Infection Genetics and Evolution最新文献_第6页

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 Epub Date: 2025-11-20 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

Virulence comparison and pathological impacts of three clinical Klebsiella pneumoniae isolates in a zebrafish larval model 三种临床肺炎克雷伯菌分离株在斑马鱼幼虫模型中的毒力比较和病理影响

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.2025.105847

Yanfei Jing , Ke Yu , Hai-yan Yu , Pei-pei Zhao , Hui-fang Wang , Zhong-bo Shang

Klebsiella pneumoniae (Kp) can cause infections in communities and hospitals. After a report of a first highly virulent strain, it has now become the important pathogens that threatens human health and can often infect patients in intensive care units (ICUs). Kp is invasive and causes damage to the liver, pancreas, blood, intestines, and even the central nervous system. Zebrafish is a model organism with many advantages in biomedicine, and it has been used as a host to evaluate the virulence of Kp. However, there are no reports using zebrafish as a host to study the pathological characteristics of Kp. In this study, three Kp strains (KP1053, KP1196, and KP1195) were isolated from two clinical patients. The genetic and drug-susceptibility properties of the strains were first studied, and then zebrafish was used as a host to evaluate their virulence and pathogenicity. The three clinical Kp strains led to a marked decrease in the zebrafish survival rate, heart rate, and swimming distance; they also impeded the development of the swim bladder and resulted in a notable increase in the number of inflammatory cells. The virulence of these three strains followed the sequence KP1196 > KP1053 > KP1195. The transcriptome analysis found that lung, liver, nerve, and other developmental processes were significantly enriched in differentially expressed genes (DEGs), indicating that Kp may affect organ pathology through these genes. Our research offers a valuable reference for comprehending the pathological mechanisms underlying Kp clinical isolates.

肺炎克雷伯菌（Kp）可在社区和医院引起感染。在报告了第一个高毒力菌株之后，它现已成为威胁人类健康的重要病原体，并且经常可以感染重症监护病房（icu）的患者。Kp具有侵袭性，可对肝脏、胰腺、血液、肠道甚至中枢神经系统造成损害。斑马鱼是一种在生物医学上具有许多优势的模式生物，已被用作评价Kp毒力的宿主。然而，目前尚无以斑马鱼为宿主研究Kp病理特征的报道。本研究从2例临床患者中分离到3株Kp菌株（KP1053、KP1196和KP1195）。首先研究菌株的遗传和药敏特性，然后以斑马鱼为宿主对其毒力和致病性进行评价。3种临床Kp菌株导致斑马鱼存活率、心率和游泳距离显著降低；它们还阻碍了鱼鳔的发育，并导致炎症细胞数量的显著增加。这3株毒株的毒力序列为KP1196 >； KP1053 > KP1195。转录组分析发现，肺、肝、神经和其他发育过程中差异表达基因（DEGs）显著富集，表明Kp可能通过这些基因影响器官病理。我们的研究为理解Kp临床分离株的病理机制提供了有价值的参考。

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引用次数: 0

Analysis of novel African swine fever variants circulating in wild boars in South Korea isolated in 2021 by deep sequencing 通过深度测序分析2021年在韩国分离的野猪中流行的新型非洲猪瘟变体

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-20 DOI: 10.1016/j.meegid.2025.105833

Van Dam Lai , Yong-kwan Kim , Min-Ho Kim , Yeeun Moon , Hyeok-Il Kwon , Weon-hwa Jheong , Jong-Soo Lee , Sung-Sik Yoo , In Pil Mo

African swine fever (ASF) is major infectious disease of concern currently circulating in swine species, causing high mortality and significant economic damage on the global scale. Since the first incident of ASF outbreak in Korea in 2019, the disease has continued to spread throughout the country despite enhanced biosecurity measures, with wild boars playing a key role. Thus, characterizing the domestic African swine fever virus (ASFV) strains including its genetic variants is crucial for both monitoring and diagnostic purposes. In this study, we sequenced and analyzed the full genome of seven Korean ASFV strains isolated from ASFV positive wild boar samples collected in 2021 from various regions. The sequences were compared with previously isolated ASFV strains to track the origin and the evolutionary trend of the ASFV variants residing in the wild boar population in Korea. A total of thirty single-nucleotide polymorphisms (SNPs) were detected which consists of ten synonymous and eighteen non-synonymous mutations, a single mutation at intergenic region (IGR), and a truncation mutation which led to a premature stop codon. Out of the mutations, thirteen were present in the MGF 505-9R gene. All seven strains contained an additional ten-nucleotides (nt) long tandem repeat sequence (TRS) between the I73R and I179L gene, similar to strains previously studied in Korea. Additionally, a new seventeen-nt long tandem repeat sequence insertion, adjacent to the MGF 505-10R, has been observed at the IGR between the MGF 505-9R and 10R genes. The results of the study provide extra insight for characterizing the ASFV virus in Korea and suggesting new molecular genetic markers for epidemiological monitoring, thus minimizing the risk of new ASF outbreaks in Korea.

非洲猪瘟（ASF）是目前在猪种中流行的令人关注的主要传染病，在全球范围内造成高死亡率和重大经济损失。自2019年韩国首次出现非洲猪瘟疫情以来，尽管加强了生物安全措施，但疫情仍在全国范围内持续蔓延，其中野猪发挥了关键作用。因此，确定国内非洲猪瘟病毒（ASFV）毒株的特征，包括其遗传变异，对于监测和诊断目的都至关重要。在这项研究中，我们对从2021年从不同地区收集的ASFV阳性野猪样本中分离的7株韩国ASFV毒株进行了全基因组测序和分析。将这些序列与先前分离的ASFV毒株进行比较，以追踪韩国野猪种群中ASFV变异的起源和进化趋势。共检测到30个单核苷酸多态性（SNPs），包括10个同义突变和18个非同义突变，1个基因间区突变（IGR）和1个截断突变（导致过早终止密码子）。在这些突变中，有13个存在于MGF 505-9R基因中。所有菌株在I73R和I179L基因之间都含有一个额外的10个核苷酸（nt）长串联重复序列（TRS），与之前在韩国研究的菌株相似。此外，在MGF 505-10R基因和MGF 505-9R基因之间的IGR上发现了一个新的17 nt长的串联重复序列插入，邻近MGF 505-10R基因。该研究结果为韩国ASFV病毒的特征提供了额外的见解，并为流行病学监测提供了新的分子遗传标记，从而最大限度地降低了韩国新的ASF暴发的风险。

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引用次数: 0

Transcriptome analysis reveals the gene expression changes in Strongyloides ratti tissue-migrating larvae 转录组分析揭示了鼠圆线虫组织迁移幼虫基因表达的变化。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-08 DOI: 10.1016/j.meegid.2025.105839

Mari Ishida , Takao Irie , Ryusei Tanaka , Haruhiko Maruyama , Ayako Yoshida

Strongyloides ratti is an intestinal nematode commonly found in rats. Unlike other Strongyloides species, the tissue-migrating third-stage larvae in S. ratti follow a unique route of invasion via the nasofrontal region before reaching the gut. Despite its importance in host invasion, the transcriptomic profile of this larval stage has not been characterized. In this study, we performed RNA sequencing (RNA-seq) to examine gene expression in head-derived tissue-migrating third-stage larvae (hL3) and infective third-stage larvae (iL3) of the S. ratti Tokyo strain. hL3 were collected from rat heads at 30 h post-infection. Differential expression analysis revealed 664 upregulated genes in hL3. Functional annotation showed enrichment of genes encoding astacin metalloproteases and sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) protein families—both associated with tissue invasion and immune modulation. Quantitative RT-PCR was used to validate selected differentially expressed genes. Seven hL3-specific astacin genes were identified, of which six belonged to the M12A group. One hL3-specific astacin gene showed domain similarity to strongylastacin, a known tissue-penetration protein. Two SCP/TAPS genes were unique to hL3 and were absent from parasitic females, suggesting distinct roles in larval migration. By contrast, G protein-coupled receptor genes, particularly those related to chemosensory functions, were not upregulated in hL3, indicating that these pathways may be less important during this stage. These results provide the first transcriptomic profile of hL3 in S. ratti, and identify potential molecular mechanisms driving larval migration and immune evasion during host infection.

圆形线虫是一种常见于大鼠的肠道线虫。与其他圆形线虫不同的是，在到达肠道之前，S. ratti的组织迁移第三阶段幼虫遵循独特的入侵途径，通过鼻额区。尽管它在宿主入侵中很重要，但这一幼虫阶段的转录组学特征尚未被表征。在这项研究中，我们采用RNA测序（RNA-seq）方法检测了东京鼠斑绦虫头源性组织迁移第三期幼虫（hL3）和感染性第三期幼虫（iL3）的基因表达。感染后30 h从大鼠头部采集hL3。差异表达分析显示，在hL3中有664个基因表达上调。功能注释显示，astacin金属蛋白酶和精子包膜蛋白/Tpx-1/Ag5/PR-1/Sc7 （SCP/TAPS）蛋白家族编码基因富集，这些基因都与组织侵袭和免疫调节有关。采用定量RT-PCR技术对选择的差异表达基因进行验证。共鉴定出7个h3特异性星酸基因，其中6个属于M12A组。一个hl3特异性的星黄素基因显示与强基星黄素（一种已知的组织渗透蛋白）结构域相似。两个SCP/TAPS基因是hL3所特有的，在寄生雌性中不存在，这表明在幼虫迁移中有不同的作用。相比之下，G蛋白偶联受体基因，特别是那些与化学感觉功能相关的基因，在hL3中没有上调，这表明这些途径在这一阶段可能不那么重要。这些结果提供了鼠形霉hL3的首个转录组谱，并确定了在宿主感染期间驱动幼虫迁移和免疫逃避的潜在分子机制。

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引用次数: 0

Characterization of genes involved in hemoglobin degradation in Plasmodium vivax isolates from Chennai, India, and species of non-human primate malaria 印度金奈间日疟原虫分离株和非人灵长类疟疾种血红蛋白降解相关基因的研究

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-11 DOI: 10.1016/j.meegid.2025.105823

Sneh Shalini , Neelima Mishra , Sonia Verma , Sonal Kale , Prashant K. Mallick , Surendra K. Prajapati , Anil Kumar , Nalini Srivastava , Hema Joshi , Alex Eapen , Om P. Singh

Background

Plasmodium vivax poses a persistent obstacle to global malaria elimination efforts. While no detectable chloroquine (CQ) resistance has been found in patient samples from India, this observation awaits confirmation. The mechanism of action of CQ continues to be debated. Hemoglobin degradation within the parasite's food vacuole (FV) is integral to its survival and serves as a promising target for antimalarial drug development.

Methods

This study investigates the molecular and structural characteristics of three key FV enzymes—plasmepsin IV (PM_IV), heme detoxification protein (HDP), and falcilysin (FLN)—in P. vivax isolates from India. Genomic DNA from 30 clinical isolates and three chloroquine (CQ)-resistant reference strains was analyzed to identify mutations and assess structural implications through homology modelling.

Results

Several nonsynonymous mutations were detected, including c.493G>A (Val165Ile) in PM_IV, c.1537A>G (Asn513Asp), and c.2027G>A (Gly676Asp) in FLN, and a novel in-frame duplication c.28_33dup (ATCGCC) in HDP. Structural modelling revealed that these mutations did not affect the active binding sites of the enzymes.

Conclusions

The genes were highly conserved across isolates, underscoring their important (essential) roles in parasite survival and their potential as drug targets. These are the first findings from the Indian subcontinent that provide critical insights into the mechanisms of chloroquine (CQ) action and resistance, paving the way for novel therapeutic strategies against Plasmodium vivax malaria.

背景：间日疟原虫对全球消除疟疾的努力构成了持续的障碍。虽然在印度患者样本中未发现可检测到的氯喹耐药性，但这一观察结果有待证实。CQ的作用机制仍有争议。寄生虫食物液泡（FV）内的血红蛋白降解是其生存所不可或缺的，也是抗疟疾药物开发的一个有希望的靶点。方法：研究印度间日疟原虫分离株中三种关键酶——plasmepsin IV （PM_IV）、血红素解毒蛋白（HDP）和falcilysin （FLN）的分子结构特征。分析了30株临床分离株和3株氯喹耐药参考株的基因组DNA，通过同源性建模鉴定突变并评估结构意义。结果：检测到多个非同同义词突变，包括PM_IV中的c.493G > A (Val165Ile)， FLN中的c.1537G > A （Asn513Asp）和c.2027G > A (Gly676Asp)，以及HDP中新的帧内重复c.36_41dup （ATCGCC）。结构模型显示，这些突变不影响酶的活性结合位点。结论：这些基因在整个分离株中高度保守，强调了它们在寄生虫生存中的重要（基本）作用和它们作为药物靶点的潜力。这些是来自印度次大陆的首次发现，为氯喹（CQ）的作用和耐药性机制提供了重要见解，为针对间日疟原虫疟疾的新治疗策略铺平了道路。

{"title":"Characterization of genes involved in hemoglobin degradation in Plasmodium vivax isolates from Chennai, India, and species of non-human primate malaria","authors":"Sneh Shalini , Neelima Mishra , Sonia Verma , Sonal Kale , Prashant K. Mallick , Surendra K. Prajapati , Anil Kumar , Nalini Srivastava , Hema Joshi , Alex Eapen , Om P. Singh","doi":"10.1016/j.meegid.2025.105823","DOIUrl":"10.1016/j.meegid.2025.105823","url":null,"abstract":"<div><h3>Background</h3><div><em>Plasmodium vivax</em> poses a persistent obstacle to global malaria elimination efforts. While no detectable chloroquine (CQ) resistance has been found in patient samples from India, this observation awaits confirmation. The mechanism of action of CQ continues to be debated. Hemoglobin degradation within the parasite's food vacuole (FV) is integral to its survival and serves as a promising target for antimalarial drug development.</div></div><div><h3>Methods</h3><div>This study investigates the molecular and structural characteristics of three key FV enzymes—plasmepsin IV (PM_IV), heme detoxification protein (HDP), and falcilysin (FLN)—in <em>P. vivax</em> isolates from India. Genomic DNA from 30 clinical isolates and three chloroquine (CQ)-resistant reference strains was analyzed to identify mutations and assess structural implications through homology modelling.</div></div><div><h3>Results</h3><div>Several nonsynonymous mutations were detected, including c.493G>A (Val165Ile) in PM_IV, c.1537A>G (Asn513Asp), and c.2027G>A (Gly676Asp) in FLN, and a novel in-frame duplication c.28_33dup (ATCGCC) in HDP. Structural modelling revealed that these mutations did not affect the active binding sites of the enzymes.</div></div><div><h3>Conclusions</h3><div>The genes were highly conserved across isolates, underscoring their important (essential) roles in parasite survival and their potential as drug targets. These are the first findings from the Indian subcontinent that provide critical insights into the mechanisms of chloroquine (CQ) action and resistance, paving the way for novel therapeutic strategies against <em>Plasmodium vivax</em> malaria.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105823"},"PeriodicalIF":2.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145058789","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

Targeted next-generation sequencing reveals pathogen mono- and co-detection patterns in pediatric Mycoplasma pneumoniae pneumonia 靶向下一代测序揭示了儿童肺炎支原体肺炎的病原体单一和共同检测模式。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-18 DOI: 10.1016/j.meegid.2025.105832

Genfeng Wu , Yuejie Zheng , Kangyan Yuan , Yanmin Bao , Li Li , Yuzheng Li , Wenjian Wang , Heping Wang

Background

Following pandemic control optimization, Mycoplasma pneumoniae (MP) has emerged as a predominant pediatric respiratory pathogen in Shenzhen. Understanding its epidemiological patterns and drug resistance is critical for managing severe MP-associated pneumonia.

Methods

This retrospective study analyzed 607 hospitalized children (February–November 2023) using targeted next-generation sequencing (tNGS) of bronchoalveolar lavage fluid. MP-positive cases were stratified by age, gender, clinical features, drug resistance genes, and co-detection profiles.

Results

Pathogens were identified in 605 cases (99.7 %), with MP constituting 85.0 % of detected pathogens. Among 209 cases with resistance genes, A2063G mutation predominated (98.1 %). Patients were categorized into: MP-positive (n = 444), MP-carriage (n = 72), and MP-negative (n = 91) groups. Age stratification revealed significantly older MP-positive patients (median 72 months, IQR 48–96) versus carriages (29.5 months, IQR 14–60) and negatives (36 months, IQR 16–60) (P < 0.001). Gender distribution showed no significant intergroup differences (χ² = 2.619, p = 0.270). The MP-positive group demonstrated lower co-detection rates of Haemophilus influenzae (12.2 % vs 37.5 %/31.5 %) and Moraxella catarrhalis (10.6 % vs 25.0 %/20.2 %) compared to carriages and negatives (P < 0.001). tNGS uncovered atypical pathogens including Tropheryma whipplei (13.3 %) and Fusobacterium nucleatum (6.3 %).

Conclusion

Post-pandemic MP resurgence correlates with increased severe pediatric pneumonia despite declining macrolide resistance rates (23.2 % in 2023 vs historical 80–90 %). MP primarily manifests as monoinfections, while M. catarrhalis and H. influenzae co-detection may confer observed co-detection pattern. These findings underscore tNGS's clinical utility in identifying atypical pathogens and guiding antimicrobial stewardship in pediatric pneumonia management.

背景：随着大流行控制的优化，肺炎支原体（MP）已成为深圳主要的儿科呼吸道病原体。了解其流行病学模式和耐药性对于管理严重的mp相关性肺炎至关重要。方法：采用支气管肺泡灌洗液靶向新一代测序（tNGS）对607例住院儿童（2023年2 - 11月）进行回顾性研究。mp阳性病例按年龄、性别、临床特征、耐药基因和共检概况进行分层。结果：检出病原菌605例（99.7 %），其中MP占检出病原菌的85.0% %。209例耐药基因中以A2063G突变为主（98.1% %）。患者分为：mp阳性组（n = 444）、mp携带组（n = 72）和mp阴性组（n = 91）。年龄分层显示，mp阳性患者（中位72 个月，IQR 48-96）与阴性患者（中位29.5 个月，IQR 14-60）和阴性患者（中位36 个月，IQR 16-60）相比（P 2 = 2.619,P = 0.270）具有显著性差异。MP-positive集团展示了co-detection利率下降的流感嗜血杆菌(12.2 vs 37.5  % % / 31.5 %)和莫拉克斯氏菌属复活(10.6 vs 25.0  % % / 20.2 %)相比,车厢和底片(P 结论:流行后议员复苏与增长尽管大环内酯物电阻率下降,严重的小儿肺炎(23.2 % 2023年和80 - 90年的历史 %)。MP主要表现为单感染，而卡塔卡分枝杆菌和流感嗜血杆菌共同检测可能会产生观察到的共同检测模式。这些发现强调了tNGS在鉴别非典型病原体和指导儿科肺炎抗菌药物管理方面的临床应用。

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引用次数: 0

Genomic mechanisms underlying the adaptation of Anaerobutyricum species to the human host 厌氧丁酸菌对人类宿主适应的基因组机制。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-16 DOI: 10.1016/j.meegid.2025.105844

Chaoyang Gu , Dezhong Wang , Kai Han , Jiarui Li , Liang Chen , Qinghui Zhuang , Tingzhu Yao , HengKun Wei , Jinglin Yue , Mingxi Hua , Chen Chen

The Anaerobutyricum genus, comprising Anaerobutyricum hallii and Anaerobutyricum soehngenii, is prevalent in the human gut microbiota and produces short-chain fatty acids (SCFAs) that influence host metabolism and inflammation. However, systematic genomic studies on this genus are limited. In this study, we conducted a comprehensive genomic analysis of 84 Anaerobutyricum genomes, based on the average nucleotide identity (ANI), average amino acid identity (AAI) and core genes phylogenetic tree analysis, we clustered the Anaerobutyricum genus to Anaerobutyricum spp., Anaerobutyricum hallii and Anaerobutyricum soehngenii. Specifically, Anaerobutyricum hallii and Anaerobutyricum soehngenii are specific to human hosts, possessing longer genomes and lower GC content. They contain more integrative and conjugative elements (ICEs), which genetically encoded dltA, mbtB and dhbE genes that responds for the biosynthesis of siderophore group nonribosomal peptides, which might contribute to its colonization. In addition, ICEs in Anaerobutyricum hallii and Anaerobutyricum soehngenii could also pose a risk for antibiotic resistance gene transfer. Our study advances the understanding the of Anaerobutyricum's and host adaptability, highlighting the importance of genomic analysis in refining taxonomic boundaries and assessing the safety of using these bacteria as probiotics.

厌氧丁酸菌属，包括哈利厌氧丁酸菌和索氏厌氧丁酸菌，普遍存在于人类肠道微生物群中，产生影响宿主代谢和炎症的短链脂肪酸（SCFAs）。然而，该属的系统基因组研究是有限的。本研究对84个厌氧丁酸菌基因组进行了全面的基因组分析，基于平均核苷酸同源性（ANI）、平均氨基酸同源性（AAI）和核心基因系统发育树分析，将厌氧丁酸菌属聚类为厌氧丁酸菌spp.、厌氧丁酸菌hallii和厌氧丁酸菌soehngenii。具体来说，哈利氏厌氧丁酸菌和索氏厌氧丁酸菌是人类宿主特有的，具有较长的基因组和较低的GC含量。它们含有更多的整合和共轭元件（ice），这些元件编码dltA， mbtB和dhbE基因，这些基因响应铁载体组非核糖体肽的生物合成，这可能有助于其定植。此外，哈利厌氧丁酸菌和索氏厌氧丁酸菌的ice也可能造成抗生素耐药基因转移的风险。我们的研究促进了对厌氧丁酸菌和宿主适应性的理解，强调了基因组分析在完善分类界限和评估使用这些细菌作为益生菌的安全性方面的重要性。

{"title":"Genomic mechanisms underlying the adaptation of Anaerobutyricum species to the human host","authors":"Chaoyang Gu , Dezhong Wang , Kai Han , Jiarui Li , Liang Chen , Qinghui Zhuang , Tingzhu Yao , HengKun Wei , Jinglin Yue , Mingxi Hua , Chen Chen","doi":"10.1016/j.meegid.2025.105844","DOIUrl":"10.1016/j.meegid.2025.105844","url":null,"abstract":"<div><div>The <em>Anaerobutyricum</em> genus, comprising <em>Anaerobutyricum hallii</em> and <em>Anaerobutyricum soehngenii</em>, is prevalent in the human gut microbiota and produces short-chain fatty acids (SCFAs) that influence host metabolism and inflammation. However, systematic genomic studies on this genus are limited. In this study, we conducted a comprehensive genomic analysis of 84 <em>Anaerobutyricum</em> genomes, based on the average nucleotide identity (ANI), average amino acid identity (AAI) and core genes phylogenetic tree analysis, we clustered the <em>Anaerobutyricum</em> genus to <em>Anaerobutyricum spp.</em>, <em>Anaerobutyricum hallii</em> and <em>Anaerobutyricum soehngenii</em>. Specifically, <em>Anaerobutyricum hallii</em> and <em>Anaerobutyricum soehngenii</em> are specific to human hosts, possessing longer genomes and lower GC content. They contain more integrative and conjugative elements (ICEs), which genetically encoded <em>dltA</em>, <em>mbtB</em> and <em>dhbE</em> genes that responds for the biosynthesis of siderophore group nonribosomal peptides, which might contribute to its colonization. In addition, ICEs in <em>Anaerobutyricum hallii</em> and <em>Anaerobutyricum soehngenii</em> could also pose a risk for antibiotic resistance gene transfer. Our study advances the understanding the of <em>Anaerobutyricum</em>'s and host adaptability, highlighting the importance of genomic analysis in refining taxonomic boundaries and assessing the safety of using these bacteria as probiotics.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"135 ","pages":"Article 105844"},"PeriodicalIF":2.6,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318981","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

Exploratory interaction of Chionis alba (snowy sheathbill) with the amatoxin-producing mushroom Galerina marginata in Antarctica 南极雪鞘喙菌与产蛋黄素的蘑菇Galerina marginata的探索相互作用。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-11 DOI: 10.1016/j.meegid.2025.105822

Fernando Augusto Bertazzo-Silva , Alice Lemos Costa , Jorge Renato Pinheiro Velloso , Flavia Helena Aires Sousa , Carlos Ernesto Gonçalves Reynaud Schaefer , Jair Putzke

We report a rare behavioral observation involving an individual of Chionis alba (snowy sheathbill) attempting to consume a basidiome of the toxic mushroom Galerina marginata on Livingston Island, Antarctica. The bird briefly picked up the basidiome before rejecting it. This event, to our knowledge, represents the first recorded interaction between an Antarctic bird and this deadly fungus, suggesting possible chemical or gustatory deterrence mechanisms. Such interactions, though anecdotal, contribute to the understanding of trophic dynamics and fungal ecology in polar environments.

我们报告了一个罕见的行为观察，涉及到一只Chionis alba（雪鞘喙）个体试图消耗有毒蘑菇Galerina marginata的担子子。这只鸟短暂地捡起了担子架，然后拒绝了它。据我们所知，这一事件代表了南极鸟类与这种致命真菌之间首次有记录的相互作用，表明可能存在化学或味觉威慑机制。这种相互作用，虽然道听途说，有助于理解营养动力学和真菌生态在极地环境。

引用次数: 0

Reassessing putative antimicrobial resistance variants in Burkholderia pseudomallei: Commentary on a recent genomic analysis 重新评估假性伯克氏菌中假定的抗菌素耐药性变异：对最近基因组分析的评论。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-10-14 DOI: 10.1016/j.meegid.2025.105842

Erin P. Price , Derek S. Sarovich

引用次数: 0

Genomic insights of two Acinetobacter non-baumannii strains with uncommon mechanisms of resistance leading to cefiderocol resistance 两种非鲍曼不动杆菌菌株的基因组见解，具有罕见的耐药机制，导致头孢地罗耐药。

IF 2.6 4区医学 Q3 INFECTIOUS DISEASES

Infection Genetics and Evolution

Pub Date : 2025-11-01 Epub Date: 2025-09-16 DOI: 10.1016/j.meegid.2025.105820

Usman Akhtar , Samyar Moheb , Carol Davies-Sala , Joshua Gutierrez , Fernando Pasteran , Marisel R. Tuttobene , Tomás Subils , Chun Fu Cheng , Quentin Valle , Rajnikant Sharma , Marcelo E. Tolmasky , Gauri Rao , Robert A. Bonomo , German M. Traglia , María Soledad Ramírez

The emergence of antimicrobial resistance in Acinetobacter species poses a significant clinical challenge, particularly in non-baumannii species, which are often overlooked in healthcare settings. In this study, we characterized two Acinetobacter clinical isolates, AMA204 and AMA207—identified as A. junii and A. haemolyticus, respectively—which exhibit uncommon resistance mechanisms that enable survival in the presence of cefiderocol, regardless of their initial minimum inhibitory concentration values. Whole-genome sequencing and comparative genomic analyses were performed to investigate the genetic determinants associated with their resistance profiles. Antimicrobial susceptibility testing confirmed multidrug resistance, with both isolates harboring key β-lactamase genes, including bla_OXA-58, and bla_NDM-1 in AMA204, and bla_OXA-58 and bla_PER-2 in AMA207. Phylogenomic analyses revealed genetic relatedness to geographically diverse isolates, suggesting possible evolutionary trends and transmission dynamics. Additionally, iron uptake systems were analysed, highlighting potential mechanisms contributing to cefiderocol resistance together with the presence of listed β-lactamase. This study underscores the clinical relevance of non-baumannii Acinetobacter species in antimicrobial resistance and emphasizes the need for continued surveillance and novel therapeutic strategies to combat these emerging threats.

不动杆菌物种抗菌素耐药性的出现构成了重大的临床挑战，特别是在非鲍曼原虫物种中，这在卫生保健环境中经常被忽视。在这项研究中，我们鉴定了两种临床分离的不动杆菌，AMA204和ama207，分别鉴定为朱尼假杆菌和溶血假杆菌，它们表现出罕见的耐药机制，能够在头孢地罗存在下存活，而不管它们的初始最低抑制浓度值如何。进行了全基因组测序和比较基因组分析，以调查与其抗性谱相关的遗传决定因素。药敏试验证实两株菌株均存在多药耐药，其中AMA204中含有blaOXA-58和blaNDM-1基因，AMA207中含有blaOXA-58和blaPER-2基因。系统基因组学分析揭示了地理上不同分离株的遗传相关性，提示可能的进化趋势和传播动态。此外，还分析了铁摄取系统，强调了导致头孢地罗耐药的潜在机制以及所列β-内酰胺酶的存在。这项研究强调了非鲍曼不动杆菌在抗菌素耐药性中的临床相关性，并强调需要持续监测和新的治疗策略来对抗这些新出现的威胁。

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引用次数: 0