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Geographical and temporal variations of serogroups and clonal types of Neisseria meningitidis involved in culture-confirmed invasive meningococcal disease in Canada, 2015-2023. 2015-2023年加拿大培养确认的侵袭性脑膜炎球菌病涉及脑膜炎奈瑟菌血清群和克隆型的地理和时间变化
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001979
Courtney Meilleur, Jianwei Zhou, Linda Hoang, Gregory Tyrrell, Jessica Minion, Paul Van Caeseele, Julianne Kus, Brigitte Lefebvre, David Haldane, Richard Garceau, George Zahariadis, Xiaofeng Ding, Kami Kandola, Sudit Ranade, Raymond S W Tsang
{"title":"Geographical and temporal variations of serogroups and clonal types of <i>Neisseria meningitidis</i> involved in culture-confirmed invasive meningococcal disease in Canada, 2015-2023.","authors":"Courtney Meilleur, Jianwei Zhou, Linda Hoang, Gregory Tyrrell, Jessica Minion, Paul Van Caeseele, Julianne Kus, Brigitte Lefebvre, David Haldane, Richard Garceau, George Zahariadis, Xiaofeng Ding, Kami Kandola, Sudit Ranade, Raymond S W Tsang","doi":"10.1099/jmm.0.001979","DOIUrl":"10.1099/jmm.0.001979","url":null,"abstract":"<p><p><b>Introduction.</b> Invasive meningococcal disease (IMD) is a nationally notifiable illness in Canada due to its potential severity and transmissibility. Vaccination strategies differ by province/territory and are informed by changes in the antigenic characteristics of circulating strains.<b>Gap Statement.</b> Though IMD statistics are tracked at a provincial/territorial level, there is a lack of published data characterizing trends in the epidemiology of this disease at a national level.<b>Aim.</b> To examine the epidemiology of culture-confirmed IMD in Canada during the period of 2015-2023.<b>Methodology.</b> Meningococcal isolates sent to the National Microbiology Laboratory Branch between 2015 and 2023 as part of routine national surveillance were characterized for serogroup by bacterial agglutination and genetic methods. Clonal analysis was done by MLST. Demographic information was derived from requisition forms accompanying the samples.<b>Results.</b> The proportion of IMD caused by serogroup W meningococci (MenW) in 2015-2023 was 30.0% with more (62.9%) MenW cases detected in western provinces. Serogroup B meningococci (MenB) IMD was more common (53.4%) in Quebec and Atlantic Canada. Clonal analysis reveals 168 distinct sequence types between 2015 and 2023, with 103 belonging to MenB. The average age of MenB cases during this time was 29.1 years, significantly younger than serogroup C (MenC) (45.3 years), serogroup Y (MenY) (48.3 years) and MenW (43.0 years) patients. Additionally, 31.5% of MenB and 21.7% of MenC IMD isolates were collected from cerebrospinal fluid (CSF) or brain samples, which were significantly higher than that for MenY (12.2%) and MenW (7.3%) isolates.<b>Conclusions.</b> Results from this and previous studies showed temporal and geographical variations in the serogroups causing IMD in Canada. MenB also showed the most genetic diversity, caused IMD in a significantly younger population and was more often isolated from CSF and brain samples than other serogroups.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Intratype variants and high genotypic diversity of human papillomavirus with polymorphisms in the antigenic hypervariable loops of the L1 protein from women living with human immunodeficiency virus in Northeastern Brazil. 巴西东北部感染人类免疫缺陷病毒的妇女L1蛋白抗原高变环多态性的人乳头瘤病毒型内变异和高基因型多样性
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001981
Melina Vieira Alves, Guilherme Oliveira Pereira, Letícia Alves Dos Santos Silva, Edilaine Dória Araújo, Brenda Evenlin Barreto da Silva, Lígia Mara Dolce de Lemos, Marcus Vinicius de Aragão Batista
{"title":"Intratype variants and high genotypic diversity of human papillomavirus with polymorphisms in the antigenic hypervariable loops of the L1 protein from women living with human immunodeficiency virus in Northeastern Brazil.","authors":"Melina Vieira Alves, Guilherme Oliveira Pereira, Letícia Alves Dos Santos Silva, Edilaine Dória Araújo, Brenda Evenlin Barreto da Silva, Lígia Mara Dolce de Lemos, Marcus Vinicius de Aragão Batista","doi":"10.1099/jmm.0.001981","DOIUrl":"10.1099/jmm.0.001981","url":null,"abstract":"<p><p><b>Introduction.</b> The human papillomavirus (HPV) is one of the main oncogenic viruses. High-risk HPV types are associated with the development of cervical cancers. In addition, it is known that some mutations in HPV genes, or variant viral lineages, have been associated with greater oncogenic risk.<b>Gap statement.</b> The L1 protein is the major component of the viral capsid and is therefore used in currently available vaccines. However, the characterization of mutations in the L1 gene, which is relevant to increasing the knowledge of the immune escape mechanisms used by the virus, is still incipient.<b>Aim.</b> This study aimed to characterize mutations associated with antigenic domains in the L1 protein of HPVs isolated from cervical samples of women living with HIV in Northeastern Brazil.<b>Methodology.</b> L1 gene sequences were obtained from the samples, and the mutations and the viral variants were characterized. Phylogenetic and functional analyses of the structure of the L1 protein were carried out.<b>Results.</b> A total of 41 HPV variant isolates were obtained, distributed among 16 different viral types. Of this, 25 non-synonymous mutations were evaluated regarding the stability of the L1 protein. It was observed that 10 of these mutations were predicted to increase, and 14 to decrease, the stability of the L1 protein and that most of them occurred in the FG hypervariable antigenic loop.<b>Conclusion.</b> These results add useful knowledge to understanding the biological and immunological aspects of HPV variants and the impact of these mutations on the development of vaccine strategies.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive toolkit integrating lifestyle and clinical questionnaires with gut microbiota profiling via rectal swabs: application in intensive care cirrhotic patients. 综合工具包整合生活方式和临床问卷,通过直肠拭子分析肠道微生物群:在重症监护肝硬化患者中的应用。
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001964
Julie Marin, Mohamed Ghalayini, Younes Kaoudji, Samira Dziri, Cecile Zylberfajn, Lorraine Blaise, Astrid Hoogvorst, Stephane Charpentier, Virginie Chaillou, Sylvie Beauchamp, Séverine Donneger, Nathalie Barget, Mathilde Touvier, Pierre Nahon, Roland Amathieu, Mathilde Lescat
{"title":"Comprehensive toolkit integrating lifestyle and clinical questionnaires with gut microbiota profiling via rectal swabs: application in intensive care cirrhotic patients.","authors":"Julie Marin, Mohamed Ghalayini, Younes Kaoudji, Samira Dziri, Cecile Zylberfajn, Lorraine Blaise, Astrid Hoogvorst, Stephane Charpentier, Virginie Chaillou, Sylvie Beauchamp, Séverine Donneger, Nathalie Barget, Mathilde Touvier, Pierre Nahon, Roland Amathieu, Mathilde Lescat","doi":"10.1099/jmm.0.001964","DOIUrl":"10.1099/jmm.0.001964","url":null,"abstract":"<p><p><b>Introduction.</b> The study of gut microbiota is now an essential dimension in many clinical studies. For instance, microbiota diversity investigation can help us to better manage cirrhotic patients by the identification of markers of severity and the identification of possible sources of pathogens.<b>Hypothesis/Gap Statement.</b> Conducting clinical research on gut microbiota for fragile patients in intensive care units, such as cirrhotic patients, poses significant challenges.<b>Aim.</b> In this study, we developed a comprehensive toolkit for investigating gut microbiota in fragile patients using rectal swabbing combined with straightforward lifestyle and clinical questionnaires.<b>Methodology</b> <i>.</i> We applied this prospective approach to 49 well-phenotyped cirrhotic patients as a function of their compensation status (compensated patients with outpatients' recruitment vs decompensated patients in intensive care units).<b>Results</b> <i>.</i> Our results, consistent with the literature, showed that liver function impairment is associated with lower microbiota diversity. Additionally, we monitored aerobic microbiota in decompensated cirrhotic patients, observing the invasion of extended spectrum beta-lactamase (ESBL)-producing <i>Escherichia coli</i> in the gut's aerobic microbiota prior to severe infection caused by these pathogens.<b>Conclusion.</b> We propose this pragmatic methodology for larger cohort studies, aiming to enhance the monitoring of immunocompromised patients by using microbiota analysis as a predictive tool for the severity of associated pathologies and the identification of agents responsible for severe infections.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Impact of the COVID-19 pandemic on invasive pneumococcal disease in American Indian communities in the Southwest US. COVID-19大流行对美国西南部美洲印第安人社区侵袭性肺炎球菌疾病的影响
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001983
Catherine G Sutcliffe, Shea Littlepage, Del Yazzie, George Brasinikas, Loretta Christensen, Shawnell Damon, Estar Denny, Sheri L Dixon, Lindsay R Grant, Marcella Harker-Jones, James McAuley, Pierrette Montanez, Dennie Parker, Alisa Reasonover, Amy Rice, Kristen Roessler, Eugene Romancito, Charis Salabye, Victoria M Sergent, Brenna Simons-Petrusa, Valerie Tenequer, Polly Thompson, Minnie Tsingine, Robert C Weatherholtz, Laura L Hammitt
{"title":"Impact of the COVID-19 pandemic on invasive pneumococcal disease in American Indian communities in the Southwest US.","authors":"Catherine G Sutcliffe, Shea Littlepage, Del Yazzie, George Brasinikas, Loretta Christensen, Shawnell Damon, Estar Denny, Sheri L Dixon, Lindsay R Grant, Marcella Harker-Jones, James McAuley, Pierrette Montanez, Dennie Parker, Alisa Reasonover, Amy Rice, Kristen Roessler, Eugene Romancito, Charis Salabye, Victoria M Sergent, Brenna Simons-Petrusa, Valerie Tenequer, Polly Thompson, Minnie Tsingine, Robert C Weatherholtz, Laura L Hammitt","doi":"10.1099/jmm.0.001983","DOIUrl":"10.1099/jmm.0.001983","url":null,"abstract":"<p><p>American Indian (AI) communities in the Southwest have a high burden of invasive pneumococcal disease (IPD) and COVID-19. Through laboratory-based surveillance, the impact of the pandemic on IPD incidence and serotype distribution was evaluated in two AI communities. IPD rates were lower during the pandemic (21.8 vs. 39.0/100 000 pre-pandemic). Rates increased in 2021 compared to 2020 but not to pre-pandemic levels. Cases with SARS-CoV-2 co-infection had a higher case fatality rate (45.2% vs. 17.6% without co-infection). No significant change in serotype distribution was observed. Continued surveillance in these communities is critical to understand the changing IPD burden as the pandemic evolves.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Predomination of hypervirulent ST283 and genetic diversity of levofloxacin resistance in multidrug-resistant, hypervirulent Streptococcus agalactiae in Thailand. 泰国多重耐药、高毒无乳链球菌高毒ST283的优势和左氧氟沙星耐药的遗传多样性
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001970
Wajeeorn Ouancharee, Anusak Kerdsin, Hien Van Doan, Chanagun Chitmanat, Kiatichai Faksri, Aroonlug Lulitanond, Aroonwadee Chanawong, Nicha Charoensri
{"title":"Predomination of hypervirulent ST283 and genetic diversity of levofloxacin resistance in multidrug-resistant, hypervirulent <i>Streptococcus agalactiae</i> in Thailand.","authors":"Wajeeorn Ouancharee, Anusak Kerdsin, Hien Van Doan, Chanagun Chitmanat, Kiatichai Faksri, Aroonlug Lulitanond, Aroonwadee Chanawong, Nicha Charoensri","doi":"10.1099/jmm.0.001970","DOIUrl":"10.1099/jmm.0.001970","url":null,"abstract":"<p><p><b>Introduction</b>. Group B <i>Streptococcus</i> (GBS) is a multi-host pathogen causing pneumonia and meningitis in humans as well as streptococcal diseases in tilapia and mastitis in cattle. Thailand has experienced a significant increase in GBS infections that greatly impact health and economics.<b>Gap statement</b>. The antimicrobial resistance (AMR) and genotype data of GBS in Thailand are still limited and require further study.<b>Aim</b>. This study aimed to describe AMR profiles and molecular characteristics, especially antimicrobial resistance genes (ARGs) and virulence factor (VF) genes of GBS in Thailand.<b>Methodology</b>. AMR profiles of 221 GBS isolates from humans, fish and freshwater were examined. Whole-genome sequencing of 41 representative isolates was used to investigate capsular genotypes and sequence types (STs), ARGs and VF genotypes.<b>Results</b>. All GBS isolates were susceptible to penicillin; the majority (99.1%) showed resistance to tetracycline. In addition, the rates of resistance to clindamycin, erythromycin and levofloxacin were 22.6%, 20.4% and 2.3%, respectively; multidrug-resistant (MDR) isolates (TE-E-CM and TE-E-CM-LVX) were 19.5%. Among 41 representative isolates, the dominant types were capsular genotype III (63.4%) and ST283 (43.9%). ARGs associated with resistance to tetracycline (<i>tetM</i>, <i>tetO</i> and <i>tetS</i>), erythromycin (<i>ermB</i>, <i>ermA</i>, <i>mefA</i> and <i>msrD</i>) and clindamycin (<i>lsaC</i>, <i>lsaE</i> and <i>lnuB</i>) were identified. Additionally, point mutations responsible for levofloxacin resistance, S81L in GyrA, S79F/Y in ParC and H221Y in ParE, were found. The MDR isolates belonged to various STs, predominantly clustering in capsular types III (60.0%) and Ib (30.0%). The MDR-hypervirulent ST17 and ST19 harboured multiple ARGs and mutations affecting quinolone resistance. Different VF gene patterns were found among hypervirulent STs (ST12, ST17, ST19 and ST283). Notably, a unique nt deletion [c.(1013_1020)delG] in <i>pilA</i> was found only in ST283.<b>Conclusion</b>. This study elucidated significant antimicrobial characteristics of a substantial number of GBS in Thailand. Moreover, the distribution of the hypervirulent ST283 and the genotypes of MDR-hypervirulent GBS were first described.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advancing rapid diagnostics for bloodstream infections: a perspective on scattered light integrated collection technology. 推进血流感染快速诊断:散射光综合采集技术透视。
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001973
Shital Shrikant Ghogale, Ketaki Niranjan Pathak
{"title":"Advancing rapid diagnostics for bloodstream infections: a perspective on scattered light integrated collection technology.","authors":"Shital Shrikant Ghogale, Ketaki Niranjan Pathak","doi":"10.1099/jmm.0.001973","DOIUrl":"10.1099/jmm.0.001973","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11903646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Surveillance of Salmonella and antimicrobial resistance in industrial poultry enterprises: biofilm-forming strains and critical control points. 工业家禽业沙门氏菌和抗菌素耐药性监测:生物膜形成菌株和关键控制点。
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001993
Birzhan Biyashev, Aygerim Zhusanbayeva, Zhumagul Kirkimbayeva, Asel Zholdasbekova, Dinara Sarybayeva
{"title":"Surveillance of <i>Salmonella</i> and antimicrobial resistance in industrial poultry enterprises: biofilm-forming strains and critical control points.","authors":"Birzhan Biyashev, Aygerim Zhusanbayeva, Zhumagul Kirkimbayeva, Asel Zholdasbekova, Dinara Sarybayeva","doi":"10.1099/jmm.0.001993","DOIUrl":"10.1099/jmm.0.001993","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Salmonella</i> contamination in the poultry industry poses substantial health risks, especially due to biofilm-forming strains that resist disinfection and antibiotic treatment. Biofilm-forming <i>Salmonella</i> strains are particularly challenging to control, as they adhere to surfaces in production environments, leading to persistent contamination. This study assesses the prevalence of <i>Salmonella</i>, examines antibiotic resistance patterns and evaluates biosecurity effectiveness at poultry farms in Kazakhstan.<b>Hypothesis/Gap Statement.</b> There is limited data on the prevalence and antibiotic resistance of biofilm-forming <i>Salmonella</i> strains in Kazakhstan's poultry industry, highlighting a need to characterize these strains to inform effective control measures.<b>Aim.</b> The purpose of this study was to systematically identify and characterize <i>Salmonella</i> strains, including biofilm-forming types, within industrial poultry enterprises in Kazakhstan.<b>Methodology.</b> A total of 660 samples were collected from various poultry production sites, including feed, water sources, cloacal flushes and shoe covers. <i>Salmonella</i> detection followed standardized protocols, and antibiotic sensitivity of identified strains was analysed to evaluate resistance patterns.<b>Results.</b> <i>Salmonella</i> was detected in 11.5% (95% CI) of the 660 samples, with the highest contamination observed in shoe covers, cloacal flushes, feed and water. This prevalence rate indicates a significant presence of the pathogen in the country's poultry production chain, falling between the higher rates seen in countries like China (22.2%) and Egypt (29.1%) and the lower rates observed in countries like Brazil (3.4%). The most prevalent strain was <i>Salmonella gallinarum-pullorum</i> (61.8%), followed by <i>Salmonella typhimurium</i> (18.4%) and <i>Salmonella enteritidis</i> (14.5%). Antibiotic sensitivity analysis revealed that <i>S. gallinarum-pullorum</i> was largely susceptible to common antibiotics, while <i>S. typhimurium</i> displayed considerable resistance, emphasizing the need for alternative treatments.<b>Conclusion.</b> The findings underscore the importance of strict sanitary and hygiene standards throughout poultry production, with a particular focus on managing biofilm-forming <i>Salmonella</i> strains. Implementing comprehensive Hazard Analysis and Critical Control Points protocols is essential to address contamination hotspots effectively. Future studies should investigate genetic mechanisms underlying biofilm formation and resistance in <i>Salmonella</i> strains to inform targeted interventions, ultimately improving food safety and public health outcomes.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sepsis in silico: definition, development and application of an electronic phenotype for sepsis. 硅脓毒症:脓毒症电子表型的定义、发展和应用。
Journal of medical microbiology Pub Date : 2025-03-01 DOI: 10.1099/jmm.0.001986
Zahraa Al-Sultani, Timothy Jj Inglis, Benjamin McFadden, Elizabeth Thomas, Mark Reynolds
{"title":"Sepsis <i>in silico</i>: definition, development and application of an electronic phenotype for sepsis.","authors":"Zahraa Al-Sultani, Timothy Jj Inglis, Benjamin McFadden, Elizabeth Thomas, Mark Reynolds","doi":"10.1099/jmm.0.001986","DOIUrl":"10.1099/jmm.0.001986","url":null,"abstract":"<p><p>Repurposing electronic health record (EHR) or electronic medical record (EMR) data holds significant promise for evidence-based epidemic intelligence and research. Key challenges include sepsis recognition by physicians and issues with EHR and EMR data. Recent advances in data-driven techniques, alongside initiatives like the Surviving Sepsis Campaign and the Severe Sepsis and Septic Shock Management Bundle (SEP-1), have improved sepsis definition, early detection, subtype characterization, prognostication and personalized treatment. This includes identifying potential biomarkers or digital signatures to enhance diagnosis, guide therapy and optimize clinical management. Machine learning applications play a crucial role in identifying biomarkers and digital signatures associated with sepsis and its sub-phenotypes. Additionally, electronic phenotyping, leveraging EHR and EMR data, has emerged as a valuable tool for evidence-based sepsis identification and management. This review examines methods for identifying sepsis cohorts, focusing on two main approaches: utilizing health administrative data with standardized diagnostic coding via the International Classification of Diseases and integrating clinical data. This overview provides a comprehensive analysis of current cohort identification and electronic phenotyping strategies for sepsis, highlighting their potential applications and challenges. The accuracy of an electronic phenotype or signature is pivotal for precision medicine, enabling a shift from subjective clinical descriptions to data-driven insights.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Preserving the antimicrobial arsenal: exploring alternatives to carbapenems in ESBL battles within the southeast of Ireland. 保存抗菌武器库:在爱尔兰东南部的ESBL战斗中探索碳青霉烯类的替代品。
Journal of medical microbiology Pub Date : 2025-02-01 DOI: 10.1099/jmm.0.001955
Saied Ali, Aideen Tobin, Susan Lapthorne, Meadhbh Collison, Doireann Murphy, Grace Chan, Maeve Doyle
{"title":"Preserving the antimicrobial arsenal: exploring alternatives to carbapenems in ESBL battles within the southeast of Ireland.","authors":"Saied Ali, Aideen Tobin, Susan Lapthorne, Meadhbh Collison, Doireann Murphy, Grace Chan, Maeve Doyle","doi":"10.1099/jmm.0.001955","DOIUrl":"10.1099/jmm.0.001955","url":null,"abstract":"<p><p><b>Introduction.</b> Carbapenems are usually employed as first-line antimicrobials against bacteria harbouring extended-spectrum beta-lactamases (ESBLs). These enzymes confer resistance often to multiple classes of antimicrobials.<b>Hypothesis/Gap Statement.</b> This indiscriminate use of carbapenems and the inevitable development of carbapenem resistance have prompted the need for carbapenem-sparing strategies.<b>Methodology.</b> The non-carbapenem antimicrobial susceptibility patterns of 60 ESBL-producing <i>Enterobacterales</i> (ESBL-PE) isolates responsible for bloodstream infections, in 2022-2023 inclusive, processed at our institution were reviewed.<b>Results.</b> The non-carbapenem antimicrobial susceptibility patterns of 60 ESBL-PE isolates from bloodstream infections during the study period were determined. <i>Escherichia coli</i> was the most common species isolated (87%, <i>n</i>=52), with the majority of cases (73.3%, <i>n</i>=44) originating from a presumed urinary source. Temocillin (TMC), mecillinam (MEC), cefiderocol (FDC), amikacin and fosfomycin (FOS) displayed excellent activity against all ESBL-PE isolates tested, with susceptibility rates of≥85%. Ciprofloxacin and amoxicillin-clavulanic acid were the least efficacious agents, with susceptibility rates≤20%.<b>Conclusions.</b> TMC, MEC, FDC and FOS offer promising alternatives to carbapenems, demonstrating efficacy against ESBL-PE. The use of these agents not only broadens the therapeutic arsenal against ESBL-PE but also mitigates the potential for escalating carbapenem resistance, especially in regions where the incidence of carbapenem resistance is increasing.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796091/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143191431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Viral vectors: design and delivery for small RNA. 病毒载体:小RNA的设计和传递。
Journal of medical microbiology Pub Date : 2025-02-01 DOI: 10.1099/jmm.0.001972
Wei Chin Koh, Khatijah Yusoff, Adelene Ai Lian Song, Norazalina Saad, Suet Lin Chia
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