</em> bacteraemias are largely driven by known risk factors and frailty, highlighting the importance of monitoring these factors and targeting modifiable risks where possible.</div></div>","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106612"},"PeriodicalIF":11.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-03DOI: 10.1016/j.jinf.2025.106611
Hao Guo , Qiao Li, , Yawen Zhang, Wenping Lin, Yan Chen, Fang He
{"title":"Cefiderocol resistance landscape: Insights into the global spread of blaPER-1-carrying Gram-negative bacteria","authors":"Hao Guo , Qiao Li, , Yawen Zhang, Wenping Lin, Yan Chen, Fang He","doi":"10.1016/j.jinf.2025.106611","DOIUrl":"10.1016/j.jinf.2025.106611","url":null,"abstract":"","PeriodicalId":50180,"journal":{"name":"Journal of Infection","volume":"91 4","pages":"Article 106611"},"PeriodicalIF":11.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-02DOI: 10.1016/j.jinf.2025.106607
Meghan A. Baker , Michael Klompas , Elizabeth Mermel Blaeser , Chanu Rhee , Elisa Abdulhayoglu , Julie Cadogan , Elizabeth Flanigan , Zach Pearson , Samantha Taffner , Marisa Winkler , Nicholas Boire , Jay Worley , Manfred Brigl , Lynn Bry , Nicole Pecora
Background
Conventional surveillance methods may miss healthcare-associated pathogen transmission, particularly for common, drug-susceptible organisms. It is unclear if prospective genomic analyses can help identify otherwise silent transmission events and inform prevention efforts.
Methods
We sequenced methicillin-susceptible Staphylococcus aureus (MSSA) surveillance and clinical isolates in the neonatal intensive care unit (NICU) of an academic hospital between February 2022 and March 2024. Insights gleaned from genomic-epidemiologic analyses were used to control a large MSSA cluster and to calibrate infection control measures thereafter.
Findings
There were 2352 babies admitted during the 26-month study period, of whom 318 became colonized or infected with MSSA. Monthly MSSA incidence rates were largely stable throughout this period, but whole genome sequencing demonstrated 16 MSSA clusters (range 2–19 babies/cluster). Sequencing data integrated with epidemiologic analyses informed escalating infection control measures to control a sustained cluster of 19 babies infected with MSSA ST30 (including increased hand hygiene monitoring, enhanced environmental and equipment cleaning, contact precautions, decolonization of MSSA carriers), a subsequent decision against further intensification (foregoing screening all staff members for MSSA carriage), and the subsequent liberalization of some interventions (dropping contact precautions for lower risk babies). While intensified infection control measures controlled the primary ST30 cluster, low-level transmission events (range 2–8 babies) were detected throughout the study period despite those interventions.
Interpretations
Integrating prospective genomic and epidemiologic analyses of healthcare-associated pathogens can help identify unrecognized transmission clusters and inform and calibrate infection control response measures.
Summary
Prospective genotyping of surveillance and clinical methicillin-susceptible Staphylococcus aureus (MSSA) isolates in a neonatal intensive care unit over a 26-month period identified multiple MSSA clusters that were otherwise unappreciated and helped to both catalyze and calibrate infection control measures.
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