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Data for action: the crucial role of hospitals in controlling Clostridioides difficile infection in England. 行动数据:英国医院在控制艰难梭状芽孢杆菌感染中的关键作用》(Data for Action: the crucial role of hospitals in controlling Clostridioides difficile infection in England)。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-19 DOI: 10.1016/j.lanmic.2024.100991
Akaninyene Otu, Dimple Chudasama, Russell Hope, Dakshika Jeyaratnam
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引用次数: 0
Global epidemiological trend of Klebsiella pneumoniae ST340: emergence of subclade KL15 co-producing K pneumoniae carbapenemase-2 and New Delhi metallo-β-lactamase-7 in the Americas. 肺炎克雷伯菌 ST340 的全球流行趋势:美洲出现了同时产生肺炎克雷伯菌碳青霉烯酶-2 和新德里金属-β-内酰胺酶-7 的 KL15 亚支系。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-17 DOI: 10.1016/j.lanmic.2024.100990
Felipe Vásquez-Ponce, Marco Vianello, Johana Becerra, Jesus G M Pariona, Karine Dantas, Gregory Melocco, Guilherme M Oliveira, Fernanda Esposito, Nilton Lincopan
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引用次数: 0
Critical loss: the effects of VEuPathDB defunding on global health. 重大损失:VEuPathDB 资金不足对全球健康的影响。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-14 DOI: 10.1016/j.lanmic.2024.100980
Christopher Fernandez-Prada, Nilmar S Moretti, Rubens L do Monte-Neto
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引用次数: 0
Pathoplexus: towards fair and transparent sequence sharing. Pathoplexus:实现公平透明的序列共享。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-13 DOI: 10.1016/j.lanmic.2024.100995
Elena Dalla Vecchia
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引用次数: 0
Antimicrobial resistance: a concise update. 抗菌药耐药性:简要更新。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-12 DOI: 10.1016/j.lanmic.2024.07.010
Charlotte S Ho, Carlos T H Wong, Thet Tun Aung, Rajamani Lakshminarayanan, Jodhbir S Mehta, Saaeha Rauz, Alan McNally, Balint Kintses, Sharon J Peacock, Cesar de la Fuente-Nunez, Robert E W Hancock, Darren S J Ting

Antimicrobial resistance (AMR) is a serious threat to global public health, with approximately 5 million deaths associated with bacterial AMR in 2019. Tackling AMR requires a multifaceted and cohesive approach that ranges from increased understanding of mechanisms and drivers at the individual and population levels, AMR surveillance, antimicrobial stewardship, improved infection prevention and control measures, and strengthened global policies and funding to development of novel antimicrobial therapeutic strategies. In this rapidly advancing field, this Review provides a concise update on AMR, encompassing epidemiology, evolution, underlying mechanisms (primarily those related to last-line or newer generation of antibiotics), infection prevention and control measures, access to antibiotics, antimicrobial stewardship, AMR surveillance, and emerging non-antibiotic therapeutic approaches. The Review also discusses the potential roles of artificial intelligence in addressing AMR, including antimicrobial susceptibility testing, AMR surveillance, antimicrobial stewardship, diagnosis, and antimicrobial drug discovery and development. This Review highlights the urgent need for addressing the global effects of AMR and for rapid advancement of relevant technology in this dynamic field.

抗菌药物耐药性(AMR)是对全球公共卫生的严重威胁,2019 年约有 500 万人死于细菌性 AMR。应对 AMR 需要采取多方面的综合方法,包括加强对个体和人群层面的机制和驱动因素的了解、AMR 监测、抗菌药物管理、改进感染预防和控制措施、加强全球政策和资金投入,以及开发新型抗菌药物治疗策略。在这一快速发展的领域,本综述简要介绍了 AMR 的最新情况,包括流行病学、演变、潜在机制(主要是与末线或新一代抗生素相关的机制)、感染预防和控制措施、抗生素的获取、抗菌药物管理、AMR 监测以及新兴的非抗生素治疗方法。该综述还讨论了人工智能在应对 AMR 方面的潜在作用,包括抗菌药物药敏试验、AMR 监测、抗菌药物管理、诊断以及抗菌药物的发现和开发。本综述强调了应对 AMR 的全球影响以及在这一动态领域快速发展相关技术的迫切需要。
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引用次数: 0
State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus. 基于微生物组的生物标记物的现状与未来:多学科德尔菲共识。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-04 DOI: 10.1016/j.lanmic.2024.07.011
Julie Rodriguez, Zahra Hassani, Carolina Alves Costa Silva, Fay Betsou, Federica Carraturo, Alessio Fasano, Mads Israelsen, Anandhi Iyappan, Aleksander Krag, Amira Metwaly, Robert Schierwagen, Jonel Trebicka, Hub Zwart, Joel Doré, Magali Cordaillat-Simmons, Celine Druart

Although microbiome signatures have been identified in various contexts (ie, pathogenesis of non-communicable diseases and treatment response), qualified microbiome-based biomarkers are currently not in use in clinical practice. The Human Microbiome Action consortium initiated a Delphi survey to establish a consensus on the needs, challenges, and limitations in developing qualified microbiome-based biomarkers. The questionnaire was developed by a scientific committee via literature review and expert interviews. To ensure broad applicability of the results, 307 experts were invited to participate; 114 of them responded to the first round of the survey, 93 of whom completed the second and final round as well. The survey highlighted the experts' confidence in the potential of microbiome-based biomarkers for several indications or pathologies. The paucity of validated analytical methods appears to be the principal factor hindering the qualification of these biomarkers. The survey also showed that clinical implementation of these biomarkers would only be possible if kitted and validated molecular assays with simple interpretation are developed. This initiative serves as a foundation for designing and implementing public-private collaborative projects to overcome the challenges and promote clinical application of microbiome-based biomarkers.

虽然微生物组特征已在各种情况下(即非传染性疾病的发病机理和治疗反应)得到确定,但目前临床实践中还没有使用合格的基于微生物组的生物标志物。人类微生物组行动联盟发起了一项德尔菲调查,以就开发合格的基于微生物组的生物标记物的需求、挑战和限制达成共识。调查问卷由科学委员会通过文献查阅和专家访谈制定。为确保调查结果的广泛适用性,邀请了 307 位专家参与;其中 114 位专家对第一轮调查做出了回应,93 位专家完成了第二轮和最后一轮调查。调查显示,专家们对基于微生物的生物标记物在若干适应症或病理方面的潜力充满信心。缺乏经过验证的分析方法似乎是阻碍这些生物标志物鉴定的主要因素。调查还显示,只有开发出配套的、经过验证的、解释简单的分子检测方法,才有可能在临床上应用这些生物标记物。该倡议为设计和实施公私合作项目奠定了基础,以克服挑战并促进基于微生物组的生物标记物的临床应用。
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引用次数: 0
First self-test for hepatitis C virus. 首次丙型肝炎病毒自我检测。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-03 DOI: 10.1016/j.lanmic.2024.100979
Priya Venkatesan
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引用次数: 0
Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study 新加坡第六个念珠菌支系的检测和特征:基因组和表型研究。
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-01 DOI: 10.1016/S2666-5247(24)00101-0
Chayaporn Suphavilai PhD , Karrie Kwan Ki Ko MD , Kar Mun Lim BSc , Mei Gie Tan MSc , Patipan Boonsimma BSc , Joash Jun Keat Chu BSc , Sui Sin Goh MSc , Prevena Rajandran BSc , Lai Chee Lee MPH , Kwee Yuen Tan MSc , Bushra Binte Shaik Ismail MSc , May Kyawt Aung MPH , Yong Yang PhD , Jean Xiang Ying Sim MBBS , Indumathi Venkatachalam MBBS , Benjamin Pei Zhi Cherng MBBS , Bram Spruijtenburg BSc , Kian Sing Chan MBBS , Lynette Lin Ean Oon MBBS , Ai Ling Tan MBBS , Niranjan Nagarajan PhD
<div><h3>Background</h3><p>The emerging fungal pathogen <em>Candida auris</em> poses a serious threat to global public health due to its worldwide distribution, multidrug resistance, high transmissibility, propensity to cause outbreaks, and high mortality. We aimed to characterise three unusual <em>C auris</em> isolates detected in Singapore, and to determine whether they constitute a novel clade distinct from all previously known <em>C auris</em> clades (I–V).</p></div><div><h3>Methods</h3><p>In this genotypic and phenotypic study, we characterised three <em>C auris</em> clinical isolates, which were cultured from epidemiologically unlinked inpatients at a large tertiary hospital in Singapore. The index isolate was detected in April, 2023. We performed whole-genome sequencing (WGS) and obtained hybrid assemblies of these <em>C auris</em> isolates. The complete genomes were compared with representative genomes of all known <em>C auris</em> clades. To provide a global context, 3651 international WGS data from the National Center for Biotechnology Information (NCBI) database were included in a high-resolution single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing was done and antifungal resistance genes, mating-type locus, and chromosomal rearrangements were characterised from the WGS data of the three investigated isolates. We further implemented Bayesian logistic regression models to classify isolates into known clades and simulate the automatic detection of isolates belonging to novel clades as their WGS data became available.</p></div><div><h3>Findings</h3><p>The three investigated isolates were separated by at least 37 000 SNPs (range 37 000–236 900) from all existing <em>C auris</em> clades. These isolates had opposite mating-type allele and different chromosomal rearrangements when compared with their closest clade IV relatives. The isolates were susceptible to all tested antifungals. Therefore, we propose that these isolates represent a new clade of <em>C auris,</em> clade VI. Furthermore, an independent WGS dataset from Bangladesh, accessed via the NCBI Sequence Read Archive, was found to belong to this new clade. As a proof-of-concept, our Bayesian logistic regression model was able to flag these outlier genomes as a potential new clade.</p></div><div><h3>Interpretation</h3><p>The discovery of a new <em>C auris</em> clade in Singapore and Bangladesh in the Indomalayan zone, showing a close relationship to clade IV members most commonly found in South America, highlights the unknown genetic diversity and origin of <em>C auris</em>, particularly in under-resourced regions. Active surveillance in clinical settings, along with effective sequencing strategies and downstream analysis, will be essential in the identification of novel strains, tracking of transmission, and containment of adverse clinical effects of <em>C auris</em> infections.</p></div><div><h3>Funding</h3><p>Duke-NUS Academic Medical Center Nurturing Cl
背景:新出现的真菌病原体念珠菌对全球公共卫生构成严重威胁,因为它分布于世界各地,具有耐多药、高传播性、易导致疾病爆发和高死亡率等特点。我们的目的是描述在新加坡检测到的三种不同寻常的念珠菌分离株的特征,并确定它们是否构成了一个新的支系,有别于之前已知的所有念珠菌支系(I-V):在这项基因型和表型研究中,我们对从新加坡一家大型三甲医院的无流行病学关联的住院病人身上培养出的三株银环蛇临床分离株进行了鉴定。指数分离株于 2023 年 4 月发现。我们对这些 C auris 分离物进行了全基因组测序(WGS)并获得了杂交组合。我们将完整的基因组与所有已知 C auris 支系的代表性基因组进行了比较。为了提供全球背景,美国国家生物技术信息中心(NCBI)数据库中的 3651 个国际 WGS 数据被纳入了高分辨率单核苷酸多态性(SNP)分析。我们进行了抗真菌药敏试验,并从三个被调查分离物的 WGS 数据中确定了抗真菌药敏基因、交配型基因座和染色体重排的特征。我们进一步采用贝叶斯逻辑回归模型将分离物归入已知支系,并模拟自动检测属于新支系的分离物,因为它们的 WGS 数据已经可用:所调查的三个分离株与所有现有的肛管癣菌支系之间至少有 37 000 个 SNPs(范围为 37 000-236 900)的差异。这些分离株与其最接近的支系 IV 亲属相比,具有相反的交配型等位基因和不同的染色体重排。这些分离物对所有测试过的抗真菌药物都敏感。因此,我们认为这些分离物代表了 C auris 的一个新支系,即支系 VI。此外,通过 NCBI Sequence Read Archive 获取的来自孟加拉国的独立 WGS 数据集也被发现属于这个新支系。作为概念验证,我们的贝叶斯逻辑回归模型能够将这些离群基因组标记为一个潜在的新支系:在新加坡和孟加拉国的印多马克拉亚区发现了一个新的C auris支系,该支系与最常见于南美洲的支系IV成员关系密切,这突显了C auris未知的遗传多样性和起源,尤其是在资源匮乏的地区。在临床环境中积极开展监测,同时采用有效的测序策略和下游分析,对于鉴定新型菌株、追踪传播情况和遏制 C auris 感染的不良临床影响至关重要:杜克大学-新加坡国立大学学术医学中心临床研究人员培养计划(Nurturing Clinician Researcher Scheme)和Genedant-GIS创新计划(Genedant-GIS Innovation Program)。
{"title":"Detection and characterisation of a sixth Candida auris clade in Singapore: a genomic and phenotypic study","authors":"Chayaporn Suphavilai PhD ,&nbsp;Karrie Kwan Ki Ko MD ,&nbsp;Kar Mun Lim BSc ,&nbsp;Mei Gie Tan MSc ,&nbsp;Patipan Boonsimma BSc ,&nbsp;Joash Jun Keat Chu BSc ,&nbsp;Sui Sin Goh MSc ,&nbsp;Prevena Rajandran BSc ,&nbsp;Lai Chee Lee MPH ,&nbsp;Kwee Yuen Tan MSc ,&nbsp;Bushra Binte Shaik Ismail MSc ,&nbsp;May Kyawt Aung MPH ,&nbsp;Yong Yang PhD ,&nbsp;Jean Xiang Ying Sim MBBS ,&nbsp;Indumathi Venkatachalam MBBS ,&nbsp;Benjamin Pei Zhi Cherng MBBS ,&nbsp;Bram Spruijtenburg BSc ,&nbsp;Kian Sing Chan MBBS ,&nbsp;Lynette Lin Ean Oon MBBS ,&nbsp;Ai Ling Tan MBBS ,&nbsp;Niranjan Nagarajan PhD","doi":"10.1016/S2666-5247(24)00101-0","DOIUrl":"10.1016/S2666-5247(24)00101-0","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;p&gt;The emerging fungal pathogen &lt;em&gt;Candida auris&lt;/em&gt; poses a serious threat to global public health due to its worldwide distribution, multidrug resistance, high transmissibility, propensity to cause outbreaks, and high mortality. We aimed to characterise three unusual &lt;em&gt;C auris&lt;/em&gt; isolates detected in Singapore, and to determine whether they constitute a novel clade distinct from all previously known &lt;em&gt;C auris&lt;/em&gt; clades (I–V).&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;p&gt;In this genotypic and phenotypic study, we characterised three &lt;em&gt;C auris&lt;/em&gt; clinical isolates, which were cultured from epidemiologically unlinked inpatients at a large tertiary hospital in Singapore. The index isolate was detected in April, 2023. We performed whole-genome sequencing (WGS) and obtained hybrid assemblies of these &lt;em&gt;C auris&lt;/em&gt; isolates. The complete genomes were compared with representative genomes of all known &lt;em&gt;C auris&lt;/em&gt; clades. To provide a global context, 3651 international WGS data from the National Center for Biotechnology Information (NCBI) database were included in a high-resolution single nucleotide polymorphism (SNP) analysis. Antifungal susceptibility testing was done and antifungal resistance genes, mating-type locus, and chromosomal rearrangements were characterised from the WGS data of the three investigated isolates. We further implemented Bayesian logistic regression models to classify isolates into known clades and simulate the automatic detection of isolates belonging to novel clades as their WGS data became available.&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Findings&lt;/h3&gt;&lt;p&gt;The three investigated isolates were separated by at least 37 000 SNPs (range 37 000–236 900) from all existing &lt;em&gt;C auris&lt;/em&gt; clades. These isolates had opposite mating-type allele and different chromosomal rearrangements when compared with their closest clade IV relatives. The isolates were susceptible to all tested antifungals. Therefore, we propose that these isolates represent a new clade of &lt;em&gt;C auris,&lt;/em&gt; clade VI. Furthermore, an independent WGS dataset from Bangladesh, accessed via the NCBI Sequence Read Archive, was found to belong to this new clade. As a proof-of-concept, our Bayesian logistic regression model was able to flag these outlier genomes as a potential new clade.&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Interpretation&lt;/h3&gt;&lt;p&gt;The discovery of a new &lt;em&gt;C auris&lt;/em&gt; clade in Singapore and Bangladesh in the Indomalayan zone, showing a close relationship to clade IV members most commonly found in South America, highlights the unknown genetic diversity and origin of &lt;em&gt;C auris&lt;/em&gt;, particularly in under-resourced regions. Active surveillance in clinical settings, along with effective sequencing strategies and downstream analysis, will be essential in the identification of novel strains, tracking of transmission, and containment of adverse clinical effects of &lt;em&gt;C auris&lt;/em&gt; infections.&lt;/p&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Funding&lt;/h3&gt;&lt;p&gt;Duke-NUS Academic Medical Center Nurturing Cl","PeriodicalId":46633,"journal":{"name":"Lancet Microbe","volume":"5 9","pages":"Article 100878"},"PeriodicalIF":20.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666524724001010/pdfft?md5=0066d8cd1c31db4feb85fd8b229654f1&pid=1-s2.0-S2666524724001010-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
To vaccinate or not against highly pathogenic avian influenza? 接种还是不接种高致病性禽流感疫苗?
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-01 DOI: 10.1016/S2666-5247(24)00107-1
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引用次数: 0
Harmonising the measurement of neutralising antibodies against chikungunya virus: a path forward for licensing of new vaccines? 统一基孔肯雅病毒中和抗体的测量方法:新疫苗许可的前进之路?
IF 20.9 1区 生物学 Q1 INFECTIOUS DISEASES Pub Date : 2024-09-01 DOI: 10.1016/S2666-5247(24)00097-1
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引用次数: 0
期刊
Lancet Microbe
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