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Origin and development of two Escherichia coli clones vertically transferred in broiler production. 两个垂直转移大肠杆菌克隆在肉鸡生产中的起源和发展。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001516
Yufei Zhao, Annet Heuvelink, John Elmerdahl Olsen, Louise Poulsen, Henrik Christensen

Investigation of clonal development of dominant persistent clones of avian pathogenic Escherichia coli (APEC) is important to understand their evolution and to gain knowledge to improve their control in poultry production. Whole-genomic sequencing, including hybrid assembled genomes of short and long reads, was used to analyse clonal persistence and evolution of APEC. Two vertically transferred E. coli clones, represented by ten isolates from sequence type (ST) 95-PFGE type 65 and eight isolates from ST131-PFGE type 47, were selected to identify genomic variations. The isolates had been sampled in broiler production during a period of 9 months in a previous study. The main differences among strains within each clone were related to plasmids, transposases, incomplete phage elements and amino acid substitutions which by far exceeded the genetic variation related to core-genome SNPs (cgSNPs). Fourier-transform infrared spectroscopy was, for the most part, only able to trace clones within the same ST. The genome-wide mutation rate was equivalent to 1.48 mutations per genome per year for ST95-PFGE65 and 2.86 for ST131-PFGE47, respectively. The most recent common ancestors were estimated back to 2009 for ST95-PFGE65 and to 2011 for ST131-PFGE47, with further divergence occurring in years until sampling in 2014-2015. The methodology introduced is able to trace the temporal origin of APEC clones. The conventional threshold of ten or fewer cgSNPs to include strains in the same clone did not consider any gain or loss of plasmids for the strains compared. On average, one plasmid transfer event was predicted every second year. For strains expected to be vertically transferred during the long production periods of great-grandparents over grandparents and parents to broilers, one to two plasmid transfers are therefore predicted, and several cgSNPs may be introduced, whereas up to one cgSNP is expected to be manifested during a broiler production cycle and rarely involving plasmid transfer.

禽致病性大肠杆菌(APEC)优势持久性克隆的克隆发育研究,对了解其进化过程和提高家禽生产中对其控制水平具有重要意义。采用全基因组测序(包括长、短序列杂交组合基因组)分析APEC的克隆持久性和进化。选取10株序列型(ST) 95-PFGE 65型和8株序列型(ST131-PFGE 47型)垂直转移的大肠杆菌克隆进行基因组变异鉴定。在先前的一项研究中,分离株在肉鸡生产中进行了为期9个月的取样。各克隆菌株间的主要差异与质粒、转座酶、不完整噬菌体元件和氨基酸取代有关,远远超过与核心基因组snp (cgsnp)相关的遗传变异。傅里叶变换红外光谱在很大程度上只能追踪同一st内的克隆,ST95-PFGE65和ST131-PFGE47的全基因组突变率分别相当于每个基因组每年1.48个突变和2.86个突变。据估计,ST95-PFGE65最近的共同祖先可追溯到2009年,ST131-PFGE47可追溯到2011年,在2014-2015年采样之前的几年里出现了进一步的分歧。所介绍的方法能够追踪APEC克隆的时间起源。在同一克隆中包含菌株的常规阈值为10个或更少的cgsnp,不考虑比较菌株的质粒的获得或损失。平均每两年预测一次质粒转移事件。对于在曾祖父母、祖父母和父母的长生产周期中垂直转移给肉鸡的菌株,因此预计会有一到两次质粒转移,并且可能会引入几个cgSNP,而在肉鸡生产周期中预计最多会出现一个cgSNP,并且很少涉及质粒转移。
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引用次数: 0
Population snapshot of Streptococcus pneumoniae causing invasive disease among adults aged ≥18 years in South Africa before and after implementation of pneumococcal conjugate vaccines in 2005-2020. 2005-2020年南非实施肺炎球菌结合疫苗前后18岁以上成年人中引起侵袭性疾病的肺炎链球菌种群快照
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001559
Kedibone Maria Ndlangisa, Cebile Lekhuleni, Happy Skosana, Linda de Gouveia, Susan Meiring, Sibongile Walaza, Vanessa Quan, Stephen D Bentley, Stephanie W Lo, Cheryl Cohen, Anne von Gottberg, Mignon du Plessis

Routine use of pneumococcal conjugate vaccines (PCV) in South Africa caused a decline in vaccine-associated invasive pneumococcal disease (IPD), followed by the emergence of non-PCV serotypes, driven mainly by pre-existing lineages. We determined the molecular epidemiology of isolates causing IPD among adults in South Africa from 2020 to 2025 before and following the implementation of PCV in 2009. We performed whole-genome sequencing on randomly selected isolates causing IPD among adults aged ≥18 years (N=1 581) during the four vaccine periods [pre-PCV (2005-2008), PCV7 (2009-2010), early-PCV13 (2011-2014) and late-PCV13 (2015-2020)]. We assigned in silico serotype, multi-locus sequence type, clonal complex (CC) and global pneumococcal sequence cluster (GPSC) and determined antimicrobial non-susceptibility profiles in silico. Poisson regression was used to calculate incidence rate ratios of imputed individual GPSC lineages using IPD incidence rate estimated per year for the three vaccine periods (PCV7, early-PCV13 and late-PCV13), compared to the pre-PCV period. Overall, our dataset represented 3.7% (n=270), 3.4% (n=128), 4.9% (n=287) and 13.5% (n=896) of adult pneumococcal isolates received during the four periods, respectively. We identified 135 GPSCs with the majority of isolates [68.7%(1 086/1 581)] clustering into 1 of 23 dominant GPSCs defined as GPSCs that comprised ≥20 genomes in the dataset. Compared to the pre-PCV7 period, a decrease in incidence of vaccine type lineages normally associated with vaccine serotypes was observed during the late-PCV13 period. GPSC2 (serotype 1) declined from 1.4 to 0.039/100,000 population (P<0.001). Some non-PCV lineages increased. GPSC26 (serotype 12F) increased from 0.07 to 0.3 (P<0.001). Of the 23 dominant GPSCs, 11 expressed ≥2 serotypes. While the majority of GPSC5/CC172 isolates expressed serotype 23F during the pre-PCV period (61.5%, 7/12), serotype 35B was the most common serotype (57.1%, 12/21) expressed by GPSC5/CC172 isolates during the late-PCV13 period. All GPSC9/CC63 isolates sequenced from the pre-PCV period (n=3) expressed serotype 14; however, during the late-PCV13 period, nearly all (88.2%, 15/17) were serotype 15A. The emergence among non-PCV13 serotypes, of lineages usually associated with PCV13 serotypes (such as GPSC5/CC172 and GPSC9/CC63), warrants continued genomic surveillance in South Africa, more so as PCV10 (Pneumosil) replaced PCV13 in South Africa in 2024.

在南非,常规使用肺炎球菌结合疫苗(PCV)导致疫苗相关的侵袭性肺炎球菌疾病(IPD)的下降,随后出现了非PCV血清型,主要是由预先存在的谱系驱动的。在2009年实施PCV之前和之后,我们确定了2020年至2025年南非成人中引起IPD的分离株的分子流行病学。我们对4个疫苗接种期[pre-PCV(2005-2008)、PCV7(2009-2010)、pcv13早期(2011-2014)和pcv13晚期(2015-2020)]中随机选取的18岁以上成人中导致IPD的分离株(N= 1581)进行了全基因组测序。我们对硅片进行了血清型、多位点序列型、克隆复合体(CC)和全球肺炎球菌序列簇(GPSC)的鉴定,并确定了硅片的抗菌非敏感性谱。使用泊松回归计算估算的三个疫苗期(PCV7、pcv13早期和pcv13晚期)每年IPD发病率与pcv前相比,估算的个体GPSC谱系的发病率比。总体而言,我们的数据集分别代表3.7% (n=270)、3.4% (n=128)、4.9% (n=287)和13.5% (n=896)在这四个时期接受的成人肺炎球菌分离株。我们鉴定了135个GPSCs,大多数分离物[68.7%(1 086/1 581)]聚类为23个显性GPSCs中的1个,这些GPSCs定义为包含≥20个基因组的GPSCs。与pcv7前期相比,在pcv13后期,通常与疫苗血清型相关的疫苗类型谱系的发病率有所下降。GPSC2(血清型1)从1.4 /10万下降到0.039/10万(PPn=3);然而,在pcv13晚期,几乎所有(88.2%,15/17)为15A血清型。在非PCV13血清型中,通常与PCV13血清型相关的谱系(如GPSC5/CC172和GPSC9/CC63)的出现,需要在南非继续进行基因组监测,尤其是在2024年南非PCV10(肺炎)取代PCV13之后。
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引用次数: 0
Genomic diversity and antimicrobial resistance of Staphylococcus aureus in Saudi Arabia: a nationwide study using whole-genome sequencing. 沙特阿拉伯金黄色葡萄球菌的基因组多样性和抗菌素耐药性:一项使用全基因组测序的全国性研究。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001540
Mohammed S Alarawi, Musaad Altammami, Mohammed Abutarboush, Maxat Kulmanov, Dalal M Alkuraithy, Senay Kafkas, Robert Radley, Marwa Abdelhakim, Hind Aldakhil, Reema A Bawazeer, Mohammed A Alolayan, Basel M Alnafjan, Abdulaziz A Huraysi, Amani Almaabadi, Bandar A Suliman, Areej G Aljohani, Hassan A Hemeg, Mohammed S Almogbel, Meshari Alazmi, Abdulrahman S Bazaid, Turki S Abujamel, Anwar M Hashem, Ibrahim A Al-Zahrani, Mohammed S Abdoh, Haya I Hobani, Rakan F Felemban, Wafaa A Alhazmi, Pei-Ying Hong, Majed F Alghoribi, Sameera Aljohani, Hanan Balkhy, Abdulrahman Alswaji, Maha Alzayer, Bassam Alalwan, Mai M Kaaki, Sharif M Hala, Omniya Ahmad Fallatah, Wesam Bahitham, Samer Zakri, Mohammad A Alshehri, Nader Kameli, Abdullah Algaissi, Edrous Alamer, Abdulaziz Alhazmi, Amjad A Shajri, Majid Ahmed Darraj, Bandar Kameli, O O Sufyani, Badreldin S Rahama, Abrar A Bakr, Fahad M Alhoshani, Azzam A Alquait, Ali M Somily, Ahmed M Albarrag, Lamia Alosaimi, Sumayh A Aldakeel, Fayez S Bahwerth, Mushtaq A Khan, Tamir T Abdelrahman, Séamus Fanning, Essam A Tawfik, Essam J Alyamani, Takashi Gojobori, Satoru Miyazaki, Mohammed B Al-Fageeh, Robert Hoehndorf

Methicillin-resistant Staphylococcus aureus (MRSA) surveillance in regions with mass gatherings presents unique challenges for public health systems. Saudi Arabia, hosting millions of pilgrims annually, provides a distinctive setting for studying how human mobility shapes bacterial populations, yet comprehensive genomic surveillance data from this region remain limited. Here, we present an integrated analysis of S. aureus isolates collected across seven Saudi Arabian regions, combining whole-genome sequencing with extensive antimicrobial susceptibility testing and standardized metadata following findability, accessibility, interoperability and reusability data principles. Our analysis revealed striking differences between pilgrimage and non-pilgrimage cities. Pilgrimage cities showed significantly higher genetic diversity and antimicrobial resistance rates, harbouring numerous international strains, including recognized clones from diverse geographic origins. Reported lineage dynamics are changing, expanding toward community clones. While genomic prediction of antimicrobial resistance showed high accuracy for some antibiotics, particularly beta-lactams, with varying performance for others, it highlights the necessity for phenotypic testing in clinical settings. Our findings demonstrate how mass gatherings drive bacterial population structures and emphasize the importance of integrated surveillance approaches in regions with significant global connectivity and travel.

在大规模人群聚集地区进行耐甲氧西林金黄色葡萄球菌(MRSA)监测对公共卫生系统提出了独特的挑战。沙特阿拉伯每年接待数百万朝圣者,为研究人类流动如何影响细菌种群提供了独特的环境,但来自该地区的全面基因组监测数据仍然有限。在此,我们对从沙特阿拉伯7个地区收集的金黄色葡萄球菌分离株进行了综合分析,结合全基因组测序和广泛的抗菌药物敏感性测试,并根据可查找性、可及性、互操作性和可重用性数据原则进行了标准化元数据。我们的分析揭示了朝圣城市和非朝圣城市之间的显著差异。朝圣城市显示出更高的遗传多样性和抗菌素耐药率,拥有许多国际菌株,包括来自不同地理来源的公认克隆。报道的血统动态正在发生变化,向社区克隆扩展。虽然抗微生物药物耐药性的基因组预测对某些抗生素,特别是β -内酰胺类抗生素显示出很高的准确性,但对其他抗生素的表现不同,但它强调了在临床环境中进行表型检测的必要性。我们的研究结果证明了大规模聚集如何驱动细菌种群结构,并强调了在具有重要全球连通性和旅行的地区采用综合监测方法的重要性。
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引用次数: 0
Gene dependence during mammalian Acinetobacter baumannii pneumonia and septicaemia infections. 哺乳动物鲍曼不动杆菌肺炎和败血症感染的基因依赖性。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001556
Faye C Morris, Francesca Short, Xenia Kostoulias, Cara Nethercott, Ying Fu, Yan Jiang, Thomas Smallman, Yusong Yu, Ian T Paulsen, John D Boyce, Anton Y Peleg

With a limited number of traditional virulence factors, the success of the nosocomial pathogen Acinetobacter baumannii is largely attributed to its ability to persist and resist. The niches encountered during infection vary significantly from the more commonly studied laboratory setting, and consequently, the genes responsible for in vivo pathogenesis have yet to be fully elucidated. This study utilized the A. baumannii AB5075-UW transposon mutant library with unbiased genome-wide transposon sequencing to identify the genetic basis for survival and fitness during pneumonia and septicaemia infections. We identified 128 genes essential for in-host survival, including 22 required for survival in all tissues. Additionally, 302 genes with significantly altered fitness in vivo were also identified. Tissue specificity was observed, highlighting the importance of genes associated with aa biosynthesis in the lungs, cell shape and structure in the kidneys and metal acquisition during septicaemia. The majority (89%) of the genes with aberrant fitness were constituents of the core A. baumannii genome. The findings were validated using a subset of targeted mutants, including those required for infection (phoB, cysI and hom) or specifically septicaemia (corA, lepA and purN) or pneumonia (argC, hisC and leuD), confirming that these observations were a result of specific in vivo fitness defects rather than aberrant in vitro growth. Taken together, these data provide the first global profile of genes required for in vivo fitness of A. baumannii during different disease states and growth in different tissues.

由于传统的毒力因素有限,医院病原体鲍曼不动杆菌的成功在很大程度上归功于其持续存在和抵抗的能力。在感染过程中遇到的生态位与更常见的实验室研究环境有很大不同,因此,负责体内发病的基因尚未完全阐明。本研究利用鲍曼不动杆菌AB5075-UW转座子突变文库和无偏倚的全基因组转座子测序来确定肺炎和败血症感染期间生存和适应的遗传基础。我们确定了128个对宿主内存活至关重要的基因,其中22个是所有组织存活所必需的。此外,还鉴定出302个在体内显著改变适应度的基因。观察到组织特异性,强调了与肺中aa生物合成、肾脏中细胞形状和结构以及败血症期间金属获取相关的基因的重要性。大多数(89%)适合度异常的基因是鲍曼不动杆菌核心基因组的组成部分。研究结果通过一组靶向突变体进行了验证,包括感染所需的突变体(phoB、cyi和homm)或特异性败血症(corA、lepA和purN)或肺炎(argC、hisC和leuD),证实了这些观察结果是体内特异性适应性缺陷的结果,而不是体外生长异常的结果。综上所述,这些数据首次提供了鲍曼不动杆菌在不同疾病状态和不同组织生长过程中体内适应性所需基因的全球概况。
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引用次数: 0
Novel roseophages provide insights into a genetically and ecologically diverse phage family. 新的玫瑰噬菌体提供了对遗传和生态多样化的噬菌体家族的见解。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001568
Zuqing Wu, Ying Wu, Chunmei Deng, Hang Xiao, Sige Wang, Songlin Ye, Yanlin Zhao, Zefeng Zhang

Roseobacters are prevalent in marine environments and play a crucial role in global carbon and sulphur cycles. Although many roseophages that infect roseobacters have been characterized, those infecting members of the ecologically dominant pelagic Roseobacter cluster (PRC) remain largely unexplored due to the challenges of culturing these organisms. In this study, we isolated 7 phylogenetically related roseophages from 3 PRC lineages and retrieved 279 uncultured viral genomes (UViGs) related to these roseophages from marine environmental viral databases. Comparative genomic and phylogenetic analyses revealed that these roseophages and their related UViGs form a novel family-level phage group (designated the CRP-822-type group) comprising at least five subgroups. These subgroups display distinct genomic features in terms of G+C content, amino acid usage and codon usage, suggesting host-range specialization. Host prediction suggests that subgroup V with low G+C content may infect the SAR86 clade, while the high G+C subgroup IV likely infects the high G+C KI89A clade. Finally, viromic read-mapping analyses revealed that CRP-822-type phages are widely distributed across the global ocean and are adapted to diverse marine environments. All members of subgroup IV were more abundant in trade, westerlies and coastal regions with high temperatures. The other four subgroups exhibited more divergent biogeographic patterns, with some members more abundant in trade and westerlies ocean regions, whereas others dominated in polar or estuarine regions. Collectively, this study elucidates the genetic diversity and ecology of a previously unrecognized marine phage group that infects PRC roseobacters and other important marine bacteria.

玫瑰杆菌普遍存在于海洋环境中,在全球碳和硫循环中起着至关重要的作用。虽然许多感染玫瑰杆菌的玫瑰噬体已经被鉴定出来,但由于培养这些生物的挑战,那些感染生态上占优势的远洋玫瑰杆菌群(PRC)成员的玫瑰噬体在很大程度上仍未被探索。在这项研究中,我们从3个PRC谱系中分离出7个系统发育相关的玫瑰噬体,并从海洋环境病毒数据库中检索到279个与这些玫瑰噬体相关的未培养病毒基因组(UViGs)。比较基因组学和系统发育分析显示,这些玫瑰噬菌体及其相关的uvig形成了一个新的家族水平噬菌体群(称为crp -822型群),包括至少五个亚群。这些亚群在G+C含量、氨基酸使用和密码子使用方面显示出不同的基因组特征,表明宿主范围特化。宿主预测表明,低G+C含量的V亚群可能感染SAR86分支,而高G+C含量的IV亚群可能感染高G+C的KI89A分支。最后,病毒组读图分析显示,crp -822型噬菌体广泛分布于全球海洋,并适应不同的海洋环境。第四亚群的所有成员在贸易、西风带和高温沿海地区更为丰富。其他4个亚群的生物地理格局差异较大,其中一些亚群分布在贸易和西风带海域,而另一些亚群分布在极地或河口地区。总的来说,这项研究阐明了一种以前未被认识的海洋噬菌体群的遗传多样性和生态学,这种噬菌体感染中华人民共和国玫瑰杆菌和其他重要的海洋细菌。
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引用次数: 0
Mycobacterium tuberculosis cultured in MGIT media for whole-genome sequencing application: a systematic literature review and meta-analysis. MGIT培养基中培养的结核分枝杆菌用于全基因组测序:系统文献综述和荟萃分析。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001565
Emilyn Costa Conceição, Felicia Wells, Abhinav Sharma, Mishka Haffejee, Brendon Mann, Justice Tresor Ngom, Shatha Omar, Johannes Loubser, Miguel de Diego Fuertes, Vincent Rennie, Anzaan Dippenaar, Tim Heupink, Túlio de Oliveira, Gian Van der Spuy, Annelies Van Rie, Robin Mark Warren

Whole-genome sequencing (WGS) holds promise for accurate and comprehensive diagnosis of drug resistance in Mycobacterium tuberculosis and identification of transmission events. 'Early positive cultures' (EPC) are increasingly used when WGS is implemented to guide clinical care to reduce the turnaround time. We performed a systematic literature review to compare methods used for EPC-based WGS and performed an individual sample data meta-analysis to identify variables associated with bioinformatic quality measures. Of 423 studies identified, 15 met eligibility criteria. We analysed 1,065 FASTQ files from 11 studies using Illumina sequencing; 96.1% passed all quality control thresholds. Median genome coverage was 65× (IQR, 63-82), with a pooled mapping percentage of 91.2%. The meta-analysis showed that the number of sequencing cycles was significantly associated with improved sequencing quality, while other laboratory variables had no consistent effect. Based on these findings, we suggest replacing the term EPC with 'clinical primary culture' and propose a standardized workflow and reporting checklist for WGS on primary Mycobacteria Growth Indicator Tube (MGIT) cultures.

全基因组测序(WGS)有望准确和全面地诊断结核分枝杆菌的耐药性并确定传播事件。在实施WGS时,“早期阳性培养”(EPC)越来越多地用于指导临床护理,以减少周转时间。我们进行了系统的文献综述,比较了基于epc的WGS方法,并进行了个体样本数据荟萃分析,以确定与生物信息学质量测量相关的变量。在确定的423项研究中,有15项符合资格标准。我们使用Illumina测序分析了来自11项研究的1,065个FASTQ文件;96.1%通过了所有质量控制阈值。基因组覆盖率中位数为65× (IQR, 63-82),汇总定位百分比为91.2%。meta分析显示,测序周期的数量与测序质量的提高显著相关,而其他实验室变量没有一致的影响。基于这些发现,我们建议将术语EPC替换为“临床原代培养”,并为原代分枝杆菌生长指示管(MGIT)培养的WGS提出标准化工作流程和报告清单。
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引用次数: 0
Microevolution associated with clonal expansion of a hypervirulent, penicillin-resistant lineage of Neisseria meningitidis in Western Australia. 在西澳大利亚,与高毒力、青霉素耐药脑膜炎奈瑟菌谱系克隆扩增相关的微进化。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001530
August Mikucki, Eng Guan Chua, Chin Yen Tay, Michael J Wise, Geoffrey W Coombs, David J Speers, Shakeel Mowlaboccus, Charlene M Kahler

Neisseria meningitidis is a colonizer of the human nasopharynx which occasionally causes invasive meningococcal disease. Despite numerous reports of penicillin-resistant isolates, antimicrobial-resistant meningococcal clones have historically not persisted over long time periods or become globally distributed, presumably due to the imposed fitness cost associated with antimicrobial resistance. One exception is a penicillin-resistant clade of serogroup W clonal complex 11 (MenW:cc11) isolates identified in Western Australia in 2013, which has since caused disease globally. Here, we investigated the genomic changes associated with penicillin resistance in MenW:cc11 isolated during the 2013-2020 Western Australian meningococcal outbreak. Seventy-six MenW:cc11 disease-causing isolates underwent short-read whole genome sequencing. Reference genomes were generated for three isolates. In accordance with previous analysis, two phylogenetically distinct clusters were identified: cluster A (12 penicillin-susceptible isolates) and cluster B (63 penicillin-resistant isolates). Genomic comparison of the cluster A and cluster B isolates revealed 128 allelic differences present at the branching point between the two lineages. The differences included polymorphisms in genes associated with cell wall regulation, pilus biogenesis and the MtrR transcriptional regulator. A further 60 allelic changes were identified in the Western Australian isolates which were not identified in globally distributed cluster B isolates. In a search of the PubMLST Neisseria database, all allelic variants associated with the emergence of cluster B were found exclusively in other hypervirulent lineages. Taken together, the data suggest the global success of the penicillin-resistant N. meningitidis is due to compensatory mutations acquired through horizontal exchange from other hypervirulent lineages.

脑膜炎奈瑟菌是人类鼻咽部的定植菌,偶尔会引起侵袭性脑膜炎球菌病。尽管有许多关于青霉素耐药分离株的报道,但抗微生物脑膜炎球菌克隆在历史上并未持续很长时间或在全球分布,可能是由于与抗微生物药物耐药性相关的强制适应成本。一个例外是2013年在西澳大利亚发现的血清W群克隆复合体11 (MenW:cc11)的耐青霉素分支,该分支已在全球范围内引起疾病。在此,我们研究了2013-2020年西澳大利亚脑膜炎球菌爆发期间分离的MenW:cc11与青霉素耐药性相关的基因组变化。76株MenW:cc11致病分离株进行了短读全基因组测序。对三个分离株进行了参考基因组的构建。根据先前的分析,确定了两个系统发育上不同的集群:集群A(12株青霉素敏感株)和集群B(63株青霉素耐药株)。A群和B群分离株的基因组比较显示,在两个谱系的分支点上存在128个等位基因差异。差异包括细胞壁调控、菌毛发生和MtrR转录调控相关基因的多态性。在西澳大利亚分离株中发现了另外60个等位基因变化,这些变化在全球分布的B群分离株中没有发现。在PubMLST奈瑟菌数据库的搜索中,所有与B群出现相关的等位基因变异都只在其他高毒谱系中被发现。综上所述,这些数据表明,耐青霉素脑膜炎奈索菌在全球范围内的成功是由于从其他高毒谱系通过水平交换获得的补偿性突变。
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引用次数: 0
Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing. 通过全基因组测序重新审视经典的大肠杆菌细胞分裂突变体。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001558
Elias Dahdouh, Isabel García-Pérez, Diana Soledad Reyes-Zuñagua, Jesús Mingorance, Miguel Vicente

Over 60 years ago, researchers started the genetic analysis of bacterial cell division by isolating conditional, temperature-sensitive mutants of essential Escherichia coli cell division genes. These early mutants were obtained by mutagenesis with chemical agents that introduced dozens to hundreds of mutations in the bacterial genomes. In this work, we present the complete genome sequences of six of these original mutants on ftsA, ftsZ and ftsQ genes, along with two of the strains used to generate them. The genomes of mutants obtained by exposure to nitrosoguanidine had 100 to 400 mutations. Transducing target alleles into a new strain effectively reduced the number of mutations, but those near the target gene were co-transduced with it. In contrast, a mutant generated by site-directed mutagenesis maintained the genomic background intact. The genomic analysis improves our understanding of these foundational strains, offering insights into the effects of historical mutagenesis techniques. These findings underscore the importance of genomic characterization in ensuring accurate interpretations of experimental results in microbiological research.

60多年前,研究人员通过分离必要的大肠杆菌细胞分裂基因的条件、温度敏感突变体,开始对细菌细胞分裂进行遗传分析。这些早期突变体是通过化学试剂诱变获得的,这些化学试剂在细菌基因组中引入了数十到数百个突变。在这项工作中,我们展示了ftsA, ftsZ和ftsQ基因上的六个原始突变体的完整基因组序列,以及用于产生它们的两个菌株。暴露于亚硝基胍获得的突变体基因组有100到400个突变。将目标等位基因转导到新菌株中可以有效地减少突变的数量,但靠近目标基因的等位基因与它共转导。相比之下,由位点定向诱变产生的突变体保持了基因组背景的完整。基因组分析提高了我们对这些基础菌株的理解,提供了对历史诱变技术影响的见解。这些发现强调了基因组表征在确保微生物学研究中准确解释实验结果方面的重要性。
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引用次数: 0
A contemporary genomic snapshot of Salmonella Paratyphi A in Pakistan. 巴基斯坦甲型副伤寒沙门氏菌的当代基因组快照。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001561
Elli Mylona, Junaid Iqbal, Jacqueline A Keane, Joana Pereira-Dias, Megan Carey, Mehreen Adnan, Aneeta Hotwani, Irim Iftikhar, Seema Irfan, Stephen Baker, Farah N Qamar

Salmonella enterica serovar Paratyphi A is a significant but under-characterised cause of enteric fever in South Asia. In Pakistan, where the typhoid conjugate vaccine has been introduced to combat S. Typhi, S. Paratyphi A remains a prominent cause of bacteraemia, raising concerns about shifts in disease burden and antimicrobial resistance (AMR). Here, we provide a comprehensive genomic and phylogenetic analysis of 354 S. Paratyphi A isolates collected from three provinces in Pakistan between 2017 and early 2022. Whole-genome sequencing revealed the dominance of genotypes 2.3.3 and 2.4.5, indicating a largely stable population structure over time, and the presence of widespread fluoroquinolone-associated gyrA mutations. Although multidrug resistance was not detected, we identified one isolate harbouring an acrB-R717Q mutation associated with azithromycin resistance. Plasmid and replicon analysis revealed low prevalence of extrachromosomal elements, including cryptic plasmids with unknown function. Phylogenetic placement of these isolates in a global context demonstrated close relatedness to contemporary South Asian organisms. Our findings establish a genomic baseline for S. Paratyphi A in Pakistan, essential for future surveillance, AMR monitoring, and evaluating the potential impact of forthcoming paratyphoid vaccines.

在南亚,沙门氏菌血清型甲型副伤寒是一种重要但特征不明确的肠道热病因。在巴基斯坦,已经引进了伤寒结合疫苗来对抗伤寒沙门氏菌,甲型副伤寒沙门氏菌仍然是引起菌血症的一个主要原因,引起了人们对疾病负担和抗菌素耐药性(AMR)变化的关注。在这里,我们提供了一个全面的基因组和系统发育分析的354 S。2017年至2022年初在巴基斯坦三个省收集的甲型副伤寒分离株。全基因组测序显示,基因型2.3.3和2.4.5占主导地位,表明随着时间的推移,种群结构基本稳定,并且存在广泛的氟喹诺酮相关gyrA突变。虽然没有检测到多药耐药,但我们发现一株分离物携带与阿奇霉素耐药相关的acrB-R717Q突变。质粒和复制子分析显示染色体外因子的患病率较低,包括功能未知的隐质粒。这些分离株在全球范围内的系统发育位置表明与当代南亚生物密切相关。我们的研究结果为巴基斯坦甲型副伤寒沙门氏菌建立了基因组基线,这对未来的监测、抗菌素耐药性监测和评估即将问世的副伤寒疫苗的潜在影响至关重要。
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引用次数: 0
Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata). 刺背鳐(Raja clavata)中一种新型乳头瘤病毒的鉴定和特征分析。
IF 4 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2025-11-01 DOI: 10.1099/mgen.0.001541
Denise da Silva Fong, Joana Abrantes, Teresa Moura, Bárbara Serra-Pereira, Raquel Xavier, Ana Veríssimo, Arvind Varsani, Fabiana Neves

Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.

乳头瘤病毒是一种非包膜的双链DNA病毒,能够感染从软骨鱼到哺乳动物等多种脊椎动物。在这项研究中,我们首次在棘鳐(Raja clavata)中鉴定出一种乳头瘤病毒,并将其命名为Raja clavata乳头瘤病毒1 (RclaPV1)。基因组序列采用宏基因组方法确定,随后通过PCR确认。RclaPV1基因组长度为5539 bp,具有典型的乳头瘤病毒组织结构,在一条DNA链上编码4个核心蛋白:两个早期基因(E1和E2)和两个晚期基因(L1和L2)。L1和E1基因的最大似然系统发育分析表明,RclaPV1属于第二乳头瘤病毒亚科,与鱼类和两栖动物乳头瘤病毒聚类,与两栖动物的进化关系比与鱼类的进化关系更密切。
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引用次数: 0
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Microbial Genomics
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