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IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-12 DOI: 10.1016/j.meegid.2025.105864

Ankur Sharma , Varshini Vadhithala , Arun Kumar , Sushma Verma , Sushma Narsing Katkuri

引用次数: 0

Genetic dynamics of the Duffy antigen receptor for chemokines gene and Plasmodium vivax circulation within sub-Saharan Africa 趋化因子基因达菲抗原受体与撒哈拉以南非洲间日疟原虫循环的遗传动力学。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-08 DOI: 10.1016/j.meegid.2025.105863

Favour Adeloye , Kaothar O. Lambe , Jennifer A. Oboh , Halima Abdulsalam , Chinatu Enyinnnaya , Roseangela Nwuba , Olumide Ogundahunsi , Umberto D'Alessandro , Alfred Amambua-Ngwa , Martin M. Meremikwu , Grant Hughes , Eva Heinz , Mary A. Oboh

Introduction

Duffy antigen receptor for chemokines (DARC) is a transmembrane receptor (glycoprotein) expressed on human red blood cells. Sub-Saharan Africa (sSA) individuals, who suffer the most of the global malaria burden, predominantly carry a Duffy negative phenotype. Expression of this gene (found among Duffy-positive individuals) is known to be essential for P. vivax invasion of RBCs. While P. falciparum is the predominant Plasmodium in sSA, the upward trend in P. vivax infection is a major threat to the malaria eradication programme in the region. Since Duffy null individuals (homozygous negative) lack DARC expression, we investigated the DARC gene dynamics in relation to the emerging presence of P. vivax infections in a previously predominant P. falciparum endemic region.

Methods

A total of 223 DARC genes were retrieved from the NCBI database across various countries, Nigeria, Cameroon, Ethiopia, Madagascar and South Africa and were used for population dynamic analysis using different population genetic metrics.

Findings

Among these sSA countries, South Africa showed the most haplotype and nucleotide diversity compared to other parts of sSA. Various selection pressures were observed in Western Africa and the Central African Republic. Population structure analysis revealed DARC population clustering of Cameroon, Nigeria and Ethiopia (despite Ethiopia's geographic distance), suggestive of shared ancestry and minimal DARC locus divergence. Conversely, South Africa and Madagascar showed a distinct genetic lineage reflecting differences in evolutionary pressures.

Conclusion

Our analysis suggests minimal genetic diversity within sSA with evidence of selection potentially attributed to the recent emergence of P. vivax infections. However, greater diversity was observed in South Africa. Evidence of selection of this gene and detection of P. vivax among Duffy-null individuals in the other regions is truly a public health concern.

达菲抗原趋化因子受体（DARC）是一种在人红细胞上表达的跨膜受体（糖蛋白）。全球疟疾负担最重的撒哈拉以南非洲（sSA）个体主要携带Duffy阴性表型。该基因的表达（在duffy阳性个体中发现）已知是间日疟原虫入侵红细胞所必需的。虽然恶性疟原虫是sSA的主要疟原虫，但间日疟原虫感染的上升趋势对该区域的疟疾根除规划构成了重大威胁。由于Duffy阴性个体（纯合子阴性）缺乏DARC表达，我们研究了DARC基因动态与以前恶性疟原虫流行地区间日疟原虫感染的新存在的关系。方法：从尼日利亚、喀麦隆、埃塞俄比亚、马达加斯加和南非等国家的NCBI数据库中检索223个DARC基因，采用不同的群体遗传指标进行群体动态分析。结果：在这些sSA国家中，与sSA其他地区相比，南非表现出最多的单倍型和核苷酸多样性。在西非和中非共和国观察到各种选择压力。种群结构分析显示，喀麦隆、尼日利亚和埃塞俄比亚的DARC种群聚类（尽管埃塞俄比亚地理距离较远），表明它们具有共同的祖先和最小的DARC位点差异。相反，南非和马达加斯加表现出不同的遗传谱系，反映了进化压力的差异。结论：我们的分析表明，sSA内的遗传多样性最小，有证据表明，这种选择可能归因于最近出现的间日疟原虫感染。然而，在南非观察到更大的多样性。该基因的选择和间日疟原虫在其他地区Duffy-null个体中检测的证据确实是一个公共卫生问题。

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引用次数: 0

Genotyping of Enterocytozoon bieneusi in Denmark and Sweden: Is the outbreak-linked genotype C a rodent-adapted genotype? Evidence from rodents and wastewater 丹麦和瑞典bieneusenterocyzoon的基因分型：与疫情相关的基因型C是啮齿动物适应的基因型吗？来自啮齿动物和废水的证据。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 DOI: 10.1016/j.meegid.2025.105861

Edgar Baz-González , Tatiana Siegler Lathrop , Anette Hansen , Marianne Lebbad , Christen Rune Stensvold

Wastewater can serve as a useful indicator of the presence of pathogens circulating in the human population, including zoonotic pathogens mainly adapted to rodents. Rodents are small mammals distributed worldwide and capable of inhabiting various ecosystems, including sewer systems. Enterocytozoon bieneusi is the main etiological agent of human microsporidiosis, a well-established zoonosis; however, little is known about the epidemiology of microsporidiosis in Scandinavia, except for two foodborne outbreaks reported in Sweden and Denmark, both of which were caused by genotype C. The aim of this study was to determine the presence and genetic diversity of E. bieneusi in wild rodent populations in Denmark and influent wastewater samples from wastewater treatment plants in Sweden. Samples were analysed using nested PCR targeting the ribosomal internal transcribed spacer (ITS) and flanking regions of E. bieneusi, followed by Sanger sequencing. Sampled species included Apodemus flavicollis, Apodemus sp., Apodemus sylvaticus, Micromys minutus, Microtus agrestis, Mus musculus, and Myodes glareolus, with an overall positivity rate of 25.0 % (95 % CI, 14.4–38.4) (14/56). Meanwhile, E. bieneusi was detected in 82.8 % (95 % CI, 64.2–94.2) (24/29) of the wastewater samples. Sequence analysis revealed the presence of two known (C, EBCMAP-032), and a novel genotype (DKE-1) in rodents, and eight established (C, CYG-4, D, EBCMAP-007, EBCMAP-031, EBCMAP-032, Type IV, WildBoar3) and four new genotypes (SweWW1–SweWW4) in Swedish wastewater. A relatively high frequency of genotype C was observed in this study, suggesting a zoonotic—and possibly rodent-adapted source of the previous foodborne outbreaks caused by this genotype in Sweden and Denmark.

废水可作为在人群中传播的病原体存在的有用指标，包括主要适用于啮齿动物的人畜共患病原体。啮齿动物是分布在世界各地的小型哺乳动物，能够在各种生态系统中生存，包括下水道系统。人微孢子虫病是一种公认的人畜共患病，双胞虫是其主要病原；然而，除了在瑞典和丹麦报告的两起由基因型c引起的食源性暴发外，对斯堪的纳维亚地区的微孢子虫病流行病学知之甚少。本研究的目的是确定丹麦野生啮齿动物种群和瑞典污水处理厂的流入废水样本中是否存在和遗传多样性。采用巢式PCR方法，对bieneusi的核糖体内部转录间隔区（ITS）和侧翼区域进行分析，然后进行Sanger测序。抽样种有黄颡鱼、姬鼠、森林姬鼠、小仓鼠、野仓鼠、小家鼠和光斑鼠，总阳性率为25.0 %(95 % CI, 14.4 ~ 38.4)（14/56）。同时，bieneusi的检出率为82.8 %(95 % CI, 64.2 ~ 94.2)（24/29）。序列分析显示，啮齿动物中存在2种已知基因型（C, EBCMAP-032）和1种新基因型（DKE-1），瑞典废水中存在8种已建立基因型（C, CYG-4， D, EBCMAP-007, EBCMAP-031, EBCMAP-032, Type IV, WildBoar3）和4种新基因型（SweWW1-SweWW4）。本研究中观察到基因型C的频率相对较高，这表明先前在瑞典和丹麦由该基因型引起的食源性暴发存在人畜共患病来源，也可能是啮齿动物适应的来源。

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引用次数: 0

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 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 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。

{"title":"Molecular epidemiology of Clostridioides difficile in border areas of Yunnan Province suggests possible transmission routes of the strains","authors":"Wenpeng Gu , Jiao Gong , Junrong Liang , Xiaofang Zhou , Lulu Bai , Wenzhu Zhang , Senquan Jia , Yongming Zhou , Xiaoqing Fu , Yuan Wu","doi":"10.1016/j.meegid.2025.105860","DOIUrl":"10.1016/j.meegid.2025.105860","url":null,"abstract":"<div><h3>Objectives</h3><div>A molecular epidemiological study of <em>Clostridioides difficile</em> was performed in the border areas of Yunnan Province.</div></div><div><h3>Methods</h3><div>Molecular surveillance, bacterial isolation and identification, antibiotic susceptibility tests and genome sequencing of the isolates were performed.</div></div><div><h3>Results</h3><div>Among the 788 total diarrhea patients, 97 (12.31 %) were positive for the <em>tpi</em> gene, and 86 (10.91 %) were positive for <em>tcdB</em> in the fecal samples. Forty-nine <em>C. difficile</em> strains were isolated, 38 of which were toxigenic (<em>tcdA</em>+/<em>tcdB</em>+) and 11 of which were nontoxigenic. Specifically, four binary toxin gene-positive <em>C. difficile</em> strains were first isolated in Hekou County of Yunnan. ST3, ST35 and ST2 were the most prevalent STs. The genotype profiles of <em>C. difficile</em> 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 <em>C. difficile</em> 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.</div></div><div><h3>Conclusions</h3><div>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.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"136 ","pages":"Article 105860"},"PeriodicalIF":2.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145624466","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

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 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。

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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 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

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 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

Foot-and-mouth disease virus variability and recombination on dairy farms in Pakistan 巴基斯坦奶牛场口蹄疫病毒变异和重组。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-12-01 DOI: 10.1016/j.meegid.2025.105858

Ian Fish , Carolina Stenfeldt , Umer Farooq , John Humphreys , Zaheer Ahmed , Jonathan Arzt

Field studies on foot-and-mouth disease virus (FMDV) have historically concentrated on viral sequences obtained from clinical cases. However, FMDV often causes several forms of subclinical infections in ruminants, which are further complicated by heterologous FMDV coinfections and reinfections. The focus of this current study was genomic analysis of FMDV isolates obtained from domestic water buffalo (Bubalus bubalis) with no visible signs of disease – subclinical infections. Over a 12-month period, buffalo from dairy farms in Islamabad, Pakistan, were repeatedly sampled. We used full-genome next-generation sequencing to analyze FMDVs isolated from 68 oropharyngeal fluid (OPF) samples, representing 44 animals across 18 farms. The analysis revealed the circulation of three distinct serotypes – O, A, and Asia-1. Examination of persistent viruses showed variable within-host evolution, with 0–25 substitutions observed between sampling points. Notably, several animals were infected by recombinant viruses derived from antigenically distinct parental strains. This included at least five different recombinants recovered from one animal, as confirmed through plaque purification of OPF samples. In several instances, recombination events were determined to have occurred within the course of the study period. These results highlight the complexity of naturally occurring subclinical FMDV infections and emphasize the role of recombination in enhancing viral diversity in endemic regions.

对口蹄疫病毒（FMDV）的实地研究历来集中于从临床病例中获得的病毒序列。然而，口蹄疫病毒经常在反刍动物中引起几种形式的亚临床感染，并因异源口蹄疫病毒合并感染和再感染而进一步复杂化。目前这项研究的重点是对从没有明显疾病迹象-亚临床感染的家养水牛（Bubalus bubalis）获得的口蹄疫病毒分离株进行基因组分析。在12个月的时间里，来自巴基斯坦伊斯兰堡奶牛场的水牛被反复取样。我们使用下一代全基因组测序分析了从68个口咽液（OPF）样本中分离的fmdv，代表了18个农场的44只动物。分析显示有三种不同的血清型——O型、A型和Asia-1型。对持久性病毒的检查显示宿主内的进化是可变的，在采样点之间观察到0-25次替换。值得注意的是，一些动物被从抗原性不同的亲本毒株衍生的重组病毒感染。这包括从一只动物身上回收的至少五种不同的重组体，通过对OPF样本的空斑纯化证实了这一点。在一些情况下，重组事件被确定发生在研究期间。这些结果突出了自然发生的亚临床FMDV感染的复杂性，并强调了重组在增强流行地区病毒多样性方面的作用。

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引用次数: 0

Correlations between incidence of syphilis and frequencies of human leukocyte antigens haplotypes in China: An ecological study 中国梅毒发病率与人白细胞抗原单倍型频率的相关性：一项生态学研究。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-19 DOI: 10.1016/j.meegid.2025.105854

Wei-Jing Lin , Hong-Fei Mi , Ning-Dai Chen , Yue Zhong , Tian-Ci Yang , Yao Xiao

In China, the incidence of syphilis varies across different regions, as do the frequencies of HLA haplotypes. The progression and stages of syphilis infection may be associated with HLA polymorphisms. This study employed an ecological study design, utilizing data from a nationwide survey on the distribution of HLA frequencies in the Chinese Bone Marrow Donor Program and the incidence of syphilis in China during the same period. Pearson and Spearman correlation analyses, adjusted for multiple testing using the Benjamini-Hochberg procedure, were performed to investigate the correlation between HLA polymorphism and the incidence of syphilis. The overall incidence of syphilis was significantly correlated with the frequencies of six specific HLA-A-C-B-DRB1-DQB1 haplotypes in China. Additionally, as many as 24 HLA-A-C-B-DRB1-DQB1 haplotypes were found to be correlated with the incidence of congenital syphilis. Nominal correlations were observed between several HLA haplotype frequencies and the incidences of secondary, tertiary, and latent syphilis prior to false discovery rate correction. These findings suggest that the frequencies of HLA haplotypes are correlated with the incidence of syphilis in China, particularly in congenital syphilis cases. Collectively, susceptibility to syphilis infection and disease progression appears to be closely linked to HLA polymorphisms.

在中国，梅毒的发病率在不同地区有所不同，HLA单倍型的频率也是如此。梅毒感染的进展和分期可能与HLA多态性有关。本研究采用了生态研究设计，利用了中国骨髓捐献计划中HLA频率分布和同期中国梅毒发病率的全国调查数据。Pearson和Spearman相关分析，使用Benjamini-Hochberg程序调整多重检验，以调查HLA多态性与梅毒发病率之间的相关性。中国梅毒总发病率与6种特异性HLA-A-C-B-DRB1-DQB1单倍型的频率显著相关。此外，发现多达24个HLA-A-C-B-DRB1-DQB1单倍型与先天性梅毒的发病率相关。在错误发现率校正之前，观察到几种HLA单倍型频率与继发性、三期和潜伏性梅毒发病率之间的名义相关性。这些发现表明，HLA单倍型的频率与中国梅毒的发病率相关，特别是在先天性梅毒病例中。总的来说，梅毒感染的易感性和疾病进展似乎与HLA多态性密切相关。

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引用次数: 0