Infection Genetics and Evolution最新文献_第5页

Inhibition of EgRad50 leads to impaired DNA repair in Echinococcus granulosus sensu stricto 抑制EgRad50导致狭义颗粒棘球绦虫DNA修复受损。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-19 DOI: 10.1016/j.meegid.2025.105855

Jinlong Zhao , Shaoquan Xu , Yun Du , Xiayidanmu Tuniyazi , Jing Li , Xia Liao , Yutong Jia , Guodong Lü , Jun Zhao

The parasitic disease known as cystic echinococcosis (CE) is a significant zoonotic condition caused by Echinococcus granulosus sensu lato (s.l.). The current lack of safe and effective pharmacological treatments necessitates urgent efforts to identify and develop novel drug targets and therapeutic molecules. This study investigates the role of DNA repair protein 50 (Rad50) in Echinococcus granulosus sensu stricto (s.s.) and evaluates whether it serve as a viable target for CE. Three small interfering RNA (siRNA) fragments targeting EgRad50 were introduced into E. granulosus s.s. via electroporation, and qRT-PCR, Western blot, and immunofluorescence were performed to assess EgRad50 localization and expression. The survival rate of E. granulosus s.s. was evaluated through in vitro culture, DNA damage was assessed using a comet assay, and the impact of EgRad50 knockdown on DNA repair and ferroptosis was analyzed via Western blot. EgRad50 is expressed during the protoscolece (PSC) and metacestode (MTC) stages of E. granulosus s.s. and the knockdown of EgRad50 reduced the viability of E. granulosus s.s. PSCs in vitro. Moreover, inhibition of EgRad50 downregulates ATR phosphorylation levels and further activates ferroptosis, leading to the death of E. granulosus s.s. This investigation sheds light on the preliminary role of EgRad50 in DNA repair, highlighting its importance for parasite survival and suggesting it as a new potential drug target for CE therapy. The selective targeting of EgRad50 may facilitate a more effective resolution to the clinical challenges presented by CE.

被称为囊性棘球蚴病（CE）的寄生虫病是由细粒棘球蚴引起的一种重要的人畜共患疾病。目前缺乏安全有效的药物治疗，迫切需要识别和开发新的药物靶点和治疗分子。本研究探讨了DNA修复蛋白50 （DNA repair protein 50, Rad50）在狭义细粒棘球蚴中的作用，并评估其是否可作为CE的可行靶点。采用电穿孔法将3个靶向EgRad50的小干扰RNA （small interfering RNA, siRNA）片段导入E. granulosus s.s，采用qRT-PCR、Western blot和免疫荧光法检测EgRad50的定位和表达。通过体外培养评估颗粒绦虫的存活率，采用彗星法评估DNA损伤，并通过Western blot分析EgRad50敲低对DNA修复和铁下垂的影响。EgRad50在颗粒棘球绦虫原节段（PSCs）和转移节段（MTC）表达，EgRad50的下调降低了颗粒棘球绦虫原节段（PSCs）的体外活力。此外，抑制EgRad50可下调ATR磷酸化水平，进一步激活铁下沉，导致颗粒绦虫死亡。该研究揭示了EgRad50在DNA修复中的初步作用，强调了其对寄生虫生存的重要性，并提示其可能是CE治疗的新潜在药物靶点。选择性靶向EgRad50可能有助于更有效地解决CE带来的临床挑战。

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引用次数: 0

Molecular epidemiology of Clostridioides difficile in border areas of Yunnan Province suggests possible transmission routes of the strains 云南省边境地区艰难梭菌分子流行病学分析提示该菌株可能的传播途径

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-27 DOI: 10.1016/j.meegid.2025.105860

Wenpeng Gu , Jiao Gong , Junrong Liang , Xiaofang Zhou , Lulu Bai , Wenzhu Zhang , Senquan Jia , Yongming Zhou , Xiaoqing Fu , Yuan Wu

Objectives

A molecular epidemiological study of Clostridioides difficile was performed in the border areas of Yunnan Province.

Methods

Molecular surveillance, bacterial isolation and identification, antibiotic susceptibility tests and genome sequencing of the isolates were performed.

Results

Among the 788 total diarrhea patients, 97 (12.31 %) were positive for the tpi gene, and 86 (10.91 %) were positive for tcdB in the fecal samples. Forty-nine C. difficile strains were isolated, 38 of which were toxigenic (tcdA+/tcdB+) and 11 of which were nontoxigenic. Specifically, four binary toxin gene-positive C. difficile strains were first isolated in Hekou County of Yunnan. ST3, ST35 and ST2 were the most prevalent STs. The genotype profiles of C. difficile from the three border areas were different from those of the isolates from the inland areas of Yunnan, indicating obvious geographical divergence. cgMLST and core genome SNP phylogenetic analyses revealed that all strains formed three clades, namely, clades 1, 3 and 4. High genetic similarity of the same ST type of C. difficile in the three border regions was identified. The isolates from the border area presented high homology with isolates from inland areas and other provinces of China but were distant from the foreign reference strains, suggesting that the possible transmission route of the border strains was most consistent with dissemination from inland to border areas.

Conclusions

The genotype profiles of the strains differ across geographic regions. Phylogenetic analyses suggested that the border area strains presented high homology with inland strains from China.

目的对云南省边境地区艰难梭菌进行分子流行病学研究。方法对分离株进行分子监测、细菌分离鉴定、药敏试验和基因组测序。结果788例腹泻患者中，粪便tpi基因阳性97例（12.31%），tdb阳性86例（10.91%）。分离到49株艰难梭菌，其中产毒株38株（tcdA+/tcdB+），非产毒株11株。其中，在云南河口县首次分离到4株双毒素基因阳性艰难梭菌。ST3、ST35和ST2是最常见的STs。3个边境地区的艰难梭菌基因型与云南内陆地区的不同，表现出明显的地理差异。cgMLST和核心基因组SNP系统发育分析显示，所有菌株形成3个支系，即1、3和4支系。在三个边境地区发现了相同ST型艰难梭菌的高度遗传相似性。边境地区分离株与中国内陆地区和其他省份分离株同源性较高，但与国外参考菌株距离较远，表明边境菌株可能的传播途径与内陆向边境地区传播最为一致。结论不同地理区域菌株的基因型谱存在差异。系统发育分析表明，边境地区菌株与中国内陆菌株具有高度同源性。

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引用次数: 0

Mutations in gyrA and gyrB among drug-resistant Mycobacterium tuberculosis isolates in South Korea 韩国耐药结核分枝杆菌分离株中gyrA和gyrB的突变

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-10-30 DOI: 10.1016/j.meegid.2025.105849

Seungmo Kim , Hwi-Jun Kim , Ryeun Heo , Hyeon-Su Kim , Jong-Myun Song , Cheon-Tae Kim , Hee-Jin Kim , Soul-hee Kim , Jeong-hui Gwon , Gicheon Bae , Sumi Kang , Kwang-Hyuk Seok , Eunseon Kim , Dae-Seon Han , Mi-So Kim , Hyeon-Ju Lee , Seonmi Shin , Arim Song , Gyeong In Lee , Seung-Heon Lee , Hee Joo Lee

Background

Group A fluoroquinolones (FLQs) are essential for treating multidrug-resistant tuberculosis (MDR-TB). Mutations in gyrA and gyrB cause FLQ resistance, but their patterns vary by region. This study evaluated FLQ-associated mutations in the gyrA and gyrB genes by analyzing minimum inhibitory concentrations (MICs) using 7H9 broth microdilution (BMD) and Löwenstein–Jensen phenotypic drug susceptibility test (L-J pDST).

Methods

A total of 304 isoniazid- and/or rifampicin-resistant isolates were analyzed. Genotypic drug susceptibility testing (gDST) was performed by sequencing gyrA (codons 74–113) and gyrB (codons 500–540). MICs for moxifloxacin (MFX) and levofloxacin (LFX) (0.0625–8.0 μg/mL) were determined using 7H9 BMD. Mutations were identified relative to the M. tuberculosis H37Rv reference. In L-J pDST, resistance breakpoints were 1.0 μg/mL for MFX and 2.0 μg/mL for LFX.

Results

Among isolates, 270 (88.81 %) were wild type and 34 (11.18 %) had mutations. D94G (44.82 %) and A90V (24.14 %) were the most frequent gyrA mutations. D500N (40 %) was the most common gyrB mutation. All gyrA mutants were MFX-resistant, while only 60 % of gyrB mutants were.

Conclusions

This study confirms gyrA mutations, especially D94G, as primary determinants of FLQ resistance in drug-resistant TB (including MDR-TB) in South Korea. gyrB mutations may also influence resistance. Combining gDST with phenotypic methods may improve resistance profiling.

背景：A类氟喹诺酮类药物（FLQs）是治疗耐多药结核病（MDR-TB）所必需的药物。gyrA和gyrB突变引起FLQ抗性，但其模式因地区而异。本研究利用7H9肉液微量稀释（BMD）和Löwenstein-Jensen表型药敏试验（L-J pDST）分析最低抑制浓度（mic），评估gyrA和gyrB基因中flq相关突变。方法：对304株异烟肼耐药和/或利福平耐药菌株进行分析。测序gyrA（密码子74 ~ 113）和gyrB（密码子500 ~ 540）进行基因型药敏试验（gDST）。采用7H9骨密度法测定莫西沙星（MFX）和左氧氟沙星（LFX）的mic（0.0625-8.0 μg/mL）。与结核分枝杆菌H37Rv参比鉴定出突变。在L-J pDST中，MFX的抗性断点为1.0 μg/mL， LFX的抗性断点为2.0 μg/mL。结果：野生型270株（88.81 %），突变株34株（11.18 %）。D94G（44.82 %）和A90V（24.14 %）是最常见的gyrA突变。D500N（40 %）是最常见的gyrB突变。所有的gyrA突变体都具有mfx抗性，而只有60% %的gyrB突变体具有mfx抗性。结论：本研究证实了gyrA突变——尤其是d94g——是韩国耐药结核病（包括耐多药结核病）中FLQ耐药的主要决定因素。gyrB突变也可能影响抗性。将gDST与表型方法结合可以改善抗性谱分析。

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引用次数: 0

Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data 微生物基因组学的生物信息学工具在过去十年中的进展和挑战：迈向生物信息学工具、数字资源和新兴技术的智能集成，用于分析复杂的生物数据

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-24 DOI: 10.1016/j.meegid.2025.105859

Cheikh Tidiane Houmenou , Cheikh Sokhna , Florence Fenollar , Oleg Mediannikov

Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.

在过去的十年中，随着测序技术和生物信息学的进步，微生物基因组学已经发生了转变，使得从目标基因标记到完整的基因组组装和生态尺度的宏基因组调查成为可能。本文综述了构建该领域的生物信息学管道的全面概述，从样品制备，PCR扩增，下一代测序（NGS）到读取预处理，基因组组装，抛光，结构和功能注释，以及提交给公共数据库。我们重点介绍了在每个阶段已经成为标准的主要工具，包括FastQC、SPAdes、Prokka、Bakta、CARD、GTDB-Tk、QIIME 2和Kraken2，同时也强调了最近的创新，如混合汇编器、本体驱动的注释框架和自动化工作流（nf-core、Bactopia）。应用扩展到微生物学领域，从抗菌素耐药性监测和系统发育分类到生态学研究，这里有三个案例研究：用16S元条形码分析白蚁肠道微生物群，描述蝙蝠巴尔通体新物种，以及灵长类动物罕见肠炎沙门氏菌血清型的基因组特征。尽管取得了这些进展，但仍然存在持续的挑战，包括不完整和有偏见的参考数据库、计算瓶颈以及排序和存储容量方面的经济差异。作为回应，国际倡议越来越多地促进开放、互操作和可重复使用的生物信息学基础设施。这些努力符合可查找、可访问、可互操作、可重用（FAIR）原则和全球基因组学与健康联盟（GA4GH）等全球框架，正在推动微生物基因组学社区更大程度的标准化、透明度和数据共享。未来的观点指向人工智能、长读和端粒到端粒（T2T）测序、云原生基础设施甚至量子计算的整合，为可预测、可复制和全球包容性的微生物基因组学铺平道路。

{"title":"Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data","authors":"Cheikh Tidiane Houmenou , Cheikh Sokhna , Florence Fenollar , Oleg Mediannikov","doi":"10.1016/j.meegid.2025.105859","DOIUrl":"10.1016/j.meegid.2025.105859","url":null,"abstract":"<div><div>Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new <em>Bartonella</em> species from bats, and the genomic characterization of rare <em>Salmonella enterica</em> serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"136 ","pages":"Article 105859"},"PeriodicalIF":2.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145624465","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}

引用次数: 0

Immunological role of IL-25 on gut-dwelling helminths IL-25对肠道蠕虫的免疫作用。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-19 DOI: 10.1016/j.meegid.2025.105856

Gashaw Azanaw Amare , Yenesew Mihret Wondmagegn , Adane Adugna , Desalegn Abebaw , Abateneh Melkamu , Habtamu Belew , Zigale Hibstu Teffera , Mamaru Getinet , Mohammed Jemal , Temesgen Baylie , Deresse Sinamaw Asmare , Abebe Yenesew , Abebe Fenta , Mesafint Woreket , Abebaw Setegn , Birhanu Malede

Interleukin-25 (IL-25) is a crucial cytokine in coordinating type 2 immunity against gut-dwelling helminths. IL-25 is produced by a variety of cells, including epithelial and immune cells, and primarily stimulates Th2-type immune responses characterized by the release of IL-13, IL-5, and IL-4, which play a vital role in eosinophilia induction, goblet cell hyperplasia, and IgE synthesis. This review critically examines IL-25's role in maintaining intestinal barrier integrity and modulating regulatory immune responses. This review addresses how IL-25 integrates signals from the epithelial interface, immune cells, and gut microbiota to calibrate appropriate host defense while preventing pathological inflammation. Furthermore, this paper presents recent evidence supporting IL-25's therapeutic potential, both as a potential adjuvant therapy to enhance parasite clearance and as a modulator of inflammatory conditions where type 2 immunity proves deficient.

白细胞介素-25 （IL-25）是协调2型免疫对抗肠道蠕虫的关键细胞因子。IL-25由多种细胞产生，包括上皮细胞和免疫细胞，主要刺激以释放IL-13、IL-5和IL-4为特征的th2型免疫反应，在嗜酸性粒细胞诱导、杯状细胞增生和IgE合成中起重要作用。本文综述了IL-25在维持肠道屏障完整性和调节调节免疫反应中的作用。本文综述了IL-25如何整合来自上皮界面、免疫细胞和肠道微生物群的信号，以校准适当的宿主防御，同时预防病理性炎症。此外，本文提出了支持IL-25治疗潜力的最新证据，既可以作为增强寄生虫清除的潜在辅助治疗，也可以作为2型免疫缺陷的炎症条件的调节剂。

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引用次数: 0

Genomic insights into Erwinia amylovora prophages: Diversity, defense strategies, and phage-host coevolution 对淀粉状欧文菌噬菌体的基因组研究：多样性、防御策略和噬菌体-宿主共同进化。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-10-31 DOI: 10.1016/j.meegid.2025.105846

Mohammadreza Rahimian , Bahman Panahi

Erwinia amylovora, the causative agent of fire blight in Rosaceae plants like apple and pear, is a major agricultural pathogen responsible for significant economic losses. This gram-negative phytopathogen has the potential to acquire antibiotic resistance and virulence genes, a situation that becomes more severe and restricts treatment options. Using an in silico approach, we analyzed 268 E. amylovora genomes and identified seven high-quality temperate prophages, all classified under Caudoviricetes, with average genome sizes of 44.2 kbp and 51 % GC content. These prophages exhibited unique genomic features, including tRNA genes (Ph-Ea644), anti-defense systems like ardc (Ph-Ea6–96), and regulatory/lysis genes (Ph-EaFC01). Comparative genomics and phylogenetic analyses grouped them into five clades, with Ph-Ea4–96, Ph-Ea3–97, and Ph-Ea2–97 being genetically identical. Functional annotation revealed streptomycin resistance genes and a CAZyme (GH23) in Ph-Ea7–3, virulence factors (e.g., alginate biosynthesis proteins), and six auxiliary metabolic genes (AMGs) linked to metabolic adaptation. Additionally, Ph-Ea644 encoded a cell wall-binding receptor protein. The prophages also carried defense systems (Gabija, CBASS) and 31 anti-CRISPR proteins (ACRs), suggesting evasion of host immunity. CRISPR-Cas analysis indicated fewer arrays and spacers in prophage-containing strains, underscoring CRISPR's role in lysogeny resistance. These findings highlight the genomic plasticity of E. amylovora prophages, their interactions with bacterial defenses, and their potential influence on pathogen evolution. This study enhances understanding of temperate phages in agricultural pathogens and underscores challenges in phage-based biocontrol strategies.

苹果、梨等蔷薇科植物的火疫病病菌是造成重大经济损失的主要农业病原菌。这种革兰氏阴性植物病原体有可能获得抗生素耐药性和毒力基因，这种情况变得更加严重，并限制了治疗选择。利用计算机方法分析了268个E. amylovora基因组，鉴定出7个高质量的温带前噬菌体，它们都属于Caudoviricetes，平均基因组大小为44.2 kbp， GC含量为51% %。这些噬菌体表现出独特的基因组特征，包括tRNA基因（Ph-Ea644）、抗防御系统如ardc （Ph-Ea6-96）和调节/裂解基因（Ph-EaFC01）。比较基因组学和系统发育分析将它们分为5个分支，其中Ph-Ea4-96、Ph-Ea3-97和Ph-Ea2-97在遗传上是相同的。功能注释揭示了Ph-Ea7-3中链霉素耐药基因和一个CAZyme （GH23）、毒力因子（如海藻酸盐生物合成蛋白）以及6个与代谢适应相关的辅助代谢基因（AMGs）。此外，Ph-Ea644编码细胞壁结合受体蛋白。这些噬菌体还携带防御系统（Gabija， CBASS）和31种抗crispr蛋白（ACRs），表明它们可以逃避宿主免疫。CRISPR- cas分析表明，在含有噬菌体的菌株中，较少的阵列和间隔物，强调了CRISPR在溶原性抗性中的作用。这些发现强调了E. amylovora噬菌体的基因组可塑性，它们与细菌防御的相互作用，以及它们对病原体进化的潜在影响。这项研究提高了对温带噬菌体在农业病原体中的认识，并强调了基于噬菌体的生物防治策略的挑战。

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引用次数: 0

Genotype diversity and evolution of noroviruses GI.3[P13] associated acute gastroenteritis outbreaks in Beijing, China from 2016 to 2019 2016 - 2019年北京地区诺如病毒GI.3[P13]相关急性胃肠炎暴发的基因型多样性和进化

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-01 DOI: 10.1016/j.meegid.2025.105850

Lingyu Shen , Jiamei Fu , Baiwei Liu , Weihong Li , Yu Wang , Yi Tian , Lei Jia , Peng Yang , Quanyi Wang , Daitao Zhang , Jie Li , Gao Zhiyong

Objectives

This study aimed to characterize the epidemiological, clinical, and genomic features of norovirus GI.3[P13] outbreaks in Beijing from 2016 to 2019.

Methods

Stool specimens from acute gastroenteritis (AGE) outbreak cases were subjected to genotyping, whole-genome sequencing, and phylogenetic analysis.

Results

From 2016 to 2019, norovirus GI.3[P13] caused 29 AGE outbreaks (452 cases) in Beijing, becoming the second most prevalent strain, followed by GII.2[P16] in 2019. Phylogenetic analysis identified three subclades, with subclade 2.2 (213 cases, 19 outbreaks) demonstrating distinct epidemiological and clinical features. This emergent subclade exhibited year-round circulation in urban/suburban areas. Multivariate analysis identified male gender (aOR = 1.79), age ≥ 13 years (aOR = 9.12), and university (aOR = 6.82) as independent risk factors. As the clinical symptom, subclade 2.2 caused more severe symptoms, including higher frequencies of vomiting (≥7 episodes/day: 18.78 % vs ≤8.67 %), diarrhea (≥7 episodes/day: 35.2 % vs ≤16.7 %), and fever (50.70 % vs ≤18.70 %). Genomic analysis revealed mutations in key structural and non-structural proteins. Bayesian analysis estimated the divergence of subclade 2.2 around mid-2017 as potential novel subgenotypes, preceding its outbreak surge in 2019.

Conclusions

Norovirus GI genotypes, like GI.3[P13], circulate continuously as sporadic and can incite outbreak surges, highlighting the necessity for improved surveillance among these genotypes.

目的：研究2016 - 2019年北京市诺如病毒GI.3[P13]暴发的流行病学、临床和基因组特征。方法：对急性胃肠炎（AGE）暴发病例的粪便标本进行基因分型、全基因组测序和系统发育分析。结果：2016 - 2019年，诺如病毒GI.3[P13]在北京市共引起29起AGE暴发（452例），成为第二大流行毒株，2019年排在第二位的是gi .2[P16]。系统发育分析确定了3个亚支，其中亚支2.2（213例，19次暴发）表现出明显的流行病学和临床特征。这一新兴亚枝在城市/郊区全年循环。多变量分析发现男性性别(aOR = 1.79),年龄 ≥  13年(aOR = 9.12),和大学(aOR = 6.82)作为独立的危险因素。作为临床症状，亚枝2.2引起的症状更为严重，包括呕吐（≥7次/天：18.78 % vs≤8.67 %）、腹泻（≥7次/天：35.2% % vs≤16.7 %）和发烧（50.70 % vs≤18.70 %）的频率更高。基因组分析揭示了关键结构蛋白和非结构蛋白的突变。贝叶斯分析估计，在2019年爆发疫情之前，2017年年中左右2.2亚支的分化是潜在的新型亚基因型。结论：诺如病毒GI基因型与GI.3[P13]一样，以散发形式持续传播，并可引发疫情激增，因此有必要加强对这些基因型的监测。

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引用次数: 0

Molecular epidemiology of Trypanosoma cruzi I infection in northern Argentina 阿根廷北部克氏锥虫感染的分子流行病学研究。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-19 DOI: 10.1016/j.meegid.2025.105857

N.P. Macchiaverna , L.P. Quebrada-Palacio , G.F. Enriquez , R.V. Piccinali , M.M. Orozco , H.D. Argibay , R.E. Gürtler , M.V. Cardinal

Trypanosoma cruzi I (TcI) infects a broad range of mammalian and triatomine species across the Americas and displays broad genetic diversity. The transmission cycles of TcI remain poorly understood. We investigated whether TcI parasites from Didelphis albiventris opossums were linked to the TcI parasites found in domestic dogs, cats and peridomestic Triatoma sordida from the Argentinean Chaco or were linked to other T. cruzi genotypes in opossums. We analyzed the intergenic region of the spliced leader (SL-IR) of the mini-exon gene sequence from direct triatomine samples and culture isolates from those hosts captured in Pampa del Indio, Amamá, and Garupá municipalities. Of 56 sequences analyzed, 29 are original to this study and 27 were available at GenBank. Fifteen TcI genotypes were detected in Pampa del Indio, with at least three sub-groups circulating simultaneously. TcId was mainly linked to D. albiventris and T. sordida, suggesting a sylvatic/peridomestic transmission cycle. TcIa was found in a domestic dog and a cat at the same household, likely originated from an unidentified source. A third sub-group of TcI, closely related to sequences from Brazilian and Misiones (Argentina) opossums, was found in T. sordida. To our knowledge, this is the first report of TcI SL-IR sub-groups in T. sordida. Whether D. albiventris opossums are introducing sylvatic parasites to the peridomicile and T. sordida are getting the TcId-infection there or sylvatic T. sordida specimens are arriving to the peridomicile already infected deserves further research.

克氏锥虫I型（TcI）在美洲广泛感染哺乳动物和triatomine物种，并表现出广泛的遗传多样性。TcI的传播周期仍然知之甚少。我们调查了来自白腹Didelphis负鼠的TcI寄生虫是否与来自阿根廷查科的家养狗、猫和家养索迪达Triatoma sordida的TcI寄生虫有关，或者是否与负鼠中的其他克氏T.基因型有关。我们分析了在Pampa del Indio， amam和garup市捕获的直接triatomine样本和培养分离物的迷你外显子基因序列的剪接先导子（SL-IR）的基因间区域。在分析的56个序列中，29个是本研究的原始序列，27个在GenBank中可用。在印第安草原共检测到15种TcI基因型，至少有3个亚群同时流行。TcId主要与albiventris和T. sordida有关，表明其传播周期为森林/家庭周围。在同一户人家的一只家狗和一只猫身上发现了TcIa，可能来源不明。在T. sordida中发现了第三个TcI亚群，与巴西负鼠和阿根廷Misiones负鼠的序列密切相关。据我们所知，这是第一次报道TcI SL-IR亚群在T. sordida。究竟是白腹袋鼠将林木寄生物引入房周而使梭形绦虫感染，还是林木梭形绦虫标本到达已感染的房周，值得进一步研究。

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引用次数: 0

Phylodynamic analysis of recent bovine viral diarrhea viruses in the Republic of Korea 韩国新近牛病毒性腹泻病毒的系统动力学分析。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-04 DOI: 10.1016/j.meegid.2025.105851

Hyung-Chul Cho , Jaehyeok Song , Kyoung-Seong Choi

Bovine viral diarrhea virus (BVDV) is a globally distributed and economically significant viral pathogen in the cattle industry. Despite ongoing circulation, molecular evolutionary and phylodynamic data on BVDV in the Republic of Korea (ROK) remain limited. This study aimed to investigate the prevalence and subtype of recent BVDVs circulating in the ROK and to analyze their phylodynamic patterns. A total of 5286 samples, including serum, blood, and diarrheic feces, were collected from Korean native cattle between 2021 and 2022. Of these, 29.9 % (1584/5286) tested positive for BVDV by real-time RT-PCR targeting the 5′UTR. BVDV was most frequently detected in serum (36.9 %), followed by feces (12.3 %) and blood (9.6 %). Sequencing analysis identified three subtypes: BVDV-1a (16.5 %), BVDV-1b (53.6 %), and BVDV-2a (29.9 %). The maximum clade credibility (MCC) tree based on the 5′UTR indicated that the most recent common ancestors of BVDV-1 and BVDV-2 in the ROK likely emerged around 1988 and 1995, respectively. The evolutionary rates of BVDV-1 and BVDV-2a were estimated at 3.99 × 10⁻³ and 4.0 × 10⁻³ substitutions/site/year, respectively, indicating rapid evolution compared with those in other countries. The MCC tree revealed an evolutionary order of BVDV-1a, -2a, and -1b. Phylogenetic analysis showed that recent BVDV-1b sequences exhibited greater genetic variation than those of other subtypes, suggesting accelerated and heterogeneous evolutionary dynamics. Bayesian skyline plot analysis demonstrated a marked increase in the viral population of BVDV-1 (especially BVDV-1b) around 2018, while BVDV-2a exhibited a more gradual expansion beginning around 2016. This was the first study to characterize the evolutionary dynamics of BVDVs in the ROK. These findings enhance understanding of the recent molecular epidemiology and evolutionary dynamics of BVDV in the ROK and underscore the need for continued molecular surveillance and control strategies.

牛病毒性腹泻病毒（Bovine viral diarrhea virus， BVDV）是一种全球分布的、具有重要经济意义的养牛业病毒性病原体。尽管正在传播，但韩国BVDV的分子进化和系统动力学数据仍然有限。本研究旨在调查韩国最近流行的BVDVs的流行情况和亚型，并分析其系统动力学模式。从2021年到2022年，从韩国本土牛身上采集了血清、血液、腹泻粪便等5286份样本。其中，29.9 %（1584/5286）通过针对5'UTR的实时RT-PCR检测BVDV阳性。BVDV以血清（36.9 %）检出率最高，其次为粪便（12.3 %）和血液（9.6 %）。测序分析鉴定出三种亚型：BVDV-1a（16.5% %）、BVDV-1b（53.6 %）和BVDV-2a（29.9 %）。基于5′utr的最大进化枝可信度（MCC）树表明，韩国BVDV-1和BVDV-2最近的共同祖先可能分别出现在1988年和1995年左右。BVDV-1和BVDV-2a的进化速率分别为3.99 × 10-3和4.0 × 10-3个替换/位点/年，与其他国家相比进化速度较快。MCC树显示了BVDV-1a、-2a和-1b的进化顺序。系统发育分析表明，最近的BVDV-1b序列比其他亚型表现出更大的遗传变异，表明其进化动力学加速且异质性。贝叶斯天际线图分析显示，BVDV-1（尤其是BVDV-1b）的病毒数量在2018年左右显著增加，而BVDV-2a的病毒数量在2016年左右开始逐渐增加。这是第一个描述韩国BVDVs进化动力学的研究。这些发现加强了对韩国BVDV最近的分子流行病学和进化动力学的理解，并强调了继续进行分子监测和控制策略的必要性。

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引用次数: 0

Decoding LL-37: Structure and antimicrobial mechanisms against microbial threats 解码LL-37：结构和对抗微生物威胁的抗菌机制。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 Epub Date: 2025-11-19 DOI: 10.1016/j.meegid.2025.105853

Alireza Neshani , Hosna Zare , Nooshin Sadat Ghiasi , Mohammad Ali Karimi , Mahdi Hosseini Bafghi

Introduction

The emergence of antibiotic-resistant pathogens is a significant global health concern that necessitates the development of new antimicrobial drugs. Due to its broad-spectrum action against bacteria, fungi, and viruses, human cathelicidin LL-37, an antimicrobial peptide (AMP), has emerged as a potential option.

Methods

Data from PubMed, Scopus, Google Scholar, and Web of Science up to March 30, 2025, were investigated in this study. Studies were considered depending on their analysis of LL-37's structure, antimicrobial abilities, and mechanisms of action. For bacterial, fungal, and viral infections, standardized tests produced quantitative data.

Results

LL-37 effectively combats over 38 bacteria, 16 fungi, and 16 viruses through various mechanisms, including membrane rupture, targeting, and biofilm suppression. These mechanisms involve cell wall destruction, membrane permeabilization, oxidative stress, cell cycle arrest, adhesion prevention, gene modification, and disruption of viral envelopes, entry, and replication.

Conclusion

LL-37 presents a potential medicinal possibility due to its broad-spectrum antimicrobial properties. However, issues such as proteolytic sensitivity and potential high-concentration toxicity must be addressed. To fully realize LL-37's therapeutic potential against multidrug-resistant infections, future studies should focus on creating stable analogs, optimizing delivery mechanisms, and exploring synergistic combinations with existing antibiotics.

抗生素耐药病原体的出现是一个重大的全球卫生问题，需要开发新的抗微生物药物。由于其对细菌、真菌和病毒的广谱作用，抗菌肽（AMP）人抗菌肽LL-37已成为一种潜在的选择。方法：对PubMed、Scopus、谷歌Scholar和Web of Science截至2025年3月30日的数据进行调查。研究的考虑取决于他们对LL-37的结构、抗菌能力和作用机制的分析。对于细菌、真菌和病毒感染，标准化测试产生定量数据。结果：LL-37通过破膜、靶向和生物膜抑制等多种机制，有效对抗38种细菌、16种真菌和16种病毒。这些机制包括细胞壁破坏、膜渗透、氧化应激、细胞周期阻滞、粘附预防、基因修饰、病毒包膜破坏、进入和复制。结论：LL-37具有广谱抗菌作用，具有潜在的药用价值。然而，必须解决诸如蛋白水解敏感性和潜在的高浓度毒性等问题。为了充分发挥LL-37对耐多药感染的治疗潜力，未来的研究应侧重于建立稳定的类似物，优化给药机制，探索与现有抗生素的协同联合。

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引用次数: 0